2023-11-25T11:02:04,433 Created temporary directory: /tmp/pip-build-tracker-gwgefcli 2023-11-25T11:02:04,434 Initialized build tracking at /tmp/pip-build-tracker-gwgefcli 2023-11-25T11:02:04,434 Created build tracker: /tmp/pip-build-tracker-gwgefcli 2023-11-25T11:02:04,435 Entered build tracker: /tmp/pip-build-tracker-gwgefcli 2023-11-25T11:02:04,435 Created temporary directory: /tmp/pip-wheel-0g8op2wo 2023-11-25T11:02:04,439 Created temporary directory: /tmp/pip-ephem-wheel-cache-5yettc_s 2023-11-25T11:02:04,460 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-25T11:02:04,463 2 location(s) to search for versions of trtools: 2023-11-25T11:02:04,463 * https://pypi.org/simple/trtools/ 2023-11-25T11:02:04,463 * https://www.piwheels.org/simple/trtools/ 2023-11-25T11:02:04,464 Fetching project page and analyzing links: https://pypi.org/simple/trtools/ 2023-11-25T11:02:04,465 Getting page https://pypi.org/simple/trtools/ 2023-11-25T11:02:04,466 Found index url https://pypi.org/simple/ 2023-11-25T11:02:04,743 Fetched page https://pypi.org/simple/trtools/ as application/vnd.pypi.simple.v1+json 2023-11-25T11:02:04,753 Found link https://files.pythonhosted.org/packages/d6/c2/0c1a331961356af54cd9f8356596bc68b3e2d2538abb5356a6b2725d0ff4/trtools-2.0.0.tar.gz (from https://pypi.org/simple/trtools/), version: 2.0.0 2023-11-25T11:02:04,754 Found link https://files.pythonhosted.org/packages/13/9e/74698b4d88dd53e5473fe16e9aec25fcf0ee21f41ee080fd856f87114744/trtools-2.0.1.tar.gz (from https://pypi.org/simple/trtools/), version: 2.0.1 2023-11-25T11:02:04,754 Found link https://files.pythonhosted.org/packages/4f/9c/67295087fa44843c078ddeca9a474ced1f37e5dc4e7fb868049dc0b4e55b/trtools-2.0.2.tar.gz (from https://pypi.org/simple/trtools/), version: 2.0.2 2023-11-25T11:02:04,755 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/90/2e/ad9f798558846f3785a06d71ba784755742964adfdc37ccb0995b47fc5e4/trtools-2.0.4-py3-none-any.whl (from https://pypi.org/simple/trtools/) 2023-11-25T11:02:04,755 Found link https://files.pythonhosted.org/packages/1c/43/ffa868b6fd05bcd3b81339d68ba6d806e26d9b5ebe6e3421474b2f1f9f61/trtools-2.0.4.tar.gz (from https://pypi.org/simple/trtools/), version: 2.0.4 2023-11-25T11:02:04,756 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/89/0a/4e3136520f7d079f0182b18e38a5c47e987e2687186e6a182ba0f24f4482/trtools-2.0.5a0-py3-none-any.whl (from https://pypi.org/simple/trtools/) 2023-11-25T11:02:04,757 Found link https://files.pythonhosted.org/packages/d2/5a/1a7a5f28f3cb29a7444bdf3013f6f3ae86a1f35f13a79072d4df90354956/trtools-2.0.5a0.tar.gz (from https://pypi.org/simple/trtools/), version: 2.0.5a0 2023-11-25T11:02:04,758 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/8b/ec/71b2e7c2e44681ae7e3d6b177ef5e62eb9776a444a8a48b09b9c0d37df09/trtools-2.0.5-py3-none-any.whl (from https://pypi.org/simple/trtools/) 2023-11-25T11:02:04,758 Found link https://files.pythonhosted.org/packages/ce/31/29d3d50bd01711693b7b309084df47107aa87c075022f1bef1f8e642c25c/trtools-2.0.5.tar.gz (from https://pypi.org/simple/trtools/), version: 2.0.5 2023-11-25T11:02:04,759 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/1c/c4/84c7e1dec17cfe2a6634a3be9b911813ab4c20590b2778c5e1d9490dcb9c/trtools-2.0.10-py3-none-any.whl (from https://pypi.org/simple/trtools/) 2023-11-25T11:02:04,759 Found link https://files.pythonhosted.org/packages/7b/22/7156a9ad5f840fd4ba158010e0082a9fbb7acfaaac31d73f62040cac6ac2/trtools-2.0.10.tar.gz (from https://pypi.org/simple/trtools/), version: 2.0.10 2023-11-25T11:02:04,760 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/2e/ff/0e9f11f41350c6b9e64c9fac03460eb584484cdbd0ae0b1d9391a4f766a7/trtools-2.0.11-py3-none-any.whl (from https://pypi.org/simple/trtools/) 2023-11-25T11:02:04,761 Found link https://files.pythonhosted.org/packages/ce/62/3e5bd5bd35241e92d2100aa2089903d06ed3b3e29f3ad7d3413ec4d2c14e/trtools-2.0.11.tar.gz (from https://pypi.org/simple/trtools/), version: 2.0.11 2023-11-25T11:02:04,761 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/53/15/7b4bd38ca30f86cf25f7394295787778c6eca02f5fa22310c98a7ab3e341/trtools-2.0.12-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,763 Found link https://files.pythonhosted.org/packages/6e/02/20ed6c89904ae91e10635d4aaa5c37aca43c46f878d0271103b0836637b4/trtools-2.0.12.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 2.0.12 2023-11-25T11:02:04,763 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/8c/0e/12849b83ec628b4bc113babe57409e6be1da304ffdcd63e654bd0e4a4b2e/trtools-2.0.13-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,764 Found link https://files.pythonhosted.org/packages/6e/61/26a4efbc30c6b0b512094a15ddea66e00aec2906ca441e674fcb33a476a6/trtools-2.0.13.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 2.0.13 2023-11-25T11:02:04,765 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/2f/cc/2e8242f489b0e95c14b37f6ded9c5623cef4254d537b8ef75c9e393d0704/trtools-2.0.14-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,765 Found link https://files.pythonhosted.org/packages/7f/b7/20d754a2b03ff641ab1353ca7392e4eac54e86683ceaea1eec634a4e1d58/trtools-2.0.14.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 2.0.14 2023-11-25T11:02:04,766 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/70/71/b62113da362afc026f8ca5124a7fae85d2eb7ebe7f0c6d5a93521cd7dbb2/trtools-2.0.15-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,767 Found link https://files.pythonhosted.org/packages/f6/ae/a38a88622b173b2d7f6c2210e99ec8c63e0a49e41bbe01fe46bdb9e99f98/trtools-2.0.15.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 2.0.15 2023-11-25T11:02:04,767 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/b0/40/64641843d19bd9e9b8617403a8cf022381422bd55af4b04694e5118657aa/trtools-2.0.16a0-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,768 Found link https://files.pythonhosted.org/packages/65/dc/d359ba078b9bd90289f1ad1d8b230dcba0134a6b0e33aabc79224703cc69/trtools-2.0.16a0.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 2.0.16a0 2023-11-25T11:02:04,769 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/94/e3/979fb8d7b397d750f3b7bc52377f2e84a7dddad882995b0c77e2f219baa3/trtools-2.0.16-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,770 Found link https://files.pythonhosted.org/packages/0e/56/9792e66952a364a91f3f3c9c0f0b52ede693e32143b996bce7478a89b5b3/trtools-2.0.16.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 2.0.16 2023-11-25T11:02:04,770 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/7e/ac/810ee9cce3b454037db1819b7ec23f3d6146fa2aee66906ff0bba83dd685/trtools-2.0.17-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,771 Found link https://files.pythonhosted.org/packages/33/fc/c78d3e8859784270109cb718532df72b721f902ddf8d87fb1e596beaa447/trtools-2.0.17.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 2.0.17 2023-11-25T11:02:04,772 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/ac/9b/faa2a206ab0560bb67f6945b662bd90dee470ba04cffdf46341a93efcd94/trtools-2.0.18-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,773 Found link https://files.pythonhosted.org/packages/46/26/4b674d19383287bb04d37ccf172954f8178566b9454d88f7651987082d21/trtools-2.0.18.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 2.0.18 2023-11-25T11:02:04,773 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/40/6e/e6d63adbffbc1e4da0b1f2a3461c044e6d94295fce812b0f77abd7a1f04e/trtools-3.0.0-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,775 Found link https://files.pythonhosted.org/packages/79/57/a253e5b40ea3432448cb37bd5bcfad1848e3c8dfe33cfa1c3e4465e63849/trtools-3.0.0.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 3.0.0 2023-11-25T11:02:04,775 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/a3/98/4485208fd15508d2c7e6a33d08bc913e0eb724abe32c7377fdc5e2a9e034/trtools-3.0.2-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,776 Found link https://files.pythonhosted.org/packages/e4/c1/38c9be188d072ec08126d3dd08a47790ffb735ad922bb220f8ccb3cb9a0d/trtools-3.0.2.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 3.0.2 2023-11-25T11:02:04,776 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/ea/6e/30181eac2e2a2f1a0ac0e479424d0f9ecaa027780f455020dd2529f2c1e1/trtools-3.0.3-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,777 Found link https://files.pythonhosted.org/packages/48/6f/145c9dad23be4c659a36849f50f047e35c60af13e0be14c38049cff5793f/trtools-3.0.3.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 3.0.3 2023-11-25T11:02:04,778 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/6d/2c/8627e50429e402cf9eccc7d1fe12895f72254a14c6a3868ff5485111c5ec/trtools-4.0.0-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,779 Found link https://files.pythonhosted.org/packages/01/8b/0c44b83dd52dcdb0ae1f2511f2b0f3073b0760edb5769d684771b0bb9dea/trtools-4.0.0.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 4.0.0 2023-11-25T11:02:04,779 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/72/7b/aaf3ddfdf1cb5f009be7494da4a10e1c59f6abdf508e1ba691cbc6c9be3e/trtools-4.0.1-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,780 Found link https://files.pythonhosted.org/packages/ee/09/6f7b6b96ed8f7c918885116a41c8f09de8507f059fdcafc4a7b7c18a634d/trtools-4.0.1.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 4.0.1 2023-11-25T11:02:04,781 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/a1/3b/bf068aa82cd56147abe63704746cef4ae221848bf57db5a7fed7ffda99a8/trtools-4.0.2-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,781 Found link https://files.pythonhosted.org/packages/b5/11/1886bc4c223cb6cfaef3a3fe3dd737bdc234ae5af176e5e25e278aca93ab/trtools-4.0.2.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 4.0.2 2023-11-25T11:02:04,782 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/b4/54/574794affdaf2891c94ea2c64d8c738869d0c51350ce7ef0636f00a92f85/trtools-4.1.0-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,783 Found link https://files.pythonhosted.org/packages/e9/83/76b93c0154b5dd8ebc54f2e8dbb6aa50c0e0f6ef738065011a900acd4db8/trtools-4.1.0.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 4.1.0 2023-11-25T11:02:04,783 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/71/77/2e510d7cf0a0202ce4b8d326fa5c92a52e5bf0adb63e0fa5447d5ef9ba7a/trtools-4.2.0-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,784 Found link https://files.pythonhosted.org/packages/77/43/f924495433d9a5a90c873484e059ad5b7e9bf34760c46f7ccaa12ef3612b/trtools-4.2.0.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 4.2.0 2023-11-25T11:02:04,785 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/da/64/ed56893f8a1955b8e5f586dcd9a55fd9afda606739ace4873daff31e6306/trtools-4.2.1-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,786 Found link https://files.pythonhosted.org/packages/1b/3e/35562ac67cc3973b72a5d0f48ae9d93c72c248ffa2dc67df1d9dbf5cff2c/trtools-4.2.1.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 4.2.1 2023-11-25T11:02:04,786 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/e8/d6/e5d29feb9aed7f87a8202b01af6dc9db125004879cfaaf6547453ec7a434/trtools-5.0.0-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,787 Found link https://files.pythonhosted.org/packages/87/b3/65724f10316ec8c39b32b47707d902761c97a760b21c7a23c5e7b46898fa/trtools-5.0.0.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 5.0.0 2023-11-25T11:02:04,788 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/61/0b/1bac0a419b59312d648fa021e11741b7adebf104dc1bb1480d287261f57b/trtools-5.0.1-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,789 Found link https://files.pythonhosted.org/packages/4c/70/85c51f9cbc15450a236004644ca15c780a040f0b3dd8fa4c4cc211932cd1/trtools-5.0.1.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 5.0.1 2023-11-25T11:02:04,789 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/e6/e6/cf6be212c2a81664fedf1500408939c5fbdfb5659c576ae331dd513fa51f/trtools-5.0.2-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,790 Found link https://files.pythonhosted.org/packages/dd/f1/f0a1ef8dc71ee1a9ebd0aade7e89dbce352d6199e0a77c7970e20c60f8b2/trtools-5.0.2.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 5.0.2 2023-11-25T11:02:04,791 Skipping link: No binaries permitted for trtools: https://files.pythonhosted.org/packages/6d/5c/8d9a0c9ba87a4e59459d868edda0e665ad755352fbb5860162aadec7ac69/trtools-5.1.0-py3-none-any.whl (from https://pypi.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,792 Found link https://files.pythonhosted.org/packages/61/ab/7a84aa588d919e83afee8774b8dac81bee5e9bdbe0fd1f9eaacea1ada271/trtools-5.1.0.tar.gz (from https://pypi.org/simple/trtools/) (requires-python:>=3.5), version: 5.1.0 2023-11-25T11:02:04,793 Fetching project page and analyzing links: https://www.piwheels.org/simple/trtools/ 2023-11-25T11:02:04,793 Getting page https://www.piwheels.org/simple/trtools/ 2023-11-25T11:02:04,794 Found index url https://www.piwheels.org/simple/ 2023-11-25T11:02:04,957 Fetched page https://www.piwheels.org/simple/trtools/ as text/html 2023-11-25T11:02:04,965 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-5.0.2-py3-none-any.whl#sha256=9f7bec4f9244efb19a6a02fab669bf433a1184cee8678dfc46c09007631fdb47 (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,966 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-5.0.1-py3-none-any.whl#sha256=edfeb2c80e1ef50327e16725a66aef26e7fff56fc885a24a8155edd407edd6f2 (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,967 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-5.0.0-py3-none-any.whl#sha256=26844ac15e38bc5ddc7eac5b555958e3017e6d0c0002429f22923a228c4d200c (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,967 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-4.2.1-py3-none-any.whl#sha256=ebebd3562f3c062688d07b88c3605a08bf518b92ee2b5e6fdd76de67b9cfdc6d (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,968 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-4.2.0-py3-none-any.whl#sha256=1ef9d092dc6fc4483b753bbd5a300f4d8bef52191b62b8f056902f3ae4d189b1 (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,969 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-4.1.0-py3-none-any.whl#sha256=08ed5dc295a7b7d3ef654e3475e64949be247fe52f9d9ad357934988acabec25 (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,969 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-4.0.2-py3-none-any.whl#sha256=f0d9347adf3962e6ccc7b8c699ce253792489f56bc9c5c6b385942f3a6a609ac (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,969 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-4.0.1-py3-none-any.whl#sha256=dd82cfbda532b867070db5e34649e5fc6cd4e271206b8862aa30377e73dca01b (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,970 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-4.0.0-py3-none-any.whl#sha256=86e29c0753ddb621b4831a35ee1941bdff0f02f2c53848770e277059613174dc (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,970 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-3.0.3-py3-none-any.whl#sha256=10d5179519b6bf8fd456e3c5228b67ea1b541c89f5b76a77d0504c37f02de3bc (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,971 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-3.0.2-py3-none-any.whl#sha256=dfa9fbed916d978acdae0478c715e5e2ebad1808f95740290b5257fdc43b0767 (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,971 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-3.0.0-py3-none-any.whl#sha256=73f567a0aecbce433c7760ffd11d10a5858dab55980683a806745080ce581871 (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,972 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.18-py3-none-any.whl#sha256=06d0176666ef34ba766796464d9d762ffc3c6d026d78146ab05a6cc89be1b0ad (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,973 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.17-py3-none-any.whl#sha256=6e88f9254697cbc0902e53ea952e077a2ecbec20168834a0f52e9ee542eb85d4 (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,973 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.16-py3-none-any.whl#sha256=a01ce9e9d89b759ac5e2a71a5e0f82354bbde8e12b4374f2ab0eed3b542abe58 (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,974 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.16a0-py3-none-any.whl#sha256=182d5181827dcba72bf1ec875d8d83000062bf55c45614ce6458eb592cedc655 (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,974 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.15-py3-none-any.whl#sha256=9c5d3f522166390056596158f13f6d535e935ab55706bcc52cafa790cbed804c (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,975 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.14-py3-none-any.whl#sha256=cc6ba1a97f107507c8566155a7bb9891d0b2e3d4ae32a707f946ea5a01e34fa1 (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,976 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.13-py3-none-any.whl#sha256=5fade8dda90eac1a149e1fde68a89a064ad6eafa6147e478745a1ab375eb3a9a (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,976 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.12-py3-none-any.whl#sha256=f706850fb174af55d1b1897fddd2ac1de60b0ad3c0484c3b489a7b5e199367f1 (from https://www.piwheels.org/simple/trtools/) (requires-python:>=3.5) 2023-11-25T11:02:04,976 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.11-py3-none-any.whl#sha256=9ee7164896ec5d3472a41e25200e8ca99df0f26889f2e53b590562b7ce9039b0 (from https://www.piwheels.org/simple/trtools/) 2023-11-25T11:02:04,977 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.10-py3-none-any.whl#sha256=286444986d285fed0601790e3c9f637ae64aad825b032773a0c50270ea56e6d6 (from https://www.piwheels.org/simple/trtools/) 2023-11-25T11:02:04,977 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.5-py3-none-any.whl#sha256=f89df9883ccd4292d6205487056b0780ccf940c3ec91b5fbbb3a471e6ea66447 (from https://www.piwheels.org/simple/trtools/) 2023-11-25T11:02:04,978 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.5a0-py3-none-any.whl#sha256=b3210fac7b838ac616da0874fd35c813c12ef363490e2935a99a268e3214db5c (from https://www.piwheels.org/simple/trtools/) 2023-11-25T11:02:04,978 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.4-py3-none-any.whl#sha256=87ea2685c2d8d1748034130c5697121827d47c484e88292a60ca3b43b3ccdc6b (from https://www.piwheels.org/simple/trtools/) 2023-11-25T11:02:04,979 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.2-py3-none-any.whl#sha256=3805a3627376d1a53015fed0f31319ad0d734fd2b15b9d302658cfc3600ee13a (from https://www.piwheels.org/simple/trtools/) 2023-11-25T11:02:04,979 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.1-py3-none-any.whl#sha256=3a320fe9a2931be26a57f1298b737a01ac153295e4f7313dcf682316af47552e (from https://www.piwheels.org/simple/trtools/) 2023-11-25T11:02:04,980 Skipping link: No binaries permitted for trtools: https://www.piwheels.org/simple/trtools/trtools-2.0.0-py3-none-any.whl#sha256=1144ee042ba8ee6972b43d40451c243ca08266b89aed89941b0237cee87b78fb (from https://www.piwheels.org/simple/trtools/) 2023-11-25T11:02:04,981 Skipping link: not a file: https://www.piwheels.org/simple/trtools/ 2023-11-25T11:02:04,981 Skipping link: not a file: https://pypi.org/simple/trtools/ 2023-11-25T11:02:05,003 Given no hashes to check 1 links for project 'trtools': discarding no candidates 2023-11-25T11:02:05,021 Collecting trtools==5.1.0 2023-11-25T11:02:05,023 Created temporary directory: /tmp/pip-unpack-inwxf8id 2023-11-25T11:02:05,243 Downloading trtools-5.1.0.tar.gz (59.6 MB) 2023-11-25T11:02:21,948 Added trtools==5.1.0 from https://files.pythonhosted.org/packages/61/ab/7a84aa588d919e83afee8774b8dac81bee5e9bdbe0fd1f9eaacea1ada271/trtools-5.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-gwgefcli' 2023-11-25T11:02:21,953 Created temporary directory: /tmp/pip-build-env-0ymunvt5 2023-11-25T11:02:21,958 Installing build dependencies: started 2023-11-25T11:02:21,959 Running command pip subprocess to install build dependencies 2023-11-25T11:02:23,326 Using pip 23.3.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-11-25T11:02:24,075 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-25T11:02:25,479 Collecting setuptools 2023-11-25T11:02:25,494 Using cached https://www.piwheels.org/simple/setuptools/setuptools-69.0.2-py3-none-any.whl (819 kB) 2023-11-25T11:02:25,793 Collecting setuptools-scm 2023-11-25T11:02:25,811 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-8.0.4-py3-none-any.whl (42 kB) 2023-11-25T11:02:26,143 Collecting packaging>=20 (from setuptools-scm) 2023-11-25T11:02:26,156 Using cached https://www.piwheels.org/simple/packaging/packaging-23.2-py3-none-any.whl (53 kB) 2023-11-25T11:02:26,265 Collecting typing-extensions (from setuptools-scm) 2023-11-25T11:02:26,279 Using cached https://www.piwheels.org/simple/typing-extensions/typing_extensions-4.8.0-py3-none-any.whl (31 kB) 2023-11-25T11:02:28,726 Installing collected packages: typing-extensions, setuptools, packaging, setuptools-scm 2023-11-25T11:02:31,403 Successfully installed packaging-23.2 setuptools-69.0.2 setuptools-scm-8.0.4 typing-extensions-4.8.0 2023-11-25T11:02:31,977 Installing build dependencies: finished with status 'done' 2023-11-25T11:02:31,980 Getting requirements to build wheel: started 2023-11-25T11:02:31,981 Running command Getting requirements to build wheel 2023-11-25T11:02:32,822 running egg_info 2023-11-25T11:02:32,827 writing trtools.egg-info/PKG-INFO 2023-11-25T11:02:32,831 writing dependency_links to trtools.egg-info/dependency_links.txt 2023-11-25T11:02:32,833 writing entry points to trtools.egg-info/entry_points.txt 2023-11-25T11:02:32,835 writing requirements to trtools.egg-info/requires.txt 2023-11-25T11:02:32,836 writing top-level names to trtools.egg-info/top_level.txt 2023-11-25T11:02:32,875 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2023-11-25T11:02:32,878 reading manifest file 'trtools.egg-info/SOURCES.txt' 2023-11-25T11:02:32,946 reading manifest template 'MANIFEST.in' 2023-11-25T11:02:32,948 warning: no previously-included files found matching 'trtools/testsupport/sample_vcfs' 2023-11-25T11:02:32,949 warning: no previously-included files found matching 'trtools/testsupport/sample_regions' 2023-11-25T11:02:32,950 warning: no previously-included files found matching 'trtools/testsupport/sample_stats' 2023-11-25T11:02:32,950 adding license file 'LICENSE.txt' 2023-11-25T11:02:32,966 writing manifest file 'trtools.egg-info/SOURCES.txt' 2023-11-25T11:02:33,083 Getting requirements to build wheel: finished with status 'done' 2023-11-25T11:02:33,094 Installing backend dependencies: started 2023-11-25T11:02:33,095 Running command pip subprocess to install backend dependencies 2023-11-25T11:02:34,315 Using pip 23.3.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-11-25T11:02:34,845 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-25T11:02:35,329 Collecting wheel 2023-11-25T11:02:35,344 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.3-py3-none-any.whl (65 kB) 2023-11-25T11:02:37,575 Installing collected packages: wheel 2023-11-25T11:02:37,797 Creating /tmp/pip-build-env-0ymunvt5/normal/local/bin 2023-11-25T11:02:37,799 changing mode of /tmp/pip-build-env-0ymunvt5/normal/local/bin/wheel to 755 2023-11-25T11:02:37,811 Successfully installed wheel-0.41.3 2023-11-25T11:02:38,345 Installing backend dependencies: finished with status 'done' 2023-11-25T11:02:38,347 Created temporary directory: /tmp/pip-modern-metadata-41bqc8kt 2023-11-25T11:02:38,349 Preparing metadata (pyproject.toml): started 2023-11-25T11:02:38,351 Running command Preparing metadata (pyproject.toml) 2023-11-25T11:02:39,214 running dist_info 2023-11-25T11:02:39,220 creating /tmp/pip-modern-metadata-41bqc8kt/trtools.egg-info 2023-11-25T11:02:39,225 writing /tmp/pip-modern-metadata-41bqc8kt/trtools.egg-info/PKG-INFO 2023-11-25T11:02:39,228 writing dependency_links to /tmp/pip-modern-metadata-41bqc8kt/trtools.egg-info/dependency_links.txt 2023-11-25T11:02:39,231 writing entry points to /tmp/pip-modern-metadata-41bqc8kt/trtools.egg-info/entry_points.txt 2023-11-25T11:02:39,232 writing requirements to /tmp/pip-modern-metadata-41bqc8kt/trtools.egg-info/requires.txt 2023-11-25T11:02:39,233 writing top-level names to /tmp/pip-modern-metadata-41bqc8kt/trtools.egg-info/top_level.txt 2023-11-25T11:02:39,235 writing manifest file '/tmp/pip-modern-metadata-41bqc8kt/trtools.egg-info/SOURCES.txt' 2023-11-25T11:02:39,273 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2023-11-25T11:02:39,277 reading manifest file '/tmp/pip-modern-metadata-41bqc8kt/trtools.egg-info/SOURCES.txt' 2023-11-25T11:02:39,279 reading manifest template 'MANIFEST.in' 2023-11-25T11:02:39,280 warning: no previously-included files found matching 'trtools/testsupport/sample_vcfs' 2023-11-25T11:02:39,281 warning: no previously-included files found matching 'trtools/testsupport/sample_regions' 2023-11-25T11:02:39,281 warning: no previously-included files found matching 'trtools/testsupport/sample_stats' 2023-11-25T11:02:39,282 adding license file 'LICENSE.txt' 2023-11-25T11:02:39,283 writing manifest file '/tmp/pip-modern-metadata-41bqc8kt/trtools.egg-info/SOURCES.txt' 2023-11-25T11:02:39,284 creating '/tmp/pip-modern-metadata-41bqc8kt/trtools-5.1.0.dist-info' 2023-11-25T11:02:39,441 Preparing metadata (pyproject.toml): finished with status 'done' 2023-11-25T11:02:39,446 Source in /tmp/pip-wheel-0g8op2wo/trtools_ce517d8850d64fab9c7ee5cd60750332 has version 5.1.0, which satisfies requirement trtools==5.1.0 from https://files.pythonhosted.org/packages/61/ab/7a84aa588d919e83afee8774b8dac81bee5e9bdbe0fd1f9eaacea1ada271/trtools-5.1.0.tar.gz 2023-11-25T11:02:39,447 Removed trtools==5.1.0 from https://files.pythonhosted.org/packages/61/ab/7a84aa588d919e83afee8774b8dac81bee5e9bdbe0fd1f9eaacea1ada271/trtools-5.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-gwgefcli' 2023-11-25T11:02:39,453 Created temporary directory: /tmp/pip-unpack-5zy_g8bq 2023-11-25T11:02:39,454 Created temporary directory: /tmp/pip-unpack-l5g4wsk8 2023-11-25T11:02:39,466 Building wheels for collected packages: trtools 2023-11-25T11:02:39,470 Created temporary directory: /tmp/pip-wheel-xcaoevmu 2023-11-25T11:02:39,471 Destination directory: /tmp/pip-wheel-xcaoevmu 2023-11-25T11:02:39,473 Building wheel for trtools (pyproject.toml): started 2023-11-25T11:02:39,474 Running command Building wheel for trtools (pyproject.toml) 2023-11-25T11:02:40,280 running bdist_wheel 2023-11-25T11:02:40,303 running build 2023-11-25T11:02:40,304 running build_py 2023-11-25T11:02:40,309 creating build 2023-11-25T11:02:40,310 creating build/lib 2023-11-25T11:02:40,310 creating build/lib/trtools 2023-11-25T11:02:40,312 copying trtools/__init__.py -> build/lib/trtools 2023-11-25T11:02:40,314 copying trtools/version.py -> build/lib/trtools 2023-11-25T11:02:40,316 running egg_info 2023-11-25T11:02:40,322 writing trtools.egg-info/PKG-INFO 2023-11-25T11:02:40,325 writing dependency_links to trtools.egg-info/dependency_links.txt 2023-11-25T11:02:40,327 writing entry points to trtools.egg-info/entry_points.txt 2023-11-25T11:02:40,328 writing requirements to trtools.egg-info/requires.txt 2023-11-25T11:02:40,329 writing top-level names to trtools.egg-info/top_level.txt 2023-11-25T11:02:40,355 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2023-11-25T11:02:40,358 reading manifest file 'trtools.egg-info/SOURCES.txt' 2023-11-25T11:02:40,430 reading manifest template 'MANIFEST.in' 2023-11-25T11:02:40,431 warning: no previously-included files found matching 'trtools/testsupport/sample_vcfs' 2023-11-25T11:02:40,432 warning: no previously-included files found matching 'trtools/testsupport/sample_regions' 2023-11-25T11:02:40,433 warning: no previously-included files found matching 'trtools/testsupport/sample_stats' 2023-11-25T11:02:40,434 adding license file 'LICENSE.txt' 2023-11-25T11:02:40,449 writing manifest file 'trtools.egg-info/SOURCES.txt' 2023-11-25T11:02:40,455 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.associaTR' is absent from the `packages` configuration. 