2023-11-30T09:52:34,001 Created temporary directory: /tmp/pip-build-tracker-moua6fai 2023-11-30T09:52:34,002 Initialized build tracking at /tmp/pip-build-tracker-moua6fai 2023-11-30T09:52:34,003 Created build tracker: /tmp/pip-build-tracker-moua6fai 2023-11-30T09:52:34,003 Entered build tracker: /tmp/pip-build-tracker-moua6fai 2023-11-30T09:52:34,004 Created temporary directory: /tmp/pip-wheel-cns_5i3f 2023-11-30T09:52:34,008 Created temporary directory: /tmp/pip-ephem-wheel-cache-tqeg_8r3 2023-11-30T09:52:34,031 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-30T09:52:34,035 2 location(s) to search for versions of meeko: 2023-11-30T09:52:34,035 * https://pypi.org/simple/meeko/ 2023-11-30T09:52:34,035 * https://www.piwheels.org/simple/meeko/ 2023-11-30T09:52:34,036 Fetching project page and analyzing links: https://pypi.org/simple/meeko/ 2023-11-30T09:52:34,037 Getting page https://pypi.org/simple/meeko/ 2023-11-30T09:52:34,038 Found index url https://pypi.org/simple/ 2023-11-30T09:52:34,247 Fetched page https://pypi.org/simple/meeko/ as application/vnd.pypi.simple.v1+json 2023-11-30T09:52:34,252 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.*) 2023-11-30T09:52:34,253 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.*) 2023-11-30T09:52:34,253 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.*) 2023-11-30T09:52:34,254 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 2023-11-30T09:52:34,255 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.*) 2023-11-30T09:52:34,256 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 2023-11-30T09:52:34,257 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.*) 2023-11-30T09:52:34,258 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 2023-11-30T09:52:34,259 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.*) 2023-11-30T09:52:34,260 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 2023-11-30T09:52:34,260 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.*) 2023-11-30T09:52:34,261 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 2023-11-30T09:52:34,262 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.*) 2023-11-30T09:52:34,263 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 2023-11-30T09:52:34,264 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.*) 2023-11-30T09:52:34,265 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 2023-11-30T09:52:34,265 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) 2023-11-30T09:52:34,266 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 2023-11-30T09:52:34,267 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) 2023-11-30T09:52:34,268 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 2023-11-30T09:52:34,269 Fetching project page and analyzing links: https://www.piwheels.org/simple/meeko/ 2023-11-30T09:52:34,269 Getting page https://www.piwheels.org/simple/meeko/ 2023-11-30T09:52:34,271 Found index url https://www.piwheels.org/simple/ 2023-11-30T09:52:34,426 Fetched page https://www.piwheels.org/simple/meeko/ as text/html 2023-11-30T09:52:34,429 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) 2023-11-30T09:52:34,430 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.*) 2023-11-30T09:52:34,431 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.*) 2023-11-30T09:52:34,431 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.*) 2023-11-30T09:52:34,432 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.*) 2023-11-30T09:52:34,433 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.*) 2023-11-30T09:52:34,433 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.*) 2023-11-30T09:52:34,434 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.