2023-11-24T15:25:38,103 Created temporary directory: /tmp/pip-build-tracker-hbu8fuxm 2023-11-24T15:25:38,104 Initialized build tracking at /tmp/pip-build-tracker-hbu8fuxm 2023-11-24T15:25:38,104 Created build tracker: /tmp/pip-build-tracker-hbu8fuxm 2023-11-24T15:25:38,105 Entered build tracker: /tmp/pip-build-tracker-hbu8fuxm 2023-11-24T15:25:38,106 Created temporary directory: /tmp/pip-wheel-swg3p64t 2023-11-24T15:25:38,109 Created temporary directory: /tmp/pip-ephem-wheel-cache-z9qyxr8o 2023-11-24T15:25:38,131 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T15:25:38,134 2 location(s) to search for versions of biocode: 2023-11-24T15:25:38,134 * https://pypi.org/simple/biocode/ 2023-11-24T15:25:38,134 * https://www.piwheels.org/simple/biocode/ 2023-11-24T15:25:38,135 Fetching project page and analyzing links: https://pypi.org/simple/biocode/ 2023-11-24T15:25:38,135 Getting page https://pypi.org/simple/biocode/ 2023-11-24T15:25:38,137 Found index url https://pypi.org/simple/ 2023-11-24T15:25:38,410 Fetched page https://pypi.org/simple/biocode/ as application/vnd.pypi.simple.v1+json 2023-11-24T15:25:38,415 Found link https://files.pythonhosted.org/packages/e1/6d/8b417c8c08f02c960801f360bc8b38927a4c14dfee8cb1418978bdfc4946/biocode-0.1.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.1.0 2023-11-24T15:25:38,416 Found link https://files.pythonhosted.org/packages/96/e5/314879e7d54bee7e0ed6db1fc358d193ae2d118e4825a99d14f3269a9322/biocode-0.1.1.tar.gz (from https://pypi.org/simple/biocode/), version: 0.1.1 2023-11-24T15:25:38,417 Found link https://files.pythonhosted.org/packages/4e/94/c999970e61e13f3082eae7989bc32d745ef7d846824252dd9a3c09cfd19c/biocode-0.1.2.tar.gz (from https://pypi.org/simple/biocode/), version: 0.1.2 2023-11-24T15:25:38,417 Found link https://files.pythonhosted.org/packages/a5/2c/85a52abaf0192795d5fbc56842c58c349bc6b58c568b4b913b8fdf591617/biocode-0.1.3.tar.gz (from https://pypi.org/simple/biocode/), version: 0.1.3 2023-11-24T15:25:38,418 Found link https://files.pythonhosted.org/packages/a5/06/562772ff9d04bcfcde87ed1ce76026eaf8f6b15cf7336fc6334bad04db00/biocode-0.1.4.tar.gz (from https://pypi.org/simple/biocode/), version: 0.1.4 2023-11-24T15:25:38,419 Found link https://files.pythonhosted.org/packages/27/c6/cdb7baa2821259f68c059a9e7385d613b817d90c00c8e727df7d3da23d2e/biocode-0.1.5.tar.gz (from https://pypi.org/simple/biocode/), version: 0.1.5 2023-11-24T15:25:38,420 Found link https://files.pythonhosted.org/packages/5d/ff/bda52fd80d3696809f96b27e1df816809c610a91587199fbb5611a82ff48/biocode-0.2.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.2.0 2023-11-24T15:25:38,420 Found link https://files.pythonhosted.org/packages/4b/d4/61d22deda78a8fb9b998ac1a7e7fee95eb3e84adcb26ab1705fda8235d31/biocode-0.3.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.3.0 2023-11-24T15:25:38,421 Found link https://files.pythonhosted.org/packages/9e/04/4a879cb84c7d4d8a11b9812e25668e5f1d4ef5e3cea429f7cc8202a0021b/biocode-0.3.1.tar.gz (from https://pypi.org/simple/biocode/), version: 0.3.1 2023-11-24T15:25:38,422 Found link https://files.pythonhosted.org/packages/72/af/9de76d7a8ae1cc6912488e33e53df8145aac259d36ddd42fc3dc803ea473/biocode-0.4.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.4.0 2023-11-24T15:25:38,423 Found link https://files.pythonhosted.org/packages/c7/93/31d3a353be167da9500e2bdff93451dba1a6a134e425767d426e297a0853/biocode-0.4.1.tar.gz (from https://pypi.org/simple/biocode/), version: 0.4.1 2023-11-24T15:25:38,423 Found link https://files.pythonhosted.org/packages/7a/24/cae23280630c49008e96590c77494485e47bbcf488f5c4b4e03ecc7b1e29/biocode-0.4.2.tar.gz (from https://pypi.org/simple/biocode/), version: 0.4.2 2023-11-24T15:25:38,424 Found link https://files.pythonhosted.org/packages/7f/5a/0d11038818cc78cee863d20da8a16a9907c20be8bfa8334ebabec4cb37e4/biocode-0.4.4.tar.gz (from https://pypi.org/simple/biocode/), version: 0.4.4 2023-11-24T15:25:38,425 Found link https://files.pythonhosted.org/packages/43/8e/107a8d911b7af9db94a561f6740801f62b69a60cb8857fc6642268f0d99d/biocode-0.4.5.tar.gz (from https://pypi.org/simple/biocode/), version: 0.4.5 2023-11-24T15:25:38,426 Found link https://files.pythonhosted.org/packages/02/e7/dc62a42fcfcb2288f397789f6bc83fd40a815d495edba4fa79e14759935c/biocode-0.4.7.tar.gz (from https://pypi.org/simple/biocode/), version: 0.4.7 2023-11-24T15:25:38,427 Found link https://files.pythonhosted.org/packages/f2/fc/483f6dad337423c04dc8a1b2756c3e5326e9381648e5560eb602a4f83413/biocode-0.5.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.5.0 2023-11-24T15:25:38,427 Found link https://files.pythonhosted.org/packages/5c/b7/035e01334320dd66ac8c65be4baa910e8cb16215c563d7b65bfdfd5b56d6/biocode-0.5.1.tar.gz (from https://pypi.org/simple/biocode/), version: 0.5.1 2023-11-24T15:25:38,428 Found link https://files.pythonhosted.org/packages/95/f7/e7ac262a9e90ac52d889c0a832aa8276b95fb6c23d0c65bf32fc2ccc1c7a/biocode-0.5.2.tar.gz (from https://pypi.org/simple/biocode/), version: 0.5.2 2023-11-24T15:25:38,429 Found link https://files.pythonhosted.org/packages/3b/2d/43287226a16b06ecdf7ed706752de718042382513bf2a3a5b0c9d2a41222/biocode-0.5.3.tar.gz (from https://pypi.org/simple/biocode/), version: 0.5.3 2023-11-24T15:25:38,429 Found link https://files.pythonhosted.org/packages/b3/e7/e8b3bd627d57954933c9c5a79bbdf28ad93073cc0792c61f71e3777f44d8/biocode-0.6.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.6.0 2023-11-24T15:25:38,430 Found link https://files.pythonhosted.org/packages/dd/d7/73e00082816c193207ea58420b38ac0a4041d345b8617f0d15501367c080/biocode-0.7.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.7.0 2023-11-24T15:25:38,430 Found link https://files.pythonhosted.org/packages/bb/7a/c073ca257a937286fec9e225190fa55c66a46132708e8dfa13569ef0cc37/biocode-0.7.1.tar.gz (from https://pypi.org/simple/biocode/), version: 0.7.1 2023-11-24T15:25:38,431 Found link https://files.pythonhosted.org/packages/a3/b5/0a5b44de28177113d5bbc0a8b510ea6e9acf82184b1e1ad5303357d1caa5/biocode-0.8.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.8.0 2023-11-24T15:25:38,432 Found link https://files.pythonhosted.org/packages/ac/58/b16f07e13b99403a0069b7782dc963882f634b6863d6e4bba85d327bd634/biocode-0.9.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.9.0 2023-11-24T15:25:38,433 Found link https://files.pythonhosted.org/packages/60/4d/1ede29387210a62ff0c6ccbb1c467e94890fb1a5802a2a3b3d37df3997cb/biocode-0.10.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.10.0 2023-11-24T15:25:38,433 Found link https://files.pythonhosted.org/packages/8e/56/e76dfd9f0785ac5a835f275a4b6b35cc4fff7c8195f85ade37fb76a133bd/biocode-0.11.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.11.0 2023-11-24T15:25:38,434 Fetching project page and analyzing links: https://www.piwheels.org/simple/biocode/ 2023-11-24T15:25:38,435 Getting page https://www.piwheels.org/simple/biocode/ 2023-11-24T15:25:38,436 Found index url https://www.piwheels.org/simple/ 2023-11-24T15:25:38,593 Fetched page https://www.piwheels.org/simple/biocode/ as text/html 2023-11-24T15:25:38,600 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.10.0-py3-none-any.whl#sha256=176b55ba344b86385e86406fceaafb4dc19b817ed6ef96cc353386889ff6e709 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,601 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.9.0-py3-none-any.whl#sha256=501bd0384472d48e49c3ff2720c2ab87757414d567897589d38475113d0cdfff (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,602 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.8.0-py3-none-any.whl#sha256=e7072ae4de4a03bb9e9643e1161fcd0d8df3f543aab05b8b275799f5172f72b6 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,602 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.7.1-py3-none-any.whl#sha256=8a4879e5efc9060b185c19b016b32d855dcc3c5ced8cb614484771c21474ac71 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,603 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.7.0-py3-none-any.whl#sha256=7440f5b1d70473f68e2c42b99ce36bb23229dac2f5c1d59d287fe59f6b9fa8c6 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,605 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.6.0-py3-none-any.whl#sha256=f638223164aad0892b1f4e3ff59e5c70bf598b95f242467fc1aa28dc100436b6 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,605 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.5.3-py3-none-any.whl#sha256=d47b9988366ce2efc4b61fa29fa149d6518a5abd2b645ef30ca873b2a156d656 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,606 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.5.2-py3-none-any.whl#sha256=87ef8c0b656cb96cbddffb44f82a3f7d40334636f9919dd335b7aac6d872331e (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,606 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.5.1-py3-none-any.whl#sha256=bf9a0479e6b373349ff4d030deed21980a2b0adab49430c21616bd78cdf290b1 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,607 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.5.0-py3-none-any.whl#sha256=6ce7d47e815c46602fb4ba8a8764d62c5f26910a6c168c63956baf4983f90a45 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,607 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.4.7-py3-none-any.whl#sha256=c6f756e5d1f8d1c212a939c1081689f81a283788ef9a4b6c034eea0031d77ac3 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,608 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.4.5-py3-none-any.whl#sha256=932e531e5c3c1007b4b797e8f95973867123104ae76b7f79a2603520f2420370 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,608 