2023-11-30T18:46:26,705 Created temporary directory: /tmp/pip-build-tracker-ouf5g25a
2023-11-30T18:46:26,706 Initialized build tracking at /tmp/pip-build-tracker-ouf5g25a
2023-11-30T18:46:26,706 Created build tracker: /tmp/pip-build-tracker-ouf5g25a
2023-11-30T18:46:26,707 Entered build tracker: /tmp/pip-build-tracker-ouf5g25a
2023-11-30T18:46:26,708 Created temporary directory: /tmp/pip-wheel-omk95uj5
2023-11-30T18:46:26,711 Created temporary directory: /tmp/pip-ephem-wheel-cache-a4s4uxdy
2023-11-30T18:46:26,739 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-11-30T18:46:26,742 2 location(s) to search for versions of meeko:
2023-11-30T18:46:26,742 * https://pypi.org/simple/meeko/
2023-11-30T18:46:26,742 * https://www.piwheels.org/simple/meeko/
2023-11-30T18:46:26,743 Fetching project page and analyzing links: https://pypi.org/simple/meeko/
2023-11-30T18:46:26,744 Getting page https://pypi.org/simple/meeko/
2023-11-30T18:46:26,746 Found index url https://pypi.org/simple/
2023-11-30T18:46:26,885 Fetched page https://pypi.org/simple/meeko/ as application/vnd.pypi.simple.v1+json
2023-11-30T18:46:26,891   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/38/c7/946dda1732a3aeca878b9cf1aa1a965066488479d67e4fc137d2379a79b6/meeko-0.1.dev1-py2.py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:26,892   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/61/30/79ecf599df2c81ead389544f3291774adddccb3ac4548eae61a7b8a62bc3/meeko-0.1.dev2-py2.py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:26,892   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/89/84/827a0ea853ba0970f0287eb09ba7d07186590a510d10a8b63a2d884ac447/meeko-0.1.dev3-py2.py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:26,893   Found link https://files.pythonhosted.org/packages/ec/d2/c1eaf8b818377fbe788daf86dc8994fcc4ae2d4b6fa00c2a5c81d8aa2ca6/meeko-0.1.dev3.tar.gz (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*), version: 0.1.dev3
2023-11-30T18:46:26,894   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/f1/b6/fe6205ca310917d121b6f96259c845d94ef627d7473fc2bd119235b5b8d3/meeko-0.2-py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:26,895   Found link https://files.pythonhosted.org/packages/23/24/36f5b53aa74cd50f5e6cea8d5d5f3b99b6f3ea1e2a059d13f5f8d51a0624/meeko-0.2.tar.gz (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*), version: 0.2
2023-11-30T18:46:26,896   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/15/e4/e0195c8d07d6c9226c9940ecb9164e6120e9502f64bee2a6303fb0a75ca1/meeko-0.3.0-py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:26,897   Found link https://files.pythonhosted.org/packages/1b/e5/ff954b3fbef337ac7cd0d29ebab8864385aad66fe528aae73d05604dddfd/meeko-0.3.0.tar.gz (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*), version: 0.3.0
2023-11-30T18:46:26,897   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/7a/ff/6e57ed90d6384e76ea2acb31a929f8f036468e07c80319764805398db9d8/meeko-0.3.1-py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:26,898   Found link https://files.pythonhosted.org/packages/33/b4/3a1d12da1c3bc0c7381c51aec8e51206f2b28b8c394b23cc4b373593c478/meeko-0.3.1.tar.gz (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*), version: 0.3.1
2023-11-30T18:46:26,899   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/1a/9d/28755e7eb7679082f4e00ef3e9ad3365e9f90c0d341e95289306a7d10831/meeko-0.3.2-py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:26,900   Found link https://files.pythonhosted.org/packages/04/fd/03d4d7fb97c6ce5789eea55cc8a5a27b3c9ba2e9e8944c46855d0356786d/meeko-0.3.2.tar.gz (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*), version: 0.3.2
2023-11-30T18:46:26,901   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/53/ae/fb019569a4c5d74bcd83434261e41b322aacfae687f38b1c8596c24be8b2/meeko-0.3.3-py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:26,902   Found link https://files.pythonhosted.org/packages/97/42/a9846a4bd8c90d8cf64857e183f3dc55f0553bad814a25ad9e454d51092b/meeko-0.3.3.tar.gz (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*), version: 0.3.3