*) 2023-11-30T09:52:34,435 Skipping link: not a file: https://www.piwheels.org/simple/meeko/ 2023-11-30T09:52:34,435 Skipping link: not a file: https://pypi.org/simple/meeko/ 2023-11-30T09:52:34,456 Given no hashes to check 1 links for project 'meeko': discarding no candidates 2023-11-30T09:52:34,476 Collecting meeko==0.6.0a0 2023-11-30T09:52:34,478 Created temporary directory: /tmp/pip-unpack-_3t5r3aq 2023-11-30T09:52:34,686 Downloading meeko-0.6.0a0.tar.gz (152 kB) 2023-11-30T09:52:34,916 Added meeko==0.6.0a0 from https://files.pythonhosted.org/packages/17/d1/0906b1cb62d6d1bad1b7f1ab8d24d13fc7b8df66759ef4d0ce4fa4378de6/meeko-0.6.0a0.tar.gz to build tracker '/tmp/pip-build-tracker-moua6fai' 2023-11-30T09:52:34,918 Running setup.py (path:/tmp/pip-wheel-cns_5i3f/meeko_b0dda3f70005420dac6be665308937d7/setup.py) egg_info for package meeko 2023-11-30T09:52:34,919 Created temporary directory: /tmp/pip-pip-egg-info-9ngczfp9 2023-11-30T09:52:34,919 Preparing metadata (setup.py): started 2023-11-30T09:52:34,921 Running command python setup.py egg_info 2023-11-30T09:52:35,927 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:314: InformationOnly: Normalizing '0.6.0-alpha' to '0.6.0a0' 2023-11-30T09:52:35,928 self.metadata.version = self._normalize_version(self.metadata.version) 2023-11-30T09:52:35,968 running egg_info 2023-11-30T09:52:35,969 creating /tmp/pip-pip-egg-info-9ngczfp9/meeko.egg-info 2023-11-30T09:52:35,995 writing /tmp/pip-pip-egg-info-9ngczfp9/meeko.egg-info/PKG-INFO 2023-11-30T09:52:36,000 writing dependency_links to /tmp/pip-pip-egg-info-9ngczfp9/meeko.egg-info/dependency_links.txt 2023-11-30T09:52:36,002 writing requirements to /tmp/pip-pip-egg-info-9ngczfp9/meeko.egg-info/requires.txt 2023-11-30T09:52:36,003 writing top-level names to /tmp/pip-pip-egg-info-9ngczfp9/meeko.egg-info/top_level.txt 2023-11-30T09:52:36,005 writing manifest file '/tmp/pip-pip-egg-info-9ngczfp9/meeko.egg-info/SOURCES.txt' 2023-11-30T09:52:36,119 reading manifest file '/tmp/pip-pip-egg-info-9ngczfp9/meeko.egg-info/SOURCES.txt' 2023-11-30T09:52:36,121 adding license file 'LICENSE' 2023-11-30T09:52:36,124 writing manifest file '/tmp/pip-pip-egg-info-9ngczfp9/meeko.egg-info/SOURCES.txt' 2023-11-30T09:52:36,233 Preparing metadata (setup.py): finished with status 'done' 2023-11-30T09:52:36,239 Source in /tmp/pip-wheel-cns_5i3f/meeko_b0dda3f70005420dac6be665308937d7 has version 0.6.0a0, which satisfies requirement meeko==0.6.0a0 from https://files.pythonhosted.org/packages/17/d1/0906b1cb62d6d1bad1b7f1ab8d24d13fc7b8df66759ef4d0ce4fa4378de6/meeko-0.6.0a0.tar.gz 2023-11-30T09:52:36,240 Removed meeko==0.6.0a0 from https://files.pythonhosted.org/packages/17/d1/0906b1cb62d6d1bad1b7f1ab8d24d13fc7b8df66759ef4d0ce4fa4378de6/meeko-0.6.0a0.tar.gz from build tracker '/tmp/pip-build-tracker-moua6fai' 2023-11-30T09:52:36,248 Created temporary directory: /tmp/pip-unpack-wucjk7x3 2023-11-30T09:52:36,249 Created temporary directory: /tmp/pip-unpack-f75zvcqk 2023-11-30T09:52:36,256 Building wheels for collected packages: meeko 2023-11-30T09:52:36,261 Created temporary directory: /tmp/pip-wheel-qgfxvwk6 2023-11-30T09:52:36,262 Building wheel for meeko (setup.py): started 2023-11-30T09:52:36,263 Destination directory: /tmp/pip-wheel-qgfxvwk6 2023-11-30T09:52:36,264 Running command python setup.py bdist_wheel 2023-11-30T09:52:37,271 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:314: InformationOnly: Normalizing '0.6.0-alpha' to '0.6.0a0' 2023-11-30T09:52:37,271 self.metadata.version = self._normalize_version(self.metadata.version) 2023-11-30T09:52:37,305 running bdist_wheel 2023-11-30T09:52:37,417 running build 2023-11-30T09:52:37,418 running build_py 2023-11-30T09:52:37,459 