2023-09-27T03:27:29,021 Created temporary directory: /tmp/pip-build-tracker-4vnf35qt 2023-09-27T03:27:29,022 Initialized build tracking at /tmp/pip-build-tracker-4vnf35qt 2023-09-27T03:27:29,023 Created build tracker: /tmp/pip-build-tracker-4vnf35qt 2023-09-27T03:27:29,023 Entered build tracker: /tmp/pip-build-tracker-4vnf35qt 2023-09-27T03:27:29,024 Created temporary directory: /tmp/pip-wheel-8rmwf1x2 2023-09-27T03:27:29,027 Created temporary directory: /tmp/pip-ephem-wheel-cache-vxv2u7bq 2023-09-27T03:27:29,052 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-27T03:27:29,055 2 location(s) to search for versions of capcruncher: 2023-09-27T03:27:29,055 * https://pypi.org/simple/capcruncher/ 2023-09-27T03:27:29,055 * https://www.piwheels.org/simple/capcruncher/ 2023-09-27T03:27:29,056 Fetching project page and analyzing links: https://pypi.org/simple/capcruncher/ 2023-09-27T03:27:29,057 Getting page https://pypi.org/simple/capcruncher/ 2023-09-27T03:27:29,058 Found index url https://pypi.org/simple/ 2023-09-27T03:27:29,199 Fetched page https://pypi.org/simple/capcruncher/ as application/vnd.pypi.simple.v1+json 2023-09-27T03:27:29,205 Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/34/0a/9e75866768f2f383fb94a19406fc1351c2752e365607839d6e2bb1d8d84b/capcruncher-0.1.0a1-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.8) 2023-09-27T03:27:29,206 Found link https://files.pythonhosted.org/packages/3c/f1/f89b867eec66701b2f41487ec19a3092f869cba76c6d15750220af30ab7b/capcruncher-0.1.0a1.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.8), version: 0.1.0a1 2023-09-27T03:27:29,207 Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/1d/1b/b3083fd403c5ea09c7ac18edb1a69b795ab753e1dce96d3837c6777c090a/capcruncher-0.1.0a2-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.8) 2023-09-27T03:27:29,207 Found link https://files.pythonhosted.org/packages/78/43/1dbd9816f26f28c8ea8e41109f7b55f3c29216ae9ee9faf3132455ee5900/capcruncher-0.1.0a2.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.8), version: 0.1.0a2 2023-09-27T03:27:29,208 Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/af/21/1bd19a95d650d782bd61f0617e2ade19b8ea9dfc2583d5188cf31fc9e2ac/capcruncher-0.1.1a0-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) 2023-09-27T03:27:29,209 Found link https://files.pythonhosted.org/packages/4b/58/8c4c26cb67c97bc632d4fd7df6b754a3d7d52d9224a12b5ef30f1551e18a/capcruncher-0.1.1a0.tar.gz (from https://pypi.org/simple/capcruncher/), version: 0.1.1a0 2023-09-27T03:27:29,209 Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/09/3a/0d4e2559f5fcd1ea08ba4a59a2174bfa9b4e362fb6fbbeff57652bc8b43b/capcruncher-0.1.1a1-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) 2023-09-27T03:27:29,210 Found link https://files.pythonhosted.org/packages/fc/38/d9f3fbb589780a7116c60af23e14e0ffec82fa966bd6fac06494df1ff972/capcruncher-0.1.1a1.tar.gz (from https://pypi.org/simple/capcruncher/), version: 0.1.1a1 2023-09-27T03:27:29,210 Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/d8/b8/f378ab302aba8e011a3548bc8e12ca018dd51bae5e175f2aeac9b7023dbe/capcruncher-0.2.0-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) 2023-09-27T03:27:29,211 Found link https://files.pythonhosted.org/packages/ab/85/07383d62359c33bab143b6f85173a09852963625a5c6e23bbfd5c54d81d4/capcruncher-0.2.0.tar.gz (from https://pypi.org/simple/capcruncher/), version: 0.2.0 2023-09-27T03:27:29,212 Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/20/fb/21512e9e9259664564498669e39be1c06854d7b9a4b2c088d640dbaed48b/capcruncher-0.2.2-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) 2023-09-27T03:27:29,212 Found link https://files.pythonhosted.org/packages/d6/8a/d499689bfadfc8c5ad88d9403619ffd62fe9169a359c304a3ef25d368b1d/capcruncher-0.2.2.tar.gz (from https://pypi.org/simple/capcruncher/), version: 0.2.2 2023-09-27T03:27:29,213 Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/37/32/8d0b33d160aeec619f8cc86611ac7771733f9a300176f3b7fbc5f94dc51a/capcruncher-0.2.3-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.8) 2023-09-27T03:27:29,214 Found link https://files.pythonhosted.org/packages/e7/da/78b7ae1ccdca4a9c2a0abdd16e308facc1909da2e159ce2d565c05fad639/capcruncher-0.2.3.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.8), version: 0.2.3 2023-09-27T03:27:29,214 Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/26/e5/2b7ada507bb60d04dfafa0655d63edd3b82cdfb5476b8672acf0cb5477b9/capcruncher-0.3.1-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10) 2023-09-27T03:27:29,215 Found link https://files.pythonhosted.org/packages/43/bd/2aabc1f9b8e2fae522852b4f3c8f27f42aadcf50016eb7bfcdfe83d499bb/capcruncher-0.3.1.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10), version: 0.3.1 2023-09-27T03:27:29,216 Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/23/34/26f733de022f420176a15aaccb50dc49d6eac08dcf68d147f08d3abb257b/capcruncher-0.3.2-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10) 2023-09-27T03:27:29,216 Found link https://files.pythonhosted.org/packages/b4/c4/a3c7065d7c993db2680c1303d40862031cc6e8535aca5b023ded383d4520/capcruncher-0.3.2.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10), version: 0.3.2 2023-09-27T03:27:29,217 Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/80/d5/ae6f38bc4ec0724841406c0125296bad843a1ca2fe9e2dfce8bb73796ae5/capcruncher-0.3.3-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10) 2023-09-27T03:27:29,218 Found link https://files.pythonhosted.org/packages/21/8f/8063b68decdfed76375774899994ce09bf6f2362453110d3a7e3091d0f47/capcruncher-0.3.3.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10), version: 0.3.3 2023-09-27T03:27:29,218 Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/61/55/adac692b940cca0f453b760ec8c3be9b325e22afb8e8693717fcebd202c0/capcruncher-0.3.4-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10) 2023-09-27T03:27:29,219 Found link https://files.pythonhosted.org/packages/b1/78/c98a2a4a6e62b5bd169af128129633b9e06bce32b0284b79c68808a8f0e5/capcruncher-0.3.4.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10), version: 0.3.4 2023-09-27T03:27:29,220 Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/a7/b0/ed93710d654d62b661c227e5ab7cd4318633571b06cf746789710ca33465/capcruncher-0.3.5-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10) 2023-09-27T03:27:29,221 Found link https://files.pythonhosted.org/packages/37/ea/966e9f14e18737107ed291ea6d3646f5a05e13a9566c2e70e0a7cd9ed172/capcruncher-0.3.5.