2023-11-30T18:46:26,903   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/a1/38/e64382d54a507d7cd9b25472e91476d105e312ae8e3f88feacbd3ed6c4ca/meeko-0.4.0-py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:26,904   Found link https://files.pythonhosted.org/packages/df/e8/5599f1f3b4d82a6fd509e9ba1494866c9be26cb9cba57cffe433fb6573e1/meeko-0.4.0.tar.gz (from https://pypi.org/simple/meeko/) (requires-python:>=3.5.*), version: 0.4.0
2023-11-30T18:46:26,904   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/0f/97/aaae239d66f408f0d58c949bf4bc7c62add39fbf9ff22733fb087937ca82/meeko-0.5.0-py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5)
2023-11-30T18:46:26,905   Found link https://files.pythonhosted.org/packages/78/17/8947c029c13d2f55f3a4833e17722dd275f94b10a7c32914374981eb8c8e/meeko-0.5.0.tar.gz (from https://pypi.org/simple/meeko/) (requires-python:>=3.5), version: 0.5.0
2023-11-30T18:46:26,906   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/0f/93/453299cc4dca86c36c7eb9c35374078bfe1aa64a062d55d850286e73b083/meeko-0.6.0a0-py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5)
2023-11-30T18:46:26,907   Found link https://files.pythonhosted.org/packages/17/d1/0906b1cb62d6d1bad1b7f1ab8d24d13fc7b8df66759ef4d0ce4fa4378de6/meeko-0.6.0a0.tar.gz (from https://pypi.org/simple/meeko/) (requires-python:>=3.5), version: 0.6.0a0
2023-11-30T18:46:26,907   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/0a/9f/774439a1db856b584ee216bea0e5319027518e7495bed613a65dbb960793/meeko-0.6.0a1-py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5)
2023-11-30T18:46:26,908   Found link https://files.pythonhosted.org/packages/6e/0f/c39e837be0f4664bf9e3d9d139cbf5e1d2d836e671ca7769522eb5326a25/meeko-0.6.0a1.tar.gz (from https://pypi.org/simple/meeko/) (requires-python:>=3.5), version: 0.6.0a1
2023-11-30T18:46:26,909   Skipping link: No binaries permitted for meeko: https://files.pythonhosted.org/packages/3b/68/0733d4e5205baefc5484705710a8754117a50ca8acb4e1059b2908c38d4a/meeko-0.6.0a2-py3-none-any.whl (from https://pypi.org/simple/meeko/) (requires-python:>=3.5)
2023-11-30T18:46:26,910   Found link https://files.pythonhosted.org/packages/53/af/920d5c0225b08924a0c97746264ef33c4ba5d9622548e7b76e0a273e4999/meeko-0.6.0a2.tar.gz (from https://pypi.org/simple/meeko/) (requires-python:>=3.5), version: 0.6.0a2
2023-11-30T18:46:26,911 Fetching project page and analyzing links: https://www.piwheels.org/simple/meeko/
2023-11-30T18:46:26,912 Getting page https://www.piwheels.org/simple/meeko/
2023-11-30T18:46:26,913 Found index url https://www.piwheels.org/simple/
2023-11-30T18:46:27,072 Fetched page https://www.piwheels.org/simple/meeko/ as text/html
2023-11-30T18:46:27,076   Skipping link: No binaries permitted for meeko: https://www.piwheels.org/simple/meeko/meeko-0.6.0a1-py3-none-any.whl#sha256=0ed52cfec48b37b3da175a1426f743aa6095efa144df31884f9cb86fb9fe40ad (from https://www.piwheels.org/simple/meeko/) (requires-python:>=3.5)
2023-11-30T18:46:27,077   Skipping link: No binaries permitted for meeko: https://www.piwheels.org/simple/meeko/meeko-0.6.0a0-py3-none-any.whl#sha256=b06250c9721d6cd2d9c001803a610364ce95f5084fded20180d0c25b77ef6b50 (from https://www.piwheels.org/simple/meeko/) (requires-python:>=3.5)
2023-11-30T18:46:27,078   Skipping link: No binaries permitted for meeko: https://www.piwheels.org/simple/meeko/meeko-0.5.0-py3-none-any.whl#sha256=716f47c9471895bb7314e06164f1748d2cb8f53987d8da9d52ec129b2c91cfc3 (from https://www.piwheels.org/simple/meeko/) (requires-python:>=3.5)
2023-11-30T18:46:27,079   Skipping link: No binaries permitted for meeko: https://www.piwheels.org/simple/meeko/meeko-0.4.0-py3-none-any.whl#sha256=ab401b9be3dd1941184d0ad836b51fc577db7d02d277f08ffc26285d54a6ee5e (from https://www.piwheels.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:27,079   Skipping link: No binaries permitted for meeko: https://www.piwheels.org/simple/meeko/meeko-0.3.3-py3-none-any.whl#sha256=f226db6d061657ac79463f4cc9b02ac1639cff39efeee9d289820c1fc6895382 (from https://www.piwheels.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:27,080   Skipping link: No binaries permitted for meeko: https://www.piwheels.org/simple/meeko/meeko-0.3.2-py3-none-any.whl#sha256=c36d011eb03705ad1d8fd598ce5e441b9c55c76b1c37011d95563b4fe5449494 (from https://www.piwheels.