2023-09-26T12:43:54,586 Created temporary directory: /tmp/pip-build-tracker-_duyjv78 2023-09-26T12:43:54,587 Initialized build tracking at /tmp/pip-build-tracker-_duyjv78 2023-09-26T12:43:54,588 Created build tracker: /tmp/pip-build-tracker-_duyjv78 2023-09-26T12:43:54,588 Entered build tracker: /tmp/pip-build-tracker-_duyjv78 2023-09-26T12:43:54,589 Created temporary directory: /tmp/pip-wheel-o_2werg_ 2023-09-26T12:43:54,592 Created temporary directory: /tmp/pip-ephem-wheel-cache-ovoa7c9s 2023-09-26T12:43:54,613 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-26T12:43:54,617 2 location(s) to search for versions of capcruncher: 2023-09-26T12:43:54,617 * https://pypi.org/simple/capcruncher/ 2023-09-26T12:43:54,617 * https://www.piwheels.org/simple/capcruncher/ 2023-09-26T12:43:54,618 Fetching project page and analyzing links: https://pypi.org/simple/capcruncher/ 2023-09-26T12:43:54,618 Getting page https://pypi.org/simple/capcruncher/ 2023-09-26T12:43:54,620 Found index url https://pypi.org/simple/ 2023-09-26T12:43:54,839 Fetched page https://pypi.org/simple/capcruncher/ as application/vnd.pypi.simple.v1+json 2023-09-26T12:43:54,845 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) 2023-09-26T12:43:54,846 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 2023-09-26T12:43:54,846 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) 2023-09-26T12:43:54,847 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 2023-09-26T12:43:54,848 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/) 2023-09-26T12:43:54,849 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 2023-09-26T12:43:54,849 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/) 2023-09-26T12:43:54,850 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 2023-09-26T12:43:54,851 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/) 2023-09-26T12:43:54,851 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 2023-09-26T12:43:54,852 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/) 2023-09-26T12:43:54,853 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 2023-09-26T12:43:54,853 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) 2023-09-26T12:43:54,855 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 2023-09-26T12:43:54,855 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) 2023-09-26T12:43:54,856 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 2023-09-26T12:43:54,856 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) 2023-09-26T12:43:54,857 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 2023-09-26T12:43:54,858 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) 2023-09-26T12:43:54,859 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 2023-09-26T12:43:54,859 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) 2023-09-26T12:43:54,860 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 2023-09-26T12:43:54,861 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) 2023-09-26T12:43:54,862 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 2023-09-26T12:43:54,862 Fetching project page and analyzing links: https://www.piwheels.org/simple/capcruncher/ 2023-09-26T12:43:54,863 Getting page https://www.piwheels.org/simple/capcruncher/ 2023-09-26T12:43:54,864 Found index url https://www.piwheels.org/simple/ 2023-09-26T12:43:55,022 Fetched page https://www.piwheels.org/simple/capcruncher/ as text/html 2023-09-26T12:43:55,025 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) 2023-09-26T12:43:55,026 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/) 2023-09-26T12:43:55,026 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/) 2023-09-26T12:43:55,027 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/) 2023-09-26T12:43:55,028 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/) 2023-09-26T12:43:55,028 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) 2023-09-26T12:43:55,029 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) 2023-09-26T12:43:55,029 Skipping link: not a file: https://www.piwheels.org/simple/capcruncher/ 2023-09-26T12:43:55,030 Skipping link: not a file: https://pypi.org/simple/capcruncher/ 2023-09-26T12:43:55,049 Given no hashes to check 1 links for project 'capcruncher': discarding no candidates 2023-09-26T12:43:55,067 Collecting capcruncher==0.3.1 2023-09-26T12:43:55,070 Created temporary directory: /tmp/pip-unpack-_iqqp0ai 2023-09-26T12:43:55,847 Downloading capcruncher-0.3.1.tar.gz (84.9 MB) 2023-09-26T12:44:19,092 Added capcruncher==0.3.1 from https://files.pythonhosted.org/packages/43/bd/2aabc1f9b8e2fae522852b4f3c8f27f42aadcf50016eb7bfcdfe83d499bb/capcruncher-0.3.1.tar.gz to build tracker '/tmp/pip-build-tracker-_duyjv78' 2023-09-26T12:44:19,100 Created temporary directory: /tmp/pip-build-env-2q92hbg9 2023-09-26T12:44:19,105 Installing build dependencies: started 2023-09-26T12:44:19,106 Running command pip subprocess to install build dependencies 2023-09-26T12:44:20,330 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-26T12:44:20,897 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-26T12:44:22,425 Collecting setuptools>=61.0 2023-09-26T12:44:22,426 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 2023-09-26T12:44:22,432 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-26T12:44:22,642 Collecting wheel 2023-09-26T12:44:22,669 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-26T12:44:22,986 Collecting setuptools_scm[toml]>=6.2 2023-09-26T12:44:22,988 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 2023-09-26T12:44:22,993 Using cached setuptools_scm-8.0.3-py3-none-any.whl.metadata (6.1 kB) 2023-09-26T12:44:23,343 Collecting packaging>=20 (from setuptools_scm[toml]>=6.2) 2023-09-26T12:44:23,360 Using cached https://www.piwheels.org/simple/packaging/packaging-23.1-py3-none-any.whl (48 kB) 2023-09-26T12:44:23,428 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-26T12:44:23,455 Using cached setuptools_scm-8.0.3-py3-none-any.whl (41 kB) 2023-09-26T12:44:25,980 Installing collected packages: wheel, setuptools, packaging, setuptools_scm 2023-09-26T12:44:26,307 Creating /tmp/pip-build-env-2q92hbg9/overlay/local/bin 2023-09-26T12:44:26,314 changing mode of /tmp/pip-build-env-2q92hbg9/overlay/local/bin/wheel to 755 2023-09-26T12:44:28,990 Successfully installed packaging-23.1 setuptools-68.2.2 setuptools_scm-8.0.3 wheel-0.41.2 2023-09-26T12:44:29,568 Installing build dependencies: finished with status 'done' 2023-09-26T12:44:29,571 Getting requirements to build wheel: started 2023-09-26T12:44:29,572 Running command Getting requirements to build wheel 2023-09-26T12:44:30,087 /tmp/pip-build-env-2q92hbg9/overlay/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` 2023-09-26T12:44:30,087 !! 