2023-09-26T16:20:24,945 Created temporary directory: /tmp/pip-build-tracker-j7a_01re 2023-09-26T16:20:24,946 Initialized build tracking at /tmp/pip-build-tracker-j7a_01re 2023-09-26T16:20:24,946 Created build tracker: /tmp/pip-build-tracker-j7a_01re 2023-09-26T16:20:24,947 Entered build tracker: /tmp/pip-build-tracker-j7a_01re 2023-09-26T16:20:24,947 Created temporary directory: /tmp/pip-wheel-ejq2j3ie 2023-09-26T16:20:24,950 Created temporary directory: /tmp/pip-ephem-wheel-cache-nsif_3ga 2023-09-26T16:20:24,973 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-26T16:20:24,977 2 location(s) to search for versions of capcruncher: 2023-09-26T16:20:24,977 * https://pypi.org/simple/capcruncher/ 2023-09-26T16:20:24,977 * https://www.piwheels.org/simple/capcruncher/ 2023-09-26T16:20:24,978 Fetching project page and analyzing links: https://pypi.org/simple/capcruncher/ 2023-09-26T16:20:24,978 Getting page https://pypi.org/simple/capcruncher/ 2023-09-26T16:20:24,980 Found index url https://pypi.org/simple/ 2023-09-26T16:20:25,121 Fetched page https://pypi.org/simple/capcruncher/ as application/vnd.pypi.simple.v1+json 2023-09-26T16:20:25,127 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) 2023-09-26T16:20:25,128 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 2023-09-26T16:20:25,128 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) 2023-09-26T16:20:25,129 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 2023-09-26T16:20:25,130 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/) 2023-09-26T16:20:25,130 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 2023-09-26T16:20:25,131 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/) 2023-09-26T16:20:25,132 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 2023-09-26T16:20:25,133 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/) 2023-09-26T16:20:25,133 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 2023-09-26T16:20:25,134 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/) 2023-09-26T16:20:25,134 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 2023-09-26T16:20:25,135 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) 2023-09-26T16:20:25,136 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 2023-09-26T16:20:25,137 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) 2023-09-26T16:20:25,138 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 2023-09-26T16:20:25,138 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) 2023-09-26T16:20:25,139 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 2023-09-26T16:20:25,139 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) 2023-09-26T16:20:25,140 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 2023-09-26T16:20:25,141 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) 2023-09-26T16:20:25,142 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 2023-09-26T16:20:25,142 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) 2023-09-26T16:20:25,143 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 2023-09-26T16:20:25,144 Fetching project page and analyzing links: https://www.piwheels.org/simple/capcruncher/ 2023-09-26T16:20:25,145 Getting page https://www.piwheels.org/simple/capcruncher/ 2023-09-26T16:20:25,146 Found index url https://www.piwheels.org/simple/ 2023-09-26T16:20:25,321 Fetched page https://www.piwheels.org/simple/capcruncher/ as text/html 2023-09-26T16:20:25,325 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) 2023-09-26T16:20:25,326 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) 2023-09-26T16:20:25,326 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/) 2023-09-26T16:20:25,327 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/) 2023-09-26T16:20:25,327 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/) 2023-09-26T16:20:25,328 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/) 2023-09-26T16:20:25,329 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) 2023-09-26T16:20:25,329 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) 2023-09-26T16:20:25,330 Skipping link: not a file: https://www.piwheels.org/simple/capcruncher/ 2023-09-26T16:20:25,330 Skipping link: not a file: https://pypi.org/simple/capcruncher/ 2023-09-26T16:20:25,350 Given no hashes to check 1 links for project 'capcruncher': discarding no candidates 2023-09-26T16:20:25,368 Collecting capcruncher==0.3.2 2023-09-26T16:20:25,370 Created temporary directory: /tmp/pip-unpack-j2pd7kop 2023-09-26T16:20:26,205 Downloading capcruncher-0.3.2.tar.gz (84.9 MB) 2023-09-26T16:20:48,710 Added capcruncher==0.3.2 from https://files.pythonhosted.org/packages/b4/c4/a3c7065d7c993db2680c1303d40862031cc6e8535aca5b023ded383d4520/capcruncher-0.3.2.tar.gz to build tracker '/tmp/pip-build-tracker-j7a_01re' 2023-09-26T16:20:48,717 Created temporary directory: /tmp/pip-build-env-fsswiyff 2023-09-26T16:20:48,722 Installing build dependencies: started 2023-09-26T16:20:48,723 Running command pip subprocess to install build dependencies 2023-09-26T16:20:49,870 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-26T16:20:50,382 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-26T16:20:51,915 Collecting setuptools>=61.0 2023-09-26T16:20:51,916 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 2023-09-26T16:20:51,921 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-26T16:20:52,128 Collecting wheel 2023-09-26T16:20:52,143 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-26T16:20:52,430 Collecting setuptools_scm[toml]>=6.2 2023-09-26T16:20:52,431 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 2023-09-26T16:20:52,436 Using cached setuptools_scm-8.0.3-py3-none-any.whl.metadata (6.1 kB) 2023-09-26T16:20:52,782 Collecting packaging>=20 (from setuptools_scm[toml]>=6.2) 2023-09-26T16:20:52,797 Using cached https://www.piwheels.org/simple/packaging/packaging-23.1-py3-none-any.whl (48 kB) 2023-09-26T16:20:52,865 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-26T16:20:52,887 Using cached setuptools_scm-8.0.3-py3-none-any.whl (41 kB) 2023-09-26T16:20:55,350 Installing collected packages: wheel, setuptools, packaging, setuptools_scm 2023-09-26T16:20:55,567 Creating /tmp/pip-build-env-fsswiyff/overlay/local/bin 2023-09-26T16:20:55,569 changing mode of /tmp/pip-build-env-fsswiyff/overlay/local/bin/wheel to 755 2023-09-26T16:20:58,135 Successfully installed packaging-23.1 setuptools-68.2.2 setuptools_scm-8.0.3 wheel-0.41.2 2023-09-26T16:20:58,641 Installing build dependencies: finished with status 'done' 2023-09-26T16:20:58,645 Getting requirements to build wheel: started 2023-09-26T16:20:58,646 Running command Getting requirements to build wheel 2023-09-26T16:20:59,172 /tmp/pip-build-env-fsswiyff/overlay/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` 2023-09-26T16:20:59,172 !! 