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:27,080   Skipping link: No binaries permitted for meeko: https://www.piwheels.org/simple/meeko/meeko-0.3.1-py3-none-any.whl#sha256=628a26bdbddab96cde118d3180a404144108c33edcbbefe3ade9e84f286cece0 (from https://www.piwheels.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:27,081   Skipping link: No binaries permitted for meeko: https://www.piwheels.org/simple/meeko/meeko-0.3.0-py3-none-any.whl#sha256=508ada8f77e474225a99c3905e6eb53c7db2a45a02c84a774d9f78a889a8da1d (from https://www.piwheels.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:27,081   Skipping link: No binaries permitted for meeko: https://www.piwheels.org/simple/meeko/meeko-0.2-py3-none-any.whl#sha256=88c75d8ed22efc73b451ac641472aa931ccbf3ef36f2f236c14a2d45d58541b2 (from https://www.piwheels.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:27,082   Skipping link: No binaries permitted for meeko: https://www.piwheels.org/simple/meeko/meeko-0.1.dev3-py2.py3-none-any.whl#sha256=feb4d48b05302efc1168ac2365ebfa920dd98fe24fca3f5cafe60376ed796caa (from https://www.piwheels.org/simple/meeko/) (requires-python:>=3.5.*)
2023-11-30T18:46:27,083 Skipping link: not a file: https://www.piwheels.org/simple/meeko/
2023-11-30T18:46:27,083 Skipping link: not a file: https://pypi.org/simple/meeko/
2023-11-30T18:46:27,104 Given no hashes to check 1 links for project 'meeko': discarding no candidates
2023-11-30T18:46:27,124 Collecting meeko==0.6.0a2
2023-11-30T18:46:27,127   Created temporary directory: /tmp/pip-unpack-e4nf8lez
2023-11-30T18:46:27,341   Downloading meeko-0.6.0a2.tar.gz (152 kB)
2023-11-30T18:46:27,565   Added meeko==0.6.0a2 from https://files.pythonhosted.org/packages/53/af/920d5c0225b08924a0c97746264ef33c4ba5d9622548e7b76e0a273e4999/meeko-0.6.0a2.tar.gz to build tracker '/tmp/pip-build-tracker-ouf5g25a'
2023-11-30T18:46:27,567   Running setup.py (path:/tmp/pip-wheel-omk95uj5/meeko_5a3bc0ec7ee643ce98eebdad9ba2b777/setup.py) egg_info for package meeko
2023-11-30T18:46:27,568   Created temporary directory: /tmp/pip-pip-egg-info-e9tz82er
2023-11-30T18:46:27,569   Preparing metadata (setup.py): started
2023-11-30T18:46:27,570   Running command python setup.py egg_info
2023-11-30T18:46:28,636   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:314: InformationOnly: Normalizing '0.6.0-alpha.2' to '0.6.0a2'
2023-11-30T18:46:28,636     self.metadata.version = self._normalize_version(self.metadata.version)
2023-11-30T18:46:28,679   running egg_info
2023-11-30T18:46:28,681   creating /tmp/pip-pip-egg-info-e9tz82er/meeko.egg-info
2023-11-30T18:46:28,708   writing /tmp/pip-pip-egg-info-e9tz82er/meeko.egg-info/PKG-INFO
2023-11-30T18:46:28,713   writing dependency_links to /tmp/pip-pip-egg-info-e9tz82er/meeko.egg-info/dependency_links.txt
2023-11-30T18:46:28,715   writing requirements to /tmp/pip-pip-egg-info-e9tz82er/meeko.egg-info/requires.txt
2023-11-30T18:46:28,717   writing top-level names to /tmp/pip-pip-egg-info-e9tz82er/meeko.egg-info/top_level.txt
2023-11-30T18:46:28,718   writing manifest file '/tmp/pip-pip-egg-info-e9tz82er/meeko.egg-info/SOURCES.txt'
2023-11-30T18:46:28,834   reading manifest file '/tmp/pip-pip-egg-info-e9tz82er/meeko.egg-info/SOURCES.txt'
2023-11-30T18:46:28,836   adding license file 'LICENSE'
2023-11-30T18:46:28,839   writing manifest file '/tmp/pip-pip-egg-info-e9tz82er/meeko.egg-info/SOURCES.txt'
2023-11-30T18:46:28,947   Preparing metadata (setup.py): finished with status 'done'
2023-11-30T18:46:28,953   Source in /tmp/pip-wheel-omk95uj5/meeko_5a3bc0ec7ee643ce98eebdad9ba2b777 has version 0.6.0a2, which satisfies requirement meeko==0.6.0a2 from https://files.pythonhosted.org/packages/53/af/920d5c0225b08924a0c97746264ef33c4ba5d9622548e7b76e0a273e4999/meeko-0.6.0a2.tar.gz
2023-11-30T18:46:28,954   Removed meeko==0.6.0a2 from https://files.pythonhosted.org/packages/53/af/920d5c0225b08924a0c97746264ef33c4ba5d9622548e7b76e0a273e4999/meeko-0.6.0a2.tar.gz from build tracker '/tmp/pip-build-tracker-ouf5g25a'
2023-11-30T18:46:28,961 Created temporary directory: /tmp/pip-unpack-svoj_69g