2023-09-26T12:44:30,088 ******************************************************************************** 2023-09-26T12:44:30,089 The license_file parameter is deprecated, use license_files instead. 2023-09-26T12:44:30,090 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T12:44:30,090 or your builds will no longer be supported. 2023-09-26T12:44:30,091 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-26T12:44:30,091 ******************************************************************************** 2023-09-26T12:44:30,092 !! 2023-09-26T12:44:30,093 parsed = self.parsers.get(option_name, lambda x: x)(value) 2023-09-26T12:44:30,284 /tmp/pip-build-env-2q92hbg9/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `classifiers` defined outside of `pyproject.toml` would be ignored. 2023-09-26T12:44:30,284 !! 2023-09-26T12:44:30,286 ******************************************************************************** 2023-09-26T12:44:30,286 ########################################################################## 2023-09-26T12:44:30,287 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-26T12:44:30,287 ########################################################################## 2023-09-26T12:44:30,288 The following seems to be defined outside of `pyproject.toml`: 2023-09-26T12:44:30,290 `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']` 2023-09-26T12:44:30,291 According to the spec (see the link below), however, setuptools CANNOT 2023-09-26T12:44:30,291 consider this value unless `classifiers` is listed as `dynamic`. 2023-09-26T12:44:30,292 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-26T12:44:30,293 For the time being, `setuptools` will still consider the given value (as a 2023-09-26T12:44:30,294 **transitional** measure), but please note that future releases of setuptools will 2023-09-26T12:44:30,295 follow strictly the standard. 2023-09-26T12:44:30,296 To prevent this warning, you can list `classifiers` under `dynamic` or alternatively 2023-09-26T12:44:30,296 remove the `[project]` table from your file and rely entirely on other means of 2023-09-26T12:44:30,297 configuration. 2023-09-26T12:44:30,298 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T12:44:30,298 or your builds will no longer be supported. 2023-09-26T12:44:30,299 ******************************************************************************** 2023-09-26T12:44:30,300 !! 2023-09-26T12:44:30,301 _handle_missing_dynamic(dist, project_table) 2023-09-26T12:44:30,301 /tmp/pip-build-env-2q92hbg9/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `scripts` defined outside of `pyproject.toml` would be ignored. 2023-09-26T12:44:30,301 !! 2023-09-26T12:44:30,302 ******************************************************************************** 2023-09-26T12:44:30,303 ########################################################################## 2023-09-26T12:44:30,303 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-26T12:44:30,304 ########################################################################## 2023-09-26T12:44:30,305 The following seems to be defined outside of `pyproject.toml`: 2023-09-26T12:44:30,305 `scripts = ['capcruncher = capcruncher.cli:cli']` 2023-09-26T12:44:30,306 According to the spec (see the link below), however, setuptools CANNOT 2023-09-26T12:44:30,307 consider this value unless `scripts` is listed as `dynamic`. 2023-09-26T12:44:30,308 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-26T12:44:30,309 For the time being, `setuptools` will still consider the given value (as a 2023-09-26T12:44:30,309 **transitional** measure), but please note that future releases of setuptools will 2023-09-26T12:44:30,310 follow strictly the standard. 2023-09-26T12:44:30,310 To prevent this warning, you can list `scripts` under `dynamic` or alternatively 2023-09-26T12:44:30,311 remove the `[project]` table from your file and rely entirely on other means of 2023-09-26T12:44:30,311 configuration. 2023-09-26T12:44:30,313 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T12:44:30,313 or your builds will no longer be supported. 2023-09-26T12:44:30,314 ******************************************************************************** 2023-09-26T12:44:30,315 !! 2023-09-26T12:44:30,316 _handle_missing_dynamic(dist, project_table) 2023-09-26T12:44:30,592 running egg_info 2023-09-26T12:44:30,597 writing capcruncher.egg-info/PKG-INFO 2023-09-26T12:44:30,603 writing dependency_links to capcruncher.egg-info/dependency_links.txt 2023-09-26T12:44:30,605 writing entry points to capcruncher.egg-info/entry_points.txt 2023-09-26T12:44:30,608 writing requirements to capcruncher.egg-info/requires.txt 2023-09-26T12:44:30,609 writing top-level names to capcruncher.egg-info/top_level.txt 2023-09-26T12:44:30,659 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2023-09-26T12:44:30,662 reading manifest file 'capcruncher.egg-info/SOURCES.txt' 2023-09-26T12:44:30,670 reading manifest template 'MANIFEST.in' 2023-09-26T12:44:30,702 adding license file 'LICENSE' 2023-09-26T12:44:30,711 writing manifest file 'capcruncher.egg-info/SOURCES.txt' 2023-09-26T12:44:30,835 Getting requirements to build wheel: finished with status 'done' 2023-09-26T12:44:30,845 Created temporary directory: /tmp/pip-modern-metadata-gm8pjjfd 2023-09-26T12:44:30,848 Preparing metadata (pyproject.toml): started 2023-09-26T12:44:30,849 Running command Preparing metadata (pyproject.toml) 2023-09-26T12:44:31,407 /tmp/pip-build-env-2q92hbg9/overlay/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` 2023-09-26T12:44:31,407 !! 