2025-06-09T19:21:19,216 Created temporary directory: /tmp/pip-build-tracker-0da3iuim 2025-06-09T19:21:19,217 Initialized build tracking at /tmp/pip-build-tracker-0da3iuim 2025-06-09T19:21:19,217 Created build tracker: /tmp/pip-build-tracker-0da3iuim 2025-06-09T19:21:19,218 Entered build tracker: /tmp/pip-build-tracker-0da3iuim 2025-06-09T19:21:19,219 Created temporary directory: /tmp/pip-wheel-bhj9g8rc 2025-06-09T19:21:19,223 Created temporary directory: /tmp/pip-ephem-wheel-cache-aj4dzlkk 2025-06-09T19:21:19,274 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-09T19:21:19,276 2 location(s) to search for versions of crem: 2025-06-09T19:21:19,276 * https://pypi.org/simple/crem/ 2025-06-09T19:21:19,276 * https://www.piwheels.org/simple/crem/ 2025-06-09T19:21:19,277 Fetching project page and analyzing links: https://pypi.org/simple/crem/ 2025-06-09T19:21:19,278 Getting page https://pypi.org/simple/crem/ 2025-06-09T19:21:19,280 Found index url https://pypi.org/simple/ 2025-06-09T19:21:19,507 Fetched page https://pypi.org/simple/crem/ as application/vnd.pypi.simple.v1+json 2025-06-09T19:21:19,512 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/a5/79/77c701c0c0eb2ce6701319a95cfd29493e8e51618c5bb621cd40bf4f0841/crem-0.1-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,513 Found link https://files.pythonhosted.org/packages/49/5e/1ae619500a3515623022dcfe0a8b1a9d1d5f008b2eb2655caf766fff025b/crem-0.1.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.1 2025-06-09T19:21:19,514 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/b0/1d/ba7abcc6068ab5ce0bec9fba20510f689c1bec42848c239eeb97fc3cdb5b/crem-0.2-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,515 Found link https://files.pythonhosted.org/packages/83/fb/667430dda039b8185d02dcdcaf4adf889cffa3d9e39514b631f8c9368e33/crem-0.2.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2 2025-06-09T19:21:19,515 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/a4/1b/947e7977be99fb67a7fee6deea4b9ac99a1ca07bb033f7959c68a4cb9350/crem-0.2.1-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,516 Found link https://files.pythonhosted.org/packages/e8/a1/458d6fdb33c0049a19a706932baa6b9aaf7549426f7f566fbc745176172d/crem-0.2.1.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.1 2025-06-09T19:21:19,517 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/50/71/5b2c839ef1a85ac2f54b82aada72e73f0c20d91b32e2a99e0ae1b0b87c7f/crem-0.2.2-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,518 Found link https://files.pythonhosted.org/packages/9c/dd/86e07879327b33981b8b281e84668c367ff5ff9eeb61a4d6fa292d9fc318/crem-0.2.2.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.2 2025-06-09T19:21:19,518 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/f6/55/84c8af59816cf3ed4b999c13589a4e201b3292f8a4ec8179f9d23ee9b830/crem-0.2.3-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,519 Found link https://files.pythonhosted.org/packages/51/bc/77ffc829cb922288e87c71e83c1dabdb9ec5e2261b01ef8f80c0577d1766/crem-0.2.3.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.3 2025-06-09T19:21:19,520 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/b2/1f/01798d61f9ea674e33e319f148d392b8f30592ecbfa95ac26618574c51b3/crem-0.2.4-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,520 Found link https://files.pythonhosted.org/packages/be/76/f16878adfd0f4d4f812e6dfd7bd12421a6b0acb228354f0d16a3ad206526/crem-0.2.4.