2023-11-30T18:46:28,962 Created temporary directory: /tmp/pip-unpack-jhfcqyby
2023-11-30T18:46:28,968 Building wheels for collected packages: meeko
2023-11-30T18:46:28,973   Created temporary directory: /tmp/pip-wheel-6vgmruzb
2023-11-30T18:46:28,973   Building wheel for meeko (setup.py): started
2023-11-30T18:46:28,974   Destination directory: /tmp/pip-wheel-6vgmruzb
2023-11-30T18:46:28,975   Running command python setup.py bdist_wheel
2023-11-30T18:46:30,005   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:314: InformationOnly: Normalizing '0.6.0-alpha.2' to '0.6.0a2'
2023-11-30T18:46:30,006     self.metadata.version = self._normalize_version(self.metadata.version)
2023-11-30T18:46:30,039   running bdist_wheel
2023-11-30T18:46:30,137   running build
2023-11-30T18:46:30,138   running build_py
2023-11-30T18:46:30,167   creating build
2023-11-30T18:46:30,167   creating build/lib
2023-11-30T18:46:30,168   creating build/lib/meeko
2023-11-30T18:46:30,170   copying meeko/macrocycle.py -> build/lib/meeko
2023-11-30T18:46:30,172   copying meeko/openff_xml_parser.py -> build/lib/meeko
2023-11-30T18:46:30,175   copying meeko/rdkit_mol_create.py -> build/lib/meeko
2023-11-30T18:46:30,178   copying meeko/reactive.py -> build/lib/meeko
2023-11-30T18:46:30,180   copying meeko/covalentbuilder.py -> build/lib/meeko
2023-11-30T18:46:30,182   copying meeko/writer.py -> build/lib/meeko
2023-11-30T18:46:30,185   copying meeko/hydrate.py -> build/lib/meeko
2023-11-30T18:46:30,188   copying meeko/__init__.py -> build/lib/meeko
2023-11-30T18:46:30,190   copying meeko/bondtyper.py -> build/lib/meeko
2023-11-30T18:46:30,192   copying meeko/receptor_pdbqt.py -> build/lib/meeko
2023-11-30T18:46:30,195   copying meeko/molecule_pdbqt.py -> build/lib/meeko
2023-11-30T18:46:30,198   copying meeko/gridbox.py -> build/lib/meeko
2023-11-30T18:46:30,200   copying meeko/preparation.py -> build/lib/meeko
2023-11-30T18:46:30,203   copying meeko/espalomatyper.py -> build/lib/meeko
2023-11-30T18:46:30,206   copying meeko/flexibility.py -> build/lib/meeko
2023-11-30T18:46:30,208   copying meeko/molsetup.py -> build/lib/meeko
2023-11-30T18:46:30,212   copying meeko/atomtyper.py -> build/lib/meeko
2023-11-30T18:46:30,214   copying meeko/linked_rdkit_chorizo.py -> build/lib/meeko
2023-11-30T18:46:30,218   creating build/lib/meeko/analysis
2023-11-30T18:46:30,219   copying meeko/analysis/fingerprint_interactions.py -> build/lib/meeko/analysis
2023-11-30T18:46:30,222   copying meeko/analysis/interactions.py -> build/lib/meeko/analysis
2023-11-30T18:46:30,225   copying meeko/analysis/__init__.py -> build/lib/meeko/analysis
2023-11-30T18:46:30,229   creating build/lib/meeko/utils
2023-11-30T18:46:30,230   copying meeko/utils/geomutils.py -> build/lib/meeko/utils
2023-11-30T18:46:30,233   copying meeko/utils/utils.py -> build/lib/meeko/utils
2023-11-30T18:46:30,237   copying meeko/utils/van_der_waals_radius_table.py -> build/lib/meeko/utils
2023-11-30T18:46:30,239   copying meeko/utils/__init__.py -> build/lib/meeko/utils
2023-11-30T18:46:30,241   copying meeko/utils/rdkitutils.py -> build/lib/meeko/utils
2023-11-30T18:46:30,244   copying meeko/utils/autodock4_atom_types_elements.py -> build/lib/meeko/utils
2023-11-30T18:46:30,246   copying meeko/utils/covalent_radius_table.py -> build/lib/meeko/utils
2023-11-30T18:46:30,249   copying meeko/utils/obutils.py -> build/lib/meeko/utils
2023-11-30T18:46:30,251   copying meeko/utils/pdbutils.py -> build/lib/meeko/utils
2023-11-30T18:46:30,253   running egg_info
2023-11-30T18:46:30,312   writing meeko.egg-info/PKG-INFO
2023-11-30T18:46:30,317   writing dependency_links to meeko.egg-info/dependency_links.txt
2023-11-30T18:46:30,319   writing requirements to meeko.egg-info/requires.txt
2023-11-30T18:46:30,320   writing top-level names to meeko.egg-info/top_level.txt
2023-11-30T18:46:30,353   reading manifest file 'meeko.egg-info/SOURCES.txt'
2023-11-30T18:46:30,356   adding license file 'LICENSE'
2023-11-30T18:46:30,360   writing manifest file 'meeko.egg-info/SOURCES.txt'
2023-11-30T18:46:30,362   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'meeko.data' is absent from the `packages` configuration.
2023-11-30T18:46:30,363   !!