creating build 2023-11-30T09:52:37,459 creating build/lib 2023-11-30T09:52:37,461 creating build/lib/meeko 2023-11-30T09:52:37,462 copying meeko/espalomatyper.py -> build/lib/meeko 2023-11-30T09:52:37,465 copying meeko/gridbox.py -> build/lib/meeko 2023-11-30T09:52:37,468 copying meeko/molecule_pdbqt.py -> build/lib/meeko 2023-11-30T09:52:37,472 copying meeko/flexibility.py -> build/lib/meeko 2023-11-30T09:52:37,475 copying meeko/bondtyper.py -> build/lib/meeko 2023-11-30T09:52:37,478 copying meeko/reactive.py -> build/lib/meeko 2023-11-30T09:52:37,481 copying meeko/macrocycle.py -> build/lib/meeko 2023-11-30T09:52:37,483 copying meeko/writer.py -> build/lib/meeko 2023-11-30T09:52:37,486 copying meeko/covalentbuilder.py -> build/lib/meeko 2023-11-30T09:52:37,488 copying meeko/preparation.py -> build/lib/meeko 2023-11-30T09:52:37,491 copying meeko/hydrate.py -> build/lib/meeko 2023-11-30T09:52:37,493 copying meeko/openff_xml_parser.py -> build/lib/meeko 2023-11-30T09:52:37,496 copying meeko/molsetup.py -> build/lib/meeko 2023-11-30T09:52:37,499 copying meeko/atomtyper.py -> build/lib/meeko 2023-11-30T09:52:37,501 copying meeko/receptor_pdbqt.py -> build/lib/meeko 2023-11-30T09:52:37,504 copying meeko/linked_rdkit_chorizo.py -> build/lib/meeko 2023-11-30T09:52:37,507 copying meeko/rdkit_mol_create.py -> build/lib/meeko 2023-11-30T09:52:37,509 copying meeko/__init__.py -> build/lib/meeko 2023-11-30T09:52:37,512 creating build/lib/meeko/utils 2023-11-30T09:52:37,513 copying meeko/utils/covalent_radius_table.py -> build/lib/meeko/utils 2023-11-30T09:52:37,515 copying meeko/utils/obutils.py -> build/lib/meeko/utils 2023-11-30T09:52:37,517 copying meeko/utils/utils.py -> build/lib/meeko/utils 2023-11-30T09:52:37,520 copying meeko/utils/pdbutils.py -> build/lib/meeko/utils 2023-11-30T09:52:37,522 copying meeko/utils/geomutils.py -> build/lib/meeko/utils 2023-11-30T09:52:37,524 copying meeko/utils/van_der_waals_radius_table.py -> build/lib/meeko/utils 2023-11-30T09:52:37,526 copying meeko/utils/rdkitutils.py -> build/lib/meeko/utils 2023-11-30T09:52:37,529 copying meeko/utils/__init__.py -> build/lib/meeko/utils 2023-11-30T09:52:37,530 copying meeko/utils/autodock4_atom_types_elements.py -> build/lib/meeko/utils 2023-11-30T09:52:37,533 creating build/lib/meeko/analysis 2023-11-30T09:52:37,534 copying meeko/analysis/interactions.py -> build/lib/meeko/analysis 2023-11-30T09:52:37,537 copying meeko/analysis/fingerprint_interactions.py -> build/lib/meeko/analysis 2023-11-30T09:52:37,539 copying meeko/analysis/__init__.py -> build/lib/meeko/analysis 2023-11-30T09:52:37,541 running egg_info 2023-11-30T09:52:37,599 writing meeko.egg-info/PKG-INFO 2023-11-30T09:52:37,603 writing dependency_links to meeko.egg-info/dependency_links.txt 2023-11-30T09:52:37,605 writing requirements to meeko.egg-info/requires.txt 2023-11-30T09:52:37,606 writing top-level names to meeko.egg-info/top_level.txt 2023-11-30T09:52:37,639 reading manifest file 'meeko.egg-info/SOURCES.txt' 2023-11-30T09:52:37,642 adding license file 'LICENSE' 2023-11-30T09:52:37,646 writing manifest file 'meeko.egg-info/SOURCES.txt' 2023-11-30T09:52:37,648 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'meeko.data' is absent from the `packages` configuration. 2023-11-30T09:52:37,649 !! 2023-11-30T09:52:37,650 ******************************************************************************** 2023-11-30T09:52:37,651 ############################ 2023-11-30T09:52:37,652 # Package would be ignored # 2023-11-30T09:52:37,652 ############################ 2023-11-30T09:52:37,653 Python recognizes 'meeko.data' as an importable package[^1], 2023-11-30T09:52:37,654 but it is absent from setuptools' `packages` configuration. 