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.4 2025-06-09T19:21:19,521 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/92/6e/00beafce3a0bb42912c9f72c2ac91e1d086e7a7856787b423140c46aff69/crem-0.2.5-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,522 Found link https://files.pythonhosted.org/packages/52/48/6407335e8b1c182a4d9639fd556f803f3c80c18ee4729dbdadc5e0f5d76c/crem-0.2.5.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.5 2025-06-09T19:21:19,523 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/8c/07/0392bf97e247e3f27da50a09b5bb58bc8bb8c24a7e3a7deedf92a5943467/crem-0.2.6-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,523 Found link https://files.pythonhosted.org/packages/da/ed/5b24420ce0453f6969091f5ae3958effe1b6c7d8012a9f910895a7752e2f/crem-0.2.6.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.6 2025-06-09T19:21:19,524 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/f2/a4/552b45d0f5653c2236eaf6ffb477752fbea008f817979bf01ead3f455055/crem-0.2.7-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,524 Found link https://files.pythonhosted.org/packages/81/a4/13c52f8d9724d9834ff70413611bd3c1e9e89338a141c7f152d797e726b3/crem-0.2.7.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.7 2025-06-09T19:21:19,525 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/4d/0c/74941ea96484349710e421c7c0493a8124936617737266e690eb1b5eff60/crem-0.2.8-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,525 Found link https://files.pythonhosted.org/packages/c7/d4/89a146b92157cbf7569c8a939e01ad870d7505c9c12901c9f901b8089544/crem-0.2.8.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.8 2025-06-09T19:21:19,526 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/89/73/7923e43f7c11d367f959031badf54ee3163e230aa7403adcd07061e3ae9e/crem-0.2.9-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,527 Found link https://files.pythonhosted.org/packages/c6/33/c596dd9f6502baa690b6903b6835c10caef68d3c2172dd0d50e14cd6a46a/crem-0.2.9.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.9 2025-06-09T19:21:19,528 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/fa/b0/7d4f2814ef2a69d9c9504eaa2cf4a6da1bad360178497a8b59d14844f382/crem-0.2.10-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,528 Found link https://files.pythonhosted.org/packages/00/91/43e7eaafcf5c50ea58f300a6ad37d371573a603e9c03310dc401c2aa9714/crem-0.2.10.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.10 2025-06-09T19:21:19,529 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/fc/b5/3e13d1c5cec67af8cf01dd9c52957e7871d7f422840973e0213949c46482/crem-0.2.11-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,530 Found link https://files.pythonhosted.org/packages/7b/24/b07783ae905db73b6f1f00e57bd37c7ec45e64a934693b41aa8cccfc6d59/crem-0.2.11.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.11 2025-06-09T19:21:19,530 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/13/10/dc2687ab4fffd43872518804508c5b1a9aaf07df0e556219f508602bd33a/crem-0.2.12-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,531 Found link https://files.pythonhosted.org/packages/45/34/cacd8789c4158ed302c525b6013361b1bccdb54238333d6020c067fc4585/crem-0.2.12.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.12 2025-06-09T19:21:19,532 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/f0/e5/83f2eb7c5281db032407ca9a32cf39f4c90746569fc428f9594528883012/crem-0.2.13-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,532 Found link https://files.pythonhosted.org/packages/84/54/21fa36717a5f3bc2d97d2e32af5e68ae73f05ad7382fd6e8071aaa29fefd/crem-0.2.13.