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10), version: 0.3.5 2023-09-27T03:27:29,222 Fetching project page and analyzing links: https://www.piwheels.org/simple/capcruncher/ 2023-09-27T03:27:29,222 Getting page https://www.piwheels.org/simple/capcruncher/ 2023-09-27T03:27:29,224 Found index url https://www.piwheels.org/simple/ 2023-09-27T03:27:29,379 Fetched page https://www.piwheels.org/simple/capcruncher/ as text/html 2023-09-27T03:27:29,383 Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.3.3-py3-none-any.whl#sha256=a622eec10ed86905ffdc0d9696093c93ede9ae0280eb0979727ed05b78c6aeed (from https://www.piwheels.org/simple/capcruncher/) (requires-python:>=3.10) 2023-09-27T03:27:29,383 Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.3.2-py3-none-any.whl#sha256=cb9bbb6e602e5e11dcbac280be5520518f0110c58eb9bc7937644b956c455a02 (from https://www.piwheels.org/simple/capcruncher/) (requires-python:>=3.10) 2023-09-27T03:27:29,384 Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.3.1-py3-none-any.whl#sha256=010cc17949484bec95ba588bf89f30d450d6476b8e7c612e14f32270db999b52 (from https://www.piwheels.org/simple/capcruncher/) (requires-python:>=3.10) 2023-09-27T03:27:29,385 Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.2.3-py3-none-any.whl#sha256=3640a41566ec698430601c7ee8ff373d698ad995981fcb1564072cbdaadeaa70 (from https://www.piwheels.org/simple/capcruncher/) (requires-python:>=3.8) 2023-09-27T03:27:29,385 Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.2.2-py3-none-any.whl#sha256=696271de6a0cfb479ebe5c059b46015c0b54a4883b28fac6d3f60d3f10360694 (from https://www.piwheels.org/simple/capcruncher/) 2023-09-27T03:27:29,386 Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.2.0-py3-none-any.whl#sha256=a376e09af30f629484777d94d245a0a18cdee37e332344294623f74a218de161 (from https://www.piwheels.org/simple/capcruncher/) 2023-09-27T03:27:29,386 Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.1.1a1-py3-none-any.whl#sha256=45ad47d1025882de7d3ae2436f95d9c690fb55f4ad3320a464754782dd2a9ce8 (from https://www.piwheels.org/simple/capcruncher/) 2023-09-27T03:27:29,387 Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.1.1a0-py3-none-any.whl#sha256=33582eed6498ac35fff342bc97adfeec48d012dca74e99a13b6c8ed596465d0d (from https://www.piwheels.org/simple/capcruncher/) 2023-09-27T03:27:29,387 Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.1.0a2-py3-none-any.whl#sha256=a9cad04a0fa53e9864f02ac8641b704ba78bd0da1a8d83c5e84199e7ae183222 (from https://www.piwheels.org/simple/capcruncher/) (requires-python:>=3.8) 2023-09-27T03:27:29,388 Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.1.0a1-py3-none-any.whl#sha256=8d0852e344db844525d67d074e33a0880f102073b0bdc5d77c2c3bd498ffee5b (from https://www.piwheels.org/simple/capcruncher/) (requires-python:>=3.8) 2023-09-27T03:27:29,388 Skipping link: not a file: https://www.piwheels.org/simple/capcruncher/ 2023-09-27T03:27:29,389 Skipping link: not a file: https://pypi.org/simple/capcruncher/ 2023-09-27T03:27:29,411 Given no hashes to check 1 links for project 'capcruncher': discarding no candidates 2023-09-27T03:27:29,429 Collecting capcruncher==0.3.4 2023-09-27T03:27:29,432 Created temporary directory: /tmp/pip-unpack-arvw40m2 2023-09-27T03:27:29,655 Downloading capcruncher-0.3.4.tar.gz (84.9 MB) 2023-09-27T03:27:49,054 Added capcruncher==0.3.4 from https://files.pythonhosted.org/packages/b1/78/c98a2a4a6e62b5bd169af128129633b9e06bce32b0284b79c68808a8f0e5/capcruncher-0.3.4.tar.gz to build tracker '/tmp/pip-build-tracker-4vnf35qt' 2023-09-27T03:27:49,062 Created temporary directory: /tmp/pip-build-env-epd4mx2e 2023-09-27T03:27:49,067 Installing build dependencies: started 2023-09-27T03:27:49,068 Running command pip subprocess to install build dependencies 2023-09-27T03:27:50,210 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-27T03:27:50,702 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-27T03:27:52,284 Collecting setuptools>=61.0 2023-09-27T03:27:52,285 Obtaining dependency information for setuptools>=61.0 from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata 2023-09-27T03:27:52,290 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-27T03:27:52,497 Collecting wheel 2023-09-27T03:27:52,512 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-27T03:27:52,801 Collecting setuptools_scm[toml]>=6.2 2023-09-27T03:27:52,802 Obtaining dependency information for setuptools_scm[toml]>=6.2 from https://files.pythonhosted.org/packages/ca/04/4ea91c627355ae6d976bf7f1fc2815372a96b1b87bf290c8d726d10a08a1/setuptools_scm-8.0.3-py3-none-any.whl.metadata 2023-09-27T03:27:52,807 Using cached setuptools_scm-8.0.3-py3-none-any.whl.metadata (6.1 kB) 2023-09-27T03:27:53,157 Collecting packaging>=20 (from setuptools_scm[toml]>=6.2) 2023-09-27T03:27:53,171 Using cached https://www.piwheels.org/simple/packaging/packaging-23.1-py3-none-any.whl (48 kB) 2023-09-27T03:27:53,239 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-27T03:27:53,258 Using cached setuptools_scm-8.0.3-py3-none-any.whl (41 kB) 2023-09-27T03:27:55,741 Installing collected packages: wheel, setuptools, packaging, setuptools_scm 2023-09-27T03:27:55,970 Creating /tmp/pip-build-env-epd4mx2e/overlay/local/bin 2023-09-27T03:27:55,972 changing mode of /tmp/pip-build-env-epd4mx2e/overlay/local/bin/wheel to 755 2023-09-27T03:27:58,499 Successfully installed packaging-23.1 setuptools-68.2.2 setuptools_scm-8.0.3 wheel-0.41.2 2023-09-27T03:27:59,000 Installing build dependencies: finished with status 'done' 2023-09-27T03:27:59,003 Getting requirements to build wheel: started 2023-09-27T03:27:59,004 Running command Getting requirements to build wheel 2023-09-27T03:27:59,543 /tmp/pip-build-env-epd4mx2e/overlay/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` 2023-09-27T03:27:59,543 !! 2023-09-27T03:27:59,544 ******************************************************************************** 2023-09-27T03:27:59,545 The license_file parameter is deprecated, use license_files instead. 2023-09-27T03:27:59,546 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-27T03:27:59,547 or your builds will no longer be supported. 2023-09-27T03:27:59,548 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-27T03:27:59,549 ******************************************************************************** 2023-09-27T03:27:59,550 !! 2023-09-27T03:27:59,551 parsed = self.parsers.get(option_name, lambda x: x)(value) 2023-09-27T03:27:59,737 /tmp/pip-build-env-epd4mx2e/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `classifiers` defined outside of `pyproject.toml` would be ignored. 2023-09-27T03:27:59,738 !! 2023-09-27T03:27:59,739 ******************************************************************************** 2023-09-27T03:27:59,739 ########################################################################## 2023-09-27T03:27:59,740 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-27T03:27:59,741 ########################################################################## 2023-09-27T03:27:59,742 The following seems to be defined outside of `pyproject.toml`: 2023-09-27T03:27:59,743 `classifiers = ['Environment :: Console', 'Intended Audience :: Science/Research', 'Operating System :: POSIX :: Linux', 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python :: 3 :: Only', 'Programming Language :: Python :: Implementation :: CPython']` 2023-09-27T03:27:59,744 According to the spec (see the link below), however, setuptools CANNOT 2023-09-27T03:27:59,744 consider this value unless `classifiers` is listed as `dynamic`. 