2023-11-30T09:52:37,655 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-30T09:52:37,655 package, please make sure that 'meeko.data' is explicitly added 2023-11-30T09:52:37,656 to the `packages` configuration field. 2023-11-30T09:52:37,657 Alternatively, you can also rely on setuptools' discovery methods 2023-11-30T09:52:37,657 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-30T09:52:37,657 instead of `find_packages(...)`/`find:`). 2023-11-30T09:52:37,658 You can read more about "package discovery" on setuptools documentation page: 2023-11-30T09:52:37,659 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-30T09:52:37,660 If you don't want 'meeko.data' to be distributed and are 2023-11-30T09:52:37,661 already explicitly excluding 'meeko.data' via 2023-11-30T09:52:37,661 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-30T09:52:37,662 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-30T09:52:37,662 combination with a more fine grained `package-data` configuration. 2023-11-30T09:52:37,663 You can read more about "package data files" on setuptools documentation page: 2023-11-30T09:52:37,664 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-30T09:52:37,666 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-30T09:52:37,667 even if it does not contain any `.py` files. 2023-11-30T09:52:37,668 On the other hand, currently there is no concept of package data 2023-11-30T09:52:37,669 directory, all directories are treated like packages. 2023-11-30T09:52:37,670 ******************************************************************************** 2023-11-30T09:52:37,671 !! 2023-11-30T09:52:37,671 check.warn(importable) 2023-11-30T09:52:37,672 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'meeko.data.params' is absent from the `packages` configuration. 2023-11-30T09:52:37,673 !! 2023-11-30T09:52:37,674 ******************************************************************************** 2023-11-30T09:52:37,674 ############################ 2023-11-30T09:52:37,675 # Package would be ignored # 2023-11-30T09:52:37,676 ############################ 2023-11-30T09:52:37,676 Python recognizes 'meeko.data.params' as an importable package[^1], 2023-11-30T09:52:37,677 but it is absent from setuptools' `packages` configuration. 2023-11-30T09:52:37,678 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-30T09:52:37,678 package, please make sure that 'meeko.data.params' is explicitly added 2023-11-30T09:52:37,679 to the `packages` configuration field. 2023-11-30T09:52:37,680 Alternatively, you can also rely on setuptools' discovery methods 2023-11-30T09:52:37,681 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-30T09:52:37,681 instead of `find_packages(...)`/`find:`). 2023-11-30T09:52:37,682 You can read more about "package discovery" on setuptools documentation page: 2023-11-30T09:52:37,684 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-30T09:52:37,685 If you don't want 'meeko.data.params' to be distributed and are 2023-11-30T09:52:37,686 already explicitly excluding 'meeko.data.params' via 2023-11-30T09:52:37,686 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-30T09:52:37,687 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-30T09:52:37,688 combination with a more fine grained `package-data` configuration. 2023-11-30T09:52:37,689 You can read more about "package data files" on setuptools documentation page: 2023-11-30T09:52:37,690 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-30T09:52:37,691 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-30T09:52:37,691 even if it does not contain any `.py` files. 