2023-09-26T16:20:59,173 ******************************************************************************** 2023-09-26T16:20:59,174 The license_file parameter is deprecated, use license_files instead. 2023-09-26T16:20:59,175 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T16:20:59,175 or your builds will no longer be supported. 2023-09-26T16:20:59,176 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-26T16:20:59,177 ******************************************************************************** 2023-09-26T16:20:59,178 !! 2023-09-26T16:20:59,179 parsed = self.parsers.get(option_name, lambda x: x)(value) 2023-09-26T16:20:59,369 /tmp/pip-build-env-fsswiyff/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `classifiers` defined outside of `pyproject.toml` would be ignored. 2023-09-26T16:20:59,369 !! 2023-09-26T16:20:59,371 ******************************************************************************** 2023-09-26T16:20:59,371 ########################################################################## 2023-09-26T16:20:59,372 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-26T16:20:59,372 ########################################################################## 2023-09-26T16:20:59,374 The following seems to be defined outside of `pyproject.toml`: 2023-09-26T16:20:59,375 `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']` 2023-09-26T16:20:59,376 According to the spec (see the link below), however, setuptools CANNOT 2023-09-26T16:20:59,376 consider this value unless `classifiers` is listed as `dynamic`. 2023-09-26T16:20:59,377 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-26T16:20:59,378 For the time being, `setuptools` will still consider the given value (as a 2023-09-26T16:20:59,379 **transitional** measure), but please note that future releases of setuptools will 2023-09-26T16:20:59,380 follow strictly the standard. 2023-09-26T16:20:59,381 To prevent this warning, you can list `classifiers` under `dynamic` or alternatively 2023-09-26T16:20:59,381 remove the `[project]` table from your file and rely entirely on other means of 2023-09-26T16:20:59,382 configuration. 2023-09-26T16:20:59,383 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T16:20:59,384 or your builds will no longer be supported. 2023-09-26T16:20:59,384 ******************************************************************************** 2023-09-26T16:20:59,385 !! 2023-09-26T16:20:59,385 _handle_missing_dynamic(dist, project_table) 2023-09-26T16:20:59,386 /tmp/pip-build-env-fsswiyff/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `scripts` defined outside of `pyproject.toml` would be ignored. 2023-09-26T16:20:59,386 !! 2023-09-26T16:20:59,387 ******************************************************************************** 2023-09-26T16:20:59,388 ########################################################################## 2023-09-26T16:20:59,388 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-26T16:20:59,388 ########################################################################## 2023-09-26T16:20:59,389 The following seems to be defined outside of `pyproject.toml`: 2023-09-26T16:20:59,391 `scripts = ['capcruncher = capcruncher.cli:cli']` 2023-09-26T16:20:59,392 According to the spec (see the link below), however, setuptools CANNOT 2023-09-26T16:20:59,392 consider this value unless `scripts` is listed as `dynamic`. 2023-09-26T16:20:59,393 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-26T16:20:59,394 For the time being, `setuptools` will still consider the given value (as a 2023-09-26T16:20:59,394 **transitional** measure), but please note that future releases of setuptools will 2023-09-26T16:20:59,395 follow strictly the standard. 2023-09-26T16:20:59,396 To prevent this warning, you can list `scripts` under `dynamic` or alternatively 2023-09-26T16:20:59,397 remove the `[project]` table from your file and rely entirely on other means of 2023-09-26T16:20:59,397 configuration. 2023-09-26T16:20:59,399 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T16:20:59,399 or your builds will no longer be supported. 2023-09-26T16:20:59,400 ******************************************************************************** 2023-09-26T16:20:59,401 !! 2023-09-26T16:20:59,402 _handle_missing_dynamic(dist, project_table) 2023-09-26T16:20:59,678 running egg_info 2023-09-26T16:20:59,683 writing capcruncher.egg-info/PKG-INFO 2023-09-26T16:20:59,689 writing dependency_links to capcruncher.egg-info/dependency_links.txt 2023-09-26T16:20:59,691 writing entry points to capcruncher.egg-info/entry_points.txt 2023-09-26T16:20:59,694 writing requirements to capcruncher.egg-info/requires.txt 2023-09-26T16:20:59,695 writing top-level names to capcruncher.egg-info/top_level.txt 2023-09-26T16:20:59,744 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2023-09-26T16:20:59,747 reading manifest file 'capcruncher.egg-info/SOURCES.txt' 2023-09-26T16:20:59,755 reading manifest template 'MANIFEST.in' 2023-09-26T16:20:59,786 adding license file 'LICENSE' 2023-09-26T16:20:59,795 writing manifest file 'capcruncher.egg-info/SOURCES.txt' 2023-09-26T16:20:59,920 Getting requirements to build wheel: finished with status 'done' 2023-09-26T16:20:59,930 Created temporary directory: /tmp/pip-modern-metadata-_h1fk6ll 2023-09-26T16:20:59,932 Preparing metadata (pyproject.toml): started 2023-09-26T16:20:59,933 Running command Preparing metadata (pyproject.toml) 2023-09-26T16:21:00,486 /tmp/pip-build-env-fsswiyff/overlay/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` 2023-09-26T16:21:00,486 !! 