2023-11-25T11:02:40,455 !! 2023-11-25T11:02:40,456 ******************************************************************************** 2023-11-25T11:02:40,456 ############################ 2023-11-25T11:02:40,457 # Package would be ignored # 2023-11-25T11:02:40,457 ############################ 2023-11-25T11:02:40,458 Python recognizes 'trtools.associaTR' as an importable package[^1], 2023-11-25T11:02:40,458 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,459 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,459 package, please make sure that 'trtools.associaTR' is explicitly added 2023-11-25T11:02:40,460 to the `packages` configuration field. 2023-11-25T11:02:40,461 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,461 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,462 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,463 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,464 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,465 If you don't want 'trtools.associaTR' to be distributed and are 2023-11-25T11:02:40,465 already explicitly excluding 'trtools.associaTR' via 2023-11-25T11:02:40,466 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,466 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,466 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,467 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,468 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,469 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,470 even if it does not contain any `.py` files. 2023-11-25T11:02:40,470 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,471 directory, all directories are treated like packages. 2023-11-25T11:02:40,471 ******************************************************************************** 2023-11-25T11:02:40,472 !! 2023-11-25T11:02:40,472 check.warn(importable) 2023-11-25T11:02:40,473 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.associaTR.tests' is absent from the `packages` configuration. 2023-11-25T11:02:40,473 !! 2023-11-25T11:02:40,474 ******************************************************************************** 2023-11-25T11:02:40,475 ############################ 2023-11-25T11:02:40,475 # Package would be ignored # 2023-11-25T11:02:40,476 ############################ 2023-11-25T11:02:40,476 Python recognizes 'trtools.associaTR.tests' as an importable package[^1], 2023-11-25T11:02:40,477 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,478 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,478 package, please make sure that 'trtools.associaTR.tests' is explicitly added 2023-11-25T11:02:40,479 to the `packages` configuration field. 2023-11-25T11:02:40,480 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,480 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,481 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,482 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,482 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,483 If you don't want 'trtools.associaTR.tests' to be distributed and are 2023-11-25T11:02:40,483 already explicitly excluding 'trtools.associaTR.tests' via 2023-11-25T11:02:40,484 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,484 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,484 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,485 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,486 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,487 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,487 even if it does not contain any `.py` files. 2023-11-25T11:02:40,488 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,488 directory, all directories are treated like packages. 2023-11-25T11:02:40,488 ******************************************************************************** 2023-11-25T11:02:40,489 !! 2023-11-25T11:02:40,489 check.warn(importable) 2023-11-25T11:02:40,490 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.compareSTR' is absent from the `packages` configuration. 2023-11-25T11:02:40,490 !! 2023-11-25T11:02:40,491 ******************************************************************************** 2023-11-25T11:02:40,492 ############################ 2023-11-25T11:02:40,492 # Package would be ignored # 2023-11-25T11:02:40,492 ############################ 2023-11-25T11:02:40,493 Python recognizes 'trtools.compareSTR' as an importable package[^1], 2023-11-25T11:02:40,493 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,494 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,495 package, please make sure that 'trtools.compareSTR' is explicitly added 2023-11-25T11:02:40,495 to the `packages` configuration field. 2023-11-25T11:02:40,496 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,496 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,497 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,498 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,498 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,499 If you don't want 'trtools.compareSTR' to be distributed and are 2023-11-25T11:02:40,500 already explicitly excluding 'trtools.compareSTR' via 2023-11-25T11:02:40,500 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,501 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,501 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,502 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,503 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,504 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,505 even if it does not contain any `.py` files. 2023-11-25T11:02:40,506 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,506 directory, all directories are treated like packages. 2023-11-25T11:02:40,506 ******************************************************************************** 2023-11-25T11:02:40,507 !! 2023-11-25T11:02:40,507 check.warn(importable) 2023-11-25T11:02:40,508 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.compareSTR.tests' is absent from the `packages` configuration. 2023-11-25T11:02:40,508 !! 2023-11-25T11:02:40,509 ******************************************************************************** 2023-11-25T11:02:40,509 ############################ 2023-11-25T11:02:40,510 # Package would be ignored # 2023-11-25T11:02:40,510 ############################ 2023-11-25T11:02:40,510 Python recognizes 'trtools.compareSTR.tests' as an importable package[^1], 2023-11-25T11:02:40,511 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,511 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,512 package, please make sure that 'trtools.compareSTR.tests' is explicitly added 2023-11-25T11:02:40,512 to the `packages` configuration field. 2023-11-25T11:02:40,513 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,513 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,513 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,514 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,515 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,516 If you don't want 'trtools.compareSTR.tests' to be distributed and are 2023-11-25T11:02:40,516 already explicitly excluding 'trtools.compareSTR.tests' via 2023-11-25T11:02:40,516 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,517 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,517 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,518 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,519 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,520 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,521 even if it does not contain any `.py` files. 2023-11-25T11:02:40,521 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,522 directory, all directories are treated like packages. 2023-11-25T11:02:40,522 ******************************************************************************** 2023-11-25T11:02:40,523 !! 2023-11-25T11:02:40,523 check.warn(importable) 2023-11-25T11:02:40,524 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.dumpSTR' is absent from the `packages` configuration. 2023-11-25T11:02:40,524 !! 2023-11-25T11:02:40,525 ******************************************************************************** 2023-11-25T11:02:40,526 ############################ 2023-11-25T11:02:40,526 # Package would be ignored # 2023-11-25T11:02:40,527 ############################ 2023-11-25T11:02:40,527 Python recognizes 'trtools.dumpSTR' as an importable package[^1], 2023-11-25T11:02:40,528 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,529 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,529 package, please make sure that 'trtools.dumpSTR' is explicitly added 2023-11-25T11:02:40,529 to the `packages` configuration field. 2023-11-25T11:02:40,530 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,530 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,531 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,531 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,532 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,533 If you don't want 'trtools.dumpSTR' to be distributed and are 2023-11-25T11:02:40,533 already explicitly excluding 'trtools.dumpSTR' via 2023-11-25T11:02:40,533 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,534 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,534 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,535 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,535 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,537 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,537 even if it does not contain any `.py` files. 2023-11-25T11:02:40,537 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,538 directory, all directories are treated like packages. 2023-11-25T11:02:40,538 ******************************************************************************** 2023-11-25T11:02:40,539 !! 2023-11-25T11:02:40,540 check.warn(importable) 2023-11-25T11:02:40,540 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.dumpSTR.Example_Files' is absent from the `packages` configuration. 2023-11-25T11:02:40,541 !! 2023-11-25T11:02:40,542 ******************************************************************************** 2023-11-25T11:02:40,542 ############################ 2023-11-25T11:02:40,543 # Package would be ignored # 2023-11-25T11:02:40,543 ############################ 2023-11-25T11:02:40,544 Python recognizes 'trtools.dumpSTR.Example_Files' as an importable package[^1], 2023-11-25T11:02:40,544 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,545 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,545 package, please make sure that 'trtools.dumpSTR.Example_Files' is explicitly added 2023-11-25T11:02:40,546 to the `packages` configuration field. 2023-11-25T11:02:40,546 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,547 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,547 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,548 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,549 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,550 If you don't want 'trtools.dumpSTR.Example_Files' to be distributed and are 2023-11-25T11:02:40,550 already explicitly excluding 'trtools.dumpSTR.Example_Files' via 2023-11-25T11:02:40,551 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,551 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,552 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,553 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,553 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,554 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,555 even if it does not contain any `.py` files. 2023-11-25T11:02:40,555 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,555 directory, all directories are treated like packages. 2023-11-25T11:02:40,556 ******************************************************************************** 2023-11-25T11:02:40,556 !! 2023-11-25T11:02:40,557 check.warn(importable) 2023-11-25T11:02:40,557 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.dumpSTR.filter_files' is absent from the `packages` configuration. 2023-11-25T11:02:40,557 !! 2023-11-25T11:02:40,558 ******************************************************************************** 2023-11-25T11:02:40,558 ############################ 2023-11-25T11:02:40,559 # Package would be ignored # 2023-11-25T11:02:40,559 ############################ 2023-11-25T11:02:40,560 Python recognizes 'trtools.dumpSTR.filter_files' as an importable package[^1], 2023-11-25T11:02:40,560 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,561 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,561 package, please make sure that 'trtools.dumpSTR.filter_files' is explicitly added 2023-11-25T11:02:40,562 to the `packages` configuration field. 2023-11-25T11:02:40,563 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,563 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,563 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,564 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,565 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,566 If you don't want 'trtools.dumpSTR.filter_files' to be distributed and are 2023-11-25T11:02:40,567 already explicitly excluding 'trtools.dumpSTR.filter_files' via 2023-11-25T11:02:40,567 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,568 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,568 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,569 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,570 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,571 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,572 even if it does not contain any `.py` files. 2023-11-25T11:02:40,572 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,572 directory, all directories are treated like packages. 2023-11-25T11:02:40,573 ******************************************************************************** 2023-11-25T11:02:40,574 !! 2023-11-25T11:02:40,574 check.warn(importable) 2023-11-25T11:02:40,575 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.dumpSTR.tests' is absent from the `packages` configuration. 2023-11-25T11:02:40,575 !! 2023-11-25T11:02:40,576 ******************************************************************************** 2023-11-25T11:02:40,576 ############################ 2023-11-25T11:02:40,577 # Package would be ignored # 2023-11-25T11:02:40,577 ############################ 2023-11-25T11:02:40,577 Python recognizes 'trtools.dumpSTR.tests' as an importable package[^1], 2023-11-25T11:02:40,578 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,578 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,579 package, please make sure that 'trtools.dumpSTR.tests' is explicitly added 2023-11-25T11:02:40,579 to the `packages` configuration field. 2023-11-25T11:02:40,580 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,580 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,580 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,581 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,582 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,583 If you don't want 'trtools.dumpSTR.tests' to be distributed and are 2023-11-25T11:02:40,583 already explicitly excluding 'trtools.dumpSTR.tests' via 2023-11-25T11:02:40,583 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,584 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,584 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,585 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,586 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,587 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,588 even if it does not contain any `.py` files. 2023-11-25T11:02:40,588 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,589 directory, all directories are treated like packages. 2023-11-25T11:02:40,589 ******************************************************************************** 2023-11-25T11:02:40,590 !! 2023-11-25T11:02:40,590 check.warn(importable) 2023-11-25T11:02:40,591 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.mergeSTR' is absent from the `packages` configuration. 2023-11-25T11:02:40,591 !! 2023-11-25T11:02:40,592 ******************************************************************************** 2023-11-25T11:02:40,592 ############################ 2023-11-25T11:02:40,593 # Package would be ignored # 2023-11-25T11:02:40,593 ############################ 2023-11-25T11:02:40,594 Python recognizes 'trtools.mergeSTR' as an importable package[^1], 2023-11-25T11:02:40,594 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,595 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,595 package, please make sure that 'trtools.mergeSTR' is explicitly added 2023-11-25T11:02:40,596 to the `packages` configuration field. 2023-11-25T11:02:40,597 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,597 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,598 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,598 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,599 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,601 If you don't want 'trtools.mergeSTR' to be distributed and are 2023-11-25T11:02:40,601 already explicitly excluding 'trtools.mergeSTR' via 2023-11-25T11:02:40,601 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,602 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,602 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,603 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,604 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,605 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,605 even if it does not contain any `.py` files. 2023-11-25T11:02:40,606 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,606 directory, all directories are treated like packages. 2023-11-25T11:02:40,607 ******************************************************************************** 2023-11-25T11:02:40,608 !! 2023-11-25T11:02:40,608 check.warn(importable) 2023-11-25T11:02:40,609 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.mergeSTR.Example_Files' is absent from the `packages` configuration. 2023-11-25T11:02:40,609 !! 2023-11-25T11:02:40,610 ******************************************************************************** 2023-11-25T11:02:40,610 ############################ 2023-11-25T11:02:40,611 # Package would be ignored # 2023-11-25T11:02:40,611 ############################ 2023-11-25T11:02:40,612 Python recognizes 'trtools.mergeSTR.Example_Files' as an importable package[^1], 2023-11-25T11:02:40,612 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,613 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,614 package, please make sure that 'trtools.mergeSTR.Example_Files' is explicitly added 2023-11-25T11:02:40,614 to the `packages` configuration field. 2023-11-25T11:02:40,615 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,615 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,616 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,617 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,618 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,619 If you don't want 'trtools.mergeSTR.Example_Files' to be distributed and are 2023-11-25T11:02:40,619 already explicitly excluding 'trtools.mergeSTR.Example_Files' via 2023-11-25T11:02:40,620 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,620 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,621 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,622 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,622 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,624 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,624 even if it does not contain any `.py` files. 2023-11-25T11:02:40,625 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,625 directory, all directories are treated like packages. 2023-11-25T11:02:40,625 ******************************************************************************** 2023-11-25T11:02:40,626 !! 2023-11-25T11:02:40,627 check.warn(importable) 2023-11-25T11:02:40,627 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.mergeSTR.tests' is absent from the `packages` configuration. 2023-11-25T11:02:40,627 !! 2023-11-25T11:02:40,628 ******************************************************************************** 2023-11-25T11:02:40,629 ############################ 2023-11-25T11:02:40,629 # Package would be ignored # 2023-11-25T11:02:40,629 ############################ 2023-11-25T11:02:40,630 Python recognizes 'trtools.mergeSTR.tests' as an importable package[^1], 2023-11-25T11:02:40,630 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,631 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,631 package, please make sure that 'trtools.mergeSTR.tests' is explicitly added 2023-11-25T11:02:40,631 to the `packages` configuration field. 2023-11-25T11:02:40,632 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,633 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,633 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,634 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,634 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,635 If you don't want 'trtools.mergeSTR.tests' to be distributed and are 2023-11-25T11:02:40,636 already explicitly excluding 'trtools.mergeSTR.tests' via 2023-11-25T11:02:40,636 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,637 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,637 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,638 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,639 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,640 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,641 even if it does not contain any `.py` files. 2023-11-25T11:02:40,641 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,641 directory, all directories are treated like packages. 2023-11-25T11:02:40,642 ******************************************************************************** 2023-11-25T11:02:40,643 !! 2023-11-25T11:02:40,643 check.warn(importable) 2023-11-25T11:02:40,644 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.prancSTR' is absent from the `packages` configuration. 2023-11-25T11:02:40,644 !! 2023-11-25T11:02:40,645 ******************************************************************************** 2023-11-25T11:02:40,646 ############################ 2023-11-25T11:02:40,646 # Package would be ignored # 2023-11-25T11:02:40,646 ############################ 2023-11-25T11:02:40,647 Python recognizes 'trtools.prancSTR' as an importable package[^1], 2023-11-25T11:02:40,647 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,648 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,649 package, please make sure that 'trtools.prancSTR' is explicitly added 2023-11-25T11:02:40,649 to the `packages` configuration field. 2023-11-25T11:02:40,650 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,651 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,651 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,652 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,653 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,653 If you don't want 'trtools.prancSTR' to be distributed and are 2023-11-25T11:02:40,654 already explicitly excluding 'trtools.prancSTR' via 2023-11-25T11:02:40,654 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,654 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,655 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,656 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,656 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,657 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,658 even if it does not contain any `.py` files. 2023-11-25T11:02:40,658 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,659 directory, all directories are treated like packages. 2023-11-25T11:02:40,659 ******************************************************************************** 2023-11-25T11:02:40,660 !! 2023-11-25T11:02:40,660 check.warn(importable) 2023-11-25T11:02:40,660 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.prancSTR.paper_draft' is absent from the `packages` configuration. 2023-11-25T11:02:40,661 !! 2023-11-25T11:02:40,662 ******************************************************************************** 2023-11-25T11:02:40,662 ############################ 2023-11-25T11:02:40,662 # Package would be ignored # 2023-11-25T11:02:40,663 ############################ 2023-11-25T11:02:40,663 Python recognizes 'trtools.prancSTR.paper_draft' as an importable package[^1], 2023-11-25T11:02:40,663 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,664 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,665 package, please make sure that 'trtools.prancSTR.paper_draft' is explicitly added 2023-11-25T11:02:40,665 to the `packages` configuration field. 2023-11-25T11:02:40,666 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,667 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,667 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,668 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,669 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,670 If you don't want 'trtools.prancSTR.paper_draft' to be distributed and are 2023-11-25T11:02:40,670 already explicitly excluding 'trtools.prancSTR.paper_draft' via 2023-11-25T11:02:40,671 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,671 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,672 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,673 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,674 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,676 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,676 even if it does not contain any `.py` files. 2023-11-25T11:02:40,677 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,677 directory, all directories are treated like packages. 2023-11-25T11:02:40,677 ******************************************************************************** 2023-11-25T11:02:40,678 !! 2023-11-25T11:02:40,678 check.warn(importable) 2023-11-25T11:02:40,679 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.prancSTR.tests' is absent from the `packages` configuration. 2023-11-25T11:02:40,679 !! 2023-11-25T11:02:40,680 ******************************************************************************** 2023-11-25T11:02:40,681 ############################ 2023-11-25T11:02:40,681 # Package would be ignored # 2023-11-25T11:02:40,682 ############################ 2023-11-25T11:02:40,682 Python recognizes 'trtools.prancSTR.tests' as an importable package[^1], 2023-11-25T11:02:40,682 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,683 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,684 package, please make sure that 'trtools.prancSTR.tests' is explicitly added 2023-11-25T11:02:40,684 to the `packages` configuration field. 