2023-11-30T09:52:37,692 On the other hand, currently there is no concept of package data 2023-11-30T09:52:37,692 directory, all directories are treated like packages. 2023-11-30T09:52:37,693 ******************************************************************************** 2023-11-30T09:52:37,694 !! 2023-11-30T09:52:37,694 check.warn(importable) 2023-11-30T09:52:37,694 creating build/lib/meeko/data 2023-11-30T09:52:37,695 copying meeko/data/atomtypes.txt -> build/lib/meeko/data 2023-11-30T09:52:37,696 copying meeko/data/flexres_templates.json -> build/lib/meeko/data 2023-11-30T09:52:37,696 copying meeko/data/pi_non_aromatic.txt -> build/lib/meeko/data 2023-11-30T09:52:37,697 copying meeko/data/prot_res_params.json -> build/lib/meeko/data 2023-11-30T09:52:37,697 copying meeko/data/residue_params.json -> build/lib/meeko/data 2023-11-30T09:52:37,698 copying meeko/data/waterfield.txt -> build/lib/meeko/data 2023-11-30T09:52:37,699 creating build/lib/meeko/data/params 2023-11-30T09:52:37,699 copying meeko/data/params/ad4_desolv_param.json -> build/lib/meeko/data/params 2023-11-30T09:52:37,700 copying meeko/data/params/ad4_desolv_volume.json -> build/lib/meeko/data/params 2023-11-30T09:52:37,701 copying meeko/data/params/ad4_types.json -> build/lib/meeko/data/params 2023-11-30T09:52:37,701 copying meeko/data/params/ad4_vdw.json -> build/lib/meeko/data/params 2023-11-30T09:52:37,701 copying meeko/data/params/example_offatom_charge.json -> build/lib/meeko/data/params 2023-11-30T09:52:37,702 copying meeko/data/params/vina_params.json -> build/lib/meeko/data/params 2023-11-30T09:52:37,704 running build_scripts 2023-11-30T09:52:37,705 creating build/scripts-3.11 2023-11-30T09:52:37,706 copying and adjusting scripts/mk_prepare_ligand.py -> build/scripts-3.11 2023-11-30T09:52:37,709 copying and adjusting scripts/mk_prepare_receptor.py -> build/scripts-3.11 2023-11-30T09:52:37,712 copying and adjusting scripts/mk_export.py -> build/scripts-3.11 2023-11-30T09:52:37,714 changing mode of build/scripts-3.11/mk_prepare_ligand.py from 644 to 755 2023-11-30T09:52:37,714 changing mode of build/scripts-3.11/mk_prepare_receptor.py from 644 to 755 2023-11-30T09:52:37,715 changing mode of build/scripts-3.11/mk_export.py from 644 to 755 2023-11-30T09:52:37,740 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-11-30T09:52:37,741 !! 2023-11-30T09:52:37,742 ******************************************************************************** 2023-11-30T09:52:37,743 Please avoid running ``setup.py`` directly. 2023-11-30T09:52:37,743 Instead, use pypa/build, pypa/installer or other 2023-11-30T09:52:37,744 standards-based tools. 2023-11-30T09:52:37,745 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-11-30T09:52:37,746 ******************************************************************************** 2023-11-30T09:52:37,747 !! 2023-11-30T09:52:37,748 self.initialize_options() 2023-11-30T09:52:37,768 installing to build/bdist.linux-aarch64/wheel 2023-11-30T09:52:37,768 running install 2023-11-30T09:52:37,793 running install_lib 2023-11-30T09:52:37,819 creating build/bdist.linux-aarch64 2023-11-30T09:52:37,820 creating build/bdist.linux-aarch64/wheel 2023-11-30T09:52:37,821 creating build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,822 copying build/lib/meeko/espalomatyper.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,825 copying build/lib/meeko/gridbox.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,827 copying build/lib/meeko/molecule_pdbqt.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,830 copying build/lib/meeko/flexibility.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,833 copying build/lib/meeko/bondtyper.