2023-09-26T16:21:00,488 ******************************************************************************** 2023-09-26T16:21:00,488 The license_file parameter is deprecated, use license_files instead. 2023-09-26T16:21:00,489 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T16:21:00,490 or your builds will no longer be supported. 2023-09-26T16:21:00,491 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-26T16:21:00,492 ******************************************************************************** 2023-09-26T16:21:00,493 !! 2023-09-26T16:21:00,493 parsed = self.parsers.get(option_name, lambda x: x)(value) 2023-09-26T16:21:00,541 /tmp/pip-build-env-fsswiyff/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `classifiers` defined outside of `pyproject.toml` would be ignored. 2023-09-26T16:21:00,541 !! 2023-09-26T16:21:00,542 ******************************************************************************** 2023-09-26T16:21:00,543 ########################################################################## 2023-09-26T16:21:00,543 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-26T16:21:00,543 ########################################################################## 2023-09-26T16:21:00,544 The following seems to be defined outside of `pyproject.toml`: 2023-09-26T16:21:00,545 `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']` 2023-09-26T16:21:00,546 According to the spec (see the link below), however, setuptools CANNOT 2023-09-26T16:21:00,547 consider this value unless `classifiers` is listed as `dynamic`. 2023-09-26T16:21:00,548 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-26T16:21:00,549 For the time being, `setuptools` will still consider the given value (as a 2023-09-26T16:21:00,550 **transitional** measure), but please note that future releases of setuptools will 2023-09-26T16:21:00,550 follow strictly the standard. 2023-09-26T16:21:00,551 To prevent this warning, you can list `classifiers` under `dynamic` or alternatively 2023-09-26T16:21:00,552 remove the `[project]` table from your file and rely entirely on other means of 2023-09-26T16:21:00,553 configuration. 2023-09-26T16:21:00,554 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T16:21:00,555 or your builds will no longer be supported. 2023-09-26T16:21:00,555 ******************************************************************************** 2023-09-26T16:21:00,556 !! 2023-09-26T16:21:00,557 _handle_missing_dynamic(dist, project_table) 2023-09-26T16:21:00,557 /tmp/pip-build-env-fsswiyff/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `scripts` defined outside of `pyproject.toml` would be ignored. 2023-09-26T16:21:00,558 !! 2023-09-26T16:21:00,559 ******************************************************************************** 2023-09-26T16:21:00,560 ########################################################################## 2023-09-26T16:21:00,560 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-26T16:21:00,561 ########################################################################## 2023-09-26T16:21:00,562 The following seems to be defined outside of `pyproject.toml`: 2023-09-26T16:21:00,564 `scripts = ['capcruncher = capcruncher.cli:cli']` 2023-09-26T16:21:00,565 According to the spec (see the link below), however, setuptools CANNOT 2023-09-26T16:21:00,566 consider this value unless `scripts` is listed as `dynamic`. 2023-09-26T16:21:00,566 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-26T16:21:00,567 For the time being, `setuptools` will still consider the given value (as a 2023-09-26T16:21:00,568 **transitional** measure), but please note that future releases of setuptools will 2023-09-26T16:21:00,568 follow strictly the standard. 2023-09-26T16:21:00,569 To prevent this warning, you can list `scripts` under `dynamic` or alternatively 2023-09-26T16:21:00,570 remove the `[project]` table from your file and rely entirely on other means of 2023-09-26T16:21:00,570 configuration. 2023-09-26T16:21:00,571 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T16:21:00,572 or your builds will no longer be supported. 2023-09-26T16:21:00,572 ******************************************************************************** 2023-09-26T16:21:00,573 !! 2023-09-26T16:21:00,573 _handle_missing_dynamic(dist, project_table) 2023-09-26T16:21:00,820 running dist_info 2023-09-26T16:21:00,826 creating /tmp/pip-modern-metadata-_h1fk6ll/capcruncher.egg-info 2023-09-26T16:21:00,831 writing /tmp/pip-modern-metadata-_h1fk6ll/capcruncher.egg-info/PKG-INFO 2023-09-26T16:21:00,838 writing dependency_links to /tmp/pip-modern-metadata-_h1fk6ll/capcruncher.egg-info/dependency_links.txt 2023-09-26T16:21:00,840 writing entry points to /tmp/pip-modern-metadata-_h1fk6ll/capcruncher.egg-info/entry_points.txt 2023-09-26T16:21:00,842 writing requirements to /tmp/pip-modern-metadata-_h1fk6ll/capcruncher.egg-info/requires.txt 2023-09-26T16:21:00,843 writing top-level names to /tmp/pip-modern-metadata-_h1fk6ll/capcruncher.egg-info/top_level.txt 2023-09-26T16:21:00,845 writing manifest file '/tmp/pip-modern-metadata-_h1fk6ll/capcruncher.egg-info/SOURCES.txt' 2023-09-26T16:21:00,889 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2023-09-26T16:21:00,892 reading manifest file '/tmp/pip-modern-metadata-_h1fk6ll/capcruncher.egg-info/SOURCES.txt' 2023-09-26T16:21:00,895 reading manifest template 'MANIFEST.in' 2023-09-26T16:21:00,924 adding license file 'LICENSE' 2023-09-26T16:21:00,928 writing manifest file '/tmp/pip-modern-metadata-_h1fk6ll/capcruncher.egg-info/SOURCES.txt' 2023-09-26T16:21:00,930 creating '/tmp/pip-modern-metadata-_h1fk6ll/capcruncher-0.3.2.dist-info' 2023-09-26T16:21:01,101 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-26T16:21:01,113 Source in /tmp/pip-wheel-ejq2j3ie/capcruncher_35adc511599f4fc6998681c8b2d7e8a7 has version 0.3.2, which satisfies requirement capcruncher==0.3.2 from