2023-09-26T12:44:31,408 ******************************************************************************** 2023-09-26T12:44:31,409 The license_file parameter is deprecated, use license_files instead. 2023-09-26T12:44:31,410 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T12:44:31,411 or your builds will no longer be supported. 2023-09-26T12:44:31,412 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-26T12:44:31,413 ******************************************************************************** 2023-09-26T12:44:31,414 !! 2023-09-26T12:44:31,414 parsed = self.parsers.get(option_name, lambda x: x)(value) 2023-09-26T12:44:31,465 /tmp/pip-build-env-2q92hbg9/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `classifiers` defined outside of `pyproject.toml` would be ignored. 2023-09-26T12:44:31,465 !! 2023-09-26T12:44:31,466 ******************************************************************************** 2023-09-26T12:44:31,467 ########################################################################## 2023-09-26T12:44:31,467 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-26T12:44:31,468 ########################################################################## 2023-09-26T12:44:31,469 The following seems to be defined outside of `pyproject.toml`: 2023-09-26T12:44:31,470 `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']` 2023-09-26T12:44:31,471 According to the spec (see the link below), however, setuptools CANNOT 2023-09-26T12:44:31,472 consider this value unless `classifiers` is listed as `dynamic`. 2023-09-26T12:44:31,472 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-26T12:44:31,473 For the time being, `setuptools` will still consider the given value (as a 2023-09-26T12:44:31,474 **transitional** measure), but please note that future releases of setuptools will 2023-09-26T12:44:31,475 follow strictly the standard. 2023-09-26T12:44:31,475 To prevent this warning, you can list `classifiers` under `dynamic` or alternatively 2023-09-26T12:44:31,476 remove the `[project]` table from your file and rely entirely on other means of 2023-09-26T12:44:31,476 configuration. 2023-09-26T12:44:31,478 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T12:44:31,478 or your builds will no longer be supported. 2023-09-26T12:44:31,479 ******************************************************************************** 2023-09-26T12:44:31,480 !! 2023-09-26T12:44:31,480 _handle_missing_dynamic(dist, project_table) 2023-09-26T12:44:31,481 /tmp/pip-build-env-2q92hbg9/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `scripts` defined outside of `pyproject.toml` would be ignored. 2023-09-26T12:44:31,482 !! 2023-09-26T12:44:31,483 ******************************************************************************** 2023-09-26T12:44:31,483 ########################################################################## 2023-09-26T12:44:31,484 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-26T12:44:31,484 ########################################################################## 2023-09-26T12:44:31,485 The following seems to be defined outside of `pyproject.toml`: 2023-09-26T12:44:31,487 `scripts = ['capcruncher = capcruncher.cli:cli']` 2023-09-26T12:44:31,488 According to the spec (see the link below), however, setuptools CANNOT 2023-09-26T12:44:31,488 consider this value unless `scripts` is listed as `dynamic`. 2023-09-26T12:44:31,489 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-26T12:44:31,491 For the time being, `setuptools` will still consider the given value (as a 2023-09-26T12:44:31,491 **transitional** measure), but please note that future releases of setuptools will 2023-09-26T12:44:31,492 follow strictly the standard. 2023-09-26T12:44:31,493 To prevent this warning, you can list `scripts` under `dynamic` or alternatively 2023-09-26T12:44:31,493 remove the `[project]` table from your file and rely entirely on other means of 2023-09-26T12:44:31,494 configuration. 2023-09-26T12:44:31,495 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T12:44:31,495 or your builds will no longer be supported. 2023-09-26T12:44:31,496 ******************************************************************************** 2023-09-26T12:44:31,496 !! 2023-09-26T12:44:31,497 _handle_missing_dynamic(dist, project_table) 2023-09-26T12:44:31,762 running dist_info 2023-09-26T12:44:31,768 creating /tmp/pip-modern-metadata-gm8pjjfd/capcruncher.egg-info 2023-09-26T12:44:31,773 writing /tmp/pip-modern-metadata-gm8pjjfd/capcruncher.egg-info/PKG-INFO 2023-09-26T12:44:31,780 writing dependency_links to /tmp/pip-modern-metadata-gm8pjjfd/capcruncher.egg-info/dependency_links.txt 2023-09-26T12:44:31,781 writing entry points to /tmp/pip-modern-metadata-gm8pjjfd/capcruncher.egg-info/entry_points.txt 2023-09-26T12:44:31,784 writing requirements to /tmp/pip-modern-metadata-gm8pjjfd/capcruncher.egg-info/requires.txt 2023-09-26T12:44:31,785 writing top-level names to /tmp/pip-modern-metadata-gm8pjjfd/capcruncher.egg-info/top_level.txt 2023-09-26T12:44:31,786 writing manifest file '/tmp/pip-modern-metadata-gm8pjjfd/capcruncher.egg-info/SOURCES.txt' 2023-09-26T12:44:31,831 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2023-09-26T12:44:31,834 reading manifest file '/tmp/pip-modern-metadata-gm8pjjfd/capcruncher.egg-info/SOURCES.txt' 2023-09-26T12:44:31,836 reading manifest template 'MANIFEST.in' 2023-09-26T12:44:31,866 adding license file 'LICENSE' 2023-09-26T12:44:31,870 writing manifest file '/tmp/pip-modern-metadata-gm8pjjfd/capcruncher.egg-info/SOURCES.txt' 2023-09-26T12:44:31,871 creating '/tmp/pip-modern-metadata-gm8pjjfd/capcruncher-0.3.1.dist-info' 2023-09-26T12:44:32,040 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-26T12:44:32,052 Source in /tmp/pip-wheel-o_2werg_/capcruncher_8b5b272d4372451ebd03fedf936022f1 has version 0.3.1, which satisfies requirement capcruncher==0.3.1 from https://files.pythonhosted.org/packages/43/bd/2aabc1f9b8e2fae522852b4f3c8f27f42aadcf50016eb7bfcdfe83d499bb/capcruncher-0.3.1.tar.gz 2023-09-26T12:44:32,053 Removed capcruncher==0.3.1 from https://files.pythonhosted.org/packages/43/bd/2aabc1f9b8e2fae522852b4f3c8f27f42aadcf50016eb7bfcdfe83d499bb/capcruncher-0.3.1.tar.gz from build tracker '/tmp/pip-build-tracker-_duyjv78' 2023-09-26T12:44:32,072 Created temporary directory: /tmp/pip-unpack-41ohmx95 2023-09-26T12:44:32,074 Created temporary directory: /tmp/pip-unpack-94_m6ikn 2023-09-26T12:44:32,122 Building wheels for collected packages: capcruncher 2023-09-26T12:44:32,127 Created temporary directory: /tmp/pip-wheel-r253ducu 2023-09-26T12:44:32,127 Destination directory: /tmp/pip-wheel-r253ducu 2023-09-26T12:44:32,129 Building wheel for capcruncher (pyproject.toml): started 2023-09-26T12:44:32,131 Running command Building wheel for capcruncher (pyproject.toml) 2023-09-26T12:44:32,709 /tmp/pip-build-env-2q92hbg9/overlay/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` 2023-09-26T12:44:32,710 !! 