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.4.4-py3-none-any.whl#sha256=b61ad63c7d700f55cd2db1a75a68d247d54f08fcd6ec9308b547a5f1ea0ce0fe (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,609 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.4.2-py3-none-any.whl#sha256=e3bae2595434c4a01ca3c8128147d556b5bde54d82faf923f41413864cea2b0d (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,609 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.4.1-py3-none-any.whl#sha256=521f2d73f74c744fbe98259bd0c5246da47360c2f15cc9673dd508810a483917 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,610 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.4.0-py3-none-any.whl#sha256=c0167fa70e63b6ae969ba2a625bde0f55968889d65db61a195bccb8c7a36301e (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,611 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.3.1-py3-none-any.whl#sha256=da177825df75c57e89f9af93b45c99d0d43e1bd1c9b98b20396d1f80ac764f09 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,611 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.3.0-py3-none-any.whl#sha256=db84b6266a91bbdab2b21a249781b03776481f1ba3521c28b2c5af244e40f6d5 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,612 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.2.0-py3-none-any.whl#sha256=552b663044ffd5a76d432ac46e0b3ed5d11cd065bb16cc3598b0bdb77595b7ff (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,613 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.1.5-py3-none-any.whl#sha256=d036768387d015aac47397bce617b23c510f102a026ef9c488626d9c0697694f (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,613 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.1.4-py3-none-any.whl#sha256=70e1a456c4373ebf44860b89f3555173e027e3c4f35c51d65c6101a574a1c8ef (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,614 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.1.3-py3-none-any.whl#sha256=550c92b8b5e8d214a4e6b7e0dfca8932059095749a2d7d77d326c867e6b19154 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,614 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.1.2-py3-none-any.whl#sha256=cccf2290fd0a5cfcf8edbf2ca2bb07a469ad361c612567cb949e326d52c77c39 (from https://www.piwheels.org/simple/biocode/) 2023-11-24T15:25:38,615 Skipping link: not a file: https://www.piwheels.org/simple/biocode/ 2023-11-24T15:25:38,616 Skipping link: not a file: https://pypi.org/simple/biocode/ 2023-11-24T15:25:38,639 Given no hashes to check 1 links for project 'biocode': discarding no candidates 2023-11-24T15:25:38,659 Collecting biocode==0.11.0 2023-11-24T15:25:38,661 Created temporary directory: /tmp/pip-unpack-sw5zctar 2023-11-24T15:25:38,909 Downloading biocode-0.11.0.tar.gz (6.5 MB) 2023-11-24T15:25:41,202 Added biocode==0.11.0 from https://files.pythonhosted.org/packages/8e/56/e76dfd9f0785ac5a835f275a4b6b35cc4fff7c8195f85ade37fb76a133bd/biocode-0.11.0.tar.gz to build tracker '/tmp/pip-build-tracker-hbu8fuxm' 2023-11-24T15:25:41,204 Running setup.py (path:/tmp/pip-wheel-swg3p64t/biocode_f7d061a82567472e8348c8ae92e96d4a/setup.py) egg_info for package biocode 2023-11-24T15:25:41,206 Created temporary directory: /tmp/pip-pip-egg-info-u8dooha8 2023-11-24T15:25:41,207 Preparing metadata (setup.py): started 2023-11-24T15:25:41,208 Running command python setup.py egg_info 2023-11-24T15:25:42,221 running egg_info 2023-11-24T15:25:42,223 creating /tmp/pip-pip-egg-info-u8dooha8/biocode.egg-info 2023-11-24T15:25:42,249 writing /tmp/pip-pip-egg-info-u8dooha8/biocode.egg-info/PKG-INFO 2023-11-24T15:25:42,252 writing dependency_links to /tmp/pip-pip-egg-info-u8dooha8/biocode.egg-info/dependency_links.txt 2023-11-24T15:25:42,254 writing requirements to /tmp/pip-pip-egg-info-u8dooha8/biocode.egg-info/requires.txt 2023-11-24T15:25:42,255 writing top-level names to /tmp/pip-pip-egg-info-u8dooha8/biocode.egg-info/top_level.txt 2023-11-24T15:25:42,257 writing manifest file '/tmp/pip-pip-egg-info-u8dooha8/biocode.egg-info/SOURCES.txt' 2023-11-24T15:25:42,367 reading manifest file '/tmp/pip-pip-egg-info-u8dooha8/biocode.egg-info/SOURCES.txt' 2023-11-24T15:25:42,368 reading manifest template 'MANIFEST.in' 2023-11-24T15:25:42,370 adding license file 'LICENSE' 2023-11-24T15:25:42,375 writing manifest file '/tmp/pip-pip-egg-info-u8dooha8/biocode.egg-info/SOURCES.txt' 2023-11-24T15:25:42,485 Preparing metadata (setup.py): finished with status 'done' 2023-11-24T15:25:42,490 Source in /tmp/pip-wheel-swg3p64t/biocode_f7d061a82567472e8348c8ae92e96d4a has version 0.11.0, which satisfies requirement biocode==0.11.0 from https://files.pythonhosted.org/packages/8e/56/e76dfd9f0785ac5a835f275a4b6b35cc4fff7c8195f85ade37fb76a133bd/biocode-0.11.0.tar.gz 2023-11-24T15:25:42,491 Removed biocode==0.11.0 from https://files.pythonhosted.org/packages/8e/56/e76dfd9f0785ac5a835f275a4b6b35cc4fff7c8195f85ade37fb76a133bd/biocode-0.11.0.tar.gz from build tracker '/tmp/pip-build-tracker-hbu8fuxm' 2023-11-24T15:25:42,496 Created temporary directory: /tmp/pip-unpack-75u928ya 2023-11-24T15:25:42,497 Created temporary directory: /tmp/pip-unpack-dvjniy5w 2023-11-24T15:25:42,505 Building wheels for collected packages: biocode 2023-11-24T15:25:42,510 Created temporary directory: /tmp/pip-wheel-o1yhuips 2023-11-24T15:25:42,510 Building wheel for biocode (setup.py): started 2023-11-24T15:25:42,512 Destination directory: /tmp/pip-wheel-o1yhuips 2023-11-24T15:25:42,512 Running command python setup.py bdist_wheel 2023-11-24T15:25:43,534 running bdist_wheel 2023-11-24T15:25:43,664 running build 2023-11-24T15:25:43,665 running build_py 2023-11-24T15:25:43,693 creating build 2023-11-24T15:25:43,694 creating build/lib 2023-11-24T15:25:43,694 creating build/lib/biocode 2023-11-24T15:25:43,696 copying biocode/utils.py -> build/lib/biocode 2023-11-24T15:25:43,698 copying biocode/genbank.py -> build/lib/biocode 2023-11-24T15:25:43,700 copying biocode/annotation.py -> build/lib/biocode 2023-11-24T15:25:43,702 copying biocode/tbl.py -> build/lib/biocode 2023-11-24T15:25:43,705 copying biocode/ncbigff.py -> build/lib/biocode 2023-11-24T15:25:43,707 copying biocode/__init__.py -> build/lib/biocode 2023-11-24T15:25:43,708 copying biocode/bed.py -> build/lib/biocode 2023-11-24T15:25:43,710 copying biocode/things.py -> build/lib/biocode 2023-11-24T15:25:43,714 copying biocode/gff.py -> build/lib/biocode 2023-11-24T15:25:43,716 running egg_info 2023-11-24T15:25:43,741 writing biocode.egg-info/PKG-INFO 2023-11-24T15:25:43,744 writing dependency_links to biocode.egg-info/dependency_links.txt 2023-11-24T15:25:43,746 writing requirements to biocode.egg-info/requires.txt 2023-11-24T15:25:43,747 writing top-level names to biocode.egg-info/top_level.txt 2023-11-24T15:25:43,790 reading manifest file 'biocode.egg-info/SOURCES.txt' 2023-11-24T15:25:43,795 reading manifest template 'MANIFEST.in' 2023-11-24T15:25:43,796 adding license file 'LICENSE' 2023-11-24T15:25:43,802 writing manifest file 'biocode.egg-info/SOURCES.txt' 2023-11-24T15:25:43,806 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'biocode.data' is absent from the `packages` configuration. 2023-11-24T15:25:43,807 !! 2023-11-24T15:25:43,808 ******************************************************************************** 2023-11-24T15:25:43,808 ############################ 2023-11-24T15:25:43,809 # Package would be ignored # 2023-11-24T15:25:43,809 ############################ 2023-11-24T15:25:43,810 Python recognizes 'biocode.data' as an importable package[^1], 2023-11-24T15:25:43,810 but it is absent from setuptools' `packages` configuration. 2023-11-24T15:25:43,811 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T15:25:43,812 package, please make sure that 'biocode.data' is explicitly added 2023-11-24T15:25:43,812 to the `packages` configuration field. 2023-11-24T15:25:43,813 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T15:25:43,814 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T15:25:43,814 instead of `find_packages(...)`/`find:`). 2023-11-24T15:25:43,815 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T15:25:43,816 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T15:25:43,817 If you don't want 'biocode.data' to be distributed and are 2023-11-24T15:25:43,817 already explicitly excluding 'biocode.data' via 2023-11-24T15:25:43,818 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T15:25:43,818 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T15:25:43,819 combination with a more fine grained `package-data` configuration. 2023-11-24T15:25:43,820 You can read more about "package data files" on setuptools documentation page: 2023-11-24T15:25:43,821 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T15:25:43,823 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T15:25:43,824 even if it does not contain any `.py` files. 2023-11-24T15:25:43,825 On the other hand, currently there is no concept of package data 2023-11-24T15:25:43,825 directory, all directories are treated like packages. 2023-11-24T15:25:43,825 ******************************************************************************** 2023-11-24T15:25:43,826 !! 