https://files.pythonhosted.org/packages/b4/c4/a3c7065d7c993db2680c1303d40862031cc6e8535aca5b023ded383d4520/capcruncher-0.3.2.tar.gz 2023-09-26T16:21:01,114 Removed capcruncher==0.3.2 from https://files.pythonhosted.org/packages/b4/c4/a3c7065d7c993db2680c1303d40862031cc6e8535aca5b023ded383d4520/capcruncher-0.3.2.tar.gz from build tracker '/tmp/pip-build-tracker-j7a_01re' 2023-09-26T16:21:01,133 Created temporary directory: /tmp/pip-unpack-8n0e5209 2023-09-26T16:21:01,134 Created temporary directory: /tmp/pip-unpack-rm56uqjo 2023-09-26T16:21:01,184 Building wheels for collected packages: capcruncher 2023-09-26T16:21:01,188 Created temporary directory: /tmp/pip-wheel-_mit_0nw 2023-09-26T16:21:01,188 Destination directory: /tmp/pip-wheel-_mit_0nw 2023-09-26T16:21:01,190 Building wheel for capcruncher (pyproject.toml): started 2023-09-26T16:21:01,192 Running command Building wheel for capcruncher (pyproject.toml) 2023-09-26T16:21:01,761 /tmp/pip-build-env-fsswiyff/overlay/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` 2023-09-26T16:21:01,761 !! 2023-09-26T16:21:01,763 ******************************************************************************** 2023-09-26T16:21:01,763 The license_file parameter is deprecated, use license_files instead. 2023-09-26T16:21:01,764 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T16:21:01,764 or your builds will no longer be supported. 2023-09-26T16:21:01,765 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-26T16:21:01,766 ******************************************************************************** 2023-09-26T16:21:01,767 !! 2023-09-26T16:21:01,768 parsed = self.parsers.get(option_name, lambda x: x)(value) 2023-09-26T16:21:01,814 /tmp/pip-build-env-fsswiyff/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `classifiers` defined outside of `pyproject.toml` would be ignored. 2023-09-26T16:21:01,815 !! 2023-09-26T16:21:01,816 ******************************************************************************** 2023-09-26T16:21:01,817 ########################################################################## 2023-09-26T16:21:01,817 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-26T16:21:01,818 ########################################################################## 2023-09-26T16:21:01,819 The following seems to be defined outside of `pyproject.toml`: 2023-09-26T16:21:01,820 `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']` 2023-09-26T16:21:01,821 According to the spec (see the link below), however, setuptools CANNOT 2023-09-26T16:21:01,822 consider this value unless `classifiers` is listed as `dynamic`. 2023-09-26T16:21:01,823 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-26T16:21:01,824 For the time being, `setuptools` will still consider the given value (as a 2023-09-26T16:21:01,825 **transitional** measure), but please note that future releases of setuptools will 2023-09-26T16:21:01,825 follow strictly the standard. 2023-09-26T16:21:01,826 To prevent this warning, you can list `classifiers` under `dynamic` or alternatively 2023-09-26T16:21:01,827 remove the `[project]` table from your file and rely entirely on other means of 2023-09-26T16:21:01,827 configuration. 2023-09-26T16:21:01,829 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T16:21:01,829 or your builds will no longer be supported. 2023-09-26T16:21:01,830 ******************************************************************************** 2023-09-26T16:21:01,831 !! 2023-09-26T16:21:01,832 _handle_missing_dynamic(dist, project_table) 2023-09-26T16:21:01,832 /tmp/pip-build-env-fsswiyff/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `scripts` defined outside of `pyproject.toml` would be ignored. 2023-09-26T16:21:01,833 !! 2023-09-26T16:21:01,834 ******************************************************************************** 2023-09-26T16:21:01,835 ########################################################################## 2023-09-26T16:21:01,836 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-26T16:21:01,836 ########################################################################## 2023-09-26T16:21:01,838 The following seems to be defined outside of `pyproject.toml`: 2023-09-26T16:21:01,839 `scripts = ['capcruncher = capcruncher.cli:cli']` 2023-09-26T16:21:01,840 According to the spec (see the link below), however, setuptools CANNOT 2023-09-26T16:21:01,841 consider this value unless `scripts` is listed as `dynamic`. 2023-09-26T16:21:01,842 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-26T16:21:01,843 For the time being, `setuptools` will still consider the given value (as a 2023-09-26T16:21:01,843 **transitional** measure), but please note that future releases of setuptools will 2023-09-26T16:21:01,844 follow strictly the standard. 2023-09-26T16:21:01,845 To prevent this warning, you can list `scripts` under `dynamic` or alternatively 2023-09-26T16:21:01,845 remove the `[project]` table from your file and rely entirely on other means of 2023-09-26T16:21:01,845 configuration. 2023-09-26T16:21:01,846 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T16:21:01,847 or your builds will no longer be supported. 2023-09-26T16:21:01,847 ******************************************************************************** 2023-09-26T16:21:01,848 !! 2023-09-26T16:21:01,849 _handle_missing_dynamic(dist, project_table) 2023-09-26T16:21:02,086 running bdist_wheel 2023-09-26T16:21:02,108 running build 2023-09-26T16:21:02,109 running build_py 2023-09-26T16:21:02,114 creating build 2023-09-26T16:21:02,114 creating build/lib 2023-09-26T16:21:02,115 creating build/lib/capcruncher 2023-09-26T16:21:02,116 copying capcruncher/utils.py -> build/lib/capcruncher 2023-09-26T16:21:02,119 copying capcruncher/__init__.py -> build/lib/capcruncher 2023-09-26T16:21:02,120 copying capcruncher/_version.py -> build/lib/capcruncher 2023-09-26T16:21:02,122 creating build/lib/capcruncher/pipeline 2023-09-26T16:21:02,123 copying capcruncher/pipeline/utils.py -> build/lib/capcruncher/pipeline 2023-09-26T16:21:02,126 creating build/lib/capcruncher/cli 2023-09-26T16:21:02,127 copying capcruncher/cli/cli_interactions.