2023-09-26T12:44:32,711 ******************************************************************************** 2023-09-26T12:44:32,711 The license_file parameter is deprecated, use license_files instead. 2023-09-26T12:44:32,713 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T12:44:32,713 or your builds will no longer be supported. 2023-09-26T12:44:32,715 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-26T12:44:32,715 ******************************************************************************** 2023-09-26T12:44:32,716 !! 2023-09-26T12:44:32,717 parsed = self.parsers.get(option_name, lambda x: x)(value) 2023-09-26T12:44:32,763 /tmp/pip-build-env-2q92hbg9/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `classifiers` defined outside of `pyproject.toml` would be ignored. 2023-09-26T12:44:32,764 !! 2023-09-26T12:44:32,765 ******************************************************************************** 2023-09-26T12:44:32,765 ########################################################################## 2023-09-26T12:44:32,766 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-26T12:44:32,766 ########################################################################## 2023-09-26T12:44:32,767 The following seems to be defined outside of `pyproject.toml`: 2023-09-26T12:44:32,768 `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']` 2023-09-26T12:44:32,769 According to the spec (see the link below), however, setuptools CANNOT 2023-09-26T12:44:32,769 consider this value unless `classifiers` is listed as `dynamic`. 2023-09-26T12:44:32,770 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-26T12:44:32,771 For the time being, `setuptools` will still consider the given value (as a 2023-09-26T12:44:32,772 **transitional** measure), but please note that future releases of setuptools will 2023-09-26T12:44:32,772 follow strictly the standard. 2023-09-26T12:44:32,773 To prevent this warning, you can list `classifiers` under `dynamic` or alternatively 2023-09-26T12:44:32,774 remove the `[project]` table from your file and rely entirely on other means of 2023-09-26T12:44:32,775 configuration. 2023-09-26T12:44:32,776 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T12:44:32,776 or your builds will no longer be supported. 2023-09-26T12:44:32,777 ******************************************************************************** 2023-09-26T12:44:32,778 !! 2023-09-26T12:44:32,778 _handle_missing_dynamic(dist, project_table) 2023-09-26T12:44:32,779 /tmp/pip-build-env-2q92hbg9/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `scripts` defined outside of `pyproject.toml` would be ignored. 2023-09-26T12:44:32,780 !! 2023-09-26T12:44:32,781 ******************************************************************************** 2023-09-26T12:44:32,781 ########################################################################## 2023-09-26T12:44:32,782 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-09-26T12:44:32,782 ########################################################################## 2023-09-26T12:44:32,783 The following seems to be defined outside of `pyproject.toml`: 2023-09-26T12:44:32,784 `scripts = ['capcruncher = capcruncher.cli:cli']` 2023-09-26T12:44:32,786 According to the spec (see the link below), however, setuptools CANNOT 2023-09-26T12:44:32,786 consider this value unless `scripts` is listed as `dynamic`. 2023-09-26T12:44:32,787 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-09-26T12:44:32,789 For the time being, `setuptools` will still consider the given value (as a 2023-09-26T12:44:32,789 **transitional** measure), but please note that future releases of setuptools will 2023-09-26T12:44:32,790 follow strictly the standard. 2023-09-26T12:44:32,791 To prevent this warning, you can list `scripts` under `dynamic` or alternatively 2023-09-26T12:44:32,791 remove the `[project]` table from your file and rely entirely on other means of 2023-09-26T12:44:32,791 configuration. 2023-09-26T12:44:32,792 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-26T12:44:32,793 or your builds will no longer be supported. 2023-09-26T12:44:32,793 ******************************************************************************** 2023-09-26T12:44:32,794 !! 2023-09-26T12:44:32,795 _handle_missing_dynamic(dist, project_table) 2023-09-26T12:44:33,039 running bdist_wheel 2023-09-26T12:44:33,060 running build 2023-09-26T12:44:33,061 running build_py 2023-09-26T12:44:33,066 creating build 2023-09-26T12:44:33,067 creating build/lib 2023-09-26T12:44:33,068 creating build/lib/capcruncher 2023-09-26T12:44:33,070 copying capcruncher/__init__.py -> build/lib/capcruncher 2023-09-26T12:44:33,072 copying capcruncher/utils.py -> build/lib/capcruncher 2023-09-26T12:44:33,075 copying capcruncher/_version.py -> build/lib/capcruncher 2023-09-26T12:44:33,078 creating build/lib/capcruncher/api 2023-09-26T12:44:33,079 copying capcruncher/api/pileup.py -> build/lib/capcruncher/api 2023-09-26T12:44:33,082 copying capcruncher/api/__init__.py -> build/lib/capcruncher/api 2023-09-26T12:44:33,084 copying capcruncher/api/digest.py -> build/lib/capcruncher/api 2023-09-26T12:44:33,087 copying capcruncher/api/filter.py -> build/lib/capcruncher/api 2023-09-26T12:44:33,090 copying capcruncher/api/plotting.py -> build/lib/capcruncher/api 2023-09-26T12:44:33,093 copying capcruncher/api/deduplicate.py -> build/lib/capcruncher/api 2023-09-26T12:44:33,095 copying capcruncher/api/count.py -> build/lib/capcruncher/api 2023-09-26T12:44:33,097 copying capcruncher/api/io.py -> build/lib/capcruncher/api 2023-09-26T12:44:33,100 copying capcruncher/api/annotate.py -> build/lib/capcruncher/api 2023-09-26T12:44:33,102 copying capcruncher/api/storage.py -> build/lib/capcruncher/api 2023-09-26T12:44:33,105 copying capcruncher/api/statistics.py -> build/lib/capcruncher/api 2023-09-26T12:44:33,108 creating build/lib/capcruncher/cli 2023-09-26T12:44:33,109 copying capcruncher/cli/cli_alignments.