2023-11-24T15:25:43,827 check.warn(importable) 2023-11-24T15:25:43,827 creating build/lib/biocode/data 2023-11-24T15:25:43,828 copying biocode/data/HMPslim.v2.1.obo -> build/lib/biocode/data 2023-11-24T15:25:43,828 copying biocode/data/__init__.py -> build/lib/biocode/data 2023-11-24T15:25:43,828 copying biocode/data/biocode_script_index.json -> build/lib/biocode/data 2023-11-24T15:25:43,829 copying biocode/data/genbank_flat_file_header.template -> build/lib/biocode/data 2023-11-24T15:25:43,829 copying biocode/data/go.obo -> build/lib/biocode/data 2023-11-24T15:25:44,365 copying biocode/data/go.pickle -> build/lib/biocode/data 2023-11-24T15:25:44,449 copying biocode/data/rsem_html_table.template -> build/lib/biocode/data 2023-11-24T15:25:44,453 running build_scripts 2023-11-24T15:25:44,454 creating build/scripts-3.11 2023-11-24T15:25:44,455 copying and adjusting bin/filter_fasta_by_type.py -> build/scripts-3.11 2023-11-24T15:25:44,457 copying and adjusting bin/uniref_to_sqlite3.py -> build/scripts-3.11 2023-11-24T15:25:44,459 copying and adjusting bin/uniprot_sprot_to_sqlite3.py -> build/scripts-3.11 2023-11-24T15:25:44,462 copying and adjusting bin/replace_homopolymeric_repeats_with_Ns.py -> build/scripts-3.11 2023-11-24T15:25:44,464 copying and adjusting bin/filter_fasta_by_abundance.py -> build/scripts-3.11 2023-11-24T15:25:44,466 copying and adjusting bin/add_gff3_locus_tags.py -> build/scripts-3.11 2023-11-24T15:25:44,468 copying and adjusting bin/detect_inverted_repeats.py -> build/scripts-3.11 2023-11-24T15:25:44,470 copying and adjusting bin/convert_blast_btab_to_bed.py -> build/scripts-3.11 2023-11-24T15:25:44,472 copying and adjusting bin/replace_gff_type_column_value.py -> build/scripts-3.11 2023-11-24T15:25:44,474 copying and adjusting bin/make_cufflinks_ids_unique.py -> build/scripts-3.11 2023-11-24T15:25:44,476 copying and adjusting bin/subsample_fasta.py -> build/scripts-3.11 2023-11-24T15:25:44,478 copying and adjusting bin/convert_cufflinks_gtf_to_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,481 copying and adjusting bin/report_or_replace_nonstandard_residues.py -> build/scripts-3.11 2023-11-24T15:25:44,483 copying and adjusting bin/convert_gff3_to_gbk.py -> build/scripts-3.11 2023-11-24T15:25:44,485 copying and adjusting bin/correct_gff3_CDS_phase_column.py -> build/scripts-3.11 2023-11-24T15:25:44,488 copying and adjusting bin/merge_bam_files.py -> build/scripts-3.11 2023-11-24T15:25:44,490 copying and adjusting bin/calculate_query_coverage_by_blast.py -> build/scripts-3.11 2023-11-24T15:25:44,492 copying and adjusting bin/get_mpilup_from_id_list.py -> build/scripts-3.11 2023-11-24T15:25:44,494 copying and adjusting bin/prepend_to_fasta_header.py -> build/scripts-3.11 2023-11-24T15:25:44,496 copying and adjusting bin/download_assemblies_from_genbank.py -> build/scripts-3.11 2023-11-24T15:25:44,499 copying and adjusting bin/remove_masked_gene_models.py -> build/scripts-3.11 2023-11-24T15:25:44,501 copying and adjusting bin/report_basic_gff_model_agreement.py -> build/scripts-3.11 2023-11-24T15:25:44,503 copying and adjusting bin/convert_scipio_gff_to_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,505 copying and adjusting bin/convert_gff3_to_ncbi_tbl.py -> build/scripts-3.11 2023-11-24T15:25:44,507 copying and adjusting bin/convert_pasa_gff_to_models.py -> build/scripts-3.11 2023-11-24T15:25:44,510 copying and adjusting bin/report_gff3_statistics.py -> build/scripts-3.11 2023-11-24T15:25:44,512 copying and adjusting bin/make_go_index.py -> build/scripts-3.11 2023-11-24T15:25:44,514 copying and adjusting bin/create_rsem_html_table.py -> build/scripts-3.11 2023-11-24T15:25:44,516 copying and adjusting bin/convert_htab_to_bed.py -> build/scripts-3.11 2023-11-24T15:25:44,519 copying and adjusting bin/convert_prodigal_to_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,521 copying and adjusting bin/add_polypeptide_to_gff3_gene_models.py -> build/scripts-3.11 2023-11-24T15:25:44,523 copying and adjusting bin/append_to_fasta_header.py -> build/scripts-3.11 2023-11-24T15:25:44,525 copying and adjusting bin/create_taxonomy_db.py -> build/scripts-3.11 2023-11-24T15:25:44,527 copying and adjusting bin/convert_genbank_to_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,530 copying and adjusting bin/merge_fasta_files_and_uniquify_ids.py -> build/scripts-3.11 2023-11-24T15:25:44,532 copying and adjusting bin/update_selected_column9_values.py -> build/scripts-3.11 2023-11-24T15:25:44,534 copying and adjusting bin/reverse_misordered_cds_coords.py -> build/scripts-3.11 2023-11-24T15:25:44,536 copying and adjusting bin/interleave_fastq.py -> build/scripts-3.11 2023-11-24T15:25:44,538 copying and adjusting bin/validate_feature_boundaries_on_molecules.py -> build/scripts-3.11 2023-11-24T15:25:44,540 copying and adjusting bin/report_go_slim_counts.py -> build/scripts-3.11 2023-11-24T15:25:44,542 copying and adjusting bin/tigrfam_info_to_sqlite3.py -> build/scripts-3.11 2023-11-24T15:25:44,544 copying and adjusting bin/report_gff_intron_and_intergenic_stats.py -> build/scripts-3.11 2023-11-24T15:25:44,547 copying and adjusting bin/select_training_and_evaluation_transcripts.py -> build/scripts-3.11 2023-11-24T15:25:44,549 copying and adjusting bin/reformat_fasta_residue_lengths.py -> build/scripts-3.11 2023-11-24T15:25:44,551 copying and adjusting bin/set_source_column.py -> build/scripts-3.11 2023-11-24T15:25:44,552 copying and adjusting bin/split_fasta_into_even_files.py -> build/scripts-3.11 2023-11-24T15:25:44,554 copying and adjusting bin/remove_duplicate_sequences.py -> build/scripts-3.11 2023-11-24T15:25:44,556 copying and adjusting bin/fasta_base_content.py -> build/scripts-3.11 2023-11-24T15:25:44,558 copying and adjusting bin/check_gff_for_internal_stops.py -> build/scripts-3.11 2023-11-24T15:25:44,560 copying and adjusting bin/convert_aat_btab_to_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,563 copying and adjusting bin/remove_orphaned_features.py -> build/scripts-3.11 2023-11-24T15:25:44,565 copying and adjusting bin/convert_gff_to_ncbi_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,566 copying and adjusting bin/convert_blast_btab_to_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,569 copying and adjusting bin/convert_glimmerHMM_gff_to_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,571 copying and adjusting bin/fastq_simple_stats.py -> build/scripts-3.11 2023-11-24T15:25:44,573 copying and adjusting bin/randomly_subsample_fastq.py -> build/scripts-3.11 2023-11-24T15:25:44,576 copying and adjusting bin/fasta_simple_stats.py -> build/scripts-3.11 2023-11-24T15:25:44,578 copying and adjusting bin/split_interleaved_sequence_file.py -> build/scripts-3.11 2023-11-24T15:25:44,580 copying and adjusting bin/join_columnar_files.py -> build/scripts-3.11 2023-11-24T15:25:44,582 copying and adjusting bin/merge_masked_fasta_files.py -> build/scripts-3.11 2023-11-24T15:25:44,584 copying and adjusting bin/check_for_embedded_fasta_headers.py -> build/scripts-3.11 2023-11-24T15:25:44,586 copying and adjusting bin/filter_gff3_by_id_list.py -> build/scripts-3.11 2023-11-24T15:25:44,588 copying and adjusting bin/convert_stringtie_gtf_to_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,591 copying and adjusting bin/validate_fasta.py -> build/scripts-3.11 2023-11-24T15:25:44,593 copying and adjusting bin/remove_fasta_from_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,595 copying and adjusting bin/fasta_size_report.py -> build/scripts-3.11 2023-11-24T15:25:44,597 copying and adjusting bin/merge_predicted_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,600 copying and adjusting bin/append_to_fastq_read_header.py -> build/scripts-3.11 2023-11-24T15:25:44,602 copying and adjusting bin/fasta_size_distribution_plot.py -> build/scripts-3.11 2023-11-24T15:25:44,604 copying and adjusting bin/convert_fastq_to_fasta.py -> build/scripts-3.11 2023-11-24T15:25:44,606 copying and adjusting bin/eggnog_to_sqlite3.py -> build/scripts-3.11 2023-11-24T15:25:44,609 copying and adjusting bin/mark_partial_genes.py -> build/scripts-3.11 2023-11-24T15:25:44,612 copying and adjusting bin/validate_mate_pairing.py -> build/scripts-3.11 2023-11-24T15:25:44,614 copying and adjusting bin/convert_metagenemark_gff_to_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,617 copying and adjusting bin/hmmlib_to_sqlite3.py -> build/scripts-3.11 2023-11-24T15:25:44,619 copying and adjusting bin/convert_fasta_contigs_to_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,621 copying and adjusting bin/convert_cegma_gff_to_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,624 copying and adjusting bin/append_to_column_9_value.py -> build/scripts-3.11 2023-11-24T15:25:44,625 copying and adjusting bin/make_go_slim_index.py -> build/scripts-3.11 2023-11-24T15:25:44,628 copying and adjusting bin/convert_gff3_to_gene_association_format.py -> build/scripts-3.11 2023-11-24T15:25:44,630 copying and adjusting bin/reorient_sequences_by_id.py -> build/scripts-3.11 2023-11-24T15:25:44,633 copying and adjusting bin/report_matrix_shape.py -> build/scripts-3.11 2023-11-24T15:25:44,634 copying and adjusting bin/make_go_slim.py -> build/scripts-3.11 2023-11-24T15:25:44,637 copying and adjusting bin/extract_fasta_regions.py -> build/scripts-3.11 2023-11-24T15:25:44,639 copying and adjusting bin/filter_fastq_by_N_content.py -> build/scripts-3.11 2023-11-24T15:25:44,641 copying and adjusting bin/filter_fasta_by_header_regex.py -> build/scripts-3.11 2023-11-24T15:25:44,643 copying and adjusting bin/filter_uniref_by_taxonomy.py -> build/scripts-3.11 2023-11-24T15:25:44,646 copying and adjusting bin/create_taxonomic_profile_from_blast.py -> build/scripts-3.11 2023-11-24T15:25:44,648 copying and adjusting bin/split_molecules_on_gaps.py -> build/scripts-3.11 2023-11-24T15:25:44,650 copying and adjusting bin/remove_duplicate_features.py -> build/scripts-3.11 2023-11-24T15:25:44,652 copying and adjusting bin/convert_gff3_to_bed.py -> build/scripts-3.11 2023-11-24T15:25:44,654 copying and adjusting bin/list_biocode.py -> build/scripts-3.11 2023-11-24T15:25:44,656 copying and adjusting bin/split_isoforms_into_individual_genes.py -> build/scripts-3.11 2023-11-24T15:25:44,658 copying and adjusting bin/interleave_fasta.py -> build/scripts-3.11 2023-11-24T15:25:44,660 copying and adjusting bin/convert_augustus_to_gff3.py -> build/scripts-3.11 2023-11-24T15:25:44,662 copying and adjusting bin/filter_uniref_by_repid.py -> build/scripts-3.11 2023-11-24T15:25:44,664 copying and adjusting bin/extend_genes_to_stops.py -> build/scripts-3.11 2023-11-24T15:25:44,666 copying and adjusting bin/compare_gene_structures.py -> build/scripts-3.11 2023-11-24T15:25:44,669 copying and adjusting bin/write_fasta_from_gff.py -> build/scripts-3.11 2023-11-24T15:25:44,672 copying and adjusting bin/calculate_gene_coverage_from_assembly.py -> build/scripts-3.11 2023-11-24T15:25:44,674 copying and adjusting bin/report_coverage_gaps.py -> build/scripts-3.11 2023-11-24T15:25:44,676 changing mode of build/scripts-3.11/filter_fasta_by_type.py from 644 to 755 2023-11-24T15:25:44,677 changing mode of build/scripts-3.11/uniref_to_sqlite3.py from 644 to 755 2023-11-24T15:25:44,677 changing mode of build/scripts-3.11/uniprot_sprot_to_sqlite3.py from 644 to 755 2023-11-24T15:25:44,678 changing mode of build/scripts-3.11/replace_homopolymeric_repeats_with_Ns.py from 644 to 755 2023-11-24T15:25:44,679 changing mode of build/scripts-3.11/filter_fasta_by_abundance.py from 644 to 755 2023-11-24T15:25:44,680 changing mode of build/scripts-3.11/add_gff3_locus_tags.py from 644 to 755 2023-11-24T15:25:44,680 changing mode of build/scripts-3.11/detect_inverted_repeats.py from 644 to 755 2023-11-24T15:25:44,681 changing mode of build/scripts-3.11/convert_blast_btab_to_bed.py from 644 to 755 2023-11-24T15:25:44,682 changing mode of build/scripts-3.11/replace_gff_type_column_value.py from 644 to 755 2023-11-24T15:25:44,683 changing mode of build/scripts-3.11/make_cufflinks_ids_unique.py from 644 to 755 2023-11-24T15:25:44,683 changing mode of build/scripts-3.11/subsample_fasta.py from 644 to 755 2023-11-24T15:25:44,684 changing mode of build/scripts-3.11/convert_cufflinks_gtf_to_gff3.py from 644 to 755 2023-11-24T15:25:44,684 changing mode of build/scripts-3.11/report_or_replace_nonstandard_residues.py from 644 to 755 2023-11-24T15:25:44,685 changing mode of build/scripts-3.11/convert_gff3_to_gbk.py from 644 to 755 2023-11-24T15:25:44,686 changing mode of build/scripts-3.11/correct_gff3_CDS_phase_column.py from 644 to 755 2023-11-24T15:25:44,686 changing mode of build/scripts-3.11/merge_bam_files.py from 644 to 755 2023-11-24T15:25:44,687 changing mode of build/scripts-3.11/calculate_query_coverage_by_blast.py from 644 to 755 2023-11-24T15:25:44,688 changing mode of build/scripts-3.11/get_mpilup_from_id_list.py from 644 to 755 2023-11-24T15:25:44,688 changing mode of build/scripts-3.11/prepend_to_fasta_header.py from 644 to 755 2023-11-24T15:25:44,689 changing mode of build/scripts-3.11/download_assemblies_from_genbank.py from 644 to 755 2023-11-24T15:25:44,690 changing mode of build/scripts-3.11/remove_masked_gene_models.py from 644 to 755 2023-11-24T15:25:44,690 changing mode of build/scripts-3.11/report_basic_gff_model_agreement.py from 644 to 755 2023-11-24T15:25:44,691 changing mode of build/scripts-3.11/convert_scipio_gff_to_gff3.py from 644 to 755 2023-11-24T15:25:44,692 changing mode of build/scripts-3.11/convert_gff3_to_ncbi_tbl.py from 644 to 755 2023-11-24T15:25:44,693 changing mode of build/scripts-3.11/convert_pasa_gff_to_models.py from 644 to 755 2023-11-24T15:25:44,693 changing mode of build/scripts-3.11/report_gff3_statistics.py from 644 to 755 2023-11-24T15:25:44,694 changing mode of build/scripts-3.11/make_go_index.py from 644 to 755 2023-11-24T15:25:44,695 changing mode of build/scripts-3.11/create_rsem_html_table.py from 644 to 755 2023-11-24T15:25:44,695 changing mode of build/scripts-3.11/convert_htab_to_bed.py from 644 to 755 2023-11-24T15:25:44,696 changing mode of build/scripts-3.11/convert_prodigal_to_gff3.py from 644 to 755 2023-11-24T15:25:44,697 changing mode of build/scripts-3.11/add_polypeptide_to_gff3_gene_models.py from 644 to 755 2023-11-24T15:25:44,698 changing mode of build/scripts-3.11/append_to_fasta_header.py from 644 to 755 2023-11-24T15:25:44,698 changing mode of build/scripts-3.11/create_taxonomy_db.py from 644 to 755 2023-11-24T15:25:44,699 changing mode of build/scripts-3.11/convert_genbank_to_gff3.py from 644 to 755 2023-11-24T15:25:44,700 changing mode of build/scripts-3.11/merge_fasta_files_and_uniquify_ids.py from 644 to 755 2023-11-24T15:25:44,701 changing mode of build/scripts-3.11/update_selected_column9_values.py from 644 to 755 2023-11-24T15:25:44,701 changing mode of build/scripts-3.11/reverse_misordered_cds_coords.py from 644 to 755 2023-11-24T15:25:44,702 changing mode of build/scripts-3.11/interleave_fastq.py from 644 to 755 2023-11-24T15:25:44,702 changing mode of build/scripts-3.11/validate_feature_boundaries_on_molecules.py from 644 to 755 2023-11-24T15:25:44,703 changing mode of build/scripts-3.11/report_go_slim_counts.py from 644 to 755 2023-11-24T15:25:44,704 changing mode of build/scripts-3.11/tigrfam_info_to_sqlite3.py from 644 to 755 2023-11-24T15:25:44,704 changing mode of build/scripts-3.11/report_gff_intron_and_intergenic_stats.py from 644 to 755 2023-11-24T15:25:44,704 changing mode of build/scripts-3.11/select_training_and_evaluation_transcripts.py from 644 to 755 2023-11-24T15:25:44,705 changing mode of build/scripts-3.11/reformat_fasta_residue_lengths.py from 644 to 755 2023-11-24T15:25:44,706 changing mode of build/scripts-3.11/set_source_column.py from 644 to 755 2023-11-24T15:25:44,706 changing mode of build/scripts-3.11/split_fasta_into_even_files.py from 644 to 755 2023-11-24T15:25:44,707 changing mode of build/scripts-3.11/remove_duplicate_sequences.py from 644 to 755 2023-11-24T15:25:44,707 changing mode of build/scripts-3.11/fasta_base_content.py from 644 to 755 2023-11-24T15:25:44,708 changing mode of build/scripts-3.11/check_gff_for_internal_stops.py from 644 to 755 2023-11-24T15:25:44,708 changing mode of build/scripts-3.11/convert_aat_btab_to_gff3.py from 644 to 755 2023-11-24T15:25:44,708 changing mode of build/scripts-3.11/remove_orphaned_features.py from 644 to 755 2023-11-24T15:25:44,709 changing mode of build/scripts-3.11/convert_gff_to_ncbi_gff3.py from 644 to 755 2023-11-24T15:25:44,709 changing mode of build/scripts-3.11/convert_blast_btab_to_gff3.py from 644 to 755 2023-11-24T15:25:44,710 changing mode of build/scripts-3.11/convert_glimmerHMM_gff_to_gff3.py from 644 to 755 2023-11-24T15:25:44,710 changing mode of build/scripts-3.11/fastq_simple_stats.py from 644 to 755 2023-11-24T15:25:44,711 changing mode of build/scripts-3.11/randomly_subsample_fastq.py from 644 to 755 2023-11-24T15:25:44,711 changing mode of build/scripts-3.11/fasta_simple_stats.py from 644 to 755 2023-11-24T15:25:44,712 changing mode of build/scripts-3.11/split_interleaved_sequence_file.py from 644 to 755 2023-11-24T15:25:44,712 changing mode of build/scripts-3.11/join_columnar_files.py from 644 to 755 2023-11-24T15:25:44,713 changing mode of build/scripts-3.11/merge_masked_fasta_files.py from 644 to 755 2023-11-24T15:25:44,713 changing mode of build/scripts-3.11/check_for_embedded_fasta_headers.py from 644 to 755 2023-11-24T15:25:44,714 changing mode of build/scripts-3.11/filter_gff3_by_id_list.py from 644 to 755 2023-11-24T15:25:44,714 changing mode of build/scripts-3.11/convert_stringtie_gtf_to_gff3.py from 644 to 755 2023-11-24T15:25:44,715 changing mode of build/scripts-3.11/validate_fasta.py from 644 to 755 2023-11-24T15:25:44,715 changing mode of build/scripts-3.11/remove_fasta_from_gff3.py from 644 to 755 2023-11-24T15:25:44,715 changing mode of build/scripts-3.11/fasta_size_report.py from 644 to 755 2023-11-24T15:25:44,716 changing mode of build/scripts-3.11/merge_predicted_gff3.py from 644 to 755 2023-11-24T15:25:44,716 changing mode of build/scripts-3.11/append_to_fastq_read_header.py from 644 to 755 2023-11-24T15:25:44,717 changing mode of build/scripts-3.11/fasta_size_distribution_plot.py from 644 to 755 2023-11-24T15:25:44,718 changing mode of build/scripts-3.11/convert_fastq_to_fasta.py from 644 to 755 2023-11-24T15:25:44,718 changing mode of build/scripts-3.11/eggnog_to_sqlite3.py from 644 to 755 2023-11-24T15:25:44,719 changing mode of build/scripts-3.11/mark_partial_genes.py from 644 to 755 2023-11-24T15:25:44,719 changing mode of build/scripts-3.11/validate_mate_pairing.py from 644 to 755 2023-11-24T15:25:44,720 changing mode of build/scripts-3.11/convert_metagenemark_gff_to_gff3.py from 644 to 755 2023-11-24T15:25:44,720 changing mode of build/scripts-3.11/hmmlib_to_sqlite3.py from 644 to 755 2023-11-24T15:25:44,721 changing mode of build/scripts-3.11/convert_fasta_contigs_to_gff3.py from 644 to 755 2023-11-24T15:25:44,721 changing mode of build/scripts-3.11/convert_cegma_gff_to_gff3.py from 644 to 755 2023-11-24T15:25:44,722 changing mode of build/scripts-3.11/append_to_column_9_value.py from 644 to 755 2023-11-24T15:25:44,722 changing mode of build/scripts-3.11/make_go_slim_index.py from 644 to 755 2023-11-24T15:25:44,723 changing mode of build/scripts-3.11/convert_gff3_to_gene_association_format.py from 644 to 755 2023-11-24T15:25:44,723 changing mode of build/scripts-3.11/reorient_sequences_by_id.py from 644 to 755 2023-11-24T15:25:44,724 changing mode of build/scripts-3.11/report_matrix_shape.py from 644 to 755 2023-11-24T15:25:44,725 changing mode of build/scripts-3.11/make_go_slim.py from 644 to 755 