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,835 creating build/bdist.linux-aarch64/wheel/meeko/utils 2023-11-30T09:52:37,836 copying build/lib/meeko/utils/covalent_radius_table.py -> build/bdist.linux-aarch64/wheel/meeko/utils 2023-11-30T09:52:37,838 copying build/lib/meeko/utils/obutils.py -> build/bdist.linux-aarch64/wheel/meeko/utils 2023-11-30T09:52:37,841 copying build/lib/meeko/utils/utils.py -> build/bdist.linux-aarch64/wheel/meeko/utils 2023-11-30T09:52:37,844 copying build/lib/meeko/utils/pdbutils.py -> build/bdist.linux-aarch64/wheel/meeko/utils 2023-11-30T09:52:37,845 copying build/lib/meeko/utils/geomutils.py -> build/bdist.linux-aarch64/wheel/meeko/utils 2023-11-30T09:52:37,848 copying build/lib/meeko/utils/van_der_waals_radius_table.py -> build/bdist.linux-aarch64/wheel/meeko/utils 2023-11-30T09:52:37,850 copying build/lib/meeko/utils/rdkitutils.py -> build/bdist.linux-aarch64/wheel/meeko/utils 2023-11-30T09:52:37,852 copying build/lib/meeko/utils/__init__.py -> build/bdist.linux-aarch64/wheel/meeko/utils 2023-11-30T09:52:37,854 copying build/lib/meeko/utils/autodock4_atom_types_elements.py -> build/bdist.linux-aarch64/wheel/meeko/utils 2023-11-30T09:52:37,856 copying build/lib/meeko/reactive.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,858 copying build/lib/meeko/macrocycle.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,861 copying build/lib/meeko/writer.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,863 copying build/lib/meeko/covalentbuilder.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,866 creating build/bdist.linux-aarch64/wheel/meeko/data 2023-11-30T09:52:37,867 copying build/lib/meeko/data/waterfield.txt -> build/bdist.linux-aarch64/wheel/meeko/data 2023-11-30T09:52:37,870 copying build/lib/meeko/data/atomtypes.txt -> build/bdist.linux-aarch64/wheel/meeko/data 2023-11-30T09:52:37,872 creating build/bdist.linux-aarch64/wheel/meeko/data/params 2023-11-30T09:52:37,873 copying build/lib/meeko/data/params/ad4_vdw.json -> build/bdist.linux-aarch64/wheel/meeko/data/params 2023-11-30T09:52:37,875 copying build/lib/meeko/data/params/ad4_types.json -> build/bdist.linux-aarch64/wheel/meeko/data/params 2023-11-30T09:52:37,877 copying build/lib/meeko/data/params/example_offatom_charge.json -> build/bdist.linux-aarch64/wheel/meeko/data/params 2023-11-30T09:52:37,879 copying build/lib/meeko/data/params/ad4_desolv_param.json -> build/bdist.linux-aarch64/wheel/meeko/data/params 2023-11-30T09:52:37,881 copying build/lib/meeko/data/params/ad4_desolv_volume.json -> build/bdist.linux-aarch64/wheel/meeko/data/params 2023-11-30T09:52:37,883 copying build/lib/meeko/data/params/vina_params.json -> build/bdist.linux-aarch64/wheel/meeko/data/params 2023-11-30T09:52:37,885 copying build/lib/meeko/data/residue_params.json -> build/bdist.linux-aarch64/wheel/meeko/data 2023-11-30T09:52:37,892 copying build/lib/meeko/data/prot_res_params.json -> build/bdist.linux-aarch64/wheel/meeko/data 2023-11-30T09:52:37,898 copying build/lib/meeko/data/flexres_templates.json -> build/bdist.linux-aarch64/wheel/meeko/data 2023-11-30T09:52:37,901 copying build/lib/meeko/data/pi_non_aromatic.txt -> build/bdist.linux-aarch64/wheel/meeko/data 2023-11-30T09:52:37,904 copying build/lib/meeko/preparation.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,907 copying build/lib/meeko/hydrate.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,910 copying build/lib/meeko/openff_xml_parser.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,913 creating build/bdist.linux-aarch64/wheel/meeko/analysis 2023-11-30T09:52:37,915 copying build/lib/meeko/analysis/interactions.py -> build/bdist.linux-aarch64/wheel/meeko/analysis 2023-11-30T09:52:37,918 copying build/lib/meeko/analysis/fingerprint_interactions.py -> build/bdist.linux-aarch64/wheel/meeko/analysis 2023-11-30T09:52:37,921 copying build/lib/meeko/analysis/__init__.py -> build/bdist.linux-aarch64/wheel/meeko/analysis 2023-11-30T09:52:37,923 copying build/lib/meeko/molsetup.