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.13 2025-06-09T19:21:19,533 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/aa/90/8842c60128cb36144fd27a76fdc43c78d264894110e709b171ded2914a35/crem-0.2.14-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,533 Found link https://files.pythonhosted.org/packages/a9/ab/0c190fe6956c7adfde6eee412257a90c9b68d6eb9343cdb8b80146895668/crem-0.2.14.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.14 2025-06-09T19:21:19,534 Skipping link: No binaries permitted for crem: https://files.pythonhosted.org/packages/9f/a9/f6fb09b49bd3ebca2a08995350a9cfca9a1e8aad0bdc15003c1553be29ab/crem-0.2.15-py3-none-any.whl (from https://pypi.org/simple/crem/) (requires-python:>=3.6) 2025-06-09T19:21:19,535 Found link https://files.pythonhosted.org/packages/30/33/092b96e91e2f15730daa7513e69b0fac9e1701d25ac70a8bb58df660cb4f/crem-0.2.15.tar.gz (from https://pypi.org/simple/crem/) (requires-python:>=3.6), version: 0.2.15 2025-06-09T19:21:19,535 Fetching project page and analyzing links: https://www.piwheels.org/simple/crem/ 2025-06-09T19:21:19,536 Getting page https://www.piwheels.org/simple/crem/ 2025-06-09T19:21:19,537 Found index url https://www.piwheels.org/simple/ 2025-06-09T19:21:19,702 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/crem/ 2025-06-09T19:21:20,362 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/crem/ 2025-06-09T19:21:21,524 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/crem/ 2025-06-09T19:21:23,686 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/crem/ 2025-06-09T19:21:27,845 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/crem/ 2025-06-09T19:21:28,007 Could not fetch URL https://www.piwheels.org/simple/crem/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/crem/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping 2025-06-09T19:21:28,009 Skipping link: not a file: https://www.piwheels.org/simple/crem/ 2025-06-09T19:21:28,009 Skipping link: not a file: https://pypi.org/simple/crem/ 2025-06-09T19:21:28,031 Given no hashes to check 1 links for project 'crem': discarding no candidates 2025-06-09T19:21:28,033 Collecting crem==0.2.15 2025-06-09T19:21:28,036 Created temporary directory: /tmp/pip-unpack-nrjs4lxz 2025-06-09T19:21:28,278 Downloading crem-0.2.15.tar.gz (700 kB) 2025-06-09T19:21:28,686 Added crem==0.2.15 from https://files.pythonhosted.org/packages/30/33/092b96e91e2f15730daa7513e69b0fac9e1701d25ac70a8bb58df660cb4f/crem-0.2.15.tar.gz to build tracker '/tmp/pip-build-tracker-0da3iuim' 2025-06-09T19:21:28,689 Running setup.py (path:/tmp/pip-wheel-bhj9g8rc/crem_d139344658a047d290f8c033500c88e8/setup.py) egg_info for package crem 2025-06-09T19:21:28,689 Created temporary directory: /tmp/pip-pip-egg-info-2ctutxla 2025-06-09T19:21:28,690 Preparing metadata (setup.py): started 2025-06-09T19:21:28,691 Running command python setup.py egg_info 2025-06-09T19:21:29,575 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-09T19:21:29,575 !! 2025-06-09T19:21:29,576 ******************************************************************************** 2025-06-09T19:21:29,577 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-09T19:21:29,578 License :: OSI Approved :: BSD License 2025-06-09T19:21:29,579 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-09T19:21:29,579 ******************************************************************************** 2025-06-09T19:21:29,580 !! 