2023-11-25T11:02:40,685 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,685 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,686 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,687 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,687 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,688 If you don't want 'trtools.prancSTR.tests' to be distributed and are 2023-11-25T11:02:40,689 already explicitly excluding 'trtools.prancSTR.tests' via 2023-11-25T11:02:40,689 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,690 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,690 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,691 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,692 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,693 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,694 even if it does not contain any `.py` files. 2023-11-25T11:02:40,694 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,695 directory, all directories are treated like packages. 2023-11-25T11:02:40,695 ******************************************************************************** 2023-11-25T11:02:40,696 !! 2023-11-25T11:02:40,697 check.warn(importable) 2023-11-25T11:02:40,697 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.qcSTR' is absent from the `packages` configuration. 2023-11-25T11:02:40,697 !! 2023-11-25T11:02:40,698 ******************************************************************************** 2023-11-25T11:02:40,699 ############################ 2023-11-25T11:02:40,699 # Package would be ignored # 2023-11-25T11:02:40,700 ############################ 2023-11-25T11:02:40,701 Python recognizes 'trtools.qcSTR' as an importable package[^1], 2023-11-25T11:02:40,701 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,702 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,702 package, please make sure that 'trtools.qcSTR' is explicitly added 2023-11-25T11:02:40,703 to the `packages` configuration field. 2023-11-25T11:02:40,703 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,704 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,704 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,705 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,705 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,706 If you don't want 'trtools.qcSTR' to be distributed and are 2023-11-25T11:02:40,706 already explicitly excluding 'trtools.qcSTR' via 2023-11-25T11:02:40,707 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,707 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,708 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,708 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,709 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,710 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,711 even if it does not contain any `.py` files. 2023-11-25T11:02:40,711 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,711 directory, all directories are treated like packages. 2023-11-25T11:02:40,712 ******************************************************************************** 2023-11-25T11:02:40,713 !! 2023-11-25T11:02:40,713 check.warn(importable) 2023-11-25T11:02:40,714 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.qcSTR.images' is absent from the `packages` configuration. 2023-11-25T11:02:40,714 !! 2023-11-25T11:02:40,715 ******************************************************************************** 2023-11-25T11:02:40,715 ############################ 2023-11-25T11:02:40,716 # Package would be ignored # 2023-11-25T11:02:40,716 ############################ 2023-11-25T11:02:40,717 Python recognizes 'trtools.qcSTR.images' as an importable package[^1], 2023-11-25T11:02:40,717 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,718 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,719 package, please make sure that 'trtools.qcSTR.images' is explicitly added 2023-11-25T11:02:40,719 to the `packages` configuration field. 2023-11-25T11:02:40,720 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,721 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,721 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,722 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,723 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,724 If you don't want 'trtools.qcSTR.images' to be distributed and are 2023-11-25T11:02:40,725 already explicitly excluding 'trtools.qcSTR.images' via 2023-11-25T11:02:40,725 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,726 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,727 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,727 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,728 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,729 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,730 even if it does not contain any `.py` files. 2023-11-25T11:02:40,730 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,730 directory, all directories are treated like packages. 2023-11-25T11:02:40,731 ******************************************************************************** 2023-11-25T11:02:40,731 !! 2023-11-25T11:02:40,732 check.warn(importable) 2023-11-25T11:02:40,732 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.qcSTR.tests' is absent from the `packages` configuration. 2023-11-25T11:02:40,733 !! 2023-11-25T11:02:40,733 ******************************************************************************** 2023-11-25T11:02:40,734 ############################ 2023-11-25T11:02:40,734 # Package would be ignored # 2023-11-25T11:02:40,734 ############################ 2023-11-25T11:02:40,735 Python recognizes 'trtools.qcSTR.tests' as an importable package[^1], 2023-11-25T11:02:40,735 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,736 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,736 package, please make sure that 'trtools.qcSTR.tests' is explicitly added 2023-11-25T11:02:40,737 to the `packages` configuration field. 2023-11-25T11:02:40,738 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,738 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,738 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,739 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,740 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,741 If you don't want 'trtools.qcSTR.tests' to be distributed and are 2023-11-25T11:02:40,742 already explicitly excluding 'trtools.qcSTR.tests' via 2023-11-25T11:02:40,742 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,743 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,743 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,745 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,746 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,748 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,749 even if it does not contain any `.py` files. 2023-11-25T11:02:40,749 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,750 directory, all directories are treated like packages. 2023-11-25T11:02:40,751 ******************************************************************************** 2023-11-25T11:02:40,752 !! 2023-11-25T11:02:40,752 check.warn(importable) 2023-11-25T11:02:40,753 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.simTR' is absent from the `packages` configuration. 2023-11-25T11:02:40,754 !! 2023-11-25T11:02:40,755 ******************************************************************************** 2023-11-25T11:02:40,755 ############################ 2023-11-25T11:02:40,755 # Package would be ignored # 2023-11-25T11:02:40,756 ############################ 2023-11-25T11:02:40,756 Python recognizes 'trtools.simTR' as an importable package[^1], 2023-11-25T11:02:40,756 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,757 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,757 package, please make sure that 'trtools.simTR' is explicitly added 2023-11-25T11:02:40,758 to the `packages` configuration field. 2023-11-25T11:02:40,759 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,759 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,760 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,760 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,761 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,762 If you don't want 'trtools.simTR' to be distributed and are 2023-11-25T11:02:40,762 already explicitly excluding 'trtools.simTR' via 2023-11-25T11:02:40,763 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,763 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,763 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,764 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,765 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,767 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,767 even if it does not contain any `.py` files. 2023-11-25T11:02:40,768 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,768 directory, all directories are treated like packages. 2023-11-25T11:02:40,769 ******************************************************************************** 2023-11-25T11:02:40,770 !! 2023-11-25T11:02:40,770 check.warn(importable) 2023-11-25T11:02:40,771 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.simTR.tests' is absent from the `packages` configuration. 2023-11-25T11:02:40,771 !! 2023-11-25T11:02:40,772 ******************************************************************************** 2023-11-25T11:02:40,773 ############################ 2023-11-25T11:02:40,773 # Package would be ignored # 2023-11-25T11:02:40,774 ############################ 2023-11-25T11:02:40,774 Python recognizes 'trtools.simTR.tests' as an importable package[^1], 2023-11-25T11:02:40,775 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,776 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,776 package, please make sure that 'trtools.simTR.tests' is explicitly added 2023-11-25T11:02:40,777 to the `packages` configuration field. 2023-11-25T11:02:40,778 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,779 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,779 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,780 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,781 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,783 If you don't want 'trtools.simTR.tests' to be distributed and are 2023-11-25T11:02:40,783 already explicitly excluding 'trtools.simTR.tests' via 2023-11-25T11:02:40,784 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,784 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,784 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,785 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,786 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,788 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,788 even if it does not contain any `.py` files. 2023-11-25T11:02:40,788 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,789 directory, all directories are treated like packages. 2023-11-25T11:02:40,789 ******************************************************************************** 2023-11-25T11:02:40,790 !! 2023-11-25T11:02:40,791 check.warn(importable) 2023-11-25T11:02:40,791 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.statSTR' is absent from the `packages` configuration. 2023-11-25T11:02:40,792 !! 2023-11-25T11:02:40,793 ******************************************************************************** 2023-11-25T11:02:40,793 ############################ 2023-11-25T11:02:40,793 # Package would be ignored # 2023-11-25T11:02:40,794 ############################ 2023-11-25T11:02:40,795 Python recognizes 'trtools.statSTR' as an importable package[^1], 2023-11-25T11:02:40,795 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,796 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,797 package, please make sure that 'trtools.statSTR' is explicitly added 2023-11-25T11:02:40,797 to the `packages` configuration field. 2023-11-25T11:02:40,798 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,799 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,799 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,800 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,801 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,802 If you don't want 'trtools.statSTR' to be distributed and are 2023-11-25T11:02:40,803 already explicitly excluding 'trtools.statSTR' via 2023-11-25T11:02:40,803 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,803 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,804 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,805 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,806 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,808 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,808 even if it does not contain any `.py` files. 2023-11-25T11:02:40,809 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,809 directory, all directories are treated like packages. 2023-11-25T11:02:40,810 ******************************************************************************** 2023-11-25T11:02:40,812 !! 2023-11-25T11:02:40,812 check.warn(importable) 2023-11-25T11:02:40,812 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.statSTR.tests' is absent from the `packages` configuration. 2023-11-25T11:02:40,813 !! 2023-11-25T11:02:40,814 ******************************************************************************** 2023-11-25T11:02:40,814 ############################ 2023-11-25T11:02:40,815 # Package would be ignored # 2023-11-25T11:02:40,815 ############################ 2023-11-25T11:02:40,816 Python recognizes 'trtools.statSTR.tests' as an importable package[^1], 2023-11-25T11:02:40,816 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,817 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,817 package, please make sure that 'trtools.statSTR.tests' is explicitly added 2023-11-25T11:02:40,818 to the `packages` configuration field. 2023-11-25T11:02:40,818 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,819 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,819 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,820 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,821 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,822 If you don't want 'trtools.statSTR.tests' to be distributed and are 2023-11-25T11:02:40,823 already explicitly excluding 'trtools.statSTR.tests' via 2023-11-25T11:02:40,823 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,827 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,830 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,833 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,834 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,836 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,836 even if it does not contain any `.py` files. 2023-11-25T11:02:40,837 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,837 directory, all directories are treated like packages. 2023-11-25T11:02:40,838 ******************************************************************************** 2023-11-25T11:02:40,839 !! 2023-11-25T11:02:40,840 check.warn(importable) 2023-11-25T11:02:40,840 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.testsupport' is absent from the `packages` configuration. 2023-11-25T11:02:40,841 !! 2023-11-25T11:02:40,842 ******************************************************************************** 2023-11-25T11:02:40,843 ############################ 2023-11-25T11:02:40,844 # Package would be ignored # 2023-11-25T11:02:40,845 ############################ 2023-11-25T11:02:40,846 Python recognizes 'trtools.testsupport' as an importable package[^1], 2023-11-25T11:02:40,847 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,849 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,850 package, please make sure that 'trtools.testsupport' is explicitly added 2023-11-25T11:02:40,853 to the `packages` configuration field. 2023-11-25T11:02:40,856 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,856 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,857 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,858 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,859 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,860 If you don't want 'trtools.testsupport' to be distributed and are 2023-11-25T11:02:40,860 already explicitly excluding 'trtools.testsupport' via 2023-11-25T11:02:40,861 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,861 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,862 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,869 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,870 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,872 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,873 even if it does not contain any `.py` files. 2023-11-25T11:02:40,874 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,874 directory, all directories are treated like packages. 2023-11-25T11:02:40,875 ******************************************************************************** 2023-11-25T11:02:40,876 !! 2023-11-25T11:02:40,876 check.warn(importable) 2023-11-25T11:02:40,877 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.testsupport.sample_regions' is absent from the `packages` configuration. 2023-11-25T11:02:40,878 !! 2023-11-25T11:02:40,881 ******************************************************************************** 2023-11-25T11:02:40,883 ############################ 2023-11-25T11:02:40,883 # Package would be ignored # 2023-11-25T11:02:40,884 ############################ 2023-11-25T11:02:40,885 Python recognizes 'trtools.testsupport.sample_regions' as an importable package[^1], 2023-11-25T11:02:40,885 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,890 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,930 package, please make sure that 'trtools.testsupport.sample_regions' is explicitly added 2023-11-25T11:02:40,931 to the `packages` configuration field. 2023-11-25T11:02:40,932 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,933 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,933 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,935 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,936 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,937 If you don't want 'trtools.testsupport.sample_regions' to be distributed and are 2023-11-25T11:02:40,937 already explicitly excluding 'trtools.testsupport.sample_regions' via 2023-11-25T11:02:40,938 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,938 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,939 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,940 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,941 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,942 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,943 even if it does not contain any `.py` files. 2023-11-25T11:02:40,943 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,944 directory, all directories are treated like packages. 2023-11-25T11:02:40,944 ******************************************************************************** 2023-11-25T11:02:40,945 !! 2023-11-25T11:02:40,946 check.warn(importable) 2023-11-25T11:02:40,946 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.testsupport.sample_simtrdata' is absent from the `packages` configuration. 2023-11-25T11:02:40,947 !! 2023-11-25T11:02:40,948 ******************************************************************************** 2023-11-25T11:02:40,948 ############################ 2023-11-25T11:02:40,949 # Package would be ignored # 2023-11-25T11:02:40,949 ############################ 2023-11-25T11:02:40,950 Python recognizes 'trtools.testsupport.sample_simtrdata' as an importable package[^1], 2023-11-25T11:02:40,950 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,951 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,952 package, please make sure that 'trtools.testsupport.sample_simtrdata' is explicitly added 2023-11-25T11:02:40,952 to the `packages` configuration field. 2023-11-25T11:02:40,953 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,954 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,954 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,955 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,956 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,957 If you don't want 'trtools.testsupport.sample_simtrdata' to be distributed and are 2023-11-25T11:02:40,958 already explicitly excluding 'trtools.testsupport.sample_simtrdata' via 2023-11-25T11:02:40,958 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,959 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,959 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,960 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,961 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,963 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,964 even if it does not contain any `.py` files. 2023-11-25T11:02:40,964 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,965 directory, all directories are treated like packages. 2023-11-25T11:02:40,966 ******************************************************************************** 2023-11-25T11:02:40,967 !! 2023-11-25T11:02:40,967 check.warn(importable) 2023-11-25T11:02:40,968 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.testsupport.sample_stats' is absent from the `packages` configuration. 2023-11-25T11:02:40,969 !! 2023-11-25T11:02:40,970 ******************************************************************************** 2023-11-25T11:02:40,970 ############################ 2023-11-25T11:02:40,971 # Package would be ignored # 2023-11-25T11:02:40,971 ############################ 2023-11-25T11:02:40,972 Python recognizes 'trtools.testsupport.sample_stats' as an importable package[^1], 2023-11-25T11:02:40,973 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:40,974 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:40,975 package, please make sure that 'trtools.testsupport.sample_stats' is explicitly added 2023-11-25T11:02:40,976 to the `packages` configuration field. 2023-11-25T11:02:40,977 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:40,977 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:40,978 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:40,979 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:40,981 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:40,982 If you don't want 'trtools.testsupport.sample_stats' to be distributed and are 2023-11-25T11:02:40,982 already explicitly excluding 'trtools.testsupport.sample_stats' via 2023-11-25T11:02:40,983 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:40,983 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:40,989 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:40,990 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:40,991 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:40,993 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:40,994 even if it does not contain any `.py` files. 2023-11-25T11:02:40,994 On the other hand, currently there is no concept of package data 2023-11-25T11:02:40,995 directory, all directories are treated like packages. 2023-11-25T11:02:40,995 ******************************************************************************** 2023-11-25T11:02:40,996 !! 2023-11-25T11:02:40,996 check.warn(importable) 2023-11-25T11:02:40,997 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.testsupport.sample_vcfs' is absent from the `packages` configuration. 2023-11-25T11:02:40,998 !! 2023-11-25T11:02:40,999 ******************************************************************************** 2023-11-25T11:02:40,999 ############################ 2023-11-25T11:02:41,000 # Package would be ignored # 2023-11-25T11:02:41,000 ############################ 2023-11-25T11:02:41,001 Python recognizes 'trtools.testsupport.sample_vcfs' as an importable package[^1], 2023-11-25T11:02:41,001 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:41,002 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:41,003 package, please make sure that 'trtools.testsupport.sample_vcfs' is explicitly added 2023-11-25T11:02:41,003 to the `packages` configuration field. 2023-11-25T11:02:41,005 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:41,005 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:41,006 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:41,007 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:41,008 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:41,009 If you don't want 'trtools.testsupport.sample_vcfs' to be distributed and are 2023-11-25T11:02:41,010 already explicitly excluding 'trtools.testsupport.sample_vcfs' via 2023-11-25T11:02:41,010 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:41,011 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:41,012 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:41,013 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:41,014 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:41,021 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:41,021 even if it does not contain any `.py` files. 2023-11-25T11:02:41,022 On the other hand, currently there is no concept of package data 2023-11-25T11:02:41,022 directory, all directories are treated like packages. 2023-11-25T11:02:41,024 ******************************************************************************** 2023-11-25T11:02:41,032 !! 2023-11-25T11:02:41,039 check.warn(importable) 2023-11-25T11:02:41,043 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.testsupport.sample_vcfs.associaTR' is absent from the `packages` configuration. 2023-11-25T11:02:41,045 !! 2023-11-25T11:02:41,046 ******************************************************************************** 2023-11-25T11:02:41,046 ############################ 2023-11-25T11:02:41,047 # Package would be ignored # 2023-11-25T11:02:41,047 ############################ 2023-11-25T11:02:41,048 Python recognizes 'trtools.testsupport.sample_vcfs.associaTR' as an importable package[^1], 2023-11-25T11:02:41,048 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:41,049 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:41,050 package, please make sure that 'trtools.testsupport.sample_vcfs.associaTR' is explicitly added 2023-11-25T11:02:41,051 to the `packages` configuration field. 2023-11-25T11:02:41,052 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:41,053 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:41,053 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:41,054 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:41,056 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:41,057 If you don't want 'trtools.testsupport.sample_vcfs.associaTR' to be distributed and are 2023-11-25T11:02:41,057 already explicitly excluding 'trtools.testsupport.sample_vcfs.associaTR' via 2023-11-25T11:02:41,058 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:41,059 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:41,059 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:41,061 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:41,062 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:41,063 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:41,064 even if it does not contain any `.py` files. 2023-11-25T11:02:41,064 On the other hand, currently there is no concept of package data 2023-11-25T11:02:41,065 directory, all directories are treated like packages. 2023-11-25T11:02:41,065 ******************************************************************************** 2023-11-25T11:02:41,066 !! 2023-11-25T11:02:41,067 check.warn(importable) 2023-11-25T11:02:41,067 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.testsupport.sample_vcfs.beagle' is absent from the `packages` configuration. 