2023-11-24T15:25:44,725 changing mode of build/scripts-3.11/extract_fasta_regions.py from 644 to 755 2023-11-24T15:25:44,726 changing mode of build/scripts-3.11/filter_fastq_by_N_content.py from 644 to 755 2023-11-24T15:25:44,727 changing mode of build/scripts-3.11/filter_fasta_by_header_regex.py from 644 to 755 2023-11-24T15:25:44,727 changing mode of build/scripts-3.11/filter_uniref_by_taxonomy.py from 644 to 755 2023-11-24T15:25:44,727 changing mode of build/scripts-3.11/create_taxonomic_profile_from_blast.py from 644 to 755 2023-11-24T15:25:44,728 changing mode of build/scripts-3.11/split_molecules_on_gaps.py from 644 to 755 2023-11-24T15:25:44,728 changing mode of build/scripts-3.11/remove_duplicate_features.py from 644 to 755 2023-11-24T15:25:44,729 changing mode of build/scripts-3.11/convert_gff3_to_bed.py from 644 to 755 2023-11-24T15:25:44,729 changing mode of build/scripts-3.11/list_biocode.py from 644 to 755 2023-11-24T15:25:44,730 changing mode of build/scripts-3.11/split_isoforms_into_individual_genes.py from 644 to 755 2023-11-24T15:25:44,730 changing mode of build/scripts-3.11/interleave_fasta.py from 644 to 755 2023-11-24T15:25:44,731 changing mode of build/scripts-3.11/convert_augustus_to_gff3.py from 644 to 755 2023-11-24T15:25:44,731 changing mode of build/scripts-3.11/filter_uniref_by_repid.py from 644 to 755 2023-11-24T15:25:44,732 changing mode of build/scripts-3.11/extend_genes_to_stops.py from 644 to 755 2023-11-24T15:25:44,732 changing mode of build/scripts-3.11/compare_gene_structures.py from 644 to 755 2023-11-24T15:25:44,733 changing mode of build/scripts-3.11/write_fasta_from_gff.py from 644 to 755 2023-11-24T15:25:44,733 changing mode of build/scripts-3.11/calculate_gene_coverage_from_assembly.py from 644 to 755 2023-11-24T15:25:44,734 changing mode of build/scripts-3.11/report_coverage_gaps.py from 644 to 755 2023-11-24T15:25:44,750 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-11-24T15:25:44,751 !! 2023-11-24T15:25:44,752 ******************************************************************************** 2023-11-24T15:25:44,753 Please avoid running ``setup.py`` directly. 2023-11-24T15:25:44,753 Instead, use pypa/build, pypa/installer or other 2023-11-24T15:25:44,754 standards-based tools. 2023-11-24T15:25:44,755 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-11-24T15:25:44,756 ******************************************************************************** 2023-11-24T15:25:44,757 !! 2023-11-24T15:25:44,757 self.initialize_options() 2023-11-24T15:25:44,776 installing to build/bdist.linux-armv7l/wheel 2023-11-24T15:25:44,777 running install 2023-11-24T15:25:44,801 running install_lib 2023-11-24T15:25:44,825 creating build/bdist.linux-armv7l 2023-11-24T15:25:44,826 creating build/bdist.linux-armv7l/wheel 2023-11-24T15:25:44,828 creating build/bdist.linux-armv7l/wheel/biocode 2023-11-24T15:25:44,829 copying build/lib/biocode/utils.py -> build/bdist.linux-armv7l/wheel/biocode 2023-11-24T15:25:44,831 copying build/lib/biocode/genbank.py -> build/bdist.linux-armv7l/wheel/biocode 2023-11-24T15:25:44,833 copying build/lib/biocode/annotation.py -> build/bdist.linux-armv7l/wheel/biocode 2023-11-24T15:25:44,836 copying build/lib/biocode/tbl.py -> build/bdist.linux-armv7l/wheel/biocode 2023-11-24T15:25:44,839 creating build/bdist.linux-armv7l/wheel/biocode/data 2023-11-24T15:25:44,840 copying build/lib/biocode/data/go.pickle -> build/bdist.linux-armv7l/wheel/biocode/data 2023-11-24T15:25:44,927 copying build/lib/biocode/data/go.obo -> build/bdist.linux-armv7l/wheel/biocode/data 2023-11-24T15:25:45,447 copying build/lib/biocode/data/HMPslim.v2.1.obo -> build/bdist.linux-armv7l/wheel/biocode/data 2023-11-24T15:25:45,450 copying build/lib/biocode/data/rsem_html_table.template -> build/bdist.linux-armv7l/wheel/biocode/data 2023-11-24T15:25:45,453 copying build/lib/biocode/data/biocode_script_index.json -> build/bdist.linux-armv7l/wheel/biocode/data 2023-11-24T15:25:45,455 copying build/lib/biocode/data/__init__.py -> build/bdist.linux-armv7l/wheel/biocode/data 2023-11-24T15:25:45,457 copying build/lib/biocode/data/genbank_flat_file_header.template -> build/bdist.linux-armv7l/wheel/biocode/data 2023-11-24T15:25:45,459 copying build/lib/biocode/ncbigff.py -> build/bdist.linux-armv7l/wheel/biocode 2023-11-24T15:25:45,462 copying build/lib/biocode/__init__.py -> build/bdist.linux-armv7l/wheel/biocode 2023-11-24T15:25:45,464 copying build/lib/biocode/bed.py -> build/bdist.linux-armv7l/wheel/biocode 2023-11-24T15:25:45,466 copying build/lib/biocode/things.py -> build/bdist.linux-armv7l/wheel/biocode 2023-11-24T15:25:45,469 copying build/lib/biocode/gff.py -> build/bdist.linux-armv7l/wheel/biocode 2023-11-24T15:25:45,471 running install_egg_info 2023-11-24T15:25:45,503 Copying biocode.egg-info to build/bdist.linux-armv7l/wheel/biocode-0.11.0-py3.11.egg-info 2023-11-24T15:25:45,515 running install_scripts 2023-11-24T15:25:45,519 creating build/bdist.linux-armv7l/wheel/biocode-0.11.0.data 2023-11-24T15:25:45,519 creating build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,521 copying build/scripts-3.11/randomly_subsample_fastq.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,523 copying build/scripts-3.11/correct_gff3_CDS_phase_column.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,525 copying build/scripts-3.11/fasta_base_content.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,527 copying build/scripts-3.11/interleave_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,529 copying build/scripts-3.11/split_isoforms_into_individual_genes.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,531 copying build/scripts-3.11/remove_duplicate_features.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,533 copying build/scripts-3.11/split_molecules_on_gaps.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,534 copying build/scripts-3.11/calculate_query_coverage_by_blast.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,537 copying build/scripts-3.11/report_matrix_shape.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,538 copying build/scripts-3.11/eggnog_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,541 copying build/scripts-3.11/report_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,543 copying build/scripts-3.11/select_training_and_evaluation_transcripts.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,545 copying build/scripts-3.11/hmmlib_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,547 copying build/scripts-3.11/detect_inverted_repeats.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,549 copying build/scripts-3.11/remove_masked_gene_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,551 copying build/scripts-3.11/convert_htab_to_bed.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,553 copying build/scripts-3.11/replace_gff_type_column_value.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,555 copying build/scripts-3.11/prepend_to_fasta_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,557 copying build/scripts-3.11/update_selected_column9_values.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,560 copying build/scripts-3.11/calculate_gene_coverage_from_assembly.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,562 copying build/scripts-3.11/append_to_fasta_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,564 copying build/scripts-3.11/split_interleaved_sequence_file.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,566 copying build/scripts-3.11/convert_gff3_to_gbk.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,568 copying build/scripts-3.11/validate_feature_boundaries_on_molecules.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,570 copying build/scripts-3.11/fastq_simple_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,572 copying build/scripts-3.11/convert_pasa_gff_to_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,573 copying build/scripts-3.11/append_to_fastq_read_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,575 copying build/scripts-3.11/report_or_replace_nonstandard_residues.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,577 copying build/scripts-3.11/reorient_sequences_by_id.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,579 copying build/scripts-3.11/append_to_column_9_value.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,581 copying build/scripts-3.11/remove_fasta_from_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,583 copying build/scripts-3.11/tigrfam_info_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,585 copying build/scripts-3.11/fasta_simple_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,587 copying build/scripts-3.11/fasta_size_distribution_plot.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,589 copying build/scripts-3.11/convert_stringtie_gtf_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,591 copying build/scripts-3.11/mark_partial_genes.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,594 copying build/scripts-3.11/create_taxonomy_db.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,596 copying build/scripts-3.11/report_basic_gff_model_agreement.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,598 copying build/scripts-3.11/remove_orphaned_features.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,600 copying build/scripts-3.11/report_gff3_statistics.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,602 copying build/scripts-3.11/download_assemblies_from_genbank.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,604 copying build/scripts-3.11/convert_gff_to_ncbi_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,606 copying build/scripts-3.11/list_biocode.