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,130 copying capcruncher/cli/cli_plot.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,131 copying capcruncher/cli/interactions_compare.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,134 copying capcruncher/cli/fastq_deduplicate.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,136 copying capcruncher/cli/interactions_count.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,138 copying capcruncher/cli/cli_genome.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,139 copying capcruncher/cli/alignments_annotate.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,141 copying capcruncher/cli/__init__.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,143 copying capcruncher/cli/cli_utilities.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,145 copying capcruncher/cli/interactions_differential.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,147 copying capcruncher/cli/genome_digest.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,149 copying capcruncher/cli/interactions_deduplicate.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,152 copying capcruncher/cli/fastq_digest.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,154 copying capcruncher/cli/cli_pipeline.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,155 copying capcruncher/cli/interactions_pileup.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,157 copying capcruncher/cli/plot.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,159 copying capcruncher/cli/fastq_split.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,161 copying capcruncher/cli/cli_fastq.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,163 copying capcruncher/cli/alignments_filter.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,165 copying capcruncher/cli/interactions_store.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,167 copying capcruncher/cli/cli_alignments.py -> build/lib/capcruncher/cli 2023-09-26T16:21:02,170 creating build/lib/capcruncher/api 2023-09-26T16:21:02,171 copying capcruncher/api/digest.py -> build/lib/capcruncher/api 2023-09-26T16:21:02,173 copying capcruncher/api/io.py -> build/lib/capcruncher/api 2023-09-26T16:21:02,175 copying capcruncher/api/pileup.py -> build/lib/capcruncher/api 2023-09-26T16:21:02,177 copying capcruncher/api/deduplicate.py -> build/lib/capcruncher/api 2023-09-26T16:21:02,179 copying capcruncher/api/__init__.py -> build/lib/capcruncher/api 2023-09-26T16:21:02,181 copying capcruncher/api/statistics.py -> build/lib/capcruncher/api 2023-09-26T16:21:02,182 copying capcruncher/api/filter.py -> build/lib/capcruncher/api 2023-09-26T16:21:02,185 copying capcruncher/api/storage.py -> build/lib/capcruncher/api 2023-09-26T16:21:02,187 copying capcruncher/api/count.py -> build/lib/capcruncher/api 2023-09-26T16:21:02,189 copying capcruncher/api/plotting.py -> build/lib/capcruncher/api 2023-09-26T16:21:02,191 copying capcruncher/api/annotate.py -> build/lib/capcruncher/api 2023-09-26T16:21:02,195 creating build/lib/capcruncher/pipeline/workflow 2023-09-26T16:21:02,196 creating build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,197 copying capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,198 copying capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,200 copying capcruncher/pipeline/workflow/scripts/combine_cis_and_trans_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,201 copying capcruncher/pipeline/workflow/scripts/combine_deduplication_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,203 copying capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,205 copying capcruncher/pipeline/workflow/scripts/combine_digestion_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,206 copying capcruncher/pipeline/workflow/scripts/combine_stats_read_level.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,208 copying capcruncher/pipeline/workflow/scripts/plot.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,209 copying capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,211 copying capcruncher/pipeline/workflow/scripts/combine_filtering_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,213 copying capcruncher/pipeline/workflow/scripts/combine_alignment_deduplication_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,215 creating build/lib/capcruncher/pipeline/workflow/report 2023-09-26T16:21:02,216 copying capcruncher/pipeline/workflow/report/make_report.py -> build/lib/capcruncher/pipeline/workflow/report 2023-09-26T16:21:02,219 running egg_info 2023-09-26T16:21:02,224 writing capcruncher.egg-info/PKG-INFO 2023-09-26T16:21:02,229 writing dependency_links to capcruncher.egg-info/dependency_links.txt 2023-09-26T16:21:02,231 writing entry points to capcruncher.egg-info/entry_points.txt 2023-09-26T16:21:02,233 writing requirements to capcruncher.egg-info/requires.txt 2023-09-26T16:21:02,234 writing top-level names to capcruncher.egg-info/top_level.txt 2023-09-26T16:21:02,268 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2023-09-26T16:21:02,271 reading manifest file 'capcruncher.egg-info/SOURCES.txt' 2023-09-26T16:21:02,277 reading manifest template 'MANIFEST.in' 2023-09-26T16:21:02,314 adding license file 'LICENSE' 2023-09-26T16:21:02,322 writing manifest file 'capcruncher.egg-info/SOURCES.txt' 2023-09-26T16:21:02,334 creating build/lib/capcruncher/data 2023-09-26T16:21:02,335 copying capcruncher/data/logo.txt -> build/lib/capcruncher/data 2023-09-26T16:21:02,337 creating build/lib/capcruncher/pipeline/config 2023-09-26T16:21:02,338 copying capcruncher/pipeline/config/cookiecutter.json -> build/lib/capcruncher/pipeline/config 2023-09-26T16:21:02,340 creating build/lib/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}} 2023-09-26T16:21:02,341 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}} 2023-09-26T16:21:02,344 copying capcruncher/pipeline/workflow/Snakefile -> build/lib/capcruncher/pipeline/workflow 2023-09-26T16:21:02,346 creating build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,347 copying capcruncher/pipeline/workflow/rules/align.