2023-11-30T18:46:30,364           ********************************************************************************
2023-11-30T18:46:30,364           ############################
2023-11-30T18:46:30,365           # Package would be ignored #
2023-11-30T18:46:30,365           ############################
2023-11-30T18:46:30,366           Python recognizes 'meeko.data' as an importable package[^1],
2023-11-30T18:46:30,367           but it is absent from setuptools' `packages` configuration.

2023-11-30T18:46:30,368           This leads to an ambiguous overall configuration. If you want to distribute this
2023-11-30T18:46:30,368           package, please make sure that 'meeko.data' is explicitly added
2023-11-30T18:46:30,369           to the `packages` configuration field.

2023-11-30T18:46:30,370           Alternatively, you can also rely on setuptools' discovery methods
2023-11-30T18:46:30,370           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-11-30T18:46:30,371           instead of `find_packages(...)`/`find:`).

2023-11-30T18:46:30,372           You can read more about "package discovery" on setuptools documentation page:

2023-11-30T18:46:30,373           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-11-30T18:46:30,374           If you don't want 'meeko.data' to be distributed and are
2023-11-30T18:46:30,375           already explicitly excluding 'meeko.data' via
2023-11-30T18:46:30,375           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-11-30T18:46:30,376           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-11-30T18:46:30,376           combination with a more fine grained `package-data` configuration.

2023-11-30T18:46:30,378           You can read more about "package data files" on setuptools documentation page:

2023-11-30T18:46:30,379           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-11-30T18:46:30,381           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-11-30T18:46:30,383                 even if it does not contain any `.py` files.
2023-11-30T18:46:30,383                 On the other hand, currently there is no concept of package data
2023-11-30T18:46:30,384                 directory, all directories are treated like packages.
2023-11-30T18:46:30,384           ********************************************************************************

2023-11-30T18:46:30,386   !!
2023-11-30T18:46:30,387     check.warn(importable)
2023-11-30T18:46:30,387   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'meeko.data.params' is absent from the `packages` configuration.
2023-11-30T18:46:30,388   !!

2023-11-30T18:46:30,389           ********************************************************************************
2023-11-30T18:46:30,390           ############################
2023-11-30T18:46:30,391           # Package would be ignored #
2023-11-30T18:46:30,391           ############################
2023-11-30T18:46:30,392           Python recognizes 'meeko.data.params' as an importable package[^1],
2023-11-30T18:46:30,392           but it is absent from setuptools' `packages` configuration.

2023-11-30T18:46:30,393           This leads to an ambiguous overall configuration. If you want to distribute this
2023-11-30T18:46:30,394           package, please make sure that 'meeko.data.params' is explicitly added
2023-11-30T18:46:30,394           to the `packages` configuration field.

2023-11-30T18:46:30,395           Alternatively, you can also rely on setuptools' discovery methods
2023-11-30T18:46:30,396           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-11-30T18:46:30,396           instead of `find_packages(...)`/`find:`).

2023-11-30T18:46:30,397           You can read more about "package discovery" on setuptools documentation page:

2023-11-30T18:46:30,398           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-11-30T18:46:30,399           If you don't want 'meeko.data.params' to be distributed and are
2023-11-30T18:46:30,400           already explicitly excluding 'meeko.data.params' via
2023-11-30T18:46:30,400           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-11-30T18:46:30,400           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-11-30T18:46:30,401           combination with a more fine grained `package-data` configuration.

2023-11-30T18:46:30,402           You can read more about "package data files" on setuptools documentation page:

2023-11-30T18:46:30,403           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-11-30T18:46:30,404           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-11-30T18:46:30,405                 even if it does not contain any `.py` files.
2023-11-30T18:46:30,405                 On the other hand, currently there is no concept of package data
2023-11-30T18:46:30,406                 directory, all directories are treated like packages.
2023-11-30T18:46:30,406           ********************************************************************************

2023-11-30T18:46:30,407   !!
2023-11-30T18:46:30,408     check.warn(importable)
2023-11-30T18:46:30,408   creating build/lib/meeko/data
2023-11-30T18:46:30,409   copying meeko/data/atomtypes.txt -> build/lib/meeko/data
2023-11-30T18:46:30,409   copying meeko/data/flexres_templates.json -> build/lib/meeko/data
2023-11-30T18:46:30,410   copying meeko/data/pi_non_aromatic.txt -> build/lib/meeko/data
2023-11-30T18:46:30,410   copying meeko/data/prot_res_params.json -> build/lib/meeko/data
2023-11-30T18:46:30,411   copying meeko/data/residue_params.json -> build/lib/meeko/data
2023-11-30T18:46:30,411   copying meeko/data/waterfield.txt -> build/lib/meeko/data
2023-11-30T18:46:30,412   creating build/lib/meeko/data/params
2023-11-30T18:46:30,412   copying meeko/data/params/ad4_desolv_param.json -> build/lib/meeko/data/params
2023-11-30T18:46:30,413   copying meeko/data/params/ad4_desolv_volume.json -> build/lib/meeko/data/params
2023-11-30T18:46:30,413   copying meeko/data/params/ad4_types.json -> build/lib/meeko/data/params
2023-11-30T18:46:30,414   copying meeko/data/params/ad4_vdw.json -> build/lib/meeko/data/params
2023-11-30T18:46:30,414   copying meeko/data/params/example_offatom_charge.json -> build/lib/meeko/data/params
2023-11-30T18:46:30,415   copying meeko/data/params/vina_params.json -> build/lib/meeko/data/params
2023-11-30T18:46:30,418   running build_scripts
2023-11-30T18:46:30,419   creating build/scripts-3.11
2023-11-30T18:46:30,420   copying and adjusting scripts/mk_prepare_ligand.py -> build/scripts-3.11
2023-11-30T18:46:30,423   copying and adjusting scripts/mk_prepare_receptor.py -> build/scripts-3.11
2023-11-30T18:46:30,426   copying and adjusting scripts/mk_export.py -> build/scripts-3.11
2023-11-30T18:46:30,428   changing mode of build/scripts-3.11/mk_prepare_ligand.py from 644 to 755
2023-11-30T18:46:30,428   changing mode of build/scripts-3.11/mk_prepare_receptor.py from 644 to 755
2023-11-30T18:46:30,429   changing mode of build/scripts-3.11/mk_export.py from 644 to 755
2023-11-30T18:46:30,454   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2023-11-30T18:46:30,454   !!