2025-06-09T19:21:29,581 self._finalize_license_expression() 2025-06-09T19:21:29,610 running egg_info 2025-06-09T19:21:29,639 creating /tmp/pip-pip-egg-info-2ctutxla/crem.egg-info 2025-06-09T19:21:29,641 writing /tmp/pip-pip-egg-info-2ctutxla/crem.egg-info/PKG-INFO 2025-06-09T19:21:29,646 writing dependency_links to /tmp/pip-pip-egg-info-2ctutxla/crem.egg-info/dependency_links.txt 2025-06-09T19:21:29,648 writing entry points to /tmp/pip-pip-egg-info-2ctutxla/crem.egg-info/entry_points.txt 2025-06-09T19:21:29,651 writing requirements to /tmp/pip-pip-egg-info-2ctutxla/crem.egg-info/requires.txt 2025-06-09T19:21:29,652 writing top-level names to /tmp/pip-pip-egg-info-2ctutxla/crem.egg-info/top_level.txt 2025-06-09T19:21:29,654 writing manifest file '/tmp/pip-pip-egg-info-2ctutxla/crem.egg-info/SOURCES.txt' 2025-06-09T19:21:29,777 reading manifest file '/tmp/pip-pip-egg-info-2ctutxla/crem.egg-info/SOURCES.txt' 2025-06-09T19:21:29,779 adding license file 'LICENSE.txt' 2025-06-09T19:21:29,782 writing manifest file '/tmp/pip-pip-egg-info-2ctutxla/crem.egg-info/SOURCES.txt' 2025-06-09T19:21:29,893 Preparing metadata (setup.py): finished with status 'done' 2025-06-09T19:21:29,898 Source in /tmp/pip-wheel-bhj9g8rc/crem_d139344658a047d290f8c033500c88e8 has version 0.2.15, which satisfies requirement crem==0.2.15 from https://files.pythonhosted.org/packages/30/33/092b96e91e2f15730daa7513e69b0fac9e1701d25ac70a8bb58df660cb4f/crem-0.2.15.tar.gz 2025-06-09T19:21:29,899 Removed crem==0.2.15 from https://files.pythonhosted.org/packages/30/33/092b96e91e2f15730daa7513e69b0fac9e1701d25ac70a8bb58df660cb4f/crem-0.2.15.tar.gz from build tracker '/tmp/pip-build-tracker-0da3iuim' 2025-06-09T19:21:29,906 Created temporary directory: /tmp/pip-unpack-rxnxz4fd 2025-06-09T19:21:29,907 Created temporary directory: /tmp/pip-unpack-j6rkc757 2025-06-09T19:21:29,908 Building wheels for collected packages: crem 2025-06-09T19:21:29,912 Created temporary directory: /tmp/pip-wheel-l6alchyh 2025-06-09T19:21:29,913 DEPRECATION: Building 'crem' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'crem'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-06-09T19:21:29,914 Building wheel for crem (setup.py): started 2025-06-09T19:21:29,915 Destination directory: /tmp/pip-wheel-l6alchyh 2025-06-09T19:21:29,916 Running command python setup.py bdist_wheel 2025-06-09T19:21:30,809 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-09T19:21:30,809 !! 2025-06-09T19:21:30,810 ******************************************************************************** 2025-06-09T19:21:30,811 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-09T19:21:30,812 License :: OSI Approved :: BSD License 2025-06-09T19:21:30,813 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-09T19:21:30,813 ******************************************************************************** 2025-06-09T19:21:30,814 !! 