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,608 copying build/scripts-3.11/remove_duplicate_sequences.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,609 copying build/scripts-3.11/convert_fasta_contigs_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,611 copying build/scripts-3.11/reverse_misordered_cds_coords.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,613 copying build/scripts-3.11/convert_glimmerHMM_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,616 copying build/scripts-3.11/convert_blast_btab_to_bed.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,617 copying build/scripts-3.11/join_columnar_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,619 copying build/scripts-3.11/uniref_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,621 copying build/scripts-3.11/convert_blast_btab_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,623 copying build/scripts-3.11/extend_genes_to_stops.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,625 copying build/scripts-3.11/make_go_slim.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,627 copying build/scripts-3.11/make_cufflinks_ids_unique.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,629 copying build/scripts-3.11/split_fasta_into_even_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,631 copying build/scripts-3.11/filter_fasta_by_type.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,633 copying build/scripts-3.11/reformat_fasta_residue_lengths.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,634 copying build/scripts-3.11/convert_cufflinks_gtf_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,636 copying build/scripts-3.11/fasta_size_report.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,638 copying build/scripts-3.11/extract_fasta_regions.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,640 copying build/scripts-3.11/merge_predicted_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,642 copying build/scripts-3.11/filter_uniref_by_repid.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,644 copying build/scripts-3.11/report_go_slim_counts.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,646 copying build/scripts-3.11/compare_gene_structures.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,649 copying build/scripts-3.11/convert_prodigal_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,651 copying build/scripts-3.11/convert_cegma_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,653 copying build/scripts-3.11/convert_gff3_to_gene_association_format.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,655 copying build/scripts-3.11/uniprot_sprot_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,657 copying build/scripts-3.11/get_mpilup_from_id_list.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,659 copying build/scripts-3.11/convert_scipio_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,661 copying build/scripts-3.11/report_gff_intron_and_intergenic_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,664 copying build/scripts-3.11/validate_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,666 copying build/scripts-3.11/merge_bam_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,668 copying build/scripts-3.11/filter_fasta_by_abundance.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,670 copying build/scripts-3.11/filter_gff3_by_id_list.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,671 copying build/scripts-3.11/add_polypeptide_to_gff3_gene_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,674 copying build/scripts-3.11/add_gff3_locus_tags.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,676 copying build/scripts-3.11/convert_metagenemark_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,678 copying build/scripts-3.11/make_go_index.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,680 copying build/scripts-3.11/convert_gff3_to_ncbi_tbl.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,681 copying build/scripts-3.11/create_taxonomic_profile_from_blast.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,684 copying build/scripts-3.11/filter_uniref_by_taxonomy.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,686 copying build/scripts-3.11/make_go_slim_index.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,688 copying build/scripts-3.11/convert_aat_btab_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,690 copying build/scripts-3.11/replace_homopolymeric_repeats_with_Ns.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,692 copying build/scripts-3.11/set_source_column.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,694 copying build/scripts-3.11/convert_genbank_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,697 copying build/scripts-3.11/create_rsem_html_table.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,699 copying build/scripts-3.11/convert_augustus_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,701 copying build/scripts-3.11/filter_fasta_by_header_regex.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,703 copying build/scripts-3.11/filter_fastq_by_N_content.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,705 copying build/scripts-3.11/convert_fastq_to_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,707 copying build/scripts-3.11/convert_gff3_to_bed.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,709 copying build/scripts-3.11/interleave_fastq.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,711 copying build/scripts-3.11/merge_masked_fasta_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,713 copying build/scripts-3.11/check_gff_for_internal_stops.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,715 copying build/scripts-3.11/validate_mate_pairing.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,717 copying build/scripts-3.11/merge_fasta_files_and_uniquify_ids.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,719 copying build/scripts-3.11/check_for_embedded_fasta_headers.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,721 copying build/scripts-3.11/write_fasta_from_gff.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,723 copying build/scripts-3.11/subsample_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts 2023-11-24T15:25:45,725 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/randomly_subsample_fastq.py to 755 2023-11-24T15:25:45,725 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/correct_gff3_CDS_phase_column.py to 755 2023-11-24T15:25:45,726 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/fasta_base_content.py to 755 2023-11-24T15:25:45,726 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/interleave_fasta.py to 755 2023-11-24T15:25:45,727 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/split_isoforms_into_individual_genes.py to 755 2023-11-24T15:25:45,727 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/remove_duplicate_features.py to 755 2023-11-24T15:25:45,728 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/split_molecules_on_gaps.py to 755 2023-11-24T15:25:45,729 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/calculate_query_coverage_by_blast.py to 755 2023-11-24T15:25:45,729 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/report_matrix_shape.py to 755 2023-11-24T15:25:45,729 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/eggnog_to_sqlite3.py to 755 2023-11-24T15:25:45,730 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/report_coverage_gaps.py to 755 2023-11-24T15:25:45,730 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/select_training_and_evaluation_transcripts.py to 755 2023-11-24T15:25:45,731 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/hmmlib_to_sqlite3.py to 755 2023-11-24T15:25:45,731 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/detect_inverted_repeats.py to 755 2023-11-24T15:25:45,732 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/remove_masked_gene_models.py to 755 2023-11-24T15:25:45,732 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_htab_to_bed.py to 755 2023-11-24T15:25:45,733 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/replace_gff_type_column_value.py to 755 2023-11-24T15:25:45,733 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/prepend_to_fasta_header.py to 755 2023-11-24T15:25:45,734 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/update_selected_column9_values.py to 755 2023-11-24T15:25:45,734 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/calculate_gene_coverage_from_assembly.py to 755 2023-11-24T15:25:45,735 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/append_to_fasta_header.py to 755 2023-11-24T15:25:45,735 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/split_interleaved_sequence_file.py to 755 2023-11-24T15:25:45,736 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_gff3_to_gbk.py to 755 2023-11-24T15:25:45,736 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/validate_feature_boundaries_on_molecules.py to 755 2023-11-24T15:25:45,737 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/fastq_simple_stats.py to 755 2023-11-24T15:25:45,737 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_pasa_gff_to_models.py to 755 2023-11-24T15:25:45,738 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/append_to_fastq_read_header.py to 755 2023-11-24T15:25:45,738 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/report_or_replace_nonstandard_residues.py to 755 2023-11-24T15:25:45,739 