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,111 copying capcruncher/cli/cli_pipeline.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,114 copying capcruncher/cli/fastq_digest.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,116 copying capcruncher/cli/interactions_compare.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,118 copying capcruncher/cli/cli_genome.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,120 copying capcruncher/cli/alignments_filter.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,122 copying capcruncher/cli/__init__.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,124 copying capcruncher/cli/genome_digest.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,126 copying capcruncher/cli/interactions_store.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,128 copying capcruncher/cli/interactions_pileup.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,131 copying capcruncher/cli/cli_interactions.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,133 copying capcruncher/cli/interactions_differential.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,136 copying capcruncher/cli/interactions_count.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,138 copying capcruncher/cli/interactions_deduplicate.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,141 copying capcruncher/cli/cli_plot.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,143 copying capcruncher/cli/fastq_deduplicate.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,146 copying capcruncher/cli/cli_utilities.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,148 copying capcruncher/cli/plot.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,150 copying capcruncher/cli/alignments_annotate.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,152 copying capcruncher/cli/cli_fastq.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,155 copying capcruncher/cli/fastq_split.py -> build/lib/capcruncher/cli 2023-09-26T12:44:33,158 creating build/lib/capcruncher/pipeline 2023-09-26T12:44:33,159 copying capcruncher/pipeline/utils.py -> build/lib/capcruncher/pipeline 2023-09-26T12:44:33,163 creating build/lib/capcruncher/pipeline/workflow 2023-09-26T12:44:33,163 creating build/lib/capcruncher/pipeline/workflow/report 2023-09-26T12:44:33,165 copying capcruncher/pipeline/workflow/report/make_report.py -> build/lib/capcruncher/pipeline/workflow/report 2023-09-26T12:44:33,169 creating build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,170 copying capcruncher/pipeline/workflow/scripts/combine_stats_read_level.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,172 copying capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,174 copying capcruncher/pipeline/workflow/scripts/combine_cis_and_trans_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,176 copying capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,179 copying capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,181 copying capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,183 copying capcruncher/pipeline/workflow/scripts/combine_deduplication_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,185 copying capcruncher/pipeline/workflow/scripts/combine_filtering_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,187 copying capcruncher/pipeline/workflow/scripts/combine_digestion_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,189 copying capcruncher/pipeline/workflow/scripts/combine_alignment_deduplication_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,191 copying capcruncher/pipeline/workflow/scripts/plot.py -> build/lib/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,195 running egg_info 2023-09-26T12:44:33,200 writing capcruncher.egg-info/PKG-INFO 2023-09-26T12:44:33,206 writing dependency_links to capcruncher.egg-info/dependency_links.txt 2023-09-26T12:44:33,208 writing entry points to capcruncher.egg-info/entry_points.txt 2023-09-26T12:44:33,210 writing requirements to capcruncher.egg-info/requires.txt 2023-09-26T12:44:33,211 writing top-level names to capcruncher.egg-info/top_level.txt 2023-09-26T12:44:33,252 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2023-09-26T12:44:33,255 reading manifest file 'capcruncher.egg-info/SOURCES.txt' 2023-09-26T12:44:33,261 reading manifest template 'MANIFEST.in' 2023-09-26T12:44:33,305 adding license file 'LICENSE' 2023-09-26T12:44:33,314 writing manifest file 'capcruncher.egg-info/SOURCES.txt' 2023-09-26T12:44:33,328 creating build/lib/capcruncher/data 2023-09-26T12:44:33,329 copying capcruncher/data/logo.txt -> build/lib/capcruncher/data 2023-09-26T12:44:33,332 copying capcruncher/pipeline/workflow/Snakefile -> build/lib/capcruncher/pipeline/workflow 2023-09-26T12:44:33,335 creating build/lib/capcruncher/pipeline/config 2023-09-26T12:44:33,336 copying capcruncher/pipeline/config/cookiecutter.json -> build/lib/capcruncher/pipeline/config 2023-09-26T12:44:33,338 creating build/lib/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}} 2023-09-26T12:44:33,339 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}} 2023-09-26T12:44:33,342 copying capcruncher/pipeline/workflow/report/capcruncher_report.qmd -> build/lib/capcruncher/pipeline/workflow/report 2023-09-26T12:44:33,344 copying capcruncher/pipeline/workflow/report/report_text.yml -> build/lib/capcruncher/pipeline/workflow/report 2023-09-26T12:44:33,346 creating build/lib/capcruncher/pipeline/workflow/data 2023-09-26T12:44:33,347 copying capcruncher/pipeline/workflow/data/annotation_defaults.json -> build/lib/capcruncher/pipeline/workflow/data 2023-09-26T12:44:33,350 creating build/lib/capcruncher/pipeline/workflow/envs 2023-09-26T12:44:33,351 copying capcruncher/pipeline/workflow/envs/environment.yml -> build/lib/capcruncher/pipeline/workflow/envs 2023-09-26T12:44:33,354 creating build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,355 copying capcruncher/pipeline/workflow/rules/align.