2023-11-25T11:02:41,067 !! 2023-11-25T11:02:41,068 ******************************************************************************** 2023-11-25T11:02:41,069 ############################ 2023-11-25T11:02:41,069 # Package would be ignored # 2023-11-25T11:02:41,069 ############################ 2023-11-25T11:02:41,070 Python recognizes 'trtools.testsupport.sample_vcfs.beagle' as an importable package[^1], 2023-11-25T11:02:41,070 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:41,071 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:41,072 package, please make sure that 'trtools.testsupport.sample_vcfs.beagle' is explicitly added 2023-11-25T11:02:41,072 to the `packages` configuration field. 2023-11-25T11:02:41,074 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:41,074 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:41,075 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:41,076 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:41,077 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:41,077 If you don't want 'trtools.testsupport.sample_vcfs.beagle' to be distributed and are 2023-11-25T11:02:41,078 already explicitly excluding 'trtools.testsupport.sample_vcfs.beagle' via 2023-11-25T11:02:41,078 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:41,079 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:41,079 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:41,081 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:41,082 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:41,083 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:41,084 even if it does not contain any `.py` files. 2023-11-25T11:02:41,084 On the other hand, currently there is no concept of package data 2023-11-25T11:02:41,084 directory, all directories are treated like packages. 2023-11-25T11:02:41,085 ******************************************************************************** 2023-11-25T11:02:41,086 !! 2023-11-25T11:02:41,087 check.warn(importable) 2023-11-25T11:02:41,087 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.testsupport.sample_vcfs.compareSTR_vcfs' is absent from the `packages` configuration. 2023-11-25T11:02:41,088 !! 2023-11-25T11:02:41,089 ******************************************************************************** 2023-11-25T11:02:41,089 ############################ 2023-11-25T11:02:41,090 # Package would be ignored # 2023-11-25T11:02:41,090 ############################ 2023-11-25T11:02:41,091 Python recognizes 'trtools.testsupport.sample_vcfs.compareSTR_vcfs' as an importable package[^1], 2023-11-25T11:02:41,091 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:41,092 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:41,093 package, please make sure that 'trtools.testsupport.sample_vcfs.compareSTR_vcfs' is explicitly added 2023-11-25T11:02:41,094 to the `packages` configuration field. 2023-11-25T11:02:41,095 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:41,095 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:41,095 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:41,096 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:41,097 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:41,098 If you don't want 'trtools.testsupport.sample_vcfs.compareSTR_vcfs' to be distributed and are 2023-11-25T11:02:41,098 already explicitly excluding 'trtools.testsupport.sample_vcfs.compareSTR_vcfs' via 2023-11-25T11:02:41,099 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:41,099 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:41,100 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:41,101 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:41,102 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:41,103 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:41,104 even if it does not contain any `.py` files. 2023-11-25T11:02:41,104 On the other hand, currently there is no concept of package data 2023-11-25T11:02:41,104 directory, all directories are treated like packages. 2023-11-25T11:02:41,105 ******************************************************************************** 2023-11-25T11:02:41,106 !! 2023-11-25T11:02:41,106 check.warn(importable) 2023-11-25T11:02:41,107 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.testsupport.sample_vcfs.dumpSTR_vcfs' is absent from the `packages` configuration. 2023-11-25T11:02:41,107 !! 2023-11-25T11:02:41,108 ******************************************************************************** 2023-11-25T11:02:41,109 ############################ 2023-11-25T11:02:41,109 # Package would be ignored # 2023-11-25T11:02:41,110 ############################ 2023-11-25T11:02:41,110 Python recognizes 'trtools.testsupport.sample_vcfs.dumpSTR_vcfs' as an importable package[^1], 2023-11-25T11:02:41,111 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:41,111 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:41,112 package, please make sure that 'trtools.testsupport.sample_vcfs.dumpSTR_vcfs' is explicitly added 2023-11-25T11:02:41,113 to the `packages` configuration field. 2023-11-25T11:02:41,114 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:41,114 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:41,114 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:41,115 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:41,116 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:41,117 If you don't want 'trtools.testsupport.sample_vcfs.dumpSTR_vcfs' to be distributed and are 2023-11-25T11:02:41,118 already explicitly excluding 'trtools.testsupport.sample_vcfs.dumpSTR_vcfs' via 2023-11-25T11:02:41,118 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:41,119 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:41,119 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:41,121 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:41,121 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:41,123 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:41,123 even if it does not contain any `.py` files. 2023-11-25T11:02:41,124 On the other hand, currently there is no concept of package data 2023-11-25T11:02:41,124 directory, all directories are treated like packages. 2023-11-25T11:02:41,124 ******************************************************************************** 2023-11-25T11:02:41,125 !! 2023-11-25T11:02:41,126 check.warn(importable) 2023-11-25T11:02:41,126 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.testsupport.sample_vcfs.dumpSTR_vcfs.pyvcf_output' is absent from the `packages` configuration. 2023-11-25T11:02:41,126 !! 2023-11-25T11:02:41,127 ******************************************************************************** 2023-11-25T11:02:41,128 ############################ 2023-11-25T11:02:41,128 # Package would be ignored # 2023-11-25T11:02:41,129 ############################ 2023-11-25T11:02:41,129 Python recognizes 'trtools.testsupport.sample_vcfs.dumpSTR_vcfs.pyvcf_output' as an importable package[^1], 2023-11-25T11:02:41,130 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:41,130 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:41,131 package, please make sure that 'trtools.testsupport.sample_vcfs.dumpSTR_vcfs.pyvcf_output' is explicitly added 2023-11-25T11:02:41,131 to the `packages` configuration field. 2023-11-25T11:02:41,132 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:41,133 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:41,133 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:41,134 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:41,135 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:41,136 If you don't want 'trtools.testsupport.sample_vcfs.dumpSTR_vcfs.pyvcf_output' to be distributed and are 2023-11-25T11:02:41,137 already explicitly excluding 'trtools.testsupport.sample_vcfs.dumpSTR_vcfs.pyvcf_output' via 2023-11-25T11:02:41,137 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:41,138 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:41,138 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:41,139 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:41,140 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:41,142 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:41,142 even if it does not contain any `.py` files. 2023-11-25T11:02:41,143 On the other hand, currently there is no concept of package data 2023-11-25T11:02:41,143 directory, all directories are treated like packages. 2023-11-25T11:02:41,144 ******************************************************************************** 2023-11-25T11:02:41,145 !! 2023-11-25T11:02:41,145 check.warn(importable) 2023-11-25T11:02:41,146 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.testsupport.sample_vcfs.mergeSTR_vcfs' is absent from the `packages` configuration. 2023-11-25T11:02:41,146 !! 2023-11-25T11:02:41,147 ******************************************************************************** 2023-11-25T11:02:41,148 ############################ 2023-11-25T11:02:41,148 # Package would be ignored # 2023-11-25T11:02:41,149 ############################ 2023-11-25T11:02:41,149 Python recognizes 'trtools.testsupport.sample_vcfs.mergeSTR_vcfs' as an importable package[^1], 2023-11-25T11:02:41,149 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:41,150 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:41,151 package, please make sure that 'trtools.testsupport.sample_vcfs.mergeSTR_vcfs' is explicitly added 2023-11-25T11:02:41,151 to the `packages` configuration field. 2023-11-25T11:02:41,152 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:41,152 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:41,153 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:41,154 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:41,154 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:41,155 If you don't want 'trtools.testsupport.sample_vcfs.mergeSTR_vcfs' to be distributed and are 2023-11-25T11:02:41,156 already explicitly excluding 'trtools.testsupport.sample_vcfs.mergeSTR_vcfs' via 2023-11-25T11:02:41,156 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:41,156 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:41,157 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:41,158 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:41,159 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:41,160 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:41,161 even if it does not contain any `.py` files. 2023-11-25T11:02:41,161 On the other hand, currently there is no concept of package data 2023-11-25T11:02:41,162 directory, all directories are treated like packages. 2023-11-25T11:02:41,162 ******************************************************************************** 2023-11-25T11:02:41,163 !! 2023-11-25T11:02:41,163 check.warn(importable) 2023-11-25T11:02:41,164 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.testsupport.sample_vcfs.qc_vcfs' is absent from the `packages` configuration. 2023-11-25T11:02:41,164 !! 2023-11-25T11:02:41,165 ******************************************************************************** 2023-11-25T11:02:41,166 ############################ 2023-11-25T11:02:41,166 # Package would be ignored # 2023-11-25T11:02:41,167 ############################ 2023-11-25T11:02:41,167 Python recognizes 'trtools.testsupport.sample_vcfs.qc_vcfs' as an importable package[^1], 2023-11-25T11:02:41,168 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:41,169 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:41,169 package, please make sure that 'trtools.testsupport.sample_vcfs.qc_vcfs' is explicitly added 2023-11-25T11:02:41,170 to the `packages` configuration field. 2023-11-25T11:02:41,171 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:41,171 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:41,172 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:41,173 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:41,174 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:41,174 If you don't want 'trtools.testsupport.sample_vcfs.qc_vcfs' to be distributed and are 2023-11-25T11:02:41,175 already explicitly excluding 'trtools.testsupport.sample_vcfs.qc_vcfs' via 2023-11-25T11:02:41,175 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:41,176 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:41,176 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:41,177 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:41,178 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:41,179 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:41,179 even if it does not contain any `.py` files. 2023-11-25T11:02:41,180 On the other hand, currently there is no concept of package data 2023-11-25T11:02:41,180 directory, all directories are treated like packages. 2023-11-25T11:02:41,181 ******************************************************************************** 2023-11-25T11:02:41,181 !! 2023-11-25T11:02:41,182 check.warn(importable) 2023-11-25T11:02:41,182 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.utils' is absent from the `packages` configuration. 2023-11-25T11:02:41,183 !! 2023-11-25T11:02:41,184 ******************************************************************************** 2023-11-25T11:02:41,184 ############################ 2023-11-25T11:02:41,184 # Package would be ignored # 2023-11-25T11:02:41,185 ############################ 2023-11-25T11:02:41,186 Python recognizes 'trtools.utils' as an importable package[^1], 2023-11-25T11:02:41,186 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:41,187 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:41,188 package, please make sure that 'trtools.utils' is explicitly added 2023-11-25T11:02:41,188 to the `packages` configuration field. 2023-11-25T11:02:41,189 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:41,190 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:41,192 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:41,193 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:41,194 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:41,200 If you don't want 'trtools.utils' to be distributed and are 2023-11-25T11:02:41,202 already explicitly excluding 'trtools.utils' via 2023-11-25T11:02:41,204 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:41,204 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:41,205 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:41,206 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:41,207 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:41,208 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:41,209 even if it does not contain any `.py` files. 2023-11-25T11:02:41,209 On the other hand, currently there is no concept of package data 2023-11-25T11:02:41,210 directory, all directories are treated like packages. 2023-11-25T11:02:41,210 ******************************************************************************** 2023-11-25T11:02:41,211 !! 2023-11-25T11:02:41,212 check.warn(importable) 2023-11-25T11:02:41,212 /tmp/pip-build-env-0ymunvt5/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'trtools.utils.tests' is absent from the `packages` configuration. 2023-11-25T11:02:41,212 !! 2023-11-25T11:02:41,213 ******************************************************************************** 2023-11-25T11:02:41,214 ############################ 2023-11-25T11:02:41,214 # Package would be ignored # 2023-11-25T11:02:41,214 ############################ 2023-11-25T11:02:41,215 Python recognizes 'trtools.utils.tests' as an importable package[^1], 2023-11-25T11:02:41,215 but it is absent from setuptools' `packages` configuration. 2023-11-25T11:02:41,216 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-25T11:02:41,217 package, please make sure that 'trtools.utils.tests' is explicitly added 2023-11-25T11:02:41,217 to the `packages` configuration field. 2023-11-25T11:02:41,218 Alternatively, you can also rely on setuptools' discovery methods 2023-11-25T11:02:41,218 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-25T11:02:41,219 instead of `find_packages(...)`/`find:`). 2023-11-25T11:02:41,220 You can read more about "package discovery" on setuptools documentation page: 2023-11-25T11:02:41,221 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-25T11:02:41,222 If you don't want 'trtools.utils.tests' to be distributed and are 2023-11-25T11:02:41,222 already explicitly excluding 'trtools.utils.tests' via 2023-11-25T11:02:41,223 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-25T11:02:41,223 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-25T11:02:41,224 combination with a more fine grained `package-data` configuration. 2023-11-25T11:02:41,225 You can read more about "package data files" on setuptools documentation page: 2023-11-25T11:02:41,226 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-25T11:02:41,227 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-25T11:02:41,228 even if it does not contain any `.py` files. 2023-11-25T11:02:41,230 On the other hand, currently there is no concept of package data 2023-11-25T11:02:41,231 directory, all directories are treated like packages. 2023-11-25T11:02:41,231 ******************************************************************************** 2023-11-25T11:02:41,232 !! 2023-11-25T11:02:41,240 check.warn(importable) 2023-11-25T11:02:41,242 creating build/lib/trtools/associaTR 2023-11-25T11:02:41,243 copying trtools/associaTR/README.rst -> build/lib/trtools/associaTR 2023-11-25T11:02:41,244 copying trtools/associaTR/__init__.py -> build/lib/trtools/associaTR 2023-11-25T11:02:41,248 copying trtools/associaTR/associaTR.py -> build/lib/trtools/associaTR 2023-11-25T11:02:41,248 copying trtools/associaTR/load_and_filter_genotypes.py -> build/lib/trtools/associaTR 2023-11-25T11:02:41,249 creating build/lib/trtools/associaTR/tests 2023-11-25T11:02:41,249 copying trtools/associaTR/tests/__init__.py -> build/lib/trtools/associaTR/tests 2023-11-25T11:02:41,250 copying trtools/associaTR/tests/test_associaTR.py -> build/lib/trtools/associaTR/tests 2023-11-25T11:02:41,251 creating build/lib/trtools/compareSTR 2023-11-25T11:02:41,251 copying trtools/compareSTR/README.rst -> build/lib/trtools/compareSTR 2023-11-25T11:02:41,252 copying trtools/compareSTR/__init__.py -> build/lib/trtools/compareSTR 2023-11-25T11:02:41,252 copying trtools/compareSTR/compareSTR.py -> build/lib/trtools/compareSTR 2023-11-25T11:02:41,253 creating build/lib/trtools/compareSTR/tests 2023-11-25T11:02:41,255 copying trtools/compareSTR/tests/__init__.py -> build/lib/trtools/compareSTR/tests 2023-11-25T11:02:41,256 copying trtools/compareSTR/tests/test_compareSTR.py -> build/lib/trtools/compareSTR/tests 2023-11-25T11:02:41,257 creating build/lib/trtools/dumpSTR 2023-11-25T11:02:41,257 copying trtools/dumpSTR/README.rst -> build/lib/trtools/dumpSTR 2023-11-25T11:02:41,258 copying trtools/dumpSTR/__init__.py -> build/lib/trtools/dumpSTR 2023-11-25T11:02:41,258 copying trtools/dumpSTR/dumpSTR.py -> build/lib/trtools/dumpSTR 2023-11-25T11:02:41,259 copying trtools/dumpSTR/filters.py -> build/lib/trtools/dumpSTR 2023-11-25T11:02:41,259 creating build/lib/trtools/dumpSTR/Example_Files 2023-11-25T11:02:41,260 copying trtools/dumpSTR/Example_Files/test_run_gangstr.vcf -> build/lib/trtools/dumpSTR/Example_Files 2023-11-25T11:02:41,260 copying trtools/dumpSTR/Example_Files/test_run_original.vcf -> build/lib/trtools/dumpSTR/Example_Files 2023-11-25T11:02:41,261 creating build/lib/trtools/dumpSTR/filter_files 2023-11-25T11:02:41,262 copying trtools/dumpSTR/filter_files/hg19_segmentalduplications.bed.gz -> build/lib/trtools/dumpSTR/filter_files 2023-11-25T11:02:41,262 copying trtools/dumpSTR/filter_files/hg19_segmentalduplications.bed.gz.tbi -> build/lib/trtools/dumpSTR/filter_files 2023-11-25T11:02:41,262 copying trtools/dumpSTR/filter_files/hs37_segmentalduplications.bed.gz -> build/lib/trtools/dumpSTR/filter_files 2023-11-25T11:02:41,263 copying trtools/dumpSTR/filter_files/hs37_segmentalduplications.bed.gz.tbi -> build/lib/trtools/dumpSTR/filter_files 2023-11-25T11:02:41,264 creating build/lib/trtools/dumpSTR/tests 2023-11-25T11:02:41,264 copying trtools/dumpSTR/tests/__init__.py -> build/lib/trtools/dumpSTR/tests 2023-11-25T11:02:41,265 copying trtools/dumpSTR/tests/test_dumpSTR.py -> build/lib/trtools/dumpSTR/tests 2023-11-25T11:02:41,265 copying trtools/dumpSTR/tests/test_filters.py -> build/lib/trtools/dumpSTR/tests 2023-11-25T11:02:41,265 creating build/lib/trtools/mergeSTR 2023-11-25T11:02:41,266 copying trtools/mergeSTR/README.rst -> build/lib/trtools/mergeSTR 2023-11-25T11:02:41,267 copying trtools/mergeSTR/__init__.py -> build/lib/trtools/mergeSTR 2023-11-25T11:02:41,267 copying trtools/mergeSTR/mergeSTR.py -> build/lib/trtools/mergeSTR 2023-11-25T11:02:41,268 creating build/lib/trtools/mergeSTR/Example_Files 2023-11-25T11:02:41,268 copying trtools/mergeSTR/Example_Files/test_run_original.vcf -> build/lib/trtools/mergeSTR/Example_Files 2023-11-25T11:02:41,269 creating build/lib/trtools/mergeSTR/tests 2023-11-25T11:02:41,269 copying trtools/mergeSTR/tests/__init__.py -> build/lib/trtools/mergeSTR/tests 2023-11-25T11:02:41,270 copying trtools/mergeSTR/tests/test_mergeSTR.py -> build/lib/trtools/mergeSTR/tests 2023-11-25T11:02:41,271 creating build/lib/trtools/prancSTR 2023-11-25T11:02:41,271 copying trtools/prancSTR/README.rst -> build/lib/trtools/prancSTR 2023-11-25T11:02:41,272 copying trtools/prancSTR/__init__.py -> build/lib/trtools/prancSTR 2023-11-25T11:02:41,272 copying trtools/prancSTR/prancSTR.py -> build/lib/trtools/prancSTR 2023-11-25T11:02:41,273 creating build/lib/trtools/prancSTR/paper_draft 2023-11-25T11:02:41,273 copying trtools/prancSTR/paper_draft/prancSTR_Manuscript_draft.pdf -> build/lib/trtools/prancSTR/paper_draft 2023-11-25T11:02:41,274 creating build/lib/trtools/prancSTR/tests 2023-11-25T11:02:41,274 copying trtools/prancSTR/tests/__init__.py -> build/lib/trtools/prancSTR/tests 2023-11-25T11:02:41,275 copying trtools/prancSTR/tests/test_prancSTR.py -> build/lib/trtools/prancSTR/tests 2023-11-25T11:02:41,275 creating build/lib/trtools/qcSTR 2023-11-25T11:02:41,276 copying trtools/qcSTR/README.rst -> build/lib/trtools/qcSTR 2023-11-25T11:02:41,276 copying trtools/qcSTR/__init__.py -> build/lib/trtools/qcSTR 2023-11-25T11:02:41,277 copying trtools/qcSTR/qcSTR.py -> build/lib/trtools/qcSTR 2023-11-25T11:02:41,277 copying trtools/qcSTR/wishlist.rst -> build/lib/trtools/qcSTR 2023-11-25T11:02:41,278 creating build/lib/trtools/qcSTR/images 2023-11-25T11:02:41,278 copying trtools/qcSTR/images/README.txt -> build/lib/trtools/qcSTR/images 2023-11-25T11:02:41,278 copying trtools/qcSTR/images/chrom-callnum.png -> build/lib/trtools/qcSTR/images 2023-11-25T11:02:41,279 copying trtools/qcSTR/images/diffref-bias.png -> build/lib/trtools/qcSTR/images 2023-11-25T11:02:41,279 copying trtools/qcSTR/images/diffref-histogram.png -> build/lib/trtools/qcSTR/images 2023-11-25T11:02:41,280 copying trtools/qcSTR/images/quality-locus-stratified.png -> build/lib/trtools/qcSTR/images 2023-11-25T11:02:41,280 copying trtools/qcSTR/images/quality-per-call.png -> build/lib/trtools/qcSTR/images 2023-11-25T11:02:41,280 copying trtools/qcSTR/images/quality-per-locus.png -> build/lib/trtools/qcSTR/images 2023-11-25T11:02:41,281 copying trtools/qcSTR/images/quality-per-sample.png -> build/lib/trtools/qcSTR/images 2023-11-25T11:02:41,281 copying trtools/qcSTR/images/quality-sample-stratified.png -> build/lib/trtools/qcSTR/images 2023-11-25T11:02:41,282 copying trtools/qcSTR/images/sample-callnum.png -> build/lib/trtools/qcSTR/images 2023-11-25T11:02:41,282 creating build/lib/trtools/qcSTR/tests 2023-11-25T11:02:41,283 copying trtools/qcSTR/tests/.bandit -> build/lib/trtools/qcSTR/tests 2023-11-25T11:02:41,283 copying trtools/qcSTR/tests/__init__.py -> build/lib/trtools/qcSTR/tests 2023-11-25T11:02:41,283 copying trtools/qcSTR/tests/test_qcSTR.py -> build/lib/trtools/qcSTR/tests 2023-11-25T11:02:41,284 creating build/lib/trtools/simTR 2023-11-25T11:02:41,284 copying trtools/simTR/README.rst -> build/lib/trtools/simTR 2023-11-25T11:02:41,285 copying trtools/simTR/__init__.py -> build/lib/trtools/simTR 2023-11-25T11:02:41,286 copying trtools/simTR/simTR.py -> build/lib/trtools/simTR 2023-11-25T11:02:41,286 creating build/lib/trtools/simTR/tests 2023-11-25T11:02:41,287 copying trtools/simTR/tests/__init__.py -> build/lib/trtools/simTR/tests 2023-11-25T11:02:41,287 copying trtools/simTR/tests/test_simTR.py -> build/lib/trtools/simTR/tests 2023-11-25T11:02:41,288 creating build/lib/trtools/statSTR 2023-11-25T11:02:41,289 copying trtools/statSTR/README.rst -> build/lib/trtools/statSTR 2023-11-25T11:02:41,289 copying trtools/statSTR/__init__.py -> build/lib/trtools/statSTR 2023-11-25T11:02:41,290 copying trtools/statSTR/statSTR.py -> build/lib/trtools/statSTR 2023-11-25T11:02:41,290 creating build/lib/trtools/statSTR/tests 2023-11-25T11:02:41,291 copying trtools/statSTR/tests/__init__.py -> build/lib/trtools/statSTR/tests 2023-11-25T11:02:41,292 copying trtools/statSTR/tests/test_statSTR.py -> build/lib/trtools/statSTR/tests 2023-11-25T11:02:41,292 creating build/lib/trtools/testsupport 2023-11-25T11:02:41,293 copying trtools/testsupport/__init__.py -> build/lib/trtools/testsupport 2023-11-25T11:02:41,293 copying trtools/testsupport/dataloader.py -> build/lib/trtools/testsupport 2023-11-25T11:02:41,294 copying trtools/testsupport/test_trtools.sh -> build/lib/trtools/testsupport 2023-11-25T11:02:41,295 copying trtools/testsupport/utils.py -> build/lib/trtools/testsupport 2023-11-25T11:02:41,295 creating build/lib/trtools/testsupport/sample_regions 2023-11-25T11:02:41,296 copying trtools/testsupport/sample_regions/README.txt -> build/lib/trtools/testsupport/sample_regions 2023-11-25T11:02:41,296 copying trtools/testsupport/sample_regions/test_regions1.bed.gz -> build/lib/trtools/testsupport/sample_regions 2023-11-25T11:02:41,297 copying trtools/testsupport/sample_regions/test_regions1.bed.gz.tbi -> build/lib/trtools/testsupport/sample_regions 2023-11-25T11:02:41,297 copying trtools/testsupport/sample_regions/test_regions2.bed.gz -> build/lib/trtools/testsupport/sample_regions 2023-11-25T11:02:41,298 copying trtools/testsupport/sample_regions/test_regions2.bed.gz.tbi -> build/lib/trtools/testsupport/sample_regions 2023-11-25T11:02:41,299 copying trtools/testsupport/sample_regions/test_regions3.bed.gz -> build/lib/trtools/testsupport/sample_regions 2023-11-25T11:02:41,300 copying trtools/testsupport/sample_regions/test_regions4.bed.gz -> build/lib/trtools/testsupport/sample_regions 2023-11-25T11:02:41,300 copying trtools/testsupport/sample_regions/test_regions4.bed.gz.tbi -> build/lib/trtools/testsupport/sample_regions 2023-11-25T11:02:41,301 creating build/lib/trtools/testsupport/sample_simtrdata 2023-11-25T11:02:41,301 copying trtools/testsupport/sample_simtrdata/CBL.fa -> build/lib/trtools/testsupport/sample_simtrdata 2023-11-25T11:02:41,301 copying trtools/testsupport/sample_simtrdata/CBL.fa.fai -> build/lib/trtools/testsupport/sample_simtrdata 2023-11-25T11:02:41,302 copying trtools/testsupport/sample_simtrdata/README.txt -> build/lib/trtools/testsupport/sample_simtrdata 2023-11-25T11:02:41,302 creating build/lib/trtools/testsupport/sample_stats 2023-11-25T11:02:41,303 copying trtools/testsupport/sample_stats/many_samples_all.tab -> build/lib/trtools/testsupport/sample_stats 2023-11-25T11:02:41,303 copying trtools/testsupport/sample_stats/many_samples_all_strat.tab -> build/lib/trtools/testsupport/sample_stats 2023-11-25T11:02:41,304 creating build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,304 copying trtools/testsupport/sample_vcfs/CEU_test.