2023-09-27T03:27:59,746 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-27T03:27:59,746 For the time being, `setuptools` will still consider the given value (as a 2023-09-27T03:27:59,747 **transitional** measure), but please note that future releases of setuptools will 2023-09-27T03:27:59,747 follow strictly the standard. 2023-09-27T03:27:59,748 To prevent this warning, you can list `classifiers` under `dynamic` or alternatively 2023-09-27T03:27:59,748 remove the `[project]` table from your file and rely entirely on other means of 2023-09-27T03:27:59,749 configuration. 2023-09-27T03:27:59,750 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-27T03:27:59,750 or your builds will no longer be supported. 2023-09-27T03:27:59,751 ******************************************************************************** 2023-09-27T03:27:59,752 !! 2023-09-27T03:27:59,752 _handle_missing_dynamic(dist, project_table) 2023-09-27T03:27:59,753 /tmp/pip-build-env-epd4mx2e/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `scripts` defined outside of `pyproject.toml` would be ignored. 2023-09-27T03:27:59,753 !! 2023-09-27T03:27:59,754 ******************************************************************************** 2023-09-27T03:27:59,755 ########################################################################## 2023-09-27T03:27:59,755 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-27T03:27:59,756 ########################################################################## 2023-09-27T03:27:59,757 The following seems to be defined outside of `pyproject.toml`: 2023-09-27T03:27:59,758 `scripts = ['capcruncher = capcruncher.cli:cli']` 2023-09-27T03:27:59,759 According to the spec (see the link below), however, setuptools CANNOT 2023-09-27T03:27:59,760 consider this value unless `scripts` is listed as `dynamic`. 2023-09-27T03:27:59,761 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-27T03:27:59,762 For the time being, `setuptools` will still consider the given value (as a 2023-09-27T03:27:59,763 **transitional** measure), but please note that future releases of setuptools will 2023-09-27T03:27:59,763 follow strictly the standard. 2023-09-27T03:27:59,764 To prevent this warning, you can list `scripts` under `dynamic` or alternatively 2023-09-27T03:27:59,765 remove the `[project]` table from your file and rely entirely on other means of 2023-09-27T03:27:59,765 configuration. 2023-09-27T03:27:59,766 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-27T03:27:59,766 or your builds will no longer be supported. 2023-09-27T03:27:59,767 ******************************************************************************** 2023-09-27T03:27:59,768 !! 2023-09-27T03:27:59,769 _handle_missing_dynamic(dist, project_table) 2023-09-27T03:28:00,030 running egg_info 2023-09-27T03:28:00,035 writing capcruncher.egg-info/PKG-INFO 2023-09-27T03:28:00,041 writing dependency_links to capcruncher.egg-info/dependency_links.txt 2023-09-27T03:28:00,043 writing entry points to capcruncher.egg-info/entry_points.txt 2023-09-27T03:28:00,046 writing requirements to capcruncher.egg-info/requires.txt 2023-09-27T03:28:00,047 writing top-level names to capcruncher.egg-info/top_level.txt 2023-09-27T03:28:00,097 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2023-09-27T03:28:00,100 reading manifest file 'capcruncher.egg-info/SOURCES.txt' 2023-09-27T03:28:00,108 reading manifest template 'MANIFEST.in' 2023-09-27T03:28:00,139 adding license file 'LICENSE' 2023-09-27T03:28:00,148 writing manifest file 'capcruncher.egg-info/SOURCES.txt' 2023-09-27T03:28:00,271 Getting requirements to build wheel: finished with status 'done' 2023-09-27T03:28:00,285 Created temporary directory: /tmp/pip-modern-metadata-t4mxck7s 2023-09-27T03:28:00,287 Preparing metadata (pyproject.toml): started 2023-09-27T03:28:00,288 Running command Preparing metadata (pyproject.toml) 2023-09-27T03:28:00,841 /tmp/pip-build-env-epd4mx2e/overlay/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` 2023-09-27T03:28:00,841 !! 2023-09-27T03:28:00,842 ******************************************************************************** 2023-09-27T03:28:00,842 The license_file parameter is deprecated, use license_files instead. 2023-09-27T03:28:00,843 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-27T03:28:00,843 or your builds will no longer be supported. 2023-09-27T03:28:00,844 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-27T03:28:00,845 ******************************************************************************** 2023-09-27T03:28:00,846 !! 2023-09-27T03:28:00,846 parsed = self.parsers.get(option_name, lambda x: x)(value) 2023-09-27T03:28:00,896 /tmp/pip-build-env-epd4mx2e/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `classifiers` defined outside of `pyproject.toml` would be ignored. 2023-09-27T03:28:00,896 !! 2023-09-27T03:28:00,897 ******************************************************************************** 2023-09-27T03:28:00,898 ########################################################################## 2023-09-27T03:28:00,898 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-27T03:28:00,899 ########################################################################## 2023-09-27T03:28:00,900 The following seems to be defined outside of `pyproject.toml`: 2023-09-27T03:28:00,901 `classifiers = ['Environment :: Console', 'Intended Audience :: Science/Research', 'Operating System :: POSIX :: Linux', 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python :: 3 :: Only', 'Programming Language :: Python :: Implementation :: CPython']` 2023-09-27T03:28:00,902 According to the spec (see the link below), however, setuptools CANNOT 2023-09-27T03:28:00,903 consider this value unless `classifiers` is listed as `dynamic`. 2023-09-27T03:28:00,904 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-27T03:28:00,905 For the time being, `setuptools` will still consider the given value (as a 2023-09-27T03:28:00,906 **transitional** measure), but please note that future releases of setuptools will 2023-09-27T03:28:00,906 follow strictly the standard. 2023-09-27T03:28:00,907 To prevent this warning, you can list `classifiers` under `dynamic` or alternatively 2023-09-27T03:28:00,908 remove the `[project]` table from your file and rely entirely on other means of 2023-09-27T03:28:00,908 configuration. 2023-09-27T03:28:00,910 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-27T03:28:00,910 or your builds will no longer be supported. 2023-09-27T03:28:00,911 ******************************************************************************** 2023-09-27T03:28:00,912 !! 