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,357 copying capcruncher/pipeline/workflow/rules/annotate.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,360 copying capcruncher/pipeline/workflow/rules/compare.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,363 copying capcruncher/pipeline/workflow/rules/digest.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,366 copying capcruncher/pipeline/workflow/rules/fastq.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,369 copying capcruncher/pipeline/workflow/rules/filter.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,372 copying capcruncher/pipeline/workflow/rules/pileup.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,375 copying capcruncher/pipeline/workflow/rules/qc.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,377 copying capcruncher/pipeline/workflow/rules/statistics.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,380 copying capcruncher/pipeline/workflow/rules/visualise.smk -> build/lib/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,383 creating build/lib/capcruncher/pipeline/workflow/envs/profiles 2023-09-26T12:44:33,383 creating build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_singularity 2023-09-26T12:44:33,385 copying capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml -> build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_singularity 2023-09-26T12:44:33,387 creating build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity 2023-09-26T12:44:33,388 copying capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity/config.yaml -> build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity 2023-09-26T12:44:33,406 installing to build/bdist.linux-armv7l/wheel 2023-09-26T12:44:33,407 running install 2023-09-26T12:44:33,431 running install_lib 2023-09-26T12:44:33,436 creating build/bdist.linux-armv7l 2023-09-26T12:44:33,437 creating build/bdist.linux-armv7l/wheel 2023-09-26T12:44:33,439 creating build/bdist.linux-armv7l/wheel/capcruncher 2023-09-26T12:44:33,440 creating build/bdist.linux-armv7l/wheel/capcruncher/data 2023-09-26T12:44:33,441 copying build/lib/capcruncher/data/logo.txt -> build/bdist.linux-armv7l/wheel/capcruncher/data 2023-09-26T12:44:33,443 creating build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T12:44:33,445 copying build/lib/capcruncher/api/pileup.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T12:44:33,447 copying build/lib/capcruncher/api/__init__.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T12:44:33,449 copying build/lib/capcruncher/api/digest.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T12:44:33,451 copying build/lib/capcruncher/api/filter.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T12:44:33,454 copying build/lib/capcruncher/api/plotting.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T12:44:33,457 copying build/lib/capcruncher/api/deduplicate.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T12:44:33,459 copying build/lib/capcruncher/api/count.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T12:44:33,461 copying build/lib/capcruncher/api/io.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T12:44:33,464 copying build/lib/capcruncher/api/annotate.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T12:44:33,466 copying build/lib/capcruncher/api/storage.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T12:44:33,468 copying build/lib/capcruncher/api/statistics.py -> build/bdist.linux-armv7l/wheel/capcruncher/api 2023-09-26T12:44:33,471 copying build/lib/capcruncher/__init__.py -> build/bdist.linux-armv7l/wheel/capcruncher 2023-09-26T12:44:33,473 creating build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,474 copying build/lib/capcruncher/cli/cli_alignments.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,477 copying build/lib/capcruncher/cli/cli_pipeline.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,479 copying build/lib/capcruncher/cli/fastq_digest.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,481 copying build/lib/capcruncher/cli/interactions_compare.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,484 copying build/lib/capcruncher/cli/cli_genome.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,486 copying build/lib/capcruncher/cli/alignments_filter.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,488 copying build/lib/capcruncher/cli/__init__.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,490 copying build/lib/capcruncher/cli/genome_digest.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,492 copying build/lib/capcruncher/cli/interactions_store.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,495 copying build/lib/capcruncher/cli/interactions_pileup.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,497 copying build/lib/capcruncher/cli/cli_interactions.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,500 copying build/lib/capcruncher/cli/interactions_differential.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,502 copying build/lib/capcruncher/cli/interactions_count.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,505 copying build/lib/capcruncher/cli/interactions_deduplicate.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,508 copying build/lib/capcruncher/cli/cli_plot.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,510 copying build/lib/capcruncher/cli/fastq_deduplicate.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,513 copying build/lib/capcruncher/cli/cli_utilities.