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,927 copying build/lib/meeko/atomtyper.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,930 copying build/lib/meeko/receptor_pdbqt.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,933 copying build/lib/meeko/linked_rdkit_chorizo.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,937 copying build/lib/meeko/rdkit_mol_create.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,941 copying build/lib/meeko/__init__.py -> build/bdist.linux-aarch64/wheel/meeko 2023-11-30T09:52:37,943 running install_data 2023-11-30T09:52:37,969 creating build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data 2023-11-30T09:52:37,970 creating build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/data 2023-11-30T09:52:37,972 copying README.md -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/data/ 2023-11-30T09:52:37,975 copying LICENSE -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/data/ 2023-11-30T09:52:37,977 creating build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/data/scripts 2023-11-30T09:52:37,978 copying scripts/mk_export.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/data/scripts 2023-11-30T09:52:37,981 copying scripts/mk_get_openff_epsilon_sigma.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/data/scripts 2023-11-30T09:52:37,983 copying scripts/mk_prepare_receptor.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/data/scripts 2023-11-30T09:52:37,986 copying scripts/mk_prepare_ligand.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/data/scripts 2023-11-30T09:52:37,988 running install_egg_info 2023-11-30T09:52:38,020 Copying meeko.egg-info to build/bdist.linux-aarch64/wheel/meeko-0.6.0a0-py3.11.egg-info 2023-11-30T09:52:38,033 running install_scripts 2023-11-30T09:52:38,034 creating build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/scripts 2023-11-30T09:52:38,035 copying build/scripts-3.11/mk_export.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/scripts 2023-11-30T09:52:38,038 copying build/scripts-3.11/mk_prepare_receptor.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/scripts 2023-11-30T09:52:38,041 copying build/scripts-3.11/mk_prepare_ligand.py -> build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/scripts 2023-11-30T09:52:38,043 changing mode of build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/scripts/mk_export.py to 755 2023-11-30T09:52:38,044 changing mode of build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/scripts/mk_prepare_receptor.py to 755 2023-11-30T09:52:38,044 changing mode of build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.data/scripts/mk_prepare_ligand.py to 755 2023-11-30T09:52:38,061 creating build/bdist.linux-aarch64/wheel/meeko-0.6.0a0.dist-info/WHEEL 2023-11-30T09:52:38,064 creating '/tmp/pip-wheel-qgfxvwk6/meeko-0.6.0a0-py3-none-any.whl' and adding 'build/bdist.linux-aarch64/wheel' to it 2023-11-30T09:52:38,067 adding 'meeko/__init__.py' 2023-11-30T09:52:38,070 adding 'meeko/atomtyper.py' 2023-11-30T09:52:38,071 adding 'meeko/bondtyper.py' 2023-11-30T09:52:38,074 adding 'meeko/covalentbuilder.py' 2023-11-30T09:52:38,076 adding 'meeko/espalomatyper.py' 2023-11-30T09:52:38,078 adding 'meeko/flexibility.py' 2023-11-30T09:52:38,080 adding 'meeko/gridbox.py' 2023-11-30T09:52:38,082 adding 'meeko/hydrate.py' 2023-11-30T09:52:38,088 adding 'meeko/linked_rdkit_chorizo.py' 2023-11-30T09:52:38,091 