2025-06-09T19:21:30,815 self._finalize_license_expression() 2025-06-09T19:21:30,815 running bdist_wheel 2025-06-09T19:21:30,950 running build 2025-06-09T19:21:30,951 running build_py 2025-06-09T19:21:30,982 creating build/lib/crem 2025-06-09T19:21:30,984 copying crem/guacamol_distribution_test.py -> build/lib/crem 2025-06-09T19:21:30,987 copying crem/crem.py -> build/lib/crem 2025-06-09T19:21:30,990 copying crem/arg_types.py -> build/lib/crem 2025-06-09T19:21:30,992 copying crem/__init__.py -> build/lib/crem 2025-06-09T19:21:30,994 copying crem/mol_context.py -> build/lib/crem 2025-06-09T19:21:30,996 copying crem/functions.py -> build/lib/crem 2025-06-09T19:21:30,998 copying crem/import_env_to_db.py -> build/lib/crem 2025-06-09T19:21:31,000 copying crem/utils.py -> build/lib/crem 2025-06-09T19:21:31,003 copying crem/guacamol_crem_test.py -> build/lib/crem 2025-06-09T19:21:31,006 copying crem/fragmentation.py -> build/lib/crem 2025-06-09T19:21:31,008 copying crem/frag_to_env_mp.py -> build/lib/crem 2025-06-09T19:21:31,010 running egg_info 2025-06-09T19:21:31,039 writing crem.egg-info/PKG-INFO 2025-06-09T19:21:31,044 writing dependency_links to crem.egg-info/dependency_links.txt 2025-06-09T19:21:31,045 writing entry points to crem.egg-info/entry_points.txt 2025-06-09T19:21:31,047 writing requirements to crem.egg-info/requires.txt 2025-06-09T19:21:31,049 writing top-level names to crem.egg-info/top_level.txt 2025-06-09T19:21:31,083 reading manifest file 'crem.egg-info/SOURCES.txt' 2025-06-09T19:21:31,086 adding license file 'LICENSE.txt' 2025-06-09T19:21:31,089 writing manifest file 'crem.egg-info/SOURCES.txt' 2025-06-09T19:21:31,092 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'crem.scripts' is absent from the `packages` configuration. 2025-06-09T19:21:31,092 !! 2025-06-09T19:21:31,093 ******************************************************************************** 2025-06-09T19:21:31,094 ############################ 2025-06-09T19:21:31,095 # Package would be ignored # 2025-06-09T19:21:31,095 ############################ 2025-06-09T19:21:31,096 Python recognizes 'crem.scripts' as an importable package[^1], 2025-06-09T19:21:31,096 but it is absent from setuptools' `packages` configuration. 2025-06-09T19:21:31,097 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-09T19:21:31,098 package, please make sure that 'crem.scripts' is explicitly added 2025-06-09T19:21:31,098 to the `packages` configuration field. 2025-06-09T19:21:31,100 Alternatively, you can also rely on setuptools' discovery methods 2025-06-09T19:21:31,100 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-09T19:21:31,101 instead of `find_packages(...)`/`find:`). 2025-06-09T19:21:31,102 You can read more about "package discovery" on setuptools documentation page: 2025-06-09T19:21:31,103 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-09T19:21:31,104 If you don't want 'crem.scripts' to be distributed and are 2025-06-09T19:21:31,105 already explicitly excluding 'crem.scripts' via 2025-06-09T19:21:31,106 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-09T19:21:31,106 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-09T19:21:31,106 combination with a more fine grained `package-data` configuration. 2025-06-09T19:21:31,107 You can read more about "package data files" on setuptools documentation page: 2025-06-09T19:21:31,108 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-09T19:21:31,110 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-09T19:21:31,110 even if it does not contain any `.py` files. 2025-06-09T19:21:31,111 On the other hand, currently there is no concept of package data 2025-06-09T19:21:31,111 directory, all directories are treated like packages. 2025-06-09T19:21:31,112 ******************************************************************************** 2025-06-09T19:21:31,113 !! 