2023-09-27T03:28:00,912 _handle_missing_dynamic(dist, project_table) 2023-09-27T03:28:00,913 /tmp/pip-build-env-epd4mx2e/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `scripts` defined outside of `pyproject.toml` would be ignored. 2023-09-27T03:28:00,914 !! 2023-09-27T03:28:00,915 ******************************************************************************** 2023-09-27T03:28:00,915 ########################################################################## 2023-09-27T03:28:00,916 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-27T03:28:00,916 ########################################################################## 2023-09-27T03:28:00,917 The following seems to be defined outside of `pyproject.toml`: 2023-09-27T03:28:00,918 `scripts = ['capcruncher = capcruncher.cli:cli']` 2023-09-27T03:28:00,919 According to the spec (see the link below), however, setuptools CANNOT 2023-09-27T03:28:00,919 consider this value unless `scripts` is listed as `dynamic`. 2023-09-27T03:28:00,920 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-27T03:28:00,921 For the time being, `setuptools` will still consider the given value (as a 2023-09-27T03:28:00,921 **transitional** measure), but please note that future releases of setuptools will 2023-09-27T03:28:00,922 follow strictly the standard. 2023-09-27T03:28:00,923 To prevent this warning, you can list `scripts` under `dynamic` or alternatively 2023-09-27T03:28:00,923 remove the `[project]` table from your file and rely entirely on other means of 2023-09-27T03:28:00,924 configuration. 2023-09-27T03:28:00,925 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-27T03:28:00,925 or your builds will no longer be supported. 2023-09-27T03:28:00,925 ******************************************************************************** 2023-09-27T03:28:00,926 !! 2023-09-27T03:28:00,927 _handle_missing_dynamic(dist, project_table) 2023-09-27T03:28:01,182 running dist_info 2023-09-27T03:28:01,188 creating /tmp/pip-modern-metadata-t4mxck7s/capcruncher.egg-info 2023-09-27T03:28:01,193 writing /tmp/pip-modern-metadata-t4mxck7s/capcruncher.egg-info/PKG-INFO 2023-09-27T03:28:01,200 writing dependency_links to /tmp/pip-modern-metadata-t4mxck7s/capcruncher.egg-info/dependency_links.txt 2023-09-27T03:28:01,201 writing entry points to /tmp/pip-modern-metadata-t4mxck7s/capcruncher.egg-info/entry_points.txt 2023-09-27T03:28:01,204 writing requirements to /tmp/pip-modern-metadata-t4mxck7s/capcruncher.egg-info/requires.txt 2023-09-27T03:28:01,205 writing top-level names to /tmp/pip-modern-metadata-t4mxck7s/capcruncher.egg-info/top_level.txt 2023-09-27T03:28:01,207 writing manifest file '/tmp/pip-modern-metadata-t4mxck7s/capcruncher.egg-info/SOURCES.txt' 2023-09-27T03:28:01,251 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2023-09-27T03:28:01,254 reading manifest file '/tmp/pip-modern-metadata-t4mxck7s/capcruncher.egg-info/SOURCES.txt' 2023-09-27T03:28:01,256 reading manifest template 'MANIFEST.in' 2023-09-27T03:28:01,288 adding license file 'LICENSE' 2023-09-27T03:28:01,292 writing manifest file '/tmp/pip-modern-metadata-t4mxck7s/capcruncher.egg-info/SOURCES.txt' 2023-09-27T03:28:01,293 creating '/tmp/pip-modern-metadata-t4mxck7s/capcruncher-0.3.4.dist-info' 2023-09-27T03:28:01,462 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-27T03:28:01,475 Source in /tmp/pip-wheel-8rmwf1x2/capcruncher_df9cc198156b40cdb905510d27745a6b has version 0.3.4, which satisfies requirement capcruncher==0.3.4 from https://files.pythonhosted.org/packages/b1/78/c98a2a4a6e62b5bd169af128129633b9e06bce32b0284b79c68808a8f0e5/capcruncher-0.3.4.tar.gz 2023-09-27T03:28:01,476 Removed capcruncher==0.3.4 from https://files.pythonhosted.org/packages/b1/78/c98a2a4a6e62b5bd169af128129633b9e06bce32b0284b79c68808a8f0e5/capcruncher-0.3.4.tar.gz from build tracker '/tmp/pip-build-tracker-4vnf35qt' 2023-09-27T03:28:01,496 Created temporary directory: /tmp/pip-unpack-n1fpy50r 2023-09-27T03:28:01,497 Created temporary directory: /tmp/pip-unpack-itatqcg5 2023-09-27T03:28:01,547 Building wheels for collected packages: capcruncher 2023-09-27T03:28:01,552 Created temporary directory: /tmp/pip-wheel-zyfk_4y0 2023-09-27T03:28:01,552 Destination directory: /tmp/pip-wheel-zyfk_4y0 2023-09-27T03:28:01,554 Building wheel for capcruncher (pyproject.toml): started 2023-09-27T03:28:01,555 Running command Building wheel for capcruncher (pyproject.toml) 2023-09-27T03:28:02,107 /tmp/pip-build-env-epd4mx2e/overlay/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` 2023-09-27T03:28:02,107 !! 2023-09-27T03:28:02,108 ******************************************************************************** 2023-09-27T03:28:02,109 The license_file parameter is deprecated, use license_files instead. 2023-09-27T03:28:02,110 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-27T03:28:02,110 or your builds will no longer be supported. 2023-09-27T03:28:02,111 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-27T03:28:02,112 ******************************************************************************** 2023-09-27T03:28:02,113 !! 2023-09-27T03:28:02,114 parsed = self.parsers.get(option_name, lambda x: x)(value) 2023-09-27T03:28:02,160 /tmp/pip-build-env-epd4mx2e/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `classifiers` defined outside of `pyproject.toml` would be ignored. 2023-09-27T03:28:02,160 !! 2023-09-27T03:28:02,162 ******************************************************************************** 2023-09-27T03:28:02,162 ########################################################################## 2023-09-27T03:28:02,163 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-27T03:28:02,163 ########################################################################## 2023-09-27T03:28:02,164 The following seems to be defined outside of `pyproject.toml`: 2023-09-27T03:28:02,165 `classifiers = ['Environment :: Console', 'Intended Audience :: Science/Research', 'Operating System :: POSIX :: Linux', 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python :: 3 :: Only', 'Programming Language :: Python :: Implementation :: CPython']` 2023-09-27T03:28:02,166 According to the spec (see the link below), however, setuptools CANNOT 2023-09-27T03:28:02,167 consider this value unless `classifiers` is listed as `dynamic`. 2023-09-27T03:28:02,168 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-27T03:28:02,169 For the time being, `setuptools` will still consider the given value (as a 2023-09-27T03:28:02,170 **transitional** measure), but please note that future releases of setuptools will 2023-09-27T03:28:02,170 follow strictly the standard. 2023-09-27T03:28:02,171 To prevent this warning, you can list `classifiers` under `dynamic` or alternatively 2023-09-27T03:28:02,172 remove the `[project]` table from your file and rely entirely on other means of 2023-09-27T03:28:02,173 configuration. 2023-09-27T03:28:02,174 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-27T03:28:02,174 or your builds will no longer be supported. 