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,349 copying capcruncher/pipeline/workflow/rules/annotate.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,351 copying capcruncher/pipeline/workflow/rules/compare.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,353 copying capcruncher/pipeline/workflow/rules/digest.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,355 copying capcruncher/pipeline/workflow/rules/fastq.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,357 copying capcruncher/pipeline/workflow/rules/filter.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,359 copying capcruncher/pipeline/workflow/rules/pileup.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,362 copying capcruncher/pipeline/workflow/rules/qc.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,364 copying capcruncher/pipeline/workflow/rules/statistics.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,366 copying capcruncher/pipeline/workflow/rules/visualise.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,368 creating build/lib/capcruncher/pipeline/workflow/data 2023-09-26T16:21:02,369 copying capcruncher/pipeline/workflow/data/annotation_defaults.json -> build/lib/capcruncher/pipeline/workflow/data 2023-09-26T16:21:02,371 creating build/lib/capcruncher/pipeline/workflow/envs 2023-09-26T16:21:02,372 copying capcruncher/pipeline/workflow/envs/environment.yml -> build/lib/capcruncher/pipeline/workflow/envs 2023-09-26T16:21:02,374 copying capcruncher/pipeline/workflow/report/capcruncher_report.qmd -> build/lib/capcruncher/pipeline/workflow/report 2023-09-26T16:21:02,376 copying capcruncher/pipeline/workflow/report/report_text.yml -> build/lib/capcruncher/pipeline/workflow/report 2023-09-26T16:21:02,378 creating build/lib/capcruncher/pipeline/workflow/envs/profiles 2023-09-26T16:21:02,379 creating build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity 2023-09-26T16:21:02,380 copying capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity/config.yaml -> build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity 2023-09-26T16:21:02,382 creating build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_singularity 2023-09-26T16:21:02,383 copying capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml -> build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_singularity 2023-09-26T16:21:02,399 installing to build/bdist.linux-armv7l/wheel 2023-09-26T16:21:02,400 running install 2023-09-26T16:21:02,423 running install_lib 2023-09-26T16:21:02,428 creating build/bdist.linux-armv7l 2023-09-26T16:21:02,428 creating build/bdist.linux-armv7l/wheel 2023-09-26T16:21:02,430 creating build/bdist.linux-armv7l/wheel/capcruncher 2023-09-26T16:21:02,431 copying build/lib/capcruncher/utils.py -> build/bdist.linux-armv7l/wheel/capcruncher 2023-09-26T16:21:02,434 creating build/bdist.linux-armv7l/wheel/capcruncher/data 2023-09-26T16:21:02,435 copying build/lib/capcruncher/data/logo.txt -> build/bdist.linux-armv7l/wheel/capcruncher/data 2023-09-26T16:21:02,438 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline 2023-09-26T16:21:02,438 copying build/lib/capcruncher/pipeline/utils.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline 2023-09-26T16:21:02,441 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config 2023-09-26T16:21:02,442 copying build/lib/capcruncher/pipeline/config/cookiecutter.json -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config 2023-09-26T16:21:02,444 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}} 2023-09-26T16:21:02,445 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}} 2023-09-26T16:21:02,447 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow 2023-09-26T16:21:02,449 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,450 copying build/lib/capcruncher/pipeline/workflow/rules/align.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,451 copying build/lib/capcruncher/pipeline/workflow/rules/annotate.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,453 copying build/lib/capcruncher/pipeline/workflow/rules/qc.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,455 copying build/lib/capcruncher/pipeline/workflow/rules/visualise.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,457 copying build/lib/capcruncher/pipeline/workflow/rules/fastq.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,459 copying build/lib/capcruncher/pipeline/workflow/rules/pileup.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,461 copying build/lib/capcruncher/pipeline/workflow/rules/statistics.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,463 copying build/lib/capcruncher/pipeline/workflow/rules/digest.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,465 copying build/lib/capcruncher/pipeline/workflow/rules/compare.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,467 copying build/lib/capcruncher/pipeline/workflow/rules/filter.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T16:21:02,470 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/data 2023-09-26T16:21:02,470 copying build/lib/capcruncher/pipeline/workflow/data/annotation_defaults.json -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/data 2023-09-26T16:21:02,473 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs 2023-09-26T16:21:02,474 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles 2023-09-26T16:21:02,475 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity 2023-09-26T16:21:02,476 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 2023-09-26T16:21:02,478 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_singularity 2023-09-26T16:21:02,479 copying build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_singularity 2023-09-26T16:21:02,481 copying build/lib/capcruncher/pipeline/workflow/envs/environment.yml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs 2023-09-26T16:21:02,483 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,484 copying build/lib/capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,486 copying build/lib/capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,487 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_cis_and_trans_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,489 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_deduplication_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,490 copying build/lib/capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,492 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_digestion_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,494 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_stats_read_level.