2025-06-09T19:21:31,113 check.warn(importable) 2025-06-09T19:21:31,114 creating build/lib/crem/scripts 2025-06-09T19:21:31,114 copying crem/scripts/__init__.py -> build/lib/crem/scripts 2025-06-09T19:21:31,115 copying crem/scripts/crem_add_prop.py -> build/lib/crem/scripts 2025-06-09T19:21:31,115 copying crem/scripts/crem_create_frag_db.sh -> build/lib/crem/scripts 2025-06-09T19:21:31,116 copying crem/scripts/enumerate_molecules.py -> build/lib/crem/scripts 2025-06-09T19:21:31,116 copying crem/scripts/get_stat.py -> build/lib/crem/scripts 2025-06-09T19:21:31,117 copying crem/scripts/r1.txt -> build/lib/crem/scripts 2025-06-09T19:21:31,255 copying crem/scripts/select_ids.py -> build/lib/crem/scripts 2025-06-09T19:21:31,258 running build_scripts 2025-06-09T19:21:31,259 creating build/scripts-3.11 2025-06-09T19:21:31,260 copying crem/scripts/crem_create_frag_db.sh -> build/scripts-3.11 2025-06-09T19:21:31,290 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-09T19:21:31,290 !! 2025-06-09T19:21:31,291 ******************************************************************************** 2025-06-09T19:21:31,292 Please avoid running ``setup.py`` directly. 2025-06-09T19:21:31,293 Instead, use pypa/build, pypa/installer or other 2025-06-09T19:21:31,293 standards-based tools. 2025-06-09T19:21:31,295 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-09T19:21:31,295 or your builds will no longer be supported. 2025-06-09T19:21:31,297 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-09T19:21:31,297 ******************************************************************************** 2025-06-09T19:21:31,298 !! 2025-06-09T19:21:31,299 self.initialize_options() 2025-06-09T19:21:31,318 installing to build/bdist.linux-armv7l/wheel 2025-06-09T19:21:31,319 running install 2025-06-09T19:21:31,343 running install_lib 2025-06-09T19:21:31,371 creating build/bdist.linux-armv7l/wheel 2025-06-09T19:21:31,373 creating build/bdist.linux-armv7l/wheel/crem 2025-06-09T19:21:31,375 copying build/lib/crem/guacamol_distribution_test.py -> build/bdist.linux-armv7l/wheel/./crem 2025-06-09T19:21:31,377 copying build/lib/crem/crem.py -> build/bdist.linux-armv7l/wheel/./crem 2025-06-09T19:21:31,380 copying build/lib/crem/arg_types.py -> build/bdist.linux-armv7l/wheel/./crem 2025-06-09T19:21:31,382 copying build/lib/crem/__init__.py -> build/bdist.linux-armv7l/wheel/./crem 2025-06-09T19:21:31,384 creating build/bdist.linux-armv7l/wheel/crem/scripts 2025-06-09T19:21:31,385 copying build/lib/crem/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./crem/scripts 2025-06-09T19:21:31,387 copying build/lib/crem/scripts/crem_create_frag_db.sh -> build/bdist.linux-armv7l/wheel/./crem/scripts 2025-06-09T19:21:31,389 copying build/lib/crem/scripts/get_stat.py -> build/bdist.linux-armv7l/wheel/./crem/scripts 2025-06-09T19:21:31,391 copying build/lib/crem/scripts/r1.txt -> build/bdist.linux-armv7l/wheel/./crem/scripts 2025-06-09T19:21:31,523 copying build/lib/crem/scripts/select_ids.py -> build/bdist.linux-armv7l/wheel/./crem/scripts 2025-06-09T19:21:31,525 copying build/lib/crem/scripts/crem_add_prop.py -> build/bdist.linux-armv7l/wheel/./crem/scripts 2025-06-09T19:21:31,527 copying build/lib/crem/scripts/enumerate_molecules.py -> build/bdist.linux-armv7l/wheel/./crem/scripts 2025-06-09T19:21:31,529 copying build/lib/crem/mol_context.py -> build/bdist.linux-armv7l/wheel/./crem 2025-06-09T19:21:31,532 copying build/lib/crem/functions.py -> build/bdist.linux-armv7l/wheel/./crem 2025-06-09T19:21:31,534 copying build/lib/crem/import_env_to_db.py -> build/bdist.linux-armv7l/wheel/./crem 2025-06-09T19:21:31,536 copying build/lib/crem/utils.py -> build/bdist.linux-armv7l/wheel/./crem 2025-06-09T19:21:31,539 copying build/lib/crem/guacamol_crem_test.py -> build/bdist.linux-armv7l/wheel/./crem 2025-06-09T19:21:31,541 copying build/lib/crem/fragmentation.py -> build/bdist.linux-armv7l/wheel/./crem 2025-06-09T19:21:31,544 copying build/lib/crem/frag_to_env_mp.py -> build/bdist.linux-armv7l/wheel/./crem 2025-06-09T19:21:31,546 running install_egg_info 2025-06-09T19:21:31,582 Copying crem.egg-info to build/bdist.linux-armv7l/wheel/./crem-0.2.15-py3.11.egg-info 2025-06-09T19:21:31,595 running install_scripts 2025-06-09T19:21:31,596 creating build/bdist.linux-armv7l/wheel/crem-0.2.15.data/scripts 2025-06-09T19:21:31,598 copying build/scripts-3.11/crem_create_frag_db.sh -> build/bdist.linux-armv7l/wheel/crem-0.2.15.data/scripts 2025-06-09T19:21:31,600 changing mode of build/bdist.linux-armv7l/wheel/crem-0.2.15.data/scripts/crem_create_frag_db.sh to 755 2025-06-09T19:21:31,614 creating build/bdist.linux-armv7l/wheel/crem-0.2.15.dist-info/WHEEL 2025-06-09T19:21:31,617 creating '/tmp/pip-wheel-l6alchyh/crem-0.2.15-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-09T19:21:31,620 adding 'crem/__init__.py' 2025-06-09T19:21:31,621 adding 'crem/arg_types.py' 2025-06-09T19:21:31,627 adding 'crem/crem.py' 2025-06-09T19:21:31,629 adding 'crem/frag_to_env_mp.py' 2025-06-09T19:21:31,631 adding 'crem/fragmentation.py' 2025-06-09T19:21:31,633 adding 'crem/functions.py' 2025-06-09T19:21:31,635 adding 'crem/guacamol_crem_test.py' 2025-06-09T19:21:31,637 adding 'crem/guacamol_distribution_test.py' 2025-06-09T19:21:31,639 adding 'crem/import_env_to_db.py' 2025-06-09T19:21:31,641 adding 'crem/mol_context.py' 2025-06-09T19:21:31,644 adding 'crem/utils.py' 2025-06-09T19:21:31,646 adding 'crem/scripts/__init__.py' 2025-06-09T19:21:31,647 adding 'crem/scripts/crem_add_prop.py' 2025-06-09T19:21:31,649 adding 'crem/scripts/crem_create_frag_db.sh' 2025-06-09T19:21:31,651 adding 'crem/scripts/enumerate_molecules.py' 2025-06-09T19:21:31,652 adding 'crem/scripts/get_stat.py' 2025-06-09T19:21:32,345 adding 'crem/scripts/r1.txt' 2025-06-09T19:21:32,402 adding 'crem/scripts/select_ids.py' 2025-06-09T19:21:32,405 adding 'crem-0.2.15.data/scripts/crem_create_frag_db.sh' 2025-06-09T19:21:32,407 adding 'crem-0.2.15.dist-info/licenses/LICENSE.txt' 2025-06-09T19:21:32,410 adding 'crem-0.2.15.dist-info/METADATA' 2025-06-09T19:21:32,412 adding 'crem-0.2.15.dist-info/WHEEL' 2025-06-09T19:21:32,413 adding 'crem-0.2.15.dist-info/entry_points.txt' 2025-06-09T19:21:32,414 adding 'crem-0.2.15.dist-info/top_level.txt' 2025-06-09T19:21:32,416 adding 'crem-0.2.15.dist-info/RECORD' 2025-06-09T19:21:32,425 removing build/bdist.linux-armv7l/wheel 2025-06-09T19:21:32,548 Building wheel for crem (setup.py): finished with status 'done' 2025-06-09T19:21:32,558 Created wheel for crem: filename=crem-0.2.15-py3-none-any.whl size=742369 sha256=541023483e57f826caf83e7fc9a63554feed7adf7d0bd3ff15c22b62b0ca26f4 2025-06-09T19:21:32,560 Stored in directory: /tmp/pip-ephem-wheel-cache-aj4dzlkk/wheels/79/de/86/8dafc2bb82fe6ba80da0c396fe91a344a68fdd344a177f948a 2025-06-09T19:21:32,574 Successfully built crem 2025-06-09T19:21:32,606 Removed build tracker: '/tmp/pip-build-tracker-0da3iuim'