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,515 copying build/lib/capcruncher/cli/plot.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,518 copying build/lib/capcruncher/cli/alignments_annotate.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,520 copying build/lib/capcruncher/cli/cli_fastq.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,523 copying build/lib/capcruncher/cli/fastq_split.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli 2023-09-26T12:44:33,526 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline 2023-09-26T12:44:33,528 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow 2023-09-26T12:44:33,529 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report 2023-09-26T12:44:33,531 copying build/lib/capcruncher/pipeline/workflow/report/capcruncher_report.qmd -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report 2023-09-26T12:44:33,534 copying build/lib/capcruncher/pipeline/workflow/report/make_report.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report 2023-09-26T12:44:33,537 copying build/lib/capcruncher/pipeline/workflow/report/report_text.yml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report 2023-09-26T12:44:33,539 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/data 2023-09-26T12:44:33,540 copying build/lib/capcruncher/pipeline/workflow/data/annotation_defaults.json -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/data 2023-09-26T12:44:33,543 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,544 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_stats_read_level.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,546 copying build/lib/capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,548 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_cis_and_trans_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,550 copying build/lib/capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,552 copying build/lib/capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,554 copying build/lib/capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,557 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_deduplication_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,559 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_filtering_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,561 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_digestion_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,563 copying build/lib/capcruncher/pipeline/workflow/scripts/combine_alignment_deduplication_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,565 copying build/lib/capcruncher/pipeline/workflow/scripts/plot.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts 2023-09-26T12:44:33,568 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs 2023-09-26T12:44:33,569 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles 2023-09-26T12:44:33,571 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_singularity 2023-09-26T12:44:33,572 copying build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_singularity 2023-09-26T12:44:33,575 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity 2023-09-26T12:44:33,576 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 2023-09-26T12:44:33,578 copying build/lib/capcruncher/pipeline/workflow/envs/environment.yml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs 2023-09-26T12:44:33,580 copying build/lib/capcruncher/pipeline/workflow/Snakefile -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow 2023-09-26T12:44:33,583 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,584 copying build/lib/capcruncher/pipeline/workflow/rules/compare.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,587 copying build/lib/capcruncher/pipeline/workflow/rules/pileup.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,589 copying build/lib/capcruncher/pipeline/workflow/rules/qc.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,591 copying build/lib/capcruncher/pipeline/workflow/rules/align.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,593 copying build/lib/capcruncher/pipeline/workflow/rules/fastq.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,595 copying build/lib/capcruncher/pipeline/workflow/rules/digest.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,597 copying build/lib/capcruncher/pipeline/workflow/rules/filter.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,599 copying build/lib/capcruncher/pipeline/workflow/rules/statistics.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,601 copying build/lib/capcruncher/pipeline/workflow/rules/visualise.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,603 copying build/lib/capcruncher/pipeline/workflow/rules/annotate.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules 2023-09-26T12:44:33,605 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config 2023-09-26T12:44:33,606 creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}} 2023-09-26T12:44:33,607 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}} 2023-09-26T12:44:33,609 copying build/lib/capcruncher/pipeline/config/cookiecutter.json -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config 2023-09-26T12:44:33,611 copying build/lib/capcruncher/pipeline/utils.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline 2023-09-26T12:44:33,614 copying build/lib/capcruncher/utils.py -> build/bdist.linux-armv7l/wheel/capcruncher 2023-09-26T12:44:33,616 copying build/lib/capcruncher/_version.py -> build/bdist.linux-armv7l/wheel/capcruncher 2023-09-26T12:44:33,618 running install_egg_info 2023-09-26T12:44:33,623 Copying capcruncher.egg-info to build/bdist.linux-armv7l/wheel/capcruncher-0.3.1-py3.11.egg-info 2023-09-26T12:44:33,637 running install_scripts 2023-09-26T12:44:33,664 creating build/bdist.linux-armv7l/wheel/capcruncher-0.3.1.dist-info/WHEEL 2023-09-26T12:44:33,666 creating '/tmp/pip-wheel-r253ducu/.tmp-nwu2bja7/capcruncher-0.3.