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,305 copying trtools/testsupport/sample_vcfs/CEU_test.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,305 copying trtools/testsupport/sample_vcfs/README.txt -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,306 copying trtools/testsupport/sample_vcfs/artificial_gangstr.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,306 copying trtools/testsupport/sample_vcfs/few_loci.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,307 copying trtools/testsupport/sample_vcfs/few_samples_few_loci.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,307 copying trtools/testsupport/sample_vcfs/few_samples_few_loci.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,308 copying trtools/testsupport/sample_vcfs/fewer_samples.txt -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,309 copying trtools/testsupport/sample_vcfs/many_samples.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,309 copying trtools/testsupport/sample_vcfs/many_samples.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,311 copying trtools/testsupport/sample_vcfs/many_samples_multiple_chroms.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,312 copying trtools/testsupport/sample_vcfs/many_samples_multiple_chroms.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,316 copying trtools/testsupport/sample_vcfs/many_samples_subsample1.txt -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,322 copying trtools/testsupport/sample_vcfs/many_samples_subsample2.txt -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,324 copying trtools/testsupport/sample_vcfs/missing_samples.txt -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,336 copying trtools/testsupport/sample_vcfs/one_sample_multiple_chroms.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,356 copying trtools/testsupport/sample_vcfs/one_sample_multiple_chroms.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,362 copying trtools/testsupport/sample_vcfs/snps.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,367 copying trtools/testsupport/sample_vcfs/test_ExpansionHunter.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,367 copying trtools/testsupport/sample_vcfs/test_ExpansionHunter_reheadered.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,368 copying trtools/testsupport/sample_vcfs/test_advntr.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,369 copying trtools/testsupport/sample_vcfs/test_beagle-4.1.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,371 copying trtools/testsupport/sample_vcfs/test_beagle_4-0.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,478 copying trtools/testsupport/sample_vcfs/test_broken.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,480 copying trtools/testsupport/sample_vcfs/test_gangstr.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,496 copying trtools/testsupport/sample_vcfs/test_gangstr_nochr.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,511 copying trtools/testsupport/sample_vcfs/test_gangstr_noqual.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,513 copying trtools/testsupport/sample_vcfs/test_gangstr_samples.txt -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,515 copying trtools/testsupport/sample_vcfs/test_hipstr.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,587 copying trtools/testsupport/sample_vcfs/test_multitype.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,589 copying trtools/testsupport/sample_vcfs/test_popstr.vcf -> build/lib/trtools/testsupport/sample_vcfs 2023-11-25T11:02:41,591 creating build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,592 copying trtools/testsupport/sample_vcfs/associaTR/.gitignore -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,594 copying trtools/testsupport/sample_vcfs/associaTR/35_samples.txt -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,596 copying trtools/testsupport/sample_vcfs/associaTR/45_samples.txt -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,598 copying trtools/testsupport/sample_vcfs/associaTR/README -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,600 copying trtools/testsupport/sample_vcfs/associaTR/ap1_dosage_header.hdr -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,602 copying trtools/testsupport/sample_vcfs/associaTR/ap1_multi_dosages.tsv.gz -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,604 copying trtools/testsupport/sample_vcfs/associaTR/ap2_dosage_header.hdr -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,606 copying trtools/testsupport/sample_vcfs/associaTR/ap2_multi_dosages.tsv.gz -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,608 copying trtools/testsupport/sample_vcfs/associaTR/combined.plink2.trait_0.glm.linear -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,611 copying trtools/testsupport/sample_vcfs/associaTR/combined_35.plink2.trait_0.glm.linear -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,614 copying trtools/testsupport/sample_vcfs/associaTR/combined_traits_for_plink.tab -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,617 copying trtools/testsupport/sample_vcfs/associaTR/generate_plink_output.sh -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,619 copying trtools/testsupport/sample_vcfs/associaTR/generate_traits.py -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,621 copying trtools/testsupport/sample_vcfs/associaTR/gp_dosage_header.hdr -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,623 copying trtools/testsupport/sample_vcfs/associaTR/make_dosages.py -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,625 copying trtools/testsupport/sample_vcfs/associaTR/many_samples_biallelic.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,632 copying trtools/testsupport/sample_vcfs/associaTR/many_samples_biallelic.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,634 copying trtools/testsupport/sample_vcfs/associaTR/many_samples_biallelic_dosages.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,644 copying trtools/testsupport/sample_vcfs/associaTR/many_samples_biallelic_dosages.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,646 copying trtools/testsupport/sample_vcfs/associaTR/many_samples_multiallelic.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,648 copying trtools/testsupport/sample_vcfs/associaTR/many_samples_multiallelic_dosages.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,651 copying trtools/testsupport/sample_vcfs/associaTR/many_samples_multiallelic_dosages.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,652 copying trtools/testsupport/sample_vcfs/associaTR/samples.txt -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,654 copying trtools/testsupport/sample_vcfs/associaTR/samples_6_to_45.txt -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,656 copying trtools/testsupport/sample_vcfs/associaTR/single.plink2.trait_0.glm.linear -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,659 copying trtools/testsupport/sample_vcfs/associaTR/single_35.plink2.trait_0.glm.linear -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,663 copying trtools/testsupport/sample_vcfs/associaTR/single_40.plink2.trait_0.glm.linear -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,666 copying trtools/testsupport/sample_vcfs/associaTR/single_40_dosages.plink2.trait_0.glm.linear -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,669 copying trtools/testsupport/sample_vcfs/associaTR/single_cutoff_5.plink2.trait_0.glm.linear -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,672 copying trtools/testsupport/sample_vcfs/associaTR/single_dosages.plink2.trait_0.glm.linear -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,675 copying trtools/testsupport/sample_vcfs/associaTR/single_traits_for_plink.tab -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,678 copying trtools/testsupport/sample_vcfs/associaTR/traits_0.npy -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,680 copying trtools/testsupport/sample_vcfs/associaTR/traits_0_40_samples.npy -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,682 copying trtools/testsupport/sample_vcfs/associaTR/traits_1.npy -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,684 copying trtools/testsupport/sample_vcfs/associaTR/traits_1_45_samples.npy -> build/lib/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:41,686 creating build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,687 copying trtools/testsupport/sample_vcfs/beagle/1kg_snpstr_21_first_100k_first_50_annotated.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,724 copying trtools/testsupport/sample_vcfs/beagle/1kg_snpstr_21_first_100k_first_50_annotated.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,726 copying trtools/testsupport/sample_vcfs/beagle/1kg_snpstr_21_first_100k_second_50_STRs_imputed.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,759 copying trtools/testsupport/sample_vcfs/beagle/1kg_snpstr_21_first_100k_second_50_STRs_imputed.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,762 copying trtools/testsupport/sample_vcfs/beagle/advntr_imputed.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,764 copying trtools/testsupport/sample_vcfs/beagle/advntr_imputed_missing_infos.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,767 copying trtools/testsupport/sample_vcfs/beagle/eh_imputed.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,770 copying trtools/testsupport/sample_vcfs/beagle/eh_imputed_missing_infos.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,773 copying trtools/testsupport/sample_vcfs/beagle/gangstr_imputed.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,777 copying trtools/testsupport/sample_vcfs/beagle/gangstr_imputed_missing_infos.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,781 copying trtools/testsupport/sample_vcfs/beagle/hipstr_imputed.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,784 copying trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_missing_infos.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:41,787 creating build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,787 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/empty_list.txt -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,789 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/sample_list.txt -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,791 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_advntr.vcf -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,793 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_better_comparability_calculation_1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,795 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_better_comparability_calculation_1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,797 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_better_comparability_calculation_2.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,799 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_better_comparability_calculation_2.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,801 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,805 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,807 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr2.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,810 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr2.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,812 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr2_wrongsamp.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,815 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr2_wrongsamp.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,817 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,827 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,829 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr_flanking_bp_flanking.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,831 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr_flanking_bp_flanking.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,833 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr_flanking_bp_non_flanking.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,835 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr_flanking_bp_non_flanking.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,837 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_no_comparable_records_1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,839 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_no_comparable_records_1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,841 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_no_comparable_records_2.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,843 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_no_comparable_records_2.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,845 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_popstr.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,852 copying trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_popstr.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:41,854 creating build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,855 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_advntr.sorted.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,860 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_advntr.sorted.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,862 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_eh.sorted.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,866 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_eh.sorted.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,869 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_popstr.sorted.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,875 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_popstr.sorted.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,878 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/advntr_filters.loclog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,880 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/advntr_filters.samplog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,882 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/advntr_filters.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,903 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/bad_preexisting_filter_ac_refac.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,905 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/bad_preexisting_het_hwep.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,908 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/bad_preexisting_hrun.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,910 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/create_test_files.sh -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,913 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/drop_filtered.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,925 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_expansion.loclog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,927 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_expansion.samplog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,929 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_expansion.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,954 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_most.loclog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,956 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_most.samplog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:41,958 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_most.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,037 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/hipstr_filters.loclog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,039 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/hipstr_filters.samplog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,041 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/hipstr_filters.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,121 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/locus_filters.loclog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,122 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/locus_filters.samplog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,124 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/locus_filters.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,205 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/popstr_filters.loclog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,207 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/popstr_filters.samplog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,209 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/popstr_filters.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,235 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/sample_region.bed.gz -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,237 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/sample_region.bed.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,239 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/sample_region2.bed.gz -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,241 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/sample_region2.bed.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,243 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_advntr.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,246 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_advntr.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,248 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_broken.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,250 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_broken.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,252 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_gangstr.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,258 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_gangstr.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,260 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_gangstr_nochr.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,265 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_gangstr_nochr.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,267 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/trio_chr21_gangstr.sorted.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,284 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/trio_chr21_gangstr.sorted.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,287 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/trio_chr21_hipstr.sorted.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,299 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/trio_chr21_hipstr.sorted.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,302 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/worrisome_preexisting_filter.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:42,304 creating build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,304 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/README -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,306 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/advntr_filters.loclog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,308 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/advntr_filters.samplog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,310 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/advntr_filters.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,325 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/drop_filtered.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,335 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_expansion.loclog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,338 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_expansion.samplog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,340 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_expansion.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,364 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_most.loclog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,366 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_most.samplog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,369 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_most.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,452 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/hipstr_filters.loclog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,455 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/hipstr_filters.samplog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,457 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/hipstr_filters.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,539 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/locus_filters.loclog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,544 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/locus_filters.samplog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,546 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/locus_filters.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,634 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/popstr_filters.loclog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,636 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/popstr_filters.samplog.tab -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,638 copying trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/popstr_filters.vcf -> build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:42,661 creating build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,662 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/advntr_merged.vcf -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,664 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/create_test_files.sh -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,666 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/eh_X_no_alt_merged.vcf -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,668 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/eh_X_no_alt_merged_swap.vcf -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,670 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/eh_merged.vcf -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,673 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/eh_no_alt_merged.vcf -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,675 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/gangstr_merged.vcf -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,705 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr-harmonized-merge-contains-flanking.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,707 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr-harmonized-merge-contains-flanking.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,709 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr-harmonized-merge-no-flanking.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,712 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr-harmonized-merge-no-flanking.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,714 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_flanking_harmonization_test_output.vcf -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,717 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_merged.vcf -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,720 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/one_sample_multiple_chroms_diff_contig_order.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,723 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/one_sample_multiple_chroms_diff_contig_order.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,725 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/popstr_merged.vcf -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,746 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_advntr1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,748 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_advntr1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,749 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_advntr2.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,751 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_advntr2.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,753 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifferent1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,755 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifferent1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,757 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifferent2.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,759 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifferent2.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,761 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifflength.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,763 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifflength.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,765 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigmissing1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,767 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigmissing1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,768 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigmissing2.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,770 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigmissing2.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,772 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,774 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,776 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh2.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,778 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh2.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,779 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_X1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,781 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_X1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,783 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_X_no_alt.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,785 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_X_no_alt.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,787 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_no_alt.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,789 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_no_alt.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,791 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,796 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,798 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr1_1contig.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,800 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr1_1contig.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,802 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr2.