2023-11-30T18:46:30,455           ********************************************************************************
2023-11-30T18:46:30,456           Please avoid running ``setup.py`` directly.
2023-11-30T18:46:30,457           Instead, use pypa/build, pypa/installer or other
2023-11-30T18:46:30,457           standards-based tools.

2023-11-30T18:46:30,458           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2023-11-30T18:46:30,459           ********************************************************************************

2023-11-30T18:46:30,460   !!
2023-11-30T18:46:30,460     self.initialize_options()
2023-11-30T18:46:30,479   installing to build/bdist.linux-aarch64/wheel
2023-11-30T18:46:30,480   running install
2023-11-30T18:46:30,503   running install_lib
2023-11-30T18:46:30,529   creating build/bdist.linux-aarch64
2023-11-30T18:46:30,530   creating build/bdist.linux-aarch64/wheel
2023-11-30T18:46:30,532   creating build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,533   copying build/lib/meeko/macrocycle.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,536   copying build/lib/meeko/openff_xml_parser.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,539   creating build/bdist.linux-aarch64/wheel/meeko/analysis
2023-11-30T18:46:30,540   copying build/lib/meeko/analysis/fingerprint_interactions.py -> build/bdist.linux-aarch64/wheel/meeko/analysis
2023-11-30T18:46:30,542   copying build/lib/meeko/analysis/interactions.py -> build/bdist.linux-aarch64/wheel/meeko/analysis
2023-11-30T18:46:30,545   copying build/lib/meeko/analysis/__init__.py -> build/bdist.linux-aarch64/wheel/meeko/analysis
2023-11-30T18:46:30,547   copying build/lib/meeko/rdkit_mol_create.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,550   copying build/lib/meeko/reactive.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,553   copying build/lib/meeko/covalentbuilder.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,556   copying build/lib/meeko/writer.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,559   copying build/lib/meeko/hydrate.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,561   copying build/lib/meeko/__init__.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,564   copying build/lib/meeko/bondtyper.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,566   copying build/lib/meeko/receptor_pdbqt.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,569   creating build/bdist.linux-aarch64/wheel/meeko/data
2023-11-30T18:46:30,570   copying build/lib/meeko/data/atomtypes.txt -> build/bdist.linux-aarch64/wheel/meeko/data
2023-11-30T18:46:30,572   copying build/lib/meeko/data/flexres_templates.json -> build/bdist.linux-aarch64/wheel/meeko/data
2023-11-30T18:46:30,574   copying build/lib/meeko/data/prot_res_params.json -> build/bdist.linux-aarch64/wheel/meeko/data
2023-11-30T18:46:30,582   creating build/bdist.linux-aarch64/wheel/meeko/data/params
2023-11-30T18:46:30,584   copying build/lib/meeko/data/params/ad4_desolv_volume.json -> build/bdist.linux-aarch64/wheel/meeko/data/params
2023-11-30T18:46:30,586   copying build/lib/meeko/data/params/ad4_types.json -> build/bdist.linux-aarch64/wheel/meeko/data/params
2023-11-30T18:46:30,588   copying build/lib/meeko/data/params/ad4_desolv_param.json -> build/bdist.linux-aarch64/wheel/meeko/data/params
2023-11-30T18:46:30,590   copying build/lib/meeko/data/params/example_offatom_charge.json -> build/bdist.linux-aarch64/wheel/meeko/data/params
2023-11-30T18:46:30,592   copying build/lib/meeko/data/params/vina_params.json -> build/bdist.linux-aarch64/wheel/meeko/data/params
2023-11-30T18:46:30,593   copying build/lib/meeko/data/params/ad4_vdw.json -> build/bdist.linux-aarch64/wheel/meeko/data/params
2023-11-30T18:46:30,596   copying build/lib/meeko/data/waterfield.txt -> build/bdist.linux-aarch64/wheel/meeko/data
2023-11-30T18:46:30,598   copying build/lib/meeko/data/pi_non_aromatic.txt -> build/bdist.linux-aarch64/wheel/meeko/data
2023-11-30T18:46:30,600   copying build/lib/meeko/data/residue_params.json -> build/bdist.linux-aarch64/wheel/meeko/data