2023-09-27T03:28:02,175 ******************************************************************************** 2023-09-27T03:28:02,176 !! 2023-09-27T03:28:02,176 _handle_missing_dynamic(dist, project_table) 2023-09-27T03:28:02,177 /tmp/pip-build-env-epd4mx2e/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `scripts` defined outside of `pyproject.toml` would be ignored. 2023-09-27T03:28:02,178 !! 2023-09-27T03:28:02,179 ******************************************************************************** 2023-09-27T03:28:02,179 ########################################################################## 2023-09-27T03:28:02,180 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-27T03:28:02,180 ########################################################################## 2023-09-27T03:28:02,181 The following seems to be defined outside of `pyproject.toml`: 2023-09-27T03:28:02,182 `scripts = ['capcruncher = capcruncher.cli:cli']` 2023-09-27T03:28:02,183 According to the spec (see the link below), however, setuptools CANNOT 2023-09-27T03:28:02,183 consider this value unless `scripts` is listed as `dynamic`. 2023-09-27T03:28:02,184 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-27T03:28:02,185 For the time being, `setuptools` will still consider the given value (as a 2023-09-27T03:28:02,185 **transitional** measure), but please note that future releases of setuptools will 2023-09-27T03:28:02,186 follow strictly the standard. 2023-09-27T03:28:02,187 To prevent this warning, you can list `scripts` under `dynamic` or alternatively 2023-09-27T03:28:02,187 remove the `[project]` table from your file and rely entirely on other means of 2023-09-27T03:28:02,188 configuration. 2023-09-27T03:28:02,188 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-27T03:28:02,189 or your builds will no longer be supported. 2023-09-27T03:28:02,189 ******************************************************************************** 2023-09-27T03:28:02,190 !! 2023-09-27T03:28:02,191 _handle_missing_dynamic(dist, project_table) 2023-09-27T03:28:02,438 running bdist_wheel 2023-09-27T03:28:02,460 running build 2023-09-27T03:28:02,461 running build_py 2023-09-27T03:28:02,467 creating build 2023-09-27T03:28:02,467 creating build/lib 2023-09-27T03:28:02,468 creating build/lib/capcruncher 2023-09-27T03:28:02,469 copying capcruncher/_version.py -> build/lib/capcruncher 2023-09-27T03:28:02,471 copying capcruncher/utils.py -> build/lib/capcruncher 2023-09-27T03:28:02,473 copying capcruncher/__init__.py -> build/lib/capcruncher 2023-09-27T03:28:02,475 creating build/lib/capcruncher/pipeline 2023-09-27T03:28:02,476 copying capcruncher/pipeline/utils.py -> build/lib/capcruncher/pipeline 2023-09-27T03:28:02,480 creating build/lib/capcruncher/cli 2023-09-27T03:28:02,481 copying capcruncher/cli/cli_plot.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,483 copying capcruncher/cli/cli_interactions.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,485 copying capcruncher/cli/interactions_compare.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,487 copying capcruncher/cli/cli_pipeline.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,489 copying capcruncher/cli/alignments_annotate.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,491 copying capcruncher/cli/interactions_differential.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,493 copying capcruncher/cli/cli_utilities.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,495 copying capcruncher/cli/interactions_deduplicate.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,497 copying capcruncher/cli/fastq_digest.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,500 copying capcruncher/cli/plot.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,502 copying capcruncher/cli/__init__.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,503 copying capcruncher/cli/interactions_pileup.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,505 copying capcruncher/cli/fastq_deduplicate.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,508 copying capcruncher/cli/cli_genome.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,510 copying capcruncher/cli/interactions_store.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,512 copying capcruncher/cli/cli_fastq.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,514 copying capcruncher/cli/cli_alignments.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,516 copying capcruncher/cli/fastq_split.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,518 copying capcruncher/cli/interactions_count.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,520 copying capcruncher/cli/genome_digest.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,522 copying capcruncher/cli/alignments_filter.py -> build/lib/capcruncher/cli 2023-09-27T03:28:02,525 creating build/lib/capcruncher/api 2023-09-27T03:28:02,526 copying capcruncher/api/io.py -> build/lib/capcruncher/api 2023-09-27T03:28:02,529 copying capcruncher/api/count.py -> build/lib/capcruncher/api 2023-09-27T03:28:02,530 copying capcruncher/api/digest.py -> build/lib/capcruncher/api 2023-09-27T03:28:02,532 copying capcruncher/api/__init__.py -> build/lib/capcruncher/api 2023-09-27T03:28:02,534 copying capcruncher/api/plotting.py -> build/lib/capcruncher/api 2023-09-27T03:28:02,537 copying capcruncher/api/storage.py -> build/lib/capcruncher/api 2023-09-27T03:28:02,540 copying capcruncher/api/annotate.py -> build/lib/capcruncher/api 2023-09-27T03:28:02,541 copying capcruncher/api/pileup.py -> build/lib/capcruncher/api 2023-09-27T03:28:02,544 copying capcruncher/api/statistics.py -> build/lib/capcruncher/api 2023-09-27T03:28:02,545 copying capcruncher/api/filter.py -> build/lib/capcruncher/api 2023-09-27T03:28:02,548 copying capcruncher/api/deduplicate.py -> build/lib/capcruncher/api 2023-09-27T03:28:02,552 creating build/lib/capcruncher/pipeline/workflow 2023-09-27T03:28:02,552 creating build/lib/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,553 copying capcruncher/pipeline/workflow/scripts/combine_filtering_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,555 copying capcruncher/pipeline/workflow/scripts/combine_digestion_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,557 copying capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,559 copying capcruncher/pipeline/workflow/scripts/plot.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,560 copying capcruncher/pipeline/workflow/scripts/combine_stats_read_level.