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,807 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr2.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,810 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr2_1contig.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,812 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr2_1contig.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,813 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_dupID.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,818 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_dupID.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,820 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_missingformat1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,822 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_missingformat1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,824 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_missinginfo1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,826 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_missinginfo1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,828 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_unindexed1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,834 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_unindexed2.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,840 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_unzipped1.vcf -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,856 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_unzipped2.vcf -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,872 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,874 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,876 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr1_badinfo.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,878 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr1_badinfo.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,880 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr2.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,882 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr2.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,884 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr2_alt_v_ref.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,887 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr2_alt_v_ref.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,889 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_popstr1.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,896 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_popstr1.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,898 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_popstr2.vcf.gz -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,904 copying trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_popstr2.vcf.gz.tbi -> build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:42,906 creating build/lib/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:42,908 copying trtools/testsupport/sample_vcfs/qc_vcfs/50by3.vcf -> build/lib/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:42,910 copying trtools/testsupport/sample_vcfs/qc_vcfs/5by50.vcf -> build/lib/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:42,913 copying trtools/testsupport/sample_vcfs/qc_vcfs/test_fakesample.txt -> build/lib/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:42,915 copying trtools/testsupport/sample_vcfs/qc_vcfs/test_popstr.vcf -> build/lib/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:42,940 copying trtools/testsupport/sample_vcfs/qc_vcfs/test_popstr_nocontig.vcf -> build/lib/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:42,962 copying trtools/testsupport/sample_vcfs/qc_vcfs/test_samplelist.txt -> build/lib/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:42,964 creating build/lib/trtools/utils 2023-11-25T11:02:42,965 copying trtools/utils/__init__.py -> build/lib/trtools/utils 2023-11-25T11:02:42,968 copying trtools/utils/common.py -> build/lib/trtools/utils 2023-11-25T11:02:42,969 copying trtools/utils/mergeutils.py -> build/lib/trtools/utils 2023-11-25T11:02:42,971 copying trtools/utils/tr_harmonizer.py -> build/lib/trtools/utils 2023-11-25T11:02:42,975 copying trtools/utils/utils.py -> build/lib/trtools/utils 2023-11-25T11:02:42,977 creating build/lib/trtools/utils/tests 2023-11-25T11:02:42,978 copying trtools/utils/tests/.bandit -> build/lib/trtools/utils/tests 2023-11-25T11:02:42,980 copying trtools/utils/tests/__init__.py -> build/lib/trtools/utils/tests 2023-11-25T11:02:42,981 copying trtools/utils/tests/test_common.py -> build/lib/trtools/utils/tests 2023-11-25T11:02:42,984 copying trtools/utils/tests/test_mergeutils.py -> build/lib/trtools/utils/tests 2023-11-25T11:02:42,986 copying trtools/utils/tests/test_trharmonizer.py -> build/lib/trtools/utils/tests 2023-11-25T11:02:42,989 copying trtools/utils/tests/test_utils.py -> build/lib/trtools/utils/tests 2023-11-25T11:02:42,993 running build_scripts 2023-11-25T11:02:42,993 creating build/scripts-3.11 2023-11-25T11:02:42,995 copying trtools/testsupport/test_trtools.sh -> build/scripts-3.11 2023-11-25T11:02:42,997 copying scripts/trtools_prep_beagle_vcf.sh -> build/scripts-3.11 2023-11-25T11:02:43,007 installing to build/bdist.linux-armv7l/wheel 2023-11-25T11:02:43,008 running install 2023-11-25T11:02:43,032 running install_lib 2023-11-25T11:02:43,037 creating build/bdist.linux-armv7l 2023-11-25T11:02:43,037 creating build/bdist.linux-armv7l/wheel 2023-11-25T11:02:43,039 creating build/bdist.linux-armv7l/wheel/trtools 2023-11-25T11:02:43,041 creating build/bdist.linux-armv7l/wheel/trtools/associaTR 2023-11-25T11:02:43,042 copying build/lib/trtools/associaTR/load_and_filter_genotypes.py -> build/bdist.linux-armv7l/wheel/trtools/associaTR 2023-11-25T11:02:43,045 creating build/bdist.linux-armv7l/wheel/trtools/associaTR/tests 2023-11-25T11:02:43,046 copying build/lib/trtools/associaTR/tests/test_associaTR.py -> build/bdist.linux-armv7l/wheel/trtools/associaTR/tests 2023-11-25T11:02:43,048 copying build/lib/trtools/associaTR/tests/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/associaTR/tests 2023-11-25T11:02:43,050 copying build/lib/trtools/associaTR/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/associaTR 2023-11-25T11:02:43,052 copying build/lib/trtools/associaTR/associaTR.py -> build/bdist.linux-armv7l/wheel/trtools/associaTR 2023-11-25T11:02:43,054 copying build/lib/trtools/associaTR/README.rst -> build/bdist.linux-armv7l/wheel/trtools/associaTR 2023-11-25T11:02:43,057 creating build/bdist.linux-armv7l/wheel/trtools/simTR 2023-11-25T11:02:43,058 creating build/bdist.linux-armv7l/wheel/trtools/simTR/tests 2023-11-25T11:02:43,059 copying build/lib/trtools/simTR/tests/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/simTR/tests 2023-11-25T11:02:43,060 copying build/lib/trtools/simTR/tests/test_simTR.py -> build/bdist.linux-armv7l/wheel/trtools/simTR/tests 2023-11-25T11:02:43,062 copying build/lib/trtools/simTR/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/simTR 2023-11-25T11:02:43,064 copying build/lib/trtools/simTR/README.rst -> build/bdist.linux-armv7l/wheel/trtools/simTR 2023-11-25T11:02:43,066 copying build/lib/trtools/simTR/simTR.py -> build/bdist.linux-armv7l/wheel/trtools/simTR 2023-11-25T11:02:43,068 creating build/bdist.linux-armv7l/wheel/trtools/compareSTR 2023-11-25T11:02:43,069 copying build/lib/trtools/compareSTR/compareSTR.py -> build/bdist.linux-armv7l/wheel/trtools/compareSTR 2023-11-25T11:02:43,072 creating build/bdist.linux-armv7l/wheel/trtools/compareSTR/tests 2023-11-25T11:02:43,073 copying build/lib/trtools/compareSTR/tests/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/compareSTR/tests 2023-11-25T11:02:43,074 copying build/lib/trtools/compareSTR/tests/test_compareSTR.py -> build/bdist.linux-armv7l/wheel/trtools/compareSTR/tests 2023-11-25T11:02:43,077 copying build/lib/trtools/compareSTR/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/compareSTR 2023-11-25T11:02:43,078 copying build/lib/trtools/compareSTR/README.rst -> build/bdist.linux-armv7l/wheel/trtools/compareSTR 2023-11-25T11:02:43,080 copying build/lib/trtools/__init__.py -> build/bdist.linux-armv7l/wheel/trtools 2023-11-25T11:02:43,082 creating build/bdist.linux-armv7l/wheel/trtools/prancSTR 2023-11-25T11:02:43,083 creating build/bdist.linux-armv7l/wheel/trtools/prancSTR/paper_draft 2023-11-25T11:02:43,084 copying build/lib/trtools/prancSTR/paper_draft/prancSTR_Manuscript_draft.pdf -> build/bdist.linux-armv7l/wheel/trtools/prancSTR/paper_draft 2023-11-25T11:02:43,117 creating build/bdist.linux-armv7l/wheel/trtools/prancSTR/tests 2023-11-25T11:02:43,118 copying build/lib/trtools/prancSTR/tests/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/prancSTR/tests 2023-11-25T11:02:43,120 copying build/lib/trtools/prancSTR/tests/test_prancSTR.py -> build/bdist.linux-armv7l/wheel/trtools/prancSTR/tests 2023-11-25T11:02:43,122 copying build/lib/trtools/prancSTR/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/prancSTR 2023-11-25T11:02:43,124 copying build/lib/trtools/prancSTR/README.rst -> build/bdist.linux-armv7l/wheel/trtools/prancSTR 2023-11-25T11:02:43,126 copying build/lib/trtools/prancSTR/prancSTR.py -> build/bdist.linux-armv7l/wheel/trtools/prancSTR 2023-11-25T11:02:43,129 creating build/bdist.linux-armv7l/wheel/trtools/utils 2023-11-25T11:02:43,130 copying build/lib/trtools/utils/mergeutils.py -> build/bdist.linux-armv7l/wheel/trtools/utils 2023-11-25T11:02:43,132 copying build/lib/trtools/utils/utils.py -> build/bdist.linux-armv7l/wheel/trtools/utils 2023-11-25T11:02:43,135 creating build/bdist.linux-armv7l/wheel/trtools/utils/tests 2023-11-25T11:02:43,136 copying build/lib/trtools/utils/tests/test_trharmonizer.py -> build/bdist.linux-armv7l/wheel/trtools/utils/tests 2023-11-25T11:02:43,139 copying build/lib/trtools/utils/tests/.bandit -> build/bdist.linux-armv7l/wheel/trtools/utils/tests 2023-11-25T11:02:43,141 copying build/lib/trtools/utils/tests/test_utils.py -> build/bdist.linux-armv7l/wheel/trtools/utils/tests 2023-11-25T11:02:43,143 copying build/lib/trtools/utils/tests/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/utils/tests 2023-11-25T11:02:43,144 copying build/lib/trtools/utils/tests/test_mergeutils.py -> build/bdist.linux-armv7l/wheel/trtools/utils/tests 2023-11-25T11:02:43,147 copying build/lib/trtools/utils/tests/test_common.py -> build/bdist.linux-armv7l/wheel/trtools/utils/tests 2023-11-25T11:02:43,148 copying build/lib/trtools/utils/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/utils 2023-11-25T11:02:43,150 copying build/lib/trtools/utils/tr_harmonizer.py -> build/bdist.linux-armv7l/wheel/trtools/utils 2023-11-25T11:02:43,154 copying build/lib/trtools/utils/common.py -> build/bdist.linux-armv7l/wheel/trtools/utils 2023-11-25T11:02:43,156 copying build/lib/trtools/version.py -> build/bdist.linux-armv7l/wheel/trtools 2023-11-25T11:02:43,158 creating build/bdist.linux-armv7l/wheel/trtools/mergeSTR 2023-11-25T11:02:43,159 copying build/lib/trtools/mergeSTR/mergeSTR.py -> build/bdist.linux-armv7l/wheel/trtools/mergeSTR 2023-11-25T11:02:43,162 creating build/bdist.linux-armv7l/wheel/trtools/mergeSTR/tests 2023-11-25T11:02:43,162 copying build/lib/trtools/mergeSTR/tests/test_mergeSTR.py -> build/bdist.linux-armv7l/wheel/trtools/mergeSTR/tests 2023-11-25T11:02:43,165 copying build/lib/trtools/mergeSTR/tests/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/mergeSTR/tests 2023-11-25T11:02:43,166 copying build/lib/trtools/mergeSTR/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/mergeSTR 2023-11-25T11:02:43,168 copying build/lib/trtools/mergeSTR/README.rst -> build/bdist.linux-armv7l/wheel/trtools/mergeSTR 2023-11-25T11:02:43,171 creating build/bdist.linux-armv7l/wheel/trtools/mergeSTR/Example_Files 2023-11-25T11:02:43,171 copying build/lib/trtools/mergeSTR/Example_Files/test_run_original.vcf -> build/bdist.linux-armv7l/wheel/trtools/mergeSTR/Example_Files 2023-11-25T11:02:43,201 creating build/bdist.linux-armv7l/wheel/trtools/dumpSTR 2023-11-25T11:02:43,202 copying build/lib/trtools/dumpSTR/dumpSTR.py -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR 2023-11-25T11:02:43,205 copying build/lib/trtools/dumpSTR/filters.py -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR 2023-11-25T11:02:43,208 creating build/bdist.linux-armv7l/wheel/trtools/dumpSTR/tests 2023-11-25T11:02:43,209 copying build/lib/trtools/dumpSTR/tests/test_dumpSTR.py -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR/tests 2023-11-25T11:02:43,211 copying build/lib/trtools/dumpSTR/tests/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR/tests 2023-11-25T11:02:43,213 copying build/lib/trtools/dumpSTR/tests/test_filters.py -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR/tests 2023-11-25T11:02:43,215 copying build/lib/trtools/dumpSTR/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR 2023-11-25T11:02:43,217 copying build/lib/trtools/dumpSTR/README.rst -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR 2023-11-25T11:02:43,219 creating build/bdist.linux-armv7l/wheel/trtools/dumpSTR/Example_Files 2023-11-25T11:02:43,220 copying build/lib/trtools/dumpSTR/Example_Files/test_run_gangstr.vcf -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR/Example_Files 2023-11-25T11:02:43,245 copying build/lib/trtools/dumpSTR/Example_Files/test_run_original.vcf -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR/Example_Files 2023-11-25T11:02:43,268 creating build/bdist.linux-armv7l/wheel/trtools/dumpSTR/filter_files 2023-11-25T11:02:43,269 copying build/lib/trtools/dumpSTR/filter_files/hg19_segmentalduplications.bed.gz -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR/filter_files 2023-11-25T11:02:43,285 copying build/lib/trtools/dumpSTR/filter_files/hs37_segmentalduplications.bed.gz -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR/filter_files 2023-11-25T11:02:43,305 copying build/lib/trtools/dumpSTR/filter_files/hg19_segmentalduplications.bed.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR/filter_files 2023-11-25T11:02:43,308 copying build/lib/trtools/dumpSTR/filter_files/hs37_segmentalduplications.bed.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/dumpSTR/filter_files 2023-11-25T11:02:43,312 creating build/bdist.linux-armv7l/wheel/trtools/testsupport 2023-11-25T11:02:43,313 creating build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:43,315 copying build/lib/trtools/testsupport/sample_vcfs/test_ExpansionHunter.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:43,317 copying build/lib/trtools/testsupport/sample_vcfs/test_broken.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:43,319 copying build/lib/trtools/testsupport/sample_vcfs/many_samples.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:43,340 copying build/lib/trtools/testsupport/sample_vcfs/test_multitype.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:43,342 copying build/lib/trtools/testsupport/sample_vcfs/few_samples_few_loci.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:43,344 copying build/lib/trtools/testsupport/sample_vcfs/one_sample_multiple_chroms.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:43,346 copying build/lib/trtools/testsupport/sample_vcfs/test_popstr.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:43,348 copying build/lib/trtools/testsupport/sample_vcfs/CEU_test.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:43,351 creating build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,352 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_gangstr.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,354 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_expansion.samplog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,355 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_broken.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,357 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_advntr.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,359 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_eh.sorted.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,362 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_expansion.loclog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,363 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/sample_region2.bed.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,365 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_gangstr.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,371 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/bad_preexisting_filter_ac_refac.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,372 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/popstr_filters.loclog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,374 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/bad_preexisting_het_hwep.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,376 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/worrisome_preexisting_filter.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,378 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/trio_chr21_hipstr.sorted.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,390 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/locus_filters.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,474 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/bad_preexisting_hrun.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,477 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_gangstr_nochr.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,482 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_broken.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,483 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/hipstr_filters.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,564 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_expansion.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,582 creating build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,583 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_expansion.samplog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,586 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_expansion.loclog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,587 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/popstr_filters.loclog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,589 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/locus_filters.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,674 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/README -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,676 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/hipstr_filters.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,763 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_expansion.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,781 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/advntr_filters.samplog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,785 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/locus_filters.samplog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,788 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/popstr_filters.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,817 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/advntr_filters.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,838 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_most.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,968 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/popstr_filters.samplog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,970 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/advntr_filters.loclog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,972 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_most.samplog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,974 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/hipstr_filters.samplog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,976 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/hipstr_filters.loclog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,978 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/locus_filters.loclog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,980 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_most.loclog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,982 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/drop_filtered.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output 2023-11-25T11:02:43,991 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/advntr_filters.samplog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,993 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/locus_filters.samplog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,995 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_gangstr_nochr.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:43,998 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/trio_chr21_gangstr.sorted.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,001 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/popstr_filters.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,030 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/advntr_filters.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,048 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/trio_chr21_gangstr.sorted.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,065 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/sample_region.bed.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,067 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_most.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,139 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/sample_region.bed.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,141 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/create_test_files.sh -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,143 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/popstr_filters.samplog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,145 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/advntr_filters.loclog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,146 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_popstr.sorted.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,149 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_popstr.sorted.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,154 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_most.samplog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,156 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_advntr.sorted.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,158 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/test_advntr.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,159 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/hipstr_filters.samplog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,161 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_advntr.sorted.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,165 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/sample_region2.bed.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,167 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/trio_chr21_hipstr.sorted.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,169 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/hipstr_filters.loclog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,171 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/locus_filters.loclog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,173 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_eh.sorted.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,178 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_most.loclog.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,179 copying build/lib/trtools/testsupport/sample_vcfs/dumpSTR_vcfs/drop_filtered.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/dumpSTR_vcfs 2023-11-25T11:02:44,188 creating build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,189 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/make_dosages.py -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,191 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/single_dosages.plink2.trait_0.glm.linear -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,194 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/traits_0.npy -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,196 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/many_samples_biallelic.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,203 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/many_samples_biallelic_dosages.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,213 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/single_40_dosages.plink2.trait_0.glm.linear -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,216 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/many_samples_biallelic.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,218 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/single.plink2.trait_0.glm.linear -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,221 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/traits_1_45_samples.npy -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,223 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/README -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,225 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/samples.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,226 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/combined_35.plink2.trait_0.glm.linear -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,229 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/many_samples_biallelic_dosages.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,231 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/ap1_multi_dosages.tsv.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,233 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/combined_traits_for_plink.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,235 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/traits_0_40_samples.npy -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,237 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/ap1_dosage_header.hdr -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,238 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/single_40.plink2.trait_0.glm.linear -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,241 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/generate_plink_output.sh -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,243 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/single_traits_for_plink.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,246 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/many_samples_multiallelic.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,248 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/single_35.plink2.trait_0.glm.linear -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,251 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/45_samples.