2023-11-30T18:46:30,605   copying build/lib/meeko/molecule_pdbqt.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,608   copying build/lib/meeko/gridbox.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,611   copying build/lib/meeko/preparation.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,614   copying build/lib/meeko/espalomatyper.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,617   copying build/lib/meeko/flexibility.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,620   creating build/bdist.linux-aarch64/wheel/meeko/utils
2023-11-30T18:46:30,622   copying build/lib/meeko/utils/geomutils.py -> build/bdist.linux-aarch64/wheel/meeko/utils
2023-11-30T18:46:30,625   copying build/lib/meeko/utils/utils.py -> build/bdist.linux-aarch64/wheel/meeko/utils
2023-11-30T18:46:30,628   copying build/lib/meeko/utils/van_der_waals_radius_table.py -> build/bdist.linux-aarch64/wheel/meeko/utils
2023-11-30T18:46:30,630   copying build/lib/meeko/utils/__init__.py -> build/bdist.linux-aarch64/wheel/meeko/utils
2023-11-30T18:46:30,633   copying build/lib/meeko/utils/rdkitutils.py -> build/bdist.linux-aarch64/wheel/meeko/utils
2023-11-30T18:46:30,635   copying build/lib/meeko/utils/autodock4_atom_types_elements.py -> build/bdist.linux-aarch64/wheel/meeko/utils
2023-11-30T18:46:30,637   copying build/lib/meeko/utils/covalent_radius_table.py -> build/bdist.linux-aarch64/wheel/meeko/utils
2023-11-30T18:46:30,640   copying build/lib/meeko/utils/obutils.py -> build/bdist.linux-aarch64/wheel/meeko/utils
2023-11-30T18:46:30,642   copying build/lib/meeko/utils/pdbutils.py -> build/bdist.linux-aarch64/wheel/meeko/utils
2023-11-30T18:46:30,644   copying build/lib/meeko/molsetup.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,648   copying build/lib/meeko/atomtyper.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,651   copying build/lib/meeko/linked_rdkit_chorizo.py -> build/bdist.linux-aarch64/wheel/meeko
2023-11-30T18:46:30,654   running install_data
2023-11-30T18:46:30,680   creating build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data
2023-11-30T18:46:30,680   creating build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/data
2023-11-30T18:46:30,682   copying README.md -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/data/
2023-11-30T18:46:30,684   copying LICENSE -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/data/
2023-11-30T18:46:30,687   creating build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/data/scripts
2023-11-30T18:46:30,688   copying scripts/mk_export.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/data/scripts
2023-11-30T18:46:30,691   copying scripts/mk_prepare_ligand.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/data/scripts
2023-11-30T18:46:30,694   copying scripts/mk_prepare_receptor.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/data/scripts
2023-11-30T18:46:30,697   copying scripts/mk_get_openff_epsilon_sigma.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/data/scripts
2023-11-30T18:46:30,699   running install_egg_info
2023-11-30T18:46:30,731   Copying meeko.egg-info to build/bdist.linux-aarch64/wheel/meeko-0.6.0a2-py3.11.egg-info
2023-11-30T18:46:30,744   running install_scripts
2023-11-30T18:46:30,746   creating build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/scripts
2023-11-30T18:46:30,746   copying build/scripts-3.11/mk_export.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/scripts
2023-11-30T18:46:30,749   copying build/scripts-3.11/mk_prepare_ligand.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/scripts
2023-11-30T18:46:30,752   copying build/scripts-3.11/mk_prepare_receptor.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/scripts
2023-11-30T18:46:30,754   changing mode of build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/scripts/mk_export.py to 755
2023-11-30T18:46:30,755   changing mode of build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/scripts/mk_prepare_ligand.py to 755
2023-11-30T18:46:30,755   changing mode of build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.data/scripts/mk_prepare_receptor.py to 755
2023-11-30T18:46:30,772   creating build/bdist.linux-aarch64/wheel/meeko-0.6.0a2.dist-info/WHEEL
2023-11-30T18:46:30,775   creating '/tmp/pip-wheel-6vgmruzb/meeko-0.6.0a2-py3-none-any.whl' and adding 'build/bdist.linux-aarch64/wheel' to it
2023-11-30T18:46:30,777   adding 'meeko/__init__.py'