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,562 copying capcruncher/pipeline/workflow/scripts/combine_deduplication_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,564 copying capcruncher/pipeline/workflow/scripts/combine_cis_and_trans_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,565 copying capcruncher/pipeline/workflow/scripts/combine_alignment_deduplication_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,567 copying capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,569 copying capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,571 copying capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,573 creating build/lib/capcruncher/pipeline/workflow/report 2023-09-27T03:28:02,574 copying capcruncher/pipeline/workflow/report/make_report.py -> build/lib/capcruncher/pipeline/workflow/report 2023-09-27T03:28:02,578 running egg_info 2023-09-27T03:28:02,583 writing capcruncher.egg-info/PKG-INFO 2023-09-27T03:28:02,588 writing dependency_links to capcruncher.egg-info/dependency_links.txt 2023-09-27T03:28:02,590 writing entry points to capcruncher.egg-info/entry_points.txt 2023-09-27T03:28:02,592 writing requirements to capcruncher.egg-info/requires.txt 2023-09-27T03:28:02,593 writing top-level names to capcruncher.egg-info/top_level.txt 2023-09-27T03:28:02,629 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2023-09-27T03:28:02,631 reading manifest file 'capcruncher.egg-info/SOURCES.txt' 2023-09-27T03:28:02,638 reading manifest template 'MANIFEST.in' 2023-09-27T03:28:02,676 adding license file 'LICENSE' 2023-09-27T03:28:02,685 writing manifest file 'capcruncher.egg-info/SOURCES.txt' 2023-09-27T03:28:02,697 creating build/lib/capcruncher/data 2023-09-27T03:28:02,698 copying capcruncher/data/logo.txt -> build/lib/capcruncher/data 2023-09-27T03:28:02,700 copying capcruncher/pipeline/workflow/Snakefile -> build/lib/capcruncher/pipeline/workflow 2023-09-27T03:28:02,703 creating build/lib/capcruncher/pipeline/config 2023-09-27T03:28:02,703 copying capcruncher/pipeline/config/cookiecutter.json -> build/lib/capcruncher/pipeline/config 2023-09-27T03:28:02,706 creating build/lib/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}} 2023-09-27T03:28:02,707 copying capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}/capcruncher_config.yml -> build/lib/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}} 2023-09-27T03:28:02,710 copying capcruncher/pipeline/workflow/report/capcruncher_report.qmd -> build/lib/capcruncher/pipeline/workflow/report 2023-09-27T03:28:02,715 copying capcruncher/pipeline/workflow/report/report_text.yml -> build/lib/capcruncher/pipeline/workflow/report 2023-09-27T03:28:02,717 creating build/lib/capcruncher/pipeline/workflow/data 2023-09-27T03:28:02,718 copying capcruncher/pipeline/workflow/data/annotation_defaults.json -> build/lib/capcruncher/pipeline/workflow/data 2023-09-27T03:28:02,720 creating build/lib/capcruncher/pipeline/workflow/envs 2023-09-27T03:28:02,721 copying capcruncher/pipeline/workflow/envs/environment.yml -> build/lib/capcruncher/pipeline/workflow/envs 2023-09-27T03:28:02,723 creating build/lib/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:02,724 copying capcruncher/pipeline/workflow/rules/align.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:02,726 copying capcruncher/pipeline/workflow/rules/annotate.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:02,728 copying capcruncher/pipeline/workflow/rules/compare.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:02,730 copying capcruncher/pipeline/workflow/rules/digest.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:02,732 copying capcruncher/pipeline/workflow/rules/fastq.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:02,735 copying capcruncher/pipeline/workflow/rules/filter.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:02,737 copying capcruncher/pipeline/workflow/rules/pileup.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:02,740 copying capcruncher/pipeline/workflow/rules/qc.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:02,742 copying capcruncher/pipeline/workflow/rules/statistics.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:02,745 copying capcruncher/pipeline/workflow/rules/visualise.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:02,747 creating build/lib/capcruncher/pipeline/workflow/envs/profiles 2023-09-27T03:28:02,748 creating build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity 2023-09-27T03:28:02,749 copying capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity/config.yaml -> build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity 2023-09-27T03:28:02,761 creating build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_singularity 2023-09-27T03:28:02,765 copying capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml -> build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_singularity 2023-09-27T03:28:02,800 installing to build/bdist.linux-armv7l/wheel 2023-09-27T03:28:02,801 running install 2023-09-27T03:28:02,825 running install_lib 2023-09-27T03:28:02,838 creating build/bdist.linux-armv7l 2023-09-27T03:28:02,841 creating build/bdist.linux-armv7l/wheel 2023-09-27T03:28:02,851 creating build/bdist.linux-armv7l/wheel/capcruncher 2023-09-27T03:28:02,855 copying build/lib/capcruncher/_version.py -> build/bdist.linux-armv7l/wheel/capcruncher 2023-09-27T03:28:02,859 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline 2023-09-27T03:28:02,860 copying build/lib/capcruncher/pipeline/utils.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline 2023-09-27T03:28:02,863 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow 2023-09-27T03:28:02,865 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,866 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_filtering_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,871 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_digestion_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,873 copying build/lib/capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,875 copying build/lib/capcruncher/pipeline/workflow/scripts/plot.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,878 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_stats_read_level.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,880 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_deduplication_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,881 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_cis_and_trans_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,883 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_alignment_deduplication_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,885 copying build/lib/capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,887 copying build/lib/capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,890 copying build/lib/capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-27T03:28:02,893 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report 2023-09-27T03:28:02,895 copying build/lib/capcruncher/pipeline/workflow/report/report_text.yml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report 2023-09-27T03:28:02,898 copying build/lib/capcruncher/pipeline/workflow/report/make_report.