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,253 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/35_samples.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,254 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/ap2_dosage_header.hdr -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,256 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/gp_dosage_header.hdr -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,258 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/combined.plink2.trait_0.glm.linear -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,261 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/single_cutoff_5.plink2.trait_0.glm.linear -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,263 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/ap2_multi_dosages.tsv.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,265 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/many_samples_multiallelic_dosages.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,267 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/many_samples_multiallelic_dosages.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,269 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/.gitignore -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,271 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/samples_6_to_45.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,272 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/traits_1.npy -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,274 copying build/lib/trtools/testsupport/sample_vcfs/associaTR/generate_traits.py -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/associaTR 2023-11-25T11:02:44,276 copying build/lib/trtools/testsupport/sample_vcfs/test_hipstr.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,351 copying build/lib/trtools/testsupport/sample_vcfs/test_beagle-4.1.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,435 copying build/lib/trtools/testsupport/sample_vcfs/many_samples_multiple_chroms.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,437 copying build/lib/trtools/testsupport/sample_vcfs/test_advntr.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,439 copying build/lib/trtools/testsupport/sample_vcfs/artificial_gangstr.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,441 copying build/lib/trtools/testsupport/sample_vcfs/test_gangstr_noqual.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,442 copying build/lib/trtools/testsupport/sample_vcfs/many_samples_multiple_chroms.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,448 creating build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,449 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr2_wrongsamp.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,453 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,462 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr_flanking_bp_non_flanking.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,463 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_better_comparability_calculation_1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,465 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr2.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,467 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,471 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_popstr.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,473 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr_flanking_bp_flanking.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,475 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_advntr.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,476 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_popstr.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,486 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/empty_list.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,487 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_no_comparable_records_1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,489 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr2.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,493 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_better_comparability_calculation_2.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,498 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr2_wrongsamp.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,499 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_better_comparability_calculation_2.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,501 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_no_comparable_records_1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,503 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,505 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr_flanking_bp_flanking.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,506 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_no_comparable_records_2.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,508 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_no_comparable_records_2.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,510 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_better_comparability_calculation_1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,512 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,513 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr_flanking_bp_non_flanking.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,515 copying build/lib/trtools/testsupport/sample_vcfs/compareSTR_vcfs/sample_list.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/compareSTR_vcfs 2023-11-25T11:02:44,517 creating build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:44,518 copying build/lib/trtools/testsupport/sample_vcfs/qc_vcfs/test_fakesample.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:44,521 copying build/lib/trtools/testsupport/sample_vcfs/qc_vcfs/test_popstr.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:44,557 copying build/lib/trtools/testsupport/sample_vcfs/qc_vcfs/test_popstr_nocontig.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:44,595 copying build/lib/trtools/testsupport/sample_vcfs/qc_vcfs/5by50.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:44,601 copying build/lib/trtools/testsupport/sample_vcfs/qc_vcfs/test_samplelist.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:44,605 copying build/lib/trtools/testsupport/sample_vcfs/qc_vcfs/50by3.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/qc_vcfs 2023-11-25T11:02:44,610 copying build/lib/trtools/testsupport/sample_vcfs/test_gangstr_samples.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,613 copying build/lib/trtools/testsupport/sample_vcfs/missing_samples.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,616 copying build/lib/trtools/testsupport/sample_vcfs/many_samples_subsample2.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,619 copying build/lib/trtools/testsupport/sample_vcfs/test_gangstr_nochr.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,651 copying build/lib/trtools/testsupport/sample_vcfs/many_samples_subsample1.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,663 creating build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,666 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_no_alt.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,673 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr2_1contig.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,676 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/one_sample_multiple_chroms_diff_contig_order.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,678 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigmissing1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,679 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr1_badinfo.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,681 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr1_badinfo.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,683 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifflength.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,685 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifferent2.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,687 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_popstr2.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,689 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr2.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,691 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_unzipped1.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,710 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,716 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_popstr1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,723 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_advntr2.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,725 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_advntr1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,727 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_popstr2.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,733 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh2.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,734 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifferent1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,736 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr2.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,742 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigmissing2.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,744 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_popstr1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,746 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigmissing1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,748 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/advntr_merged.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,750 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr1_1contig.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,752 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr-harmonized-merge-contains-flanking.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,754 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_advntr2.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,755 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/eh_no_alt_merged.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,757 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/gangstr_merged.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,777 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh2.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,779 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_missinginfo1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,781 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr-harmonized-merge-no-flanking.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,783 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_dupID.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,790 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr2.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,792 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/eh_merged.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,794 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_X_no_alt.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,796 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr2_alt_v_ref.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,798 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifferent2.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,800 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifflength.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,803 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr2_1contig.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,804 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_flanking_harmonization_test_output.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,807 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/create_test_files.sh -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,809 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,811 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,813 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_merged.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,816 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/one_sample_multiple_chroms_diff_contig_order.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,819 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr1_1contig.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,822 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr-harmonized-merge-no-flanking.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,824 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_X1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,826 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_X_no_alt.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,828 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_dupID.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,831 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_unindexed2.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,837 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr-harmonized-merge-contains-flanking.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,839 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_missingformat1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,842 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_no_alt.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,844 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_missinginfo1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,846 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifferent1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,848 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigmissing2.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,850 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/eh_X_no_alt_merged_swap.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,852 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_unindexed1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,859 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr2_alt_v_ref.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,861 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,863 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_X1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,865 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_missingformat1.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,867 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/popstr_merged.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,887 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,888 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/eh_X_no_alt_merged.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,890 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_advntr1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,892 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr2.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,894 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr1.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,895 copying build/lib/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_unzipped2.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/mergeSTR_vcfs 2023-11-25T11:02:44,911 copying build/lib/trtools/testsupport/sample_vcfs/README.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,912 copying build/lib/trtools/testsupport/sample_vcfs/CEU_test.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,915 copying build/lib/trtools/testsupport/sample_vcfs/few_loci.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,918 copying build/lib/trtools/testsupport/sample_vcfs/few_samples_few_loci.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,919 copying build/lib/trtools/testsupport/sample_vcfs/test_ExpansionHunter_reheadered.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,922 copying build/lib/trtools/testsupport/sample_vcfs/test_gangstr.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,937 copying build/lib/trtools/testsupport/sample_vcfs/snps.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,939 copying build/lib/trtools/testsupport/sample_vcfs/fewer_samples.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,940 copying build/lib/trtools/testsupport/sample_vcfs/one_sample_multiple_chroms.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:44,943 creating build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:44,943 copying build/lib/trtools/testsupport/sample_vcfs/beagle/hipstr_imputed.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:44,946 copying build/lib/trtools/testsupport/sample_vcfs/beagle/1kg_snpstr_21_first_100k_second_50_STRs_imputed.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:44,997 copying build/lib/trtools/testsupport/sample_vcfs/beagle/1kg_snpstr_21_first_100k_first_50_annotated.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:45,000 copying build/lib/trtools/testsupport/sample_vcfs/beagle/eh_imputed.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:45,003 copying build/lib/trtools/testsupport/sample_vcfs/beagle/gangstr_imputed.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:45,008 copying build/lib/trtools/testsupport/sample_vcfs/beagle/advntr_imputed.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:45,011 copying build/lib/trtools/testsupport/sample_vcfs/beagle/eh_imputed_missing_infos.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:45,015 copying build/lib/trtools/testsupport/sample_vcfs/beagle/gangstr_imputed_missing_infos.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:45,020 copying build/lib/trtools/testsupport/sample_vcfs/beagle/advntr_imputed_missing_infos.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:45,024 copying build/lib/trtools/testsupport/sample_vcfs/beagle/1kg_snpstr_21_first_100k_second_50_STRs_imputed.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:45,027 copying build/lib/trtools/testsupport/sample_vcfs/beagle/1kg_snpstr_21_first_100k_first_50_annotated.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:45,076 copying build/lib/trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_missing_infos.vcf.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs/beagle 2023-11-25T11:02:45,079 copying build/lib/trtools/testsupport/sample_vcfs/many_samples.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:45,081 copying build/lib/trtools/testsupport/sample_vcfs/test_beagle_4-0.vcf -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_vcfs 2023-11-25T11:02:45,170 copying build/lib/trtools/testsupport/dataloader.py -> build/bdist.linux-armv7l/wheel/trtools/testsupport 2023-11-25T11:02:45,172 copying build/lib/trtools/testsupport/utils.py -> build/bdist.linux-armv7l/wheel/trtools/testsupport 2023-11-25T11:02:45,174 copying build/lib/trtools/testsupport/test_trtools.sh -> build/bdist.linux-armv7l/wheel/trtools/testsupport 2023-11-25T11:02:45,177 copying build/lib/trtools/testsupport/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/testsupport 2023-11-25T11:02:45,179 creating build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_stats 2023-11-25T11:02:45,180 copying build/lib/trtools/testsupport/sample_stats/many_samples_all.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_stats 2023-11-25T11:02:45,188 copying build/lib/trtools/testsupport/sample_stats/many_samples_all_strat.tab -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_stats 2023-11-25T11:02:45,199 creating build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_regions 2023-11-25T11:02:45,200 copying build/lib/trtools/testsupport/sample_regions/test_regions3.bed.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_regions 2023-11-25T11:02:45,202 copying build/lib/trtools/testsupport/sample_regions/test_regions2.bed.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_regions 2023-11-25T11:02:45,204 copying build/lib/trtools/testsupport/sample_regions/test_regions1.bed.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_regions 2023-11-25T11:02:45,206 copying build/lib/trtools/testsupport/sample_regions/test_regions4.bed.gz -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_regions 2023-11-25T11:02:45,208 copying build/lib/trtools/testsupport/sample_regions/test_regions4.bed.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_regions 2023-11-25T11:02:45,211 copying build/lib/trtools/testsupport/sample_regions/test_regions1.bed.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_regions 2023-11-25T11:02:45,213 copying build/lib/trtools/testsupport/sample_regions/test_regions2.bed.gz.tbi -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_regions 2023-11-25T11:02:45,215 copying build/lib/trtools/testsupport/sample_regions/README.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_regions 2023-11-25T11:02:45,217 creating build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_simtrdata 2023-11-25T11:02:45,218 copying build/lib/trtools/testsupport/sample_simtrdata/CBL.fa -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_simtrdata 2023-11-25T11:02:45,221 copying build/lib/trtools/testsupport/sample_simtrdata/README.txt -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_simtrdata 2023-11-25T11:02:45,223 copying build/lib/trtools/testsupport/sample_simtrdata/CBL.fa.fai -> build/bdist.linux-armv7l/wheel/trtools/testsupport/sample_simtrdata 2023-11-25T11:02:45,225 creating build/bdist.linux-armv7l/wheel/trtools/statSTR 2023-11-25T11:02:45,226 copying build/lib/trtools/statSTR/statSTR.py -> build/bdist.linux-armv7l/wheel/trtools/statSTR 2023-11-25T11:02:45,230 creating build/bdist.linux-armv7l/wheel/trtools/statSTR/tests 2023-11-25T11:02:45,231 copying build/lib/trtools/statSTR/tests/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/statSTR/tests 2023-11-25T11:02:45,233 copying build/lib/trtools/statSTR/tests/test_statSTR.py -> build/bdist.linux-armv7l/wheel/trtools/statSTR/tests 2023-11-25T11:02:45,236 copying build/lib/trtools/statSTR/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/statSTR 2023-11-25T11:02:45,238 copying build/lib/trtools/statSTR/README.rst -> build/bdist.linux-armv7l/wheel/trtools/statSTR 2023-11-25T11:02:45,240 creating build/bdist.linux-armv7l/wheel/trtools/qcSTR 2023-11-25T11:02:45,242 creating build/bdist.linux-armv7l/wheel/trtools/qcSTR/images 2023-11-25T11:02:45,243 copying build/lib/trtools/qcSTR/images/quality-per-sample.png -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/images 2023-11-25T11:02:45,246 copying build/lib/trtools/qcSTR/images/diffref-bias.png -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/images 2023-11-25T11:02:45,251 copying build/lib/trtools/qcSTR/images/quality-per-call.png -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/images 2023-11-25T11:02:45,254 copying build/lib/trtools/qcSTR/images/README.txt -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/images 2023-11-25T11:02:45,255 copying build/lib/trtools/qcSTR/images/diffref-histogram.png -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/images 2023-11-25T11:02:45,258 copying build/lib/trtools/qcSTR/images/quality-sample-stratified.png -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/images 2023-11-25T11:02:45,260 copying build/lib/trtools/qcSTR/images/chrom-callnum.png -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/images 2023-11-25T11:02:45,263 copying build/lib/trtools/qcSTR/images/quality-locus-stratified.png -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/images 2023-11-25T11:02:45,266 copying build/lib/trtools/qcSTR/images/sample-callnum.png -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/images 2023-11-25T11:02:45,268 copying build/lib/trtools/qcSTR/images/quality-per-locus.png -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/images 2023-11-25T11:02:45,271 creating build/bdist.linux-armv7l/wheel/trtools/qcSTR/tests 2023-11-25T11:02:45,272 copying build/lib/trtools/qcSTR/tests/.bandit -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/tests 2023-11-25T11:02:45,273 copying build/lib/trtools/qcSTR/tests/test_qcSTR.py -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/tests 2023-11-25T11:02:45,276 copying build/lib/trtools/qcSTR/tests/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/qcSTR/tests 2023-11-25T11:02:45,277 copying build/lib/trtools/qcSTR/__init__.py -> build/bdist.linux-armv7l/wheel/trtools/qcSTR 2023-11-25T11:02:45,279 copying build/lib/trtools/qcSTR/README.rst -> build/bdist.linux-armv7l/wheel/trtools/qcSTR 2023-11-25T11:02:45,281 copying build/lib/trtools/qcSTR/qcSTR.py -> build/bdist.linux-armv7l/wheel/trtools/qcSTR 2023-11-25T11:02:45,283 copying build/lib/trtools/qcSTR/wishlist.rst -> build/bdist.linux-armv7l/wheel/trtools/qcSTR 2023-11-25T11:02:45,285 running install_egg_info 2023-11-25T11:02:45,290 Copying trtools.egg-info to build/bdist.linux-armv7l/wheel/trtools-5.1.0-py3.11.egg-info 2023-11-25T11:02:45,302 running install_scripts 2023-11-25T11:02:45,303 creating build/bdist.linux-armv7l/wheel/trtools-5.1.0.data 2023-11-25T11:02:45,304 creating build/bdist.linux-armv7l/wheel/trtools-5.1.0.data/scripts 2023-11-25T11:02:45,305 copying build/scripts-3.11/trtools_prep_beagle_vcf.sh -> build/bdist.linux-armv7l/wheel/trtools-5.1.0.data/scripts 2023-11-25T11:02:45,307 copying build/scripts-3.11/test_trtools.sh -> build/bdist.linux-armv7l/wheel/trtools-5.1.0.data/scripts 2023-11-25T11:02:45,309 changing mode of build/bdist.linux-armv7l/wheel/trtools-5.1.0.data/scripts/trtools_prep_beagle_vcf.sh to 755 2023-11-25T11:02:45,309 changing mode of build/bdist.linux-armv7l/wheel/trtools-5.1.0.data/scripts/test_trtools.sh to 755 2023-11-25T11:02:45,326 creating build/bdist.linux-armv7l/wheel/trtools-5.1.0.dist-info/WHEEL 2023-11-25T11:02:45,328 creating '/tmp/pip-wheel-xcaoevmu/.tmp-00s2aji4/trtools-5.1.