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,495 copying build/lib/capcruncher/pipeline/workflow/scripts/plot.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,497 copying build/lib/capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,499 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_filtering_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,501 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_alignment_deduplication_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T16:21:02,503 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report 2023-09-26T16:21:02,504 copying build/lib/capcruncher/pipeline/workflow/report/make_report.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report 2023-09-26T16:21:02,506 copying build/lib/capcruncher/pipeline/workflow/report/capcruncher_report.qmd -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report 2023-09-26T16:21:02,509 copying build/lib/capcruncher/pipeline/workflow/report/report_text.yml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report 2023-09-26T16:21:02,511 copying build/lib/capcruncher/pipeline/workflow/Snakefile -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow 2023-09-26T16:21:02,513 copying build/lib/capcruncher/__init__.py -> build/bdist.linux-armv7l/wheel/capcruncher 2023-09-26T16:21:02,514 copying build/lib/capcruncher/_version.py -> build/bdist.linux-armv7l/wheel/capcruncher 2023-09-26T16:21:02,516 creating build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,517 copying build/lib/capcruncher/cli/cli_interactions.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,519 copying build/lib/capcruncher/cli/cli_plot.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,521 copying build/lib/capcruncher/cli/interactions_compare.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,523 copying build/lib/capcruncher/cli/fastq_deduplicate.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,525 copying build/lib/capcruncher/cli/interactions_count.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,527 copying build/lib/capcruncher/cli/cli_genome.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,529 copying build/lib/capcruncher/cli/alignments_annotate.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,531 copying build/lib/capcruncher/cli/__init__.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,533 copying build/lib/capcruncher/cli/cli_utilities.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,535 copying build/lib/capcruncher/cli/interactions_differential.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,537 copying build/lib/capcruncher/cli/genome_digest.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,539 copying build/lib/capcruncher/cli/interactions_deduplicate.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,541 copying build/lib/capcruncher/cli/fastq_digest.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,543 copying build/lib/capcruncher/cli/cli_pipeline.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,545 copying build/lib/capcruncher/cli/interactions_pileup.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,546 copying build/lib/capcruncher/cli/plot.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,548 copying build/lib/capcruncher/cli/fastq_split.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,550 copying build/lib/capcruncher/cli/cli_fastq.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,552 copying build/lib/capcruncher/cli/alignments_filter.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,554 copying build/lib/capcruncher/cli/interactions_store.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,557 copying build/lib/capcruncher/cli/cli_alignments.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T16:21:02,559 creating build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T16:21:02,560 copying build/lib/capcruncher/api/digest.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T16:21:02,562 copying build/lib/capcruncher/api/io.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T16:21:02,565 copying build/lib/capcruncher/api/pileup.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T16:21:02,567 copying build/lib/capcruncher/api/deduplicate.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T16:21:02,569 copying build/lib/capcruncher/api/__init__.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T16:21:02,571 copying build/lib/capcruncher/api/statistics.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T16:21:02,573 copying build/lib/capcruncher/api/filter.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T16:21:02,576 copying build/lib/capcruncher/api/storage.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T16:21:02,578 copying build/lib/capcruncher/api/count.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T16:21:02,580 copying build/lib/capcruncher/api/plotting.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T16:21:02,583 copying build/lib/capcruncher/api/annotate.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T16:21:02,584 running install_egg_info 2023-09-26T16:21:02,589 Copying capcruncher.egg-info to build/bdist.linux-armv7l/wheel/capcruncher-0.3.2-py3.11.egg-info 2023-09-26T16:21:02,603 running install_scripts 2023-09-26T16:21:02,629 creating build/bdist.linux-armv7l/wheel/capcruncher-0.3.2.dist-info/WHEEL 2023-09-26T16:21:02,631 creating '/tmp/pip-wheel-_mit_0nw/.tmp-wo2_im7m/capcruncher-0.3.