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-26T12:44:33,668 adding 'capcruncher/__init__.py' 2023-09-26T12:44:33,669 adding 'capcruncher/_version.py' 2023-09-26T12:44:33,672 adding 'capcruncher/utils.py' 2023-09-26T12:44:33,674 adding 'capcruncher/api/__init__.py' 2023-09-26T12:44:33,675 adding 'capcruncher/api/annotate.py' 2023-09-26T12:44:33,677 adding 'capcruncher/api/count.py' 2023-09-26T12:44:33,679 adding 'capcruncher/api/deduplicate.py' 2023-09-26T12:44:33,681 adding 'capcruncher/api/digest.py' 2023-09-26T12:44:33,686 adding 'capcruncher/api/filter.py' 2023-09-26T12:44:33,689 adding 'capcruncher/api/io.py' 2023-09-26T12:44:33,691 adding 'capcruncher/api/pileup.py' 2023-09-26T12:44:33,695 adding 'capcruncher/api/plotting.py' 2023-09-26T12:44:33,696 adding 'capcruncher/api/statistics.py' 2023-09-26T12:44:33,699 adding 'capcruncher/api/storage.py' 2023-09-26T12:44:33,701 adding 'capcruncher/cli/__init__.py' 2023-09-26T12:44:33,702 adding 'capcruncher/cli/alignments_annotate.py' 2023-09-26T12:44:33,704 adding 'capcruncher/cli/alignments_filter.py' 2023-09-26T12:44:33,706 adding 'capcruncher/cli/cli_alignments.py' 2023-09-26T12:44:33,707 adding 'capcruncher/cli/cli_fastq.py' 2023-09-26T12:44:33,708 adding 'capcruncher/cli/cli_genome.py' 2023-09-26T12:44:33,710 adding 'capcruncher/cli/cli_interactions.py' 2023-09-26T12:44:33,711 adding 'capcruncher/cli/cli_pipeline.py' 2023-09-26T12:44:33,713 adding 'capcruncher/cli/cli_plot.py' 2023-09-26T12:44:33,714 adding 'capcruncher/cli/cli_utilities.py' 2023-09-26T12:44:33,716 adding 'capcruncher/cli/fastq_deduplicate.py' 2023-09-26T12:44:33,718 adding 'capcruncher/cli/fastq_digest.py' 2023-09-26T12:44:33,719 adding 'capcruncher/cli/fastq_split.py' 2023-09-26T12:44:33,721 adding 'capcruncher/cli/genome_digest.py' 2023-09-26T12:44:33,722 adding 'capcruncher/cli/interactions_compare.py' 2023-09-26T12:44:33,724 adding 'capcruncher/cli/interactions_count.py' 2023-09-26T12:44:33,726 adding 'capcruncher/cli/interactions_deduplicate.py' 2023-09-26T12:44:33,728 adding 'capcruncher/cli/interactions_differential.py' 2023-09-26T12:44:33,729 adding 'capcruncher/cli/interactions_pileup.py' 2023-09-26T12:44:33,730 adding 'capcruncher/cli/interactions_store.py' 2023-09-26T12:44:33,732 adding 'capcruncher/cli/plot.py' 2023-09-26T12:44:33,734 adding 'capcruncher/data/logo.txt' 2023-09-26T12:44:33,736 adding 'capcruncher/pipeline/utils.py' 2023-09-26T12:44:33,738 adding 'capcruncher/pipeline/config/cookiecutter.json' 2023-09-26T12:44:33,740 adding 'capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}/capcruncher_config.yml' 2023-09-26T12:44:33,742 adding 'capcruncher/pipeline/workflow/Snakefile' 2023-09-26T12:44:33,744 adding 'capcruncher/pipeline/workflow/data/annotation_defaults.json' 2023-09-26T12:44:33,746 adding 'capcruncher/pipeline/workflow/envs/environment.yml' 2023-09-26T12:44:33,748 adding 'capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity/config.yaml' 2023-09-26T12:44:33,749 adding 'capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml' 2023-09-26T12:44:33,752 adding 'capcruncher/pipeline/workflow/report/capcruncher_report.qmd' 2023-09-26T12:44:33,754 adding 'capcruncher/pipeline/workflow/report/make_report.py' 2023-09-26T12:44:33,756 adding 'capcruncher/pipeline/workflow/report/report_text.yml' 2023-09-26T12:44:33,758 adding 'capcruncher/pipeline/workflow/rules/align.smk' 2023-09-26T12:44:33,759 adding 'capcruncher/pipeline/workflow/rules/annotate.smk' 2023-09-26T12:44:33,760 adding 'capcruncher/pipeline/workflow/rules/compare.smk' 2023-09-26T12:44:33,762 adding 'capcruncher/pipeline/workflow/rules/digest.smk' 2023-09-26T12:44:33,764 adding 'capcruncher/pipeline/workflow/rules/fastq.smk' 2023-09-26T12:44:33,765 adding 'capcruncher/pipeline/workflow/rules/filter.smk' 2023-09-26T12:44:33,767 adding 'capcruncher/pipeline/workflow/rules/pileup.smk' 2023-09-26T12:44:33,768 adding 'capcruncher/pipeline/workflow/rules/qc.smk' 2023-09-26T12:44:33,770 adding 'capcruncher/pipeline/workflow/rules/statistics.smk' 2023-09-26T12:44:33,771 adding 'capcruncher/pipeline/workflow/rules/visualise.smk' 2023-09-26T12:44:33,773 adding 'capcruncher/pipeline/workflow/scripts/combine_alignment_deduplication_stats.py' 2023-09-26T12:44:33,774 adding 'capcruncher/pipeline/workflow/scripts/combine_cis_and_trans_stats.py' 2023-09-26T12:44:33,776 adding 'capcruncher/pipeline/workflow/scripts/combine_deduplication_stats.py' 2023-09-26T12:44:33,777 adding 'capcruncher/pipeline/workflow/scripts/combine_digestion_stats.py' 2023-09-26T12:44:33,778 adding 'capcruncher/pipeline/workflow/scripts/combine_filtering_stats.py' 2023-09-26T12:44:33,779 adding 'capcruncher/pipeline/workflow/scripts/combine_stats_read_level.py' 2023-09-26T12:44:33,780 adding 'capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py' 2023-09-26T12:44:33,781 adding 'capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py' 2023-09-26T12:44:33,783 adding 'capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py' 2023-09-26T12:44:33,784 adding 'capcruncher/pipeline/workflow/scripts/plot.py' 2023-09-26T12:44:33,785 adding 'capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py' 2023-09-26T12:44:33,792 adding 'capcruncher-0.3.1.dist-info/LICENSE' 2023-09-26T12:44:33,799 adding 'capcruncher-0.3.1.dist-info/METADATA' 2023-09-26T12:44:33,801 adding 'capcruncher-0.3.1.dist-info/WHEEL' 2023-09-26T12:44:33,802 adding 'capcruncher-0.3.1.dist-info/entry_points.txt' 2023-09-26T12:44:33,803 adding 'capcruncher-0.3.1.dist-info/top_level.txt' 2023-09-26T12:44:33,804 adding 'capcruncher-0.3.1.dist-info/RECORD' 2023-09-26T12:44:33,808 removing build/bdist.linux-armv7l/wheel 2023-09-26T12:44:33,961 Building wheel for capcruncher (pyproject.toml): finished with status 'done' 2023-09-26T12:44:33,973 Created wheel for capcruncher: filename=capcruncher-0.3.1-py3-none-any.whl size=159510 sha256=010cc17949484bec95ba588bf89f30d450d6476b8e7c612e14f32270db999b52 2023-09-26T12:44:33,974 Stored in directory: /tmp/pip-ephem-wheel-cache-ovoa7c9s/wheels/19/ce/77/179e32a9557152011f5a6dfd6fbbc6ed2559d5514a94adbed8 2023-09-26T12:44:34,031 Successfully built capcruncher 2023-09-26T12:44:34,039 Removed build tracker: '/tmp/pip-build-tracker-_duyjv78'