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-11-25T11:02:45,331 adding 'trtools/__init__.py' 2023-11-25T11:02:45,332 adding 'trtools/version.py' 2023-11-25T11:02:45,334 adding 'trtools/associaTR/README.rst' 2023-11-25T11:02:45,336 adding 'trtools/associaTR/__init__.py' 2023-11-25T11:02:45,339 adding 'trtools/associaTR/associaTR.py' 2023-11-25T11:02:45,341 adding 'trtools/associaTR/load_and_filter_genotypes.py' 2023-11-25T11:02:45,343 adding 'trtools/associaTR/tests/__init__.py' 2023-11-25T11:02:45,345 adding 'trtools/associaTR/tests/test_associaTR.py' 2023-11-25T11:02:45,347 adding 'trtools/compareSTR/README.rst' 2023-11-25T11:02:45,348 adding 'trtools/compareSTR/__init__.py' 2023-11-25T11:02:45,353 adding 'trtools/compareSTR/compareSTR.py' 2023-11-25T11:02:45,355 adding 'trtools/compareSTR/tests/__init__.py' 2023-11-25T11:02:45,356 adding 'trtools/compareSTR/tests/test_compareSTR.py' 2023-11-25T11:02:45,359 adding 'trtools/dumpSTR/README.rst' 2023-11-25T11:02:45,360 adding 'trtools/dumpSTR/__init__.py' 2023-11-25T11:02:45,366 adding 'trtools/dumpSTR/dumpSTR.py' 2023-11-25T11:02:45,369 adding 'trtools/dumpSTR/filters.py' 2023-11-25T11:02:45,469 adding 'trtools/dumpSTR/Example_Files/test_run_gangstr.vcf' 2023-11-25T11:02:45,578 adding 'trtools/dumpSTR/Example_Files/test_run_original.vcf' 2023-11-25T11:02:45,648 adding 'trtools/dumpSTR/filter_files/hg19_segmentalduplications.bed.gz' 2023-11-25T11:02:45,661 adding 'trtools/dumpSTR/filter_files/hg19_segmentalduplications.bed.gz.tbi' 2023-11-25T11:02:45,723 adding 'trtools/dumpSTR/filter_files/hs37_segmentalduplications.bed.gz' 2023-11-25T11:02:45,735 adding 'trtools/dumpSTR/filter_files/hs37_segmentalduplications.bed.gz.tbi' 2023-11-25T11:02:45,737 adding 'trtools/dumpSTR/tests/__init__.py' 2023-11-25T11:02:45,740 adding 'trtools/dumpSTR/tests/test_dumpSTR.py' 2023-11-25T11:02:45,742 adding 'trtools/dumpSTR/tests/test_filters.py' 2023-11-25T11:02:45,744 adding 'trtools/mergeSTR/README.rst' 2023-11-25T11:02:45,745 adding 'trtools/mergeSTR/__init__.py' 2023-11-25T11:02:45,748 adding 'trtools/mergeSTR/mergeSTR.py' 2023-11-25T11:02:45,900 adding 'trtools/mergeSTR/Example_Files/test_run_original.vcf' 2023-11-25T11:02:45,910 adding 'trtools/mergeSTR/tests/__init__.py' 2023-11-25T11:02:45,911 adding 'trtools/mergeSTR/tests/test_mergeSTR.py' 2023-11-25T11:02:45,913 adding 'trtools/prancSTR/README.rst' 2023-11-25T11:02:45,915 adding 'trtools/prancSTR/__init__.py' 2023-11-25T11:02:45,917 adding 'trtools/prancSTR/prancSTR.py' 2023-11-25T11:02:46,115 adding 'trtools/prancSTR/paper_draft/prancSTR_Manuscript_draft.pdf' 2023-11-25T11:02:46,128 adding 'trtools/prancSTR/tests/__init__.py' 2023-11-25T11:02:46,130 adding 'trtools/prancSTR/tests/test_prancSTR.py' 2023-11-25T11:02:46,132 adding 'trtools/qcSTR/README.rst' 2023-11-25T11:02:46,133 adding 'trtools/qcSTR/__init__.py' 2023-11-25T11:02:46,136 adding 'trtools/qcSTR/qcSTR.py' 2023-11-25T11:02:46,138 adding 'trtools/qcSTR/wishlist.rst' 2023-11-25T11:02:46,139 adding 'trtools/qcSTR/images/README.txt' 2023-11-25T11:02:46,142 adding 'trtools/qcSTR/images/chrom-callnum.png' 2023-11-25T11:02:46,168 adding 'trtools/qcSTR/images/diffref-bias.png' 2023-11-25T11:02:46,173 adding 'trtools/qcSTR/images/diffref-histogram.png' 2023-11-25T11:02:46,176 adding 'trtools/qcSTR/images/quality-locus-stratified.png' 2023-11-25T11:02:46,179 adding 'trtools/qcSTR/images/quality-per-call.png' 2023-11-25T11:02:46,183 adding 'trtools/qcSTR/images/quality-per-locus.png' 2023-11-25T11:02:46,186 adding 'trtools/qcSTR/images/quality-per-sample.png' 2023-11-25T11:02:46,190 adding 'trtools/qcSTR/images/quality-sample-stratified.png' 2023-11-25T11:02:46,192 adding 'trtools/qcSTR/images/sample-callnum.png' 2023-11-25T11:02:46,194 adding 'trtools/qcSTR/tests/.bandit' 2023-11-25T11:02:46,195 adding 'trtools/qcSTR/tests/__init__.py' 2023-11-25T11:02:46,197 adding 'trtools/qcSTR/tests/test_qcSTR.py' 2023-11-25T11:02:46,199 adding 'trtools/simTR/README.rst' 2023-11-25T11:02:46,200 adding 'trtools/simTR/__init__.py' 2023-11-25T11:02:46,202 adding 'trtools/simTR/simTR.py' 2023-11-25T11:02:46,204 adding 'trtools/simTR/tests/__init__.py' 2023-11-25T11:02:46,206 adding 'trtools/simTR/tests/test_simTR.py' 2023-11-25T11:02:46,208 adding 'trtools/statSTR/README.rst' 2023-11-25T11:02:46,209 adding 'trtools/statSTR/__init__.py' 2023-11-25T11:02:46,212 adding 'trtools/statSTR/statSTR.py' 2023-11-25T11:02:46,214 adding 'trtools/statSTR/tests/__init__.py' 2023-11-25T11:02:46,215 adding 'trtools/statSTR/tests/test_statSTR.py' 2023-11-25T11:02:46,217 adding 'trtools/testsupport/__init__.py' 2023-11-25T11:02:46,218 adding 'trtools/testsupport/dataloader.py' 2023-11-25T11:02:46,220 adding 'trtools/testsupport/test_trtools.sh' 2023-11-25T11:02:46,221 adding 'trtools/testsupport/utils.py' 2023-11-25T11:02:46,223 adding 'trtools/testsupport/sample_regions/README.txt' 2023-11-25T11:02:46,225 adding 'trtools/testsupport/sample_regions/test_regions1.bed.gz' 2023-11-25T11:02:46,226 adding 'trtools/testsupport/sample_regions/test_regions1.bed.gz.tbi' 2023-11-25T11:02:46,227 adding 'trtools/testsupport/sample_regions/test_regions2.bed.gz' 2023-11-25T11:02:46,229 adding 'trtools/testsupport/sample_regions/test_regions2.bed.gz.tbi' 2023-11-25T11:02:46,230 adding 'trtools/testsupport/sample_regions/test_regions3.bed.gz' 2023-11-25T11:02:46,231 adding 'trtools/testsupport/sample_regions/test_regions4.bed.gz' 2023-11-25T11:02:46,233 adding 'trtools/testsupport/sample_regions/test_regions4.bed.gz.tbi' 2023-11-25T11:02:46,238 adding 'trtools/testsupport/sample_simtrdata/CBL.fa' 2023-11-25T11:02:46,239 adding 'trtools/testsupport/sample_simtrdata/CBL.fa.fai' 2023-11-25T11:02:46,240 adding 'trtools/testsupport/sample_simtrdata/README.txt' 2023-11-25T11:02:46,285 adding 'trtools/testsupport/sample_stats/many_samples_all.tab' 2023-11-25T11:02:46,343 adding 'trtools/testsupport/sample_stats/many_samples_all_strat.tab' 2023-11-25T11:02:46,351 adding 'trtools/testsupport/sample_vcfs/CEU_test.vcf.gz' 2023-11-25T11:02:46,352 adding 'trtools/testsupport/sample_vcfs/CEU_test.vcf.gz.tbi' 2023-11-25T11:02:46,353 adding 'trtools/testsupport/sample_vcfs/README.txt' 2023-11-25T11:02:46,354 adding 'trtools/testsupport/sample_vcfs/artificial_gangstr.vcf' 2023-11-25T11:02:46,359 adding 'trtools/testsupport/sample_vcfs/few_loci.vcf' 2023-11-25T11:02:46,361 adding 'trtools/testsupport/sample_vcfs/few_samples_few_loci.vcf.gz' 2023-11-25T11:02:46,362 adding 'trtools/testsupport/sample_vcfs/few_samples_few_loci.vcf.gz.tbi' 2023-11-25T11:02:46,363 adding 'trtools/testsupport/sample_vcfs/fewer_samples.txt' 2023-11-25T11:02:46,512 adding 'trtools/testsupport/sample_vcfs/many_samples.vcf.gz' 2023-11-25T11:02:46,522 adding 'trtools/testsupport/sample_vcfs/many_samples.vcf.gz.tbi' 2023-11-25T11:02:46,548 adding 'trtools/testsupport/sample_vcfs/many_samples_multiple_chroms.vcf.gz' 2023-11-25T11:02:46,550 adding 'trtools/testsupport/sample_vcfs/many_samples_multiple_chroms.vcf.gz.tbi' 2023-11-25T11:02:46,551 adding 'trtools/testsupport/sample_vcfs/many_samples_subsample1.txt' 2023-11-25T11:02:46,553 adding 'trtools/testsupport/sample_vcfs/many_samples_subsample2.txt' 2023-11-25T11:02:46,554 adding 'trtools/testsupport/sample_vcfs/missing_samples.txt' 2023-11-25T11:02:46,556 adding 'trtools/testsupport/sample_vcfs/one_sample_multiple_chroms.vcf.gz' 2023-11-25T11:02:46,558 adding 'trtools/testsupport/sample_vcfs/one_sample_multiple_chroms.vcf.gz.tbi' 2023-11-25T11:02:46,559 adding 'trtools/testsupport/sample_vcfs/snps.vcf' 2023-11-25T11:02:46,560 adding 'trtools/testsupport/sample_vcfs/test_ExpansionHunter.vcf' 2023-11-25T11:02:46,562 adding 'trtools/testsupport/sample_vcfs/test_ExpansionHunter_reheadered.vcf' 2023-11-25T11:02:46,563 adding 'trtools/testsupport/sample_vcfs/test_advntr.vcf' 2023-11-25T11:02:47,170 adding 'trtools/testsupport/sample_vcfs/test_beagle-4.1.vcf' 2023-11-25T11:02:47,361 adding 'trtools/testsupport/sample_vcfs/test_beagle_4-0.vcf' 2023-11-25T11:02:47,399 adding 'trtools/testsupport/sample_vcfs/test_broken.vcf' 2023-11-25T11:02:47,498 adding 'trtools/testsupport/sample_vcfs/test_gangstr.vcf' 2023-11-25T11:02:47,605 adding 'trtools/testsupport/sample_vcfs/test_gangstr_nochr.vcf' 2023-11-25T11:02:47,612 adding 'trtools/testsupport/sample_vcfs/test_gangstr_noqual.vcf' 2023-11-25T11:02:47,613 adding 'trtools/testsupport/sample_vcfs/test_gangstr_samples.txt' 2023-11-25T11:02:47,860 adding 'trtools/testsupport/sample_vcfs/test_hipstr.vcf' 2023-11-25T11:02:47,887 adding 'trtools/testsupport/sample_vcfs/test_multitype.vcf' 2023-11-25T11:02:47,890 adding 'trtools/testsupport/sample_vcfs/test_popstr.vcf' 2023-11-25T11:02:47,892 adding 'trtools/testsupport/sample_vcfs/associaTR/.gitignore' 2023-11-25T11:02:47,893 adding 'trtools/testsupport/sample_vcfs/associaTR/35_samples.txt' 2023-11-25T11:02:47,895 adding 'trtools/testsupport/sample_vcfs/associaTR/45_samples.txt' 2023-11-25T11:02:47,896 adding 'trtools/testsupport/sample_vcfs/associaTR/README' 2023-11-25T11:02:47,897 adding 'trtools/testsupport/sample_vcfs/associaTR/ap1_dosage_header.hdr' 2023-11-25T11:02:47,898 adding 'trtools/testsupport/sample_vcfs/associaTR/ap1_multi_dosages.tsv.gz' 2023-11-25T11:02:47,899 adding 'trtools/testsupport/sample_vcfs/associaTR/ap2_dosage_header.hdr' 2023-11-25T11:02:47,900 adding 'trtools/testsupport/sample_vcfs/associaTR/ap2_multi_dosages.tsv.gz' 2023-11-25T11:02:47,909 adding 'trtools/testsupport/sample_vcfs/associaTR/combined.plink2.trait_0.glm.linear' 2023-11-25T11:02:47,918 adding 'trtools/testsupport/sample_vcfs/associaTR/combined_35.plink2.trait_0.glm.linear' 2023-11-25T11:02:47,921 adding 'trtools/testsupport/sample_vcfs/associaTR/combined_traits_for_plink.tab' 2023-11-25T11:02:47,922 adding 'trtools/testsupport/sample_vcfs/associaTR/generate_plink_output.sh' 2023-11-25T11:02:47,923 adding 'trtools/testsupport/sample_vcfs/associaTR/generate_traits.py' 2023-11-25T11:02:47,924 adding 'trtools/testsupport/sample_vcfs/associaTR/gp_dosage_header.hdr' 2023-11-25T11:02:47,925 adding 'trtools/testsupport/sample_vcfs/associaTR/make_dosages.py' 2023-11-25T11:02:47,958 adding 'trtools/testsupport/sample_vcfs/associaTR/many_samples_biallelic.vcf.gz' 2023-11-25T11:02:47,961 adding 'trtools/testsupport/sample_vcfs/associaTR/many_samples_biallelic.vcf.gz.tbi' 2023-11-25T11:02:48,024 adding 'trtools/testsupport/sample_vcfs/associaTR/many_samples_biallelic_dosages.vcf.gz' 2023-11-25T11:02:48,028 adding 'trtools/testsupport/sample_vcfs/associaTR/many_samples_biallelic_dosages.vcf.gz.tbi' 2023-11-25T11:02:48,030 adding 'trtools/testsupport/sample_vcfs/associaTR/many_samples_multiallelic.vcf.gz' 2023-11-25T11:02:48,032 adding 'trtools/testsupport/sample_vcfs/associaTR/many_samples_multiallelic_dosages.vcf.gz' 2023-11-25T11:02:48,033 adding 'trtools/testsupport/sample_vcfs/associaTR/many_samples_multiallelic_dosages.vcf.gz.tbi' 2023-11-25T11:02:48,034 adding 'trtools/testsupport/sample_vcfs/associaTR/samples.txt' 2023-11-25T11:02:48,035 adding 'trtools/testsupport/sample_vcfs/associaTR/samples_6_to_45.txt' 2023-11-25T11:02:48,044 adding 'trtools/testsupport/sample_vcfs/associaTR/single.plink2.trait_0.glm.linear' 2023-11-25T11:02:48,053 adding 'trtools/testsupport/sample_vcfs/associaTR/single_35.plink2.trait_0.glm.linear' 2023-11-25T11:02:48,062 adding 'trtools/testsupport/sample_vcfs/associaTR/single_40.plink2.trait_0.glm.linear' 2023-11-25T11:02:48,071 adding 'trtools/testsupport/sample_vcfs/associaTR/single_40_dosages.plink2.trait_0.glm.linear' 2023-11-25T11:02:48,077 adding 'trtools/testsupport/sample_vcfs/associaTR/single_cutoff_5.plink2.trait_0.glm.linear' 2023-11-25T11:02:48,086 adding 'trtools/testsupport/sample_vcfs/associaTR/single_dosages.plink2.trait_0.glm.linear' 2023-11-25T11:02:48,088 adding 'trtools/testsupport/sample_vcfs/associaTR/single_traits_for_plink.tab' 2023-11-25T11:02:48,090 adding 'trtools/testsupport/sample_vcfs/associaTR/traits_0.npy' 2023-11-25T11:02:48,091 adding 'trtools/testsupport/sample_vcfs/associaTR/traits_0_40_samples.npy' 2023-11-25T11:02:48,093 adding 'trtools/testsupport/sample_vcfs/associaTR/traits_1.npy' 2023-11-25T11:02:48,094 adding 'trtools/testsupport/sample_vcfs/associaTR/traits_1_45_samples.npy' 2023-11-25T11:02:48,361 adding 'trtools/testsupport/sample_vcfs/beagle/1kg_snpstr_21_first_100k_first_50_annotated.vcf.gz' 2023-11-25T11:02:48,376 adding 'trtools/testsupport/sample_vcfs/beagle/1kg_snpstr_21_first_100k_first_50_annotated.vcf.gz.tbi' 2023-11-25T11:02:48,647 adding 'trtools/testsupport/sample_vcfs/beagle/1kg_snpstr_21_first_100k_second_50_STRs_imputed.vcf.gz' 2023-11-25T11:02:48,662 adding 'trtools/testsupport/sample_vcfs/beagle/1kg_snpstr_21_first_100k_second_50_STRs_imputed.vcf.gz.tbi' 2023-11-25T11:02:48,665 adding 'trtools/testsupport/sample_vcfs/beagle/advntr_imputed.vcf.gz' 2023-11-25T11:02:48,667 adding 'trtools/testsupport/sample_vcfs/beagle/advntr_imputed_missing_infos.vcf.gz' 2023-11-25T11:02:48,671 adding 'trtools/testsupport/sample_vcfs/beagle/eh_imputed.vcf.gz' 2023-11-25T11:02:48,676 adding 'trtools/testsupport/sample_vcfs/beagle/eh_imputed_missing_infos.vcf.gz' 2023-11-25T11:02:48,687 adding 'trtools/testsupport/sample_vcfs/beagle/gangstr_imputed.vcf.gz' 2023-11-25T11:02:48,699 adding 'trtools/testsupport/sample_vcfs/beagle/gangstr_imputed_missing_infos.vcf.gz' 2023-11-25T11:02:48,704 adding 'trtools/testsupport/sample_vcfs/beagle/hipstr_imputed.vcf.gz' 2023-11-25T11:02:48,709 adding 'trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_missing_infos.vcf.gz' 2023-11-25T11:02:48,711 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/empty_list.txt' 2023-11-25T11:02:48,712 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/sample_list.txt' 2023-11-25T11:02:48,713 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_advntr.vcf' 2023-11-25T11:02:48,714 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_better_comparability_calculation_1.vcf.gz' 2023-11-25T11:02:48,715 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_better_comparability_calculation_1.vcf.gz.tbi' 2023-11-25T11:02:48,717 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_better_comparability_calculation_2.vcf.gz' 2023-11-25T11:02:48,718 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_better_comparability_calculation_2.vcf.gz.tbi' 2023-11-25T11:02:48,725 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_gangstr1.vcf.gz' 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2023-11-25T11:02:48,807 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr_flanking_bp_non_flanking.vcf.gz' 2023-11-25T11:02:48,808 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_hipstr_flanking_bp_non_flanking.vcf.gz.tbi' 2023-11-25T11:02:48,809 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_no_comparable_records_1.vcf.gz' 2023-11-25T11:02:48,810 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_no_comparable_records_1.vcf.gz.tbi' 2023-11-25T11:02:48,811 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_no_comparable_records_2.vcf.gz' 2023-11-25T11:02:48,813 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_no_comparable_records_2.vcf.gz.tbi' 2023-11-25T11:02:48,852 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_popstr.vcf.gz' 2023-11-25T11:02:48,857 adding 'trtools/testsupport/sample_vcfs/compareSTR_vcfs/test_popstr.vcf.gz.tbi' 2023-11-25T11:02:48,873 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_advntr.sorted.vcf.gz' 2023-11-25T11:02:48,876 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_advntr.sorted.vcf.gz.tbi' 2023-11-25T11:02:48,893 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_eh.sorted.vcf.gz' 2023-11-25T11:02:48,896 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_eh.sorted.vcf.gz.tbi' 2023-11-25T11:02:48,919 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_popstr.sorted.vcf.gz' 2023-11-25T11:02:48,923 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/NA12878_chr21_popstr.sorted.vcf.gz.tbi' 2023-11-25T11:02:48,925 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/advntr_filters.loclog.tab' 2023-11-25T11:02:48,926 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/advntr_filters.samplog.tab' 2023-11-25T11:02:49,065 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/advntr_filters.vcf' 2023-11-25T11:02:49,071 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/bad_preexisting_filter_ac_refac.vcf' 2023-11-25T11:02:49,072 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/bad_preexisting_het_hwep.vcf' 2023-11-25T11:02:49,074 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/bad_preexisting_hrun.vcf' 2023-11-25T11:02:49,075 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/create_test_files.sh' 2023-11-25T11:02:49,114 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/drop_filtered.vcf' 2023-11-25T11:02:49,117 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_expansion.loclog.tab' 2023-11-25T11:02:49,118 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_expansion.samplog.tab' 2023-11-25T11:02:49,195 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_expansion.vcf' 2023-11-25T11:02:49,202 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_most.loclog.tab' 2023-11-25T11:02:49,203 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_most.samplog.tab' 2023-11-25T11:02:49,621 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/gangstr_filters_most.vcf' 2023-11-25T11:02:49,653 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/hipstr_filters.loclog.tab' 2023-11-25T11:02:49,654 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/hipstr_filters.samplog.tab' 2023-11-25T11:02:49,989 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/hipstr_filters.vcf' 2023-11-25T11:02:50,024 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/locus_filters.loclog.tab' 2023-11-25T11:02:50,025 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/locus_filters.samplog.tab' 2023-11-25T11:02:50,379 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/locus_filters.vcf' 2023-11-25T11:02:50,415 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/popstr_filters.loclog.tab' 2023-11-25T11:02:50,416 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/popstr_filters.samplog.tab' 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adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/advntr_filters.loclog.tab' 2023-11-25T11:02:50,800 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/advntr_filters.samplog.tab' 2023-11-25T11:02:50,938 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/advntr_filters.vcf' 2023-11-25T11:02:50,982 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/drop_filtered.vcf' 2023-11-25T11:02:50,986 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_expansion.loclog.tab' 2023-11-25T11:02:50,987 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_expansion.samplog.tab' 2023-11-25T11:02:51,056 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_expansion.vcf' 2023-11-25T11:02:51,064 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_most.loclog.tab' 2023-11-25T11:02:51,065 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_most.samplog.tab' 2023-11-25T11:02:51,481 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/gangstr_filters_most.vcf' 2023-11-25T11:02:51,515 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/hipstr_filters.loclog.tab' 2023-11-25T11:02:51,516 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/hipstr_filters.samplog.tab' 2023-11-25T11:02:51,855 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/hipstr_filters.vcf' 2023-11-25T11:02:51,892 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/locus_filters.loclog.tab' 2023-11-25T11:02:51,893 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/locus_filters.samplog.tab' 2023-11-25T11:02:52,254 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/locus_filters.vcf' 2023-11-25T11:02:52,291 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/popstr_filters.loclog.tab' 2023-11-25T11:02:52,293 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/popstr_filters.samplog.tab' 2023-11-25T11:02:52,402 adding 'trtools/testsupport/sample_vcfs/dumpSTR_vcfs/pyvcf_output/popstr_filters.vcf' 2023-11-25T11:02:52,613 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/advntr_merged.vcf' 2023-11-25T11:02:52,686 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/create_test_files.sh' 2023-11-25T11:02:52,694 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/eh_X_no_alt_merged.vcf' 2023-11-25T11:02:52,710 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/eh_X_no_alt_merged_swap.vcf' 2023-11-25T11:02:52,712 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/eh_merged.vcf' 2023-11-25T11:02:52,714 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/eh_no_alt_merged.vcf' 2023-11-25T11:02:52,852 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/gangstr_merged.vcf' 2023-11-25T11:02:53,068 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr-harmonized-merge-contains-flanking.vcf.gz' 2023-11-25T11:02:53,317 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr-harmonized-merge-contains-flanking.vcf.gz.tbi' 2023-11-25T11:02:53,382 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr-harmonized-merge-no-flanking.vcf.gz' 2023-11-25T11:02:53,388 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr-harmonized-merge-no-flanking.vcf.gz.tbi' 2023-11-25T11:02:53,396 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_flanking_harmonization_test_output.vcf' 2023-11-25T11:02:53,399 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_merged.vcf' 2023-11-25T11:02:53,419 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/one_sample_multiple_chroms_diff_contig_order.vcf.gz' 2023-11-25T11:02:53,426 adding 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'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifferent2.vcf.gz.tbi' 2023-11-25T11:02:55,032 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifflength.vcf.gz' 2023-11-25T11:02:55,035 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigdifflength.vcf.gz.tbi' 2023-11-25T11:02:55,038 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigmissing1.vcf.gz' 2023-11-25T11:02:55,041 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigmissing1.vcf.gz.tbi' 2023-11-25T11:02:55,044 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigmissing2.vcf.gz' 2023-11-25T11:02:55,046 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_contigmissing2.vcf.gz.tbi' 2023-11-25T11:02:55,049 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh1.vcf.gz' 2023-11-25T11:02:55,052 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh1.vcf.gz.tbi' 2023-11-25T11:02:55,055 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh2.vcf.gz' 2023-11-25T11:02:55,059 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh2.vcf.gz.tbi' 2023-11-25T11:02:55,061 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_X1.vcf.gz' 2023-11-25T11:02:55,066 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_X1.vcf.gz.tbi' 2023-11-25T11:02:55,068 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_X_no_alt.vcf.gz' 2023-11-25T11:02:55,070 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_X_no_alt.vcf.gz.tbi' 2023-11-25T11:02:55,072 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_no_alt.vcf.gz' 2023-11-25T11:02:55,074 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_eh_no_alt.vcf.gz.tbi' 2023-11-25T11:02:55,117 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr1.vcf.gz' 2023-11-25T11:02:55,122 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr1.vcf.gz.tbi' 2023-11-25T11:02:55,125 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr1_1contig.vcf.gz' 2023-11-25T11:02:55,127 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr1_1contig.vcf.gz.tbi' 2023-11-25T11:02:55,166 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr2.vcf.gz' 2023-11-25T11:02:55,169 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr2.vcf.gz.tbi' 2023-11-25T11:02:55,171 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr2_1contig.vcf.gz' 2023-11-25T11:02:55,172 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr2_1contig.vcf.gz.tbi' 2023-11-25T11:02:55,195 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_dupID.vcf.gz' 2023-11-25T11:02:55,198 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_dupID.vcf.gz.tbi' 2023-11-25T11:02:55,200 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_missingformat1.vcf.gz' 2023-11-25T11:02:55,202 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_missingformat1.vcf.gz.tbi' 2023-11-25T11:02:55,203 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_missinginfo1.vcf.gz' 2023-11-25T11:02:55,205 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_missinginfo1.vcf.gz.tbi' 2023-11-25T11:02:55,228 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_unindexed1.vcf.gz' 2023-11-25T11:02:55,252 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_unindexed2.vcf.gz' 2023-11-25T11:02:55,353 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_unzipped1.vcf' 2023-11-25T11:02:55,456 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_gangstr_unzipped2.vcf' 2023-11-25T11:02:55,463 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr1.vcf.gz' 2023-11-25T11:02:55,464 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr1.vcf.gz.tbi' 2023-11-25T11:02:55,466 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr1_badinfo.vcf.gz' 2023-11-25T11:02:55,467 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr1_badinfo.vcf.gz.tbi' 2023-11-25T11:02:55,469 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr2.vcf.gz' 2023-11-25T11:02:55,470 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr2.vcf.gz.tbi' 2023-11-25T11:02:55,471 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr2_alt_v_ref.vcf.gz' 2023-11-25T11:02:55,472 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_hipstr2_alt_v_ref.vcf.gz.tbi' 2023-11-25T11:02:55,506 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_popstr1.vcf.gz' 2023-11-25T11:02:55,511 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_popstr1.vcf.gz.tbi' 2023-11-25T11:02:55,535 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_popstr2.vcf.gz' 2023-11-25T11:02:55,540 adding 'trtools/testsupport/sample_vcfs/mergeSTR_vcfs/test_file_popstr2.vcf.gz.tbi' 2023-11-25T11:02:55,543 adding 'trtools/testsupport/sample_vcfs/qc_vcfs/50by3.vcf' 2023-11-25T11:02:55,547 adding 'trtools/testsupport/sample_vcfs/qc_vcfs/5by50.vcf' 2023-11-25T11:02:55,548 adding 'trtools/testsupport/sample_vcfs/qc_vcfs/test_fakesample.txt' 2023-11-25T11:02:55,786 adding 'trtools/testsupport/sample_vcfs/qc_vcfs/test_popstr.vcf' 2023-11-25T11:02:56,033 adding 'trtools/testsupport/sample_vcfs/qc_vcfs/test_popstr_nocontig.vcf' 2023-11-25T11:02:56,043 adding 'trtools/testsupport/sample_vcfs/qc_vcfs/test_samplelist.txt' 2023-11-25T11:02:56,045 adding 'trtools/utils/__init__.py' 2023-11-25T11:02:56,047 adding 'trtools/utils/common.py' 2023-11-25T11:02:56,049 adding 'trtools/utils/mergeutils.py' 2023-11-25T11:02:56,057 adding 'trtools/utils/tr_harmonizer.py' 2023-11-25T11:02:56,060 adding 'trtools/utils/utils.py' 2023-11-25T11:02:56,062 adding 'trtools/utils/tests/.bandit' 2023-11-25T11:02:56,063 adding 'trtools/utils/tests/__init__.py' 2023-11-25T11:02:56,073 adding 'trtools/utils/tests/test_common.py' 2023-11-25T11:02:56,075 adding 'trtools/utils/tests/test_mergeutils.py' 2023-11-25T11:02:56,079 adding 'trtools/utils/tests/test_trharmonizer.py' 2023-11-25T11:02:56,082 adding 'trtools/utils/tests/test_utils.py' 2023-11-25T11:02:56,085 adding 'trtools-5.1.0.data/scripts/test_trtools.sh' 2023-11-25T11:02:56,087 adding 'trtools-5.1.0.data/scripts/trtools_prep_beagle_vcf.sh' 2023-11-25T11:02:56,089 adding 'trtools-5.1.0.dist-info/LICENSE.txt' 2023-11-25T11:02:56,092 adding 'trtools-5.1.0.dist-info/METADATA' 2023-11-25T11:02:56,093 adding 'trtools-5.1.0.dist-info/WHEEL' 2023-11-25T11:02:56,095 adding 'trtools-5.1.0.dist-info/entry_points.txt' 2023-11-25T11:02:56,097 adding 'trtools-5.1.0.dist-info/top_level.txt' 2023-11-25T11:02:56,103 adding 'trtools-5.1.0.dist-info/RECORD' 2023-11-25T11:02:57,232 removing build/bdist.linux-armv7l/wheel 2023-11-25T11:02:57,566 Building wheel for trtools (pyproject.toml): finished with status 'done' 2023-11-25T11:02:58,184 Created wheel for trtools: filename=trtools-5.1.0-py3-none-any.whl size=25204055 sha256=7466770e0cc5efe8756d1974d90afb228f46fac2fa5f16ff8a7a785dbae7b9c6 2023-11-25T11:02:58,186 Stored in directory: /tmp/pip-ephem-wheel-cache-5yettc_s/wheels/fd/2d/3d/d06b43855778b0cef3529c6f188496e1c4f8935c939880af63 2023-11-25T11:02:58,215 Successfully built trtools 2023-11-25T11:02:58,815 Removed build tracker: '/tmp/pip-build-tracker-gwgefcli'