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/reorient_sequences_by_id.py to 755 2023-11-24T15:25:45,739 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/append_to_column_9_value.py to 755 2023-11-24T15:25:45,740 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/remove_fasta_from_gff3.py to 755 2023-11-24T15:25:45,740 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/tigrfam_info_to_sqlite3.py to 755 2023-11-24T15:25:45,741 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/fasta_simple_stats.py to 755 2023-11-24T15:25:45,742 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/fasta_size_distribution_plot.py to 755 2023-11-24T15:25:45,742 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_stringtie_gtf_to_gff3.py to 755 2023-11-24T15:25:45,743 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/mark_partial_genes.py to 755 2023-11-24T15:25:45,743 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/create_taxonomy_db.py to 755 2023-11-24T15:25:45,744 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/report_basic_gff_model_agreement.py to 755 2023-11-24T15:25:45,744 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/remove_orphaned_features.py to 755 2023-11-24T15:25:45,744 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/report_gff3_statistics.py to 755 2023-11-24T15:25:45,745 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/download_assemblies_from_genbank.py to 755 2023-11-24T15:25:45,745 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_gff_to_ncbi_gff3.py to 755 2023-11-24T15:25:45,746 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/list_biocode.py to 755 2023-11-24T15:25:45,746 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/remove_duplicate_sequences.py to 755 2023-11-24T15:25:45,747 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_fasta_contigs_to_gff3.py to 755 2023-11-24T15:25:45,747 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/reverse_misordered_cds_coords.py to 755 2023-11-24T15:25:45,748 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_glimmerHMM_gff_to_gff3.py to 755 2023-11-24T15:25:45,748 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_blast_btab_to_bed.py to 755 2023-11-24T15:25:45,748 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/join_columnar_files.py to 755 2023-11-24T15:25:45,749 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/uniref_to_sqlite3.py to 755 2023-11-24T15:25:45,749 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_blast_btab_to_gff3.py to 755 2023-11-24T15:25:45,750 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/extend_genes_to_stops.py to 755 2023-11-24T15:25:45,750 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/make_go_slim.py to 755 2023-11-24T15:25:45,751 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/make_cufflinks_ids_unique.py to 755 2023-11-24T15:25:45,751 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/split_fasta_into_even_files.py to 755 2023-11-24T15:25:45,752 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/filter_fasta_by_type.py to 755 2023-11-24T15:25:45,753 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/reformat_fasta_residue_lengths.py to 755 2023-11-24T15:25:45,753 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_cufflinks_gtf_to_gff3.py to 755 2023-11-24T15:25:45,753 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/fasta_size_report.py to 755 2023-11-24T15:25:45,754 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/extract_fasta_regions.py to 755 2023-11-24T15:25:45,754 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/merge_predicted_gff3.py to 755 2023-11-24T15:25:45,755 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/filter_uniref_by_repid.py to 755 2023-11-24T15:25:45,755 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/report_go_slim_counts.py to 755 2023-11-24T15:25:45,756 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/compare_gene_structures.py to 755 2023-11-24T15:25:45,757 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_prodigal_to_gff3.py to 755 2023-11-24T15:25:45,757 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_cegma_gff_to_gff3.py to 755 2023-11-24T15:25:45,758 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_gff3_to_gene_association_format.py to 755 2023-11-24T15:25:45,758 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/uniprot_sprot_to_sqlite3.py to 755 2023-11-24T15:25:45,759 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/get_mpilup_from_id_list.py to 755 2023-11-24T15:25:45,759 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_scipio_gff_to_gff3.py to 755 2023-11-24T15:25:45,759 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/report_gff_intron_and_intergenic_stats.py to 755 2023-11-24T15:25:45,760 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/validate_fasta.py to 755 2023-11-24T15:25:45,760 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/merge_bam_files.py to 755 2023-11-24T15:25:45,761 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/filter_fasta_by_abundance.py to 755 2023-11-24T15:25:45,761 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/filter_gff3_by_id_list.py to 755 2023-11-24T15:25:45,762 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/add_polypeptide_to_gff3_gene_models.py to 755 2023-11-24T15:25:45,762 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/add_gff3_locus_tags.py to 755 2023-11-24T15:25:45,762 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_metagenemark_gff_to_gff3.py to 755 2023-11-24T15:25:45,763 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/make_go_index.py to 755 2023-11-24T15:25:45,763 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_gff3_to_ncbi_tbl.py to 755 2023-11-24T15:25:45,764 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/create_taxonomic_profile_from_blast.py to 755 2023-11-24T15:25:45,764 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/filter_uniref_by_taxonomy.py to 755 2023-11-24T15:25:45,765 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/make_go_slim_index.py to 755 2023-11-24T15:25:45,765 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_aat_btab_to_gff3.py to 755 2023-11-24T15:25:45,766 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/replace_homopolymeric_repeats_with_Ns.py to 755 2023-11-24T15:25:45,766 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/set_source_column.py to 755 2023-11-24T15:25:45,767 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_genbank_to_gff3.py to 755 2023-11-24T15:25:45,767 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/create_rsem_html_table.py to 755 2023-11-24T15:25:45,768 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_augustus_to_gff3.py to 755 2023-11-24T15:25:45,768 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/filter_fasta_by_header_regex.py to 755 2023-11-24T15:25:45,769 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/filter_fastq_by_N_content.py to 755 2023-11-24T15:25:45,770 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_fastq_to_fasta.py to 755 2023-11-24T15:25:45,770 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/convert_gff3_to_bed.py to 755 2023-11-24T15:25:45,771 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/interleave_fastq.py to 755 2023-11-24T15:25:45,771 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/merge_masked_fasta_files.py to 755 2023-11-24T15:25:45,772 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/check_gff_for_internal_stops.py to 755 2023-11-24T15:25:45,773 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/validate_mate_pairing.py to 755 2023-11-24T15:25:45,773 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/merge_fasta_files_and_uniquify_ids.py to 755 2023-11-24T15:25:45,774 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/check_for_embedded_fasta_headers.py to 755 2023-11-24T15:25:45,774 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/write_fasta_from_gff.py to 755 2023-11-24T15:25:45,775 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.11.0.data/scripts/subsample_fasta.py to 755 2023-11-24T15:25:45,784 creating build/bdist.linux-armv7l/wheel/biocode-0.11.0.dist-info/WHEEL 2023-11-24T15:25:45,787 creating '/tmp/pip-wheel-o1yhuips/biocode-0.11.