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report 2023-09-27T03:28:02,901 copying build/lib/capcruncher/pipeline/workflow/report/capcruncher_report.qmd -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report 2023-09-27T03:28:02,906 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/data 2023-09-27T03:28:02,907 copying build/lib/capcruncher/pipeline/workflow/data/annotation_defaults.json -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/data 2023-09-27T03:28:02,912 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs 2023-09-27T03:28:02,913 copying build/lib/capcruncher/pipeline/workflow/envs/environment.yml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs 2023-09-27T03:28:02,929 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles 2023-09-27T03:28:03,252 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity 2023-09-27T03:28:03,557 copying build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity/config.yaml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity 2023-09-27T03:28:03,902 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_singularity 2023-09-27T03:28:03,904 copying build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_singularity 2023-09-27T03:28:03,911 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:03,914 copying build/lib/capcruncher/pipeline/workflow/rules/statistics.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:03,922 copying build/lib/capcruncher/pipeline/workflow/rules/pileup.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:03,933 copying build/lib/capcruncher/pipeline/workflow/rules/annotate.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:03,942 copying build/lib/capcruncher/pipeline/workflow/rules/fastq.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:03,970 copying build/lib/capcruncher/pipeline/workflow/rules/qc.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:03,973 copying build/lib/capcruncher/pipeline/workflow/rules/filter.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:03,977 copying build/lib/capcruncher/pipeline/workflow/rules/align.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:03,980 copying build/lib/capcruncher/pipeline/workflow/rules/visualise.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:03,983 copying build/lib/capcruncher/pipeline/workflow/rules/digest.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:03,986 copying build/lib/capcruncher/pipeline/workflow/rules/compare.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-27T03:28:03,989 copying build/lib/capcruncher/pipeline/workflow/Snakefile -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow 2023-09-27T03:28:04,004 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config 2023-09-27T03:28:04,006 copying build/lib/capcruncher/pipeline/config/cookiecutter.json -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config 2023-09-27T03:28:04,013 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}} 2023-09-27T03:28:04,016 copying build/lib/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}/capcruncher_config.yml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}} 2023-09-27T03:28:04,032 creating build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,034 copying build/lib/capcruncher/cli/cli_plot.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,039 copying build/lib/capcruncher/cli/cli_interactions.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,044 copying build/lib/capcruncher/cli/interactions_compare.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,047 copying build/lib/capcruncher/cli/cli_pipeline.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,050 copying build/lib/capcruncher/cli/alignments_annotate.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,054 copying build/lib/capcruncher/cli/interactions_differential.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,058 copying build/lib/capcruncher/cli/cli_utilities.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,063 copying build/lib/capcruncher/cli/interactions_deduplicate.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,069 copying build/lib/capcruncher/cli/fastq_digest.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,074 copying build/lib/capcruncher/cli/plot.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,078 copying build/lib/capcruncher/cli/__init__.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,081 copying build/lib/capcruncher/cli/interactions_pileup.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,085 copying build/lib/capcruncher/cli/fastq_deduplicate.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,089 copying build/lib/capcruncher/cli/cli_genome.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,092 copying build/lib/capcruncher/cli/interactions_store.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,096 copying build/lib/capcruncher/cli/cli_fastq.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,099 copying build/lib/capcruncher/cli/cli_alignments.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,103 copying build/lib/capcruncher/cli/fastq_split.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,107 copying build/lib/capcruncher/cli/interactions_count.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,110 copying build/lib/capcruncher/cli/genome_digest.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,113 copying build/lib/capcruncher/cli/alignments_filter.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-27T03:28:04,117 copying build/lib/capcruncher/utils.py -> build/bdist.linux-armv7l/wheel/capcruncher 2023-09-27T03:28:04,121 copying build/lib/capcruncher/__init__.py -> build/bdist.linux-armv7l/wheel/capcruncher 2023-09-27T03:28:04,124 creating build/bdist.linux-armv7l/wheel/capcruncher/data 2023-09-27T03:28:04,126 copying build/lib/capcruncher/data/logo.txt -> build/bdist.linux-armv7l/wheel/capcruncher/data 2023-09-27T03:28:04,129 creating build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-27T03:28:04,131 copying build/lib/capcruncher/api/io.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-27T03:28:04,135 copying build/lib/capcruncher/api/count.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-27T03:28:04,138 copying build/lib/capcruncher/api/digest.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-27T03:28:04,146 copying build/lib/capcruncher/api/__init__.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-27T03:28:04,149 copying build/lib/capcruncher/api/plotting.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-27T03:28:04,153 copying build/lib/capcruncher/api/storage.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-27T03:28:04,157 copying build/lib/capcruncher/api/annotate.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-27T03:28:04,159 copying build/lib/capcruncher/api/pileup.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-27T03:28:04,162 copying build/lib/capcruncher/api/statistics.