2023-11-30T18:46:30,780   adding 'meeko/atomtyper.py'
2023-11-30T18:46:30,782   adding 'meeko/bondtyper.py'
2023-11-30T18:46:30,784   adding 'meeko/covalentbuilder.py'
2023-11-30T18:46:30,786   adding 'meeko/espalomatyper.py'
2023-11-30T18:46:30,788   adding 'meeko/flexibility.py'
2023-11-30T18:46:30,790   adding 'meeko/gridbox.py'
2023-11-30T18:46:30,792   adding 'meeko/hydrate.py'
2023-11-30T18:46:30,798   adding 'meeko/linked_rdkit_chorizo.py'
2023-11-30T18:46:30,801   adding 'meeko/macrocycle.py'
2023-11-30T18:46:30,805   adding 'meeko/molecule_pdbqt.py'
2023-11-30T18:46:30,811   adding 'meeko/molsetup.py'
2023-11-30T18:46:30,813   adding 'meeko/openff_xml_parser.py'
2023-11-30T18:46:30,816   adding 'meeko/preparation.py'
2023-11-30T18:46:30,819   adding 'meeko/rdkit_mol_create.py'
2023-11-30T18:46:30,821   adding 'meeko/reactive.py'
2023-11-30T18:46:30,824   adding 'meeko/receptor_pdbqt.py'
2023-11-30T18:46:30,827   adding 'meeko/writer.py'
2023-11-30T18:46:30,830   adding 'meeko/analysis/__init__.py'
2023-11-30T18:46:30,831   adding 'meeko/analysis/fingerprint_interactions.py'
2023-11-30T18:46:30,833   adding 'meeko/analysis/interactions.py'
2023-11-30T18:46:30,835   adding 'meeko/data/atomtypes.txt'
2023-11-30T18:46:30,837   adding 'meeko/data/flexres_templates.json'
2023-11-30T18:46:30,838   adding 'meeko/data/pi_non_aromatic.txt'
2023-11-30T18:46:30,848   adding 'meeko/data/prot_res_params.json'
2023-11-30T18:46:30,859   adding 'meeko/data/residue_params.json'
2023-11-30T18:46:30,862   adding 'meeko/data/waterfield.txt'
2023-11-30T18:46:30,864   adding 'meeko/data/params/ad4_desolv_param.json'
2023-11-30T18:46:30,865   adding 'meeko/data/params/ad4_desolv_volume.json'
2023-11-30T18:46:30,867   adding 'meeko/data/params/ad4_types.json'
2023-11-30T18:46:30,868   adding 'meeko/data/params/ad4_vdw.json'
2023-11-30T18:46:30,870   adding 'meeko/data/params/example_offatom_charge.json'
2023-11-30T18:46:30,871   adding 'meeko/data/params/vina_params.json'
2023-11-30T18:46:30,873   adding 'meeko/utils/__init__.py'
2023-11-30T18:46:30,875   adding 'meeko/utils/autodock4_atom_types_elements.py'
2023-11-30T18:46:30,876   adding 'meeko/utils/covalent_radius_table.py'
2023-11-30T18:46:30,879   adding 'meeko/utils/geomutils.py'
2023-11-30T18:46:30,881   adding 'meeko/utils/obutils.py'
2023-11-30T18:46:30,882   adding 'meeko/utils/pdbutils.py'
2023-11-30T18:46:30,884   adding 'meeko/utils/rdkitutils.py'
2023-11-30T18:46:30,886   adding 'meeko/utils/utils.py'
2023-11-30T18:46:30,888   adding 'meeko/utils/van_der_waals_radius_table.py'
2023-11-30T18:46:30,893   adding 'meeko-0.6.0a2.data/data/LICENSE'
2023-11-30T18:46:30,896   adding 'meeko-0.6.0a2.data/data/README.md'
2023-11-30T18:46:30,899   adding 'meeko-0.6.0a2.data/data/scripts/mk_export.py'
2023-11-30T18:46:30,900   adding 'meeko-0.6.0a2.data/data/scripts/mk_get_openff_epsilon_sigma.py'
2023-11-30T18:46:30,902   adding 'meeko-0.6.0a2.data/data/scripts/mk_prepare_ligand.py'
2023-11-30T18:46:30,906   adding 'meeko-0.6.0a2.data/data/scripts/mk_prepare_receptor.py'
2023-11-30T18:46:30,908   adding 'meeko-0.6.0a2.data/scripts/mk_export.py'
2023-11-30T18:46:30,911   adding 'meeko-0.6.0a2.data/scripts/mk_prepare_ligand.py'
2023-11-30T18:46:30,914   adding 'meeko-0.6.0a2.data/scripts/mk_prepare_receptor.py'
2023-11-30T18:46:30,919   adding 'meeko-0.6.0a2.dist-info/LICENSE'
2023-11-30T18:46:30,922   adding 'meeko-0.6.0a2.dist-info/METADATA'
2023-11-30T18:46:30,923   adding 'meeko-0.6.0a2.dist-info/WHEEL'
2023-11-30T18:46:30,924   adding 'meeko-0.6.0a2.dist-info/top_level.txt'
2023-11-30T18:46:30,925   adding 'meeko-0.6.0a2.dist-info/RECORD'
2023-11-30T18:46:30,930   removing build/bdist.linux-aarch64/wheel
2023-11-30T18:46:31,060   Building wheel for meeko (setup.py): finished with status 'done'
2023-11-30T18:46:31,065   Created wheel for meeko: filename=meeko-0.6.0a2-py3-none-any.whl size=190374 sha256=20994b5df8114eec204a0608030a8291e15c7a9214fdb1728b27489c3920027b
2023-11-30T18:46:31,066   Stored in directory: /tmp/pip-ephem-wheel-cache-a4s4uxdy/wheels/53/3d/c3/458b4d09ab933fdc388fe3cfd884cc2032deaf9c9f66c705e2
2023-11-30T18:46:31,082 Successfully built meeko
2023-11-30T18:46:31,091 Removed build tracker: '/tmp/pip-build-tracker-ouf5g25a'