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-11-24T15:25:45,789 adding 'biocode/__init__.py' 2023-11-24T15:25:45,792 adding 'biocode/annotation.py' 2023-11-24T15:25:45,794 adding 'biocode/bed.py' 2023-11-24T15:25:45,796 adding 'biocode/genbank.py' 2023-11-24T15:25:45,800 adding 'biocode/gff.py' 2023-11-24T15:25:45,802 adding 'biocode/ncbigff.py' 2023-11-24T15:25:45,804 adding 'biocode/tbl.py' 2023-11-24T15:25:45,811 adding 'biocode/things.py' 2023-11-24T15:25:45,814 adding 'biocode/utils.py' 2023-11-24T15:25:45,819 adding 'biocode/data/HMPslim.v2.1.obo' 2023-11-24T15:25:45,820 adding 'biocode/data/__init__.py' 2023-11-24T15:25:45,822 adding 'biocode/data/biocode_script_index.json' 2023-11-24T15:25:45,823 adding 'biocode/data/genbank_flat_file_header.template' 2023-11-24T15:25:48,417 adding 'biocode/data/go.obo' 2023-11-24T15:25:49,550 adding 'biocode/data/go.pickle' 2023-11-24T15:25:49,597 adding 'biocode/data/rsem_html_table.template' 2023-11-24T15:25:49,601 adding 'biocode-0.11.0.data/scripts/add_gff3_locus_tags.py' 2023-11-24T15:25:49,603 adding 'biocode-0.11.0.data/scripts/add_polypeptide_to_gff3_gene_models.py' 2023-11-24T15:25:49,604 adding 'biocode-0.11.0.data/scripts/append_to_column_9_value.py' 2023-11-24T15:25:49,606 adding 'biocode-0.11.0.data/scripts/append_to_fasta_header.py' 2023-11-24T15:25:49,607 adding 'biocode-0.11.0.data/scripts/append_to_fastq_read_header.py' 2023-11-24T15:25:49,609 adding 'biocode-0.11.0.data/scripts/calculate_gene_coverage_from_assembly.py' 2023-11-24T15:25:49,610 adding 'biocode-0.11.0.data/scripts/calculate_query_coverage_by_blast.py' 2023-11-24T15:25:49,612 adding 'biocode-0.11.0.data/scripts/check_for_embedded_fasta_headers.py' 2023-11-24T15:25:49,613 adding 'biocode-0.11.0.data/scripts/check_gff_for_internal_stops.py' 2023-11-24T15:25:49,616 adding 'biocode-0.11.0.data/scripts/compare_gene_structures.py' 2023-11-24T15:25:49,618 adding 'biocode-0.11.0.data/scripts/convert_aat_btab_to_gff3.py' 2023-11-24T15:25:49,620 adding 'biocode-0.11.0.data/scripts/convert_augustus_to_gff3.py' 2023-11-24T15:25:49,622 adding 'biocode-0.11.0.data/scripts/convert_blast_btab_to_bed.py' 2023-11-24T15:25:49,623 adding 'biocode-0.11.0.data/scripts/convert_blast_btab_to_gff3.py' 2023-11-24T15:25:49,625 adding 'biocode-0.11.0.data/scripts/convert_cegma_gff_to_gff3.py' 2023-11-24T15:25:49,627 adding 'biocode-0.11.0.data/scripts/convert_cufflinks_gtf_to_gff3.py' 2023-11-24T15:25:49,628 adding 'biocode-0.11.0.data/scripts/convert_fasta_contigs_to_gff3.py' 2023-11-24T15:25:49,630 adding 'biocode-0.11.0.data/scripts/convert_fastq_to_fasta.py' 2023-11-24T15:25:49,631 adding 'biocode-0.11.0.data/scripts/convert_genbank_to_gff3.py' 2023-11-24T15:25:49,633 adding 'biocode-0.11.0.data/scripts/convert_gff3_to_bed.py' 2023-11-24T15:25:49,634 adding 'biocode-0.11.0.data/scripts/convert_gff3_to_gbk.py' 2023-11-24T15:25:49,636 adding 'biocode-0.11.0.data/scripts/convert_gff3_to_gene_association_format.py' 2023-11-24T15:25:49,638 adding 'biocode-0.11.0.data/scripts/convert_gff3_to_ncbi_tbl.py' 2023-11-24T15:25:49,639 adding 'biocode-0.11.0.data/scripts/convert_gff_to_ncbi_gff3.py' 2023-11-24T15:25:49,640 adding 'biocode-0.11.0.data/scripts/convert_glimmerHMM_gff_to_gff3.py' 2023-11-24T15:25:49,642 adding 'biocode-0.11.0.data/scripts/convert_htab_to_bed.py' 2023-11-24T15:25:49,643 adding 'biocode-0.11.0.data/scripts/convert_metagenemark_gff_to_gff3.py' 2023-11-24T15:25:49,644 adding 'biocode-0.11.0.data/scripts/convert_pasa_gff_to_models.py' 2023-11-24T15:25:49,646 adding 'biocode-0.11.0.data/scripts/convert_prodigal_to_gff3.py' 2023-11-24T15:25:49,647 adding 'biocode-0.11.0.data/scripts/convert_scipio_gff_to_gff3.py' 2023-11-24T15:25:49,649 adding 'biocode-0.11.0.data/scripts/convert_stringtie_gtf_to_gff3.py' 2023-11-24T15:25:49,650 adding 'biocode-0.11.0.data/scripts/correct_gff3_CDS_phase_column.py' 2023-11-24T15:25:49,652 adding 'biocode-0.11.0.data/scripts/create_rsem_html_table.py' 2023-11-24T15:25:49,654 adding 'biocode-0.11.0.data/scripts/create_taxonomic_profile_from_blast.py' 2023-11-24T15:25:49,656 adding 'biocode-0.11.0.data/scripts/create_taxonomy_db.py' 2023-11-24T15:25:49,657 adding 'biocode-0.11.0.data/scripts/detect_inverted_repeats.py' 2023-11-24T15:25:49,659 adding 'biocode-0.11.0.data/scripts/download_assemblies_from_genbank.py' 2023-11-24T15:25:49,660 adding 'biocode-0.11.0.data/scripts/eggnog_to_sqlite3.py' 2023-11-24T15:25:49,662 adding 'biocode-0.11.0.data/scripts/extend_genes_to_stops.py' 2023-11-24T15:25:49,663 adding 'biocode-0.11.0.data/scripts/extract_fasta_regions.py' 2023-11-24T15:25:49,664 adding 'biocode-0.11.0.data/scripts/fasta_base_content.py' 2023-11-24T15:25:49,666 adding 'biocode-0.11.0.data/scripts/fasta_simple_stats.py' 2023-11-24T15:25:49,667 adding 'biocode-0.11.0.data/scripts/fasta_size_distribution_plot.py' 2023-11-24T15:25:49,669 adding 'biocode-0.11.0.data/scripts/fasta_size_report.py' 2023-11-24T15:25:49,670 adding 'biocode-0.11.0.data/scripts/fastq_simple_stats.py' 2023-11-24T15:25:49,672 adding 'biocode-0.11.0.data/scripts/filter_fasta_by_abundance.py' 2023-11-24T15:25:49,673 adding 'biocode-0.11.0.data/scripts/filter_fasta_by_header_regex.py' 2023-11-24T15:25:49,674 adding 'biocode-0.11.0.data/scripts/filter_fasta_by_type.py' 2023-11-24T15:25:49,676 adding 'biocode-0.11.0.data/scripts/filter_fastq_by_N_content.py' 2023-11-24T15:25:49,677 adding 'biocode-0.11.0.data/scripts/filter_gff3_by_id_list.py' 2023-11-24T15:25:49,678 adding 'biocode-0.11.0.data/scripts/filter_uniref_by_repid.py' 2023-11-24T15:25:49,680 adding 'biocode-0.11.0.data/scripts/filter_uniref_by_taxonomy.py' 2023-11-24T15:25:49,681 adding 'biocode-0.11.0.data/scripts/get_mpilup_from_id_list.py' 2023-11-24T15:25:49,683 adding 'biocode-0.11.0.data/scripts/hmmlib_to_sqlite3.py' 2023-11-24T15:25:49,685 adding 'biocode-0.11.0.data/scripts/interleave_fasta.py' 2023-11-24T15:25:49,686 adding 'biocode-0.11.0.data/scripts/interleave_fastq.py' 2023-11-24T15:25:49,687 adding 'biocode-0.11.0.data/scripts/join_columnar_files.py' 2023-11-24T15:25:49,688 adding 'biocode-0.11.0.data/scripts/list_biocode.py' 2023-11-24T15:25:49,690 adding 'biocode-0.11.0.data/scripts/make_cufflinks_ids_unique.py' 2023-11-24T15:25:49,691 adding 'biocode-0.11.0.data/scripts/make_go_index.py' 2023-11-24T15:25:49,693 adding 'biocode-0.11.0.data/scripts/make_go_slim.py' 2023-11-24T15:25:49,695 adding 'biocode-0.11.0.data/scripts/make_go_slim_index.py' 2023-11-24T15:25:49,696 adding 'biocode-0.11.0.data/scripts/mark_partial_genes.py' 2023-11-24T15:25:49,698 adding 'biocode-0.11.0.data/scripts/merge_bam_files.py' 2023-11-24T15:25:49,699 adding 'biocode-0.11.0.data/scripts/merge_fasta_files_and_uniquify_ids.py' 2023-11-24T15:25:49,700 adding 'biocode-0.11.0.data/scripts/merge_masked_fasta_files.py' 2023-11-24T15:25:49,702 adding 'biocode-0.11.0.data/scripts/merge_predicted_gff3.py' 2023-11-24T15:25:49,703 adding 'biocode-0.11.0.data/scripts/prepend_to_fasta_header.py' 2023-11-24T15:25:49,705 adding 'biocode-0.11.0.data/scripts/randomly_subsample_fastq.py' 2023-11-24T15:25:49,706 adding 'biocode-0.11.0.data/scripts/reformat_fasta_residue_lengths.py' 2023-11-24T15:25:49,708 adding 'biocode-0.11.0.data/scripts/remove_duplicate_features.py' 2023-11-24T15:25:49,709 adding 'biocode-0.11.0.data/scripts/remove_duplicate_sequences.py' 2023-11-24T15:25:49,710 adding 'biocode-0.11.0.data/scripts/remove_fasta_from_gff3.py' 2023-11-24T15:25:49,711 adding 'biocode-0.11.0.data/scripts/remove_masked_gene_models.py' 2023-11-24T15:25:49,713 adding 'biocode-0.11.0.data/scripts/remove_orphaned_features.py' 2023-11-24T15:25:49,714 adding 'biocode-0.11.0.data/scripts/reorient_sequences_by_id.py' 2023-11-24T15:25:49,715 adding 'biocode-0.11.0.data/scripts/replace_gff_type_column_value.py' 2023-11-24T15:25:49,716 adding 'biocode-0.11.0.data/scripts/replace_homopolymeric_repeats_with_Ns.py' 2023-11-24T15:25:49,718 adding 'biocode-0.11.0.data/scripts/report_basic_gff_model_agreement.py' 2023-11-24T15:25:49,719 adding 'biocode-0.11.0.data/scripts/report_coverage_gaps.py' 2023-11-24T15:25:49,720 adding 'biocode-0.11.0.data/scripts/report_gff3_statistics.py' 2023-11-24T15:25:49,722 adding 'biocode-0.11.0.data/scripts/report_gff_intron_and_intergenic_stats.py' 2023-11-24T15:25:49,724 adding 'biocode-0.11.0.data/scripts/report_go_slim_counts.py' 2023-11-24T15:25:49,725 adding 'biocode-0.11.0.data/scripts/report_matrix_shape.py' 2023-11-24T15:25:49,726 adding 'biocode-0.11.0.data/scripts/report_or_replace_nonstandard_residues.py' 2023-11-24T15:25:49,728 adding 'biocode-0.11.0.data/scripts/reverse_misordered_cds_coords.py' 2023-11-24T15:25:49,729 adding 'biocode-0.11.0.data/scripts/select_training_and_evaluation_transcripts.py' 2023-11-24T15:25:49,730 adding 'biocode-0.11.0.data/scripts/set_source_column.py' 2023-11-24T15:25:49,732 adding 'biocode-0.11.0.data/scripts/split_fasta_into_even_files.py' 2023-11-24T15:25:49,733 adding 'biocode-0.11.0.data/scripts/split_interleaved_sequence_file.py' 2023-11-24T15:25:49,734 adding 'biocode-0.11.0.data/scripts/split_isoforms_into_individual_genes.py' 2023-11-24T15:25:49,736 adding 'biocode-0.11.0.data/scripts/split_molecules_on_gaps.py' 2023-11-24T15:25:49,737 adding 'biocode-0.11.0.data/scripts/subsample_fasta.py' 2023-11-24T15:25:49,738 adding 'biocode-0.11.0.data/scripts/tigrfam_info_to_sqlite3.py' 2023-11-24T15:25:49,740 adding 'biocode-0.11.0.data/scripts/uniprot_sprot_to_sqlite3.py' 2023-11-24T15:25:49,742 adding 'biocode-0.11.0.data/scripts/uniref_to_sqlite3.py' 2023-11-24T15:25:49,743 adding 'biocode-0.11.0.data/scripts/update_selected_column9_values.py' 2023-11-24T15:25:49,745 adding 'biocode-0.11.0.data/scripts/validate_fasta.py' 2023-11-24T15:25:49,746 adding 'biocode-0.11.0.data/scripts/validate_feature_boundaries_on_molecules.py' 2023-11-24T15:25:49,747 adding 'biocode-0.11.0.data/scripts/validate_mate_pairing.py' 2023-11-24T15:25:49,749 adding 'biocode-0.11.0.data/scripts/write_fasta_from_gff.py' 2023-11-24T15:25:49,751 adding 'biocode-0.11.0.dist-info/LICENSE' 2023-11-24T15:25:49,753 adding 'biocode-0.11.0.dist-info/METADATA' 2023-11-24T15:25:49,754 adding 'biocode-0.11.0.dist-info/WHEEL' 2023-11-24T15:25:49,755 adding 'biocode-0.11.0.dist-info/top_level.txt' 2023-11-24T15:25:49,757 adding 'biocode-0.11.0.dist-info/RECORD' 2023-11-24T15:25:49,856 removing build/bdist.linux-armv7l/wheel 2023-11-24T15:25:50,010 Building wheel for biocode (setup.py): finished with status 'done' 2023-11-24T15:25:50,090 Created wheel for biocode: filename=biocode-0.11.0-py3-none-any.whl size=6578354 sha256=12935f1029ccce1fa148acb48dcdd715b3ead3f188052f41158f6beb93820b96 2023-11-24T15:25:50,091 Stored in directory: /tmp/pip-ephem-wheel-cache-z9qyxr8o/wheels/54/9b/f8/b4f8e0a87c913edd44dfd3516fe5d32e02b46914476ceaa306 2023-11-24T15:25:50,108 Successfully built biocode 2023-11-24T15:25:50,272 Removed build tracker: '/tmp/pip-build-tracker-hbu8fuxm'