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-27T03:28:04,164 copying build/lib/capcruncher/api/filter.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-27T03:28:04,168 copying build/lib/capcruncher/api/deduplicate.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-27T03:28:04,170 running install_egg_info 2023-09-27T03:28:04,176 Copying capcruncher.egg-info to build/bdist.linux-armv7l/wheel/capcruncher-0.3.4-py3.11.egg-info 2023-09-27T03:28:04,193 running install_scripts 2023-09-27T03:28:04,222 creating build/bdist.linux-armv7l/wheel/capcruncher-0.3.4.dist-info/WHEEL 2023-09-27T03:28:04,225 creating '/tmp/pip-wheel-zyfk_4y0/.tmp-9qer_idn/capcruncher-0.3.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-27T03:28:04,227 adding 'capcruncher/__init__.py' 2023-09-27T03:28:04,229 adding 'capcruncher/_version.py' 2023-09-27T03:28:04,232 adding 'capcruncher/utils.py' 2023-09-27T03:28:04,234 adding 'capcruncher/api/__init__.py' 2023-09-27T03:28:04,236 adding 'capcruncher/api/annotate.py' 2023-09-27T03:28:04,238 adding 'capcruncher/api/count.py' 2023-09-27T03:28:04,240 adding 'capcruncher/api/deduplicate.py' 2023-09-27T03:28:04,243 adding 'capcruncher/api/digest.py' 2023-09-27T03:28:04,247 adding 'capcruncher/api/filter.py' 2023-09-27T03:28:04,251 adding 'capcruncher/api/io.py' 2023-09-27T03:28:04,254 adding 'capcruncher/api/pileup.py' 2023-09-27T03:28:04,258 adding 'capcruncher/api/plotting.py' 2023-09-27T03:28:04,260 adding 'capcruncher/api/statistics.py' 2023-09-27T03:28:04,263 adding 'capcruncher/api/storage.py' 2023-09-27T03:28:04,265 adding 'capcruncher/cli/__init__.py' 2023-09-27T03:28:04,267 adding 'capcruncher/cli/alignments_annotate.py' 2023-09-27T03:28:04,269 adding 'capcruncher/cli/alignments_filter.py' 2023-09-27T03:28:04,271 adding 'capcruncher/cli/cli_alignments.py' 2023-09-27T03:28:04,272 adding 'capcruncher/cli/cli_fastq.py' 2023-09-27T03:28:04,273 adding 'capcruncher/cli/cli_genome.py' 2023-09-27T03:28:04,275 adding 'capcruncher/cli/cli_interactions.py' 2023-09-27T03:28:04,277 adding 'capcruncher/cli/cli_pipeline.py' 2023-09-27T03:28:04,278 adding 'capcruncher/cli/cli_plot.py' 2023-09-27T03:28:04,280 adding 'capcruncher/cli/cli_utilities.py' 2023-09-27T03:28:04,282 adding 'capcruncher/cli/fastq_deduplicate.py' 2023-09-27T03:28:04,283 adding 'capcruncher/cli/fastq_digest.py' 2023-09-27T03:28:04,284 adding 'capcruncher/cli/fastq_split.py' 2023-09-27T03:28:04,286 adding 'capcruncher/cli/genome_digest.py' 2023-09-27T03:28:04,288 adding 'capcruncher/cli/interactions_compare.py' 2023-09-27T03:28:04,289 adding 'capcruncher/cli/interactions_count.py' 2023-09-27T03:28:04,291 adding 'capcruncher/cli/interactions_deduplicate.py' 2023-09-27T03:28:04,292 adding 'capcruncher/cli/interactions_differential.py' 2023-09-27T03:28:04,294 adding 'capcruncher/cli/interactions_pileup.py' 2023-09-27T03:28:04,295 adding 'capcruncher/cli/interactions_store.py' 2023-09-27T03:28:04,297 adding 'capcruncher/cli/plot.py' 2023-09-27T03:28:04,299 adding 'capcruncher/data/logo.txt' 2023-09-27T03:28:04,301 adding 'capcruncher/pipeline/utils.py' 2023-09-27T03:28:04,303 adding 'capcruncher/pipeline/config/cookiecutter.json' 2023-09-27T03:28:04,305 adding 'capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}/capcruncher_config.yml' 2023-09-27T03:28:04,307 adding 'capcruncher/pipeline/workflow/Snakefile' 2023-09-27T03:28:04,309 adding 'capcruncher/pipeline/workflow/data/annotation_defaults.json' 2023-09-27T03:28:04,311 adding 'capcruncher/pipeline/workflow/envs/environment.yml' 2023-09-27T03:28:04,313 adding 'capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity/config.yaml' 2023-09-27T03:28:04,315 adding 'capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml' 2023-09-27T03:28:04,317 adding 'capcruncher/pipeline/workflow/report/capcruncher_report.qmd' 2023-09-27T03:28:04,320 adding 'capcruncher/pipeline/workflow/report/make_report.py' 2023-09-27T03:28:04,321 adding 'capcruncher/pipeline/workflow/report/report_text.yml' 2023-09-27T03:28:04,323 adding 'capcruncher/pipeline/workflow/rules/align.smk' 2023-09-27T03:28:04,325 adding 'capcruncher/pipeline/workflow/rules/annotate.smk' 2023-09-27T03:28:04,326 adding 'capcruncher/pipeline/workflow/rules/compare.smk' 2023-09-27T03:28:04,327 adding 'capcruncher/pipeline/workflow/rules/digest.smk' 2023-09-27T03:28:04,329 adding 'capcruncher/pipeline/workflow/rules/fastq.smk' 2023-09-27T03:28:04,331 adding 'capcruncher/pipeline/workflow/rules/filter.smk' 2023-09-27T03:28:04,332 adding 'capcruncher/pipeline/workflow/rules/pileup.smk' 2023-09-27T03:28:04,333 adding 'capcruncher/pipeline/workflow/rules/qc.smk' 2023-09-27T03:28:04,335 adding 'capcruncher/pipeline/workflow/rules/statistics.smk' 2023-09-27T03:28:04,336 adding 'capcruncher/pipeline/workflow/rules/visualise.smk' 2023-09-27T03:28:04,338 adding 'capcruncher/pipeline/workflow/scripts/combine_alignment_deduplication_stats.py' 2023-09-27T03:28:04,339 adding 'capcruncher/pipeline/workflow/scripts/combine_cis_and_trans_stats.py' 2023-09-27T03:28:04,340 adding 'capcruncher/pipeline/workflow/scripts/combine_deduplication_stats.py' 2023-09-27T03:28:04,341 adding 'capcruncher/pipeline/workflow/scripts/combine_digestion_stats.py' 2023-09-27T03:28:04,342 adding 'capcruncher/pipeline/workflow/scripts/combine_filtering_stats.py' 2023-09-27T03:28:04,343 adding 'capcruncher/pipeline/workflow/scripts/combine_stats_read_level.py' 2023-09-27T03:28:04,344 adding 'capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py' 2023-09-27T03:28:04,345 adding 'capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py' 2023-09-27T03:28:04,346 adding 'capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py' 2023-09-27T03:28:04,348 adding 'capcruncher/pipeline/workflow/scripts/plot.py' 2023-09-27T03:28:04,349 adding 'capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py' 2023-09-27T03:28:04,356 adding 'capcruncher-0.3.4.dist-info/LICENSE' 2023-09-27T03:28:04,363 adding 'capcruncher-0.3.4.dist-info/METADATA' 2023-09-27T03:28:04,364 adding 'capcruncher-0.3.4.dist-info/WHEEL' 2023-09-27T03:28:04,365 adding 'capcruncher-0.3.4.dist-info/entry_points.txt' 2023-09-27T03:28:04,366 adding 'capcruncher-0.3.4.dist-info/top_level.txt' 2023-09-27T03:28:04,368 adding 'capcruncher-0.3.4.dist-info/RECORD' 2023-09-27T03:28:04,371 removing build/bdist.linux-armv7l/wheel 2023-09-27T03:28:04,517 Building wheel for capcruncher (pyproject.toml): finished with status 'done' 2023-09-27T03:28:04,526 Created wheel for capcruncher: filename=capcruncher-0.3.4-py3-none-any.whl size=159216 sha256=1f430b5ce16f4b15f8b8c7eae415267929912ca0a78616fde3f593f9d458918e 2023-09-27T03:28:04,528 Stored in directory: /tmp/pip-ephem-wheel-cache-vxv2u7bq/wheels/57/03/7c/e0ac1b94724dcf78b96814b6925dddf9985ba2ecacc4927e81 2023-09-27T03:28:04,562 Successfully built capcruncher 2023-09-27T03:28:04,571 Removed build tracker: '/tmp/pip-build-tracker-4vnf35qt'