adding 'meeko/macrocycle.py' 2023-11-30T09:52:38,095 adding 'meeko/molecule_pdbqt.py' 2023-11-30T09:52:38,101 adding 'meeko/molsetup.py' 2023-11-30T09:52:38,103 adding 'meeko/openff_xml_parser.py' 2023-11-30T09:52:38,106 adding 'meeko/preparation.py' 2023-11-30T09:52:38,108 adding 'meeko/rdkit_mol_create.py' 2023-11-30T09:52:38,110 adding 'meeko/reactive.py' 2023-11-30T09:52:38,113 adding 'meeko/receptor_pdbqt.py' 2023-11-30T09:52:38,116 adding 'meeko/writer.py' 2023-11-30T09:52:38,118 adding 'meeko/analysis/__init__.py' 2023-11-30T09:52:38,120 adding 'meeko/analysis/fingerprint_interactions.py' 2023-11-30T09:52:38,122 adding 'meeko/analysis/interactions.py' 2023-11-30T09:52:38,124 adding 'meeko/data/atomtypes.txt' 2023-11-30T09:52:38,125 adding 'meeko/data/flexres_templates.json' 2023-11-30T09:52:38,127 adding 'meeko/data/pi_non_aromatic.txt' 2023-11-30T09:52:38,136 adding 'meeko/data/prot_res_params.json' 2023-11-30T09:52:38,147 adding 'meeko/data/residue_params.json' 2023-11-30T09:52:38,150 adding 'meeko/data/waterfield.txt' 2023-11-30T09:52:38,152 adding 'meeko/data/params/ad4_desolv_param.json' 2023-11-30T09:52:38,153 adding 'meeko/data/params/ad4_desolv_volume.json' 2023-11-30T09:52:38,154 adding 'meeko/data/params/ad4_types.json' 2023-11-30T09:52:38,156 adding 'meeko/data/params/ad4_vdw.json' 2023-11-30T09:52:38,157 adding 'meeko/data/params/example_offatom_charge.json' 2023-11-30T09:52:38,158 adding 'meeko/data/params/vina_params.json' 2023-11-30T09:52:38,160 adding 'meeko/utils/__init__.py' 2023-11-30T09:52:38,161 adding 'meeko/utils/autodock4_atom_types_elements.py' 2023-11-30T09:52:38,163 adding 'meeko/utils/covalent_radius_table.py' 2023-11-30T09:52:38,166 adding 'meeko/utils/geomutils.py' 2023-11-30T09:52:38,167 adding 'meeko/utils/obutils.py' 2023-11-30T09:52:38,169 adding 'meeko/utils/pdbutils.py' 2023-11-30T09:52:38,170 adding 'meeko/utils/rdkitutils.py' 2023-11-30T09:52:38,172 adding 'meeko/utils/utils.py' 2023-11-30T09:52:38,174 adding 'meeko/utils/van_der_waals_radius_table.py' 2023-11-30T09:52:38,180 adding 'meeko-0.6.0a0.data/data/LICENSE' 2023-11-30T09:52:38,182 adding 'meeko-0.6.0a0.data/data/README.md' 2023-11-30T09:52:38,185 adding 'meeko-0.6.0a0.data/data/scripts/mk_export.py' 2023-11-30T09:52:38,186 adding 'meeko-0.6.0a0.data/data/scripts/mk_get_openff_epsilon_sigma.py' 2023-11-30T09:52:38,189 adding 'meeko-0.6.0a0.data/data/scripts/mk_prepare_ligand.py' 2023-11-30T09:52:38,192 adding 'meeko-0.6.0a0.data/data/scripts/mk_prepare_receptor.py' 2023-11-30T09:52:38,195 adding 'meeko-0.6.0a0.data/scripts/mk_export.py' 2023-11-30T09:52:38,197 adding 'meeko-0.6.0a0.data/scripts/mk_prepare_ligand.py' 2023-11-30T09:52:38,201 adding 'meeko-0.6.0a0.data/scripts/mk_prepare_receptor.py' 2023-11-30T09:52:38,206 adding 'meeko-0.6.0a0.dist-info/LICENSE' 2023-11-30T09:52:38,209 adding 'meeko-0.6.0a0.dist-info/METADATA' 2023-11-30T09:52:38,210 adding 'meeko-0.6.0a0.dist-info/WHEEL' 2023-11-30T09:52:38,212 adding 'meeko-0.6.0a0.dist-info/top_level.txt' 2023-11-30T09:52:38,213 adding 'meeko-0.6.0a0.dist-info/RECORD' 2023-11-30T09:52:38,219 removing build/bdist.linux-aarch64/wheel 2023-11-30T09:52:38,349 Building wheel for meeko (setup.py): finished with status 'done' 2023-11-30T09:52:38,354 Created wheel for meeko: filename=meeko-0.6.0a0-py3-none-any.whl size=190190 sha256=b06250c9721d6cd2d9c001803a610364ce95f5084fded20180d0c25b77ef6b50 2023-11-30T09:52:38,355 Stored in directory: /tmp/pip-ephem-wheel-cache-tqeg_8r3/wheels/56/17/80/bf98146ae2f7b3ad4e2ff1b6d7e84ccdae66191479dfb14271 2023-11-30T09:52:38,371 Successfully built meeko 2023-11-30T09:52:38,384 Removed build tracker: '/tmp/pip-build-tracker-moua6fai'