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-26T16:21:02,633 adding 'capcruncher/__init__.py' 2023-09-26T16:21:02,635 adding 'capcruncher/_version.py' 2023-09-26T16:21:02,637 adding 'capcruncher/utils.py' 2023-09-26T16:21:02,639 adding 'capcruncher/api/__init__.py' 2023-09-26T16:21:02,640 adding 'capcruncher/api/annotate.py' 2023-09-26T16:21:02,642 adding 'capcruncher/api/count.py' 2023-09-26T16:21:02,644 adding 'capcruncher/api/deduplicate.py' 2023-09-26T16:21:02,646 adding 'capcruncher/api/digest.py' 2023-09-26T16:21:02,650 adding 'capcruncher/api/filter.py' 2023-09-26T16:21:02,653 adding 'capcruncher/api/io.py' 2023-09-26T16:21:02,655 adding 'capcruncher/api/pileup.py' 2023-09-26T16:21:02,658 adding 'capcruncher/api/plotting.py' 2023-09-26T16:21:02,659 adding 'capcruncher/api/statistics.py' 2023-09-26T16:21:02,662 adding 'capcruncher/api/storage.py' 2023-09-26T16:21:02,664 adding 'capcruncher/cli/__init__.py' 2023-09-26T16:21:02,666 adding 'capcruncher/cli/alignments_annotate.py' 2023-09-26T16:21:02,667 adding 'capcruncher/cli/alignments_filter.py' 2023-09-26T16:21:02,669 adding 'capcruncher/cli/cli_alignments.py' 2023-09-26T16:21:02,670 adding 'capcruncher/cli/cli_fastq.py' 2023-09-26T16:21:02,671 adding 'capcruncher/cli/cli_genome.py' 2023-09-26T16:21:02,674 adding 'capcruncher/cli/cli_interactions.py' 2023-09-26T16:21:02,675 adding 'capcruncher/cli/cli_pipeline.py' 2023-09-26T16:21:02,676 adding 'capcruncher/cli/cli_plot.py' 2023-09-26T16:21:02,678 adding 'capcruncher/cli/cli_utilities.py' 2023-09-26T16:21:02,679 adding 'capcruncher/cli/fastq_deduplicate.py' 2023-09-26T16:21:02,681 adding 'capcruncher/cli/fastq_digest.py' 2023-09-26T16:21:02,683 adding 'capcruncher/cli/fastq_split.py' 2023-09-26T16:21:02,684 adding 'capcruncher/cli/genome_digest.py' 2023-09-26T16:21:02,685 adding 'capcruncher/cli/interactions_compare.py' 2023-09-26T16:21:02,687 adding 'capcruncher/cli/interactions_count.py' 2023-09-26T16:21:02,689 adding 'capcruncher/cli/interactions_deduplicate.py' 2023-09-26T16:21:02,691 adding 'capcruncher/cli/interactions_differential.py' 2023-09-26T16:21:02,692 adding 'capcruncher/cli/interactions_pileup.py' 2023-09-26T16:21:02,694 adding 'capcruncher/cli/interactions_store.py' 2023-09-26T16:21:02,695 adding 'capcruncher/cli/plot.py' 2023-09-26T16:21:02,697 adding 'capcruncher/data/logo.txt' 2023-09-26T16:21:02,699 adding 'capcruncher/pipeline/utils.py' 2023-09-26T16:21:02,701 adding 'capcruncher/pipeline/config/cookiecutter.json' 2023-09-26T16:21:02,704 adding 'capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}/capcruncher_config.yml' 2023-09-26T16:21:02,706 adding 'capcruncher/pipeline/workflow/Snakefile' 2023-09-26T16:21:02,707 adding 'capcruncher/pipeline/workflow/data/annotation_defaults.json' 2023-09-26T16:21:02,709 adding 'capcruncher/pipeline/workflow/envs/environment.yml' 2023-09-26T16:21:02,711 adding 'capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity/config.yaml' 2023-09-26T16:21:02,713 adding 'capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml' 2023-09-26T16:21:02,716 adding 'capcruncher/pipeline/workflow/report/capcruncher_report.qmd' 2023-09-26T16:21:02,718 adding 'capcruncher/pipeline/workflow/report/make_report.py' 2023-09-26T16:21:02,719 adding 'capcruncher/pipeline/workflow/report/report_text.yml' 2023-09-26T16:21:02,721 adding 'capcruncher/pipeline/workflow/rules/align.smk' 2023-09-26T16:21:02,723 adding 'capcruncher/pipeline/workflow/rules/annotate.smk' 2023-09-26T16:21:02,724 adding 'capcruncher/pipeline/workflow/rules/compare.smk' 2023-09-26T16:21:02,725 adding 'capcruncher/pipeline/workflow/rules/digest.smk' 2023-09-26T16:21:02,727 adding 'capcruncher/pipeline/workflow/rules/fastq.smk' 2023-09-26T16:21:02,729 adding 'capcruncher/pipeline/workflow/rules/filter.smk' 2023-09-26T16:21:02,730 adding 'capcruncher/pipeline/workflow/rules/pileup.smk' 2023-09-26T16:21:02,732 adding 'capcruncher/pipeline/workflow/rules/qc.smk' 2023-09-26T16:21:02,733 adding 'capcruncher/pipeline/workflow/rules/statistics.smk' 2023-09-26T16:21:02,734 adding 'capcruncher/pipeline/workflow/rules/visualise.smk' 2023-09-26T16:21:02,736 adding 'capcruncher/pipeline/workflow/scripts/combine_alignment_deduplication_stats.py' 2023-09-26T16:21:02,738 adding 'capcruncher/pipeline/workflow/scripts/combine_cis_and_trans_stats.py' 2023-09-26T16:21:02,739 adding 'capcruncher/pipeline/workflow/scripts/combine_deduplication_stats.py' 2023-09-26T16:21:02,740 adding 'capcruncher/pipeline/workflow/scripts/combine_digestion_stats.py' 2023-09-26T16:21:02,741 adding 'capcruncher/pipeline/workflow/scripts/combine_filtering_stats.py' 2023-09-26T16:21:02,742 adding 'capcruncher/pipeline/workflow/scripts/combine_stats_read_level.py' 2023-09-26T16:21:02,743 adding 'capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py' 2023-09-26T16:21:02,744 adding 'capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py' 2023-09-26T16:21:02,745 adding 'capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py' 2023-09-26T16:21:02,747 adding 'capcruncher/pipeline/workflow/scripts/plot.py' 2023-09-26T16:21:02,748 adding 'capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py' 2023-09-26T16:21:02,755 adding 'capcruncher-0.3.2.dist-info/LICENSE' 2023-09-26T16:21:02,762 adding 'capcruncher-0.3.2.dist-info/METADATA' 2023-09-26T16:21:02,763 adding 'capcruncher-0.3.2.dist-info/WHEEL' 2023-09-26T16:21:02,764 adding 'capcruncher-0.3.2.dist-info/entry_points.txt' 2023-09-26T16:21:02,765 adding 'capcruncher-0.3.2.dist-info/top_level.txt' 2023-09-26T16:21:02,766 adding 'capcruncher-0.3.2.dist-info/RECORD' 2023-09-26T16:21:02,770 removing build/bdist.linux-armv7l/wheel 2023-09-26T16:21:02,934 Building wheel for capcruncher (pyproject.toml): finished with status 'done' 2023-09-26T16:21:02,942 Created wheel for capcruncher: filename=capcruncher-0.3.2-py3-none-any.whl size=159882 sha256=cb9bbb6e602e5e11dcbac280be5520518f0110c58eb9bc7937644b956c455a02 2023-09-26T16:21:02,943 Stored in directory: /tmp/pip-ephem-wheel-cache-nsif_3ga/wheels/68/4a/08/6fd9d44f83c073588ef4b1a2e59ef1e206e09c0fb56b93f42a 2023-09-26T16:21:02,978 Successfully built capcruncher 2023-09-26T16:21:02,985 Removed build tracker: '/tmp/pip-build-tracker-j7a_01re'