2025-09-09T02:44:25,174 Created temporary directory: /tmp/pip-build-tracker-l9ea6b2z 2025-09-09T02:44:25,175 Initialized build tracking at /tmp/pip-build-tracker-l9ea6b2z 2025-09-09T02:44:25,175 Created build tracker: /tmp/pip-build-tracker-l9ea6b2z 2025-09-09T02:44:25,175 Entered build tracker: /tmp/pip-build-tracker-l9ea6b2z 2025-09-09T02:44:25,175 Created temporary directory: /tmp/pip-wheel-w3bq3vzx 2025-09-09T02:44:25,178 Created temporary directory: /tmp/pip-ephem-wheel-cache-p8w15v1g 2025-09-09T02:44:25,235 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-09T02:44:25,238 2 location(s) to search for versions of molmod: 2025-09-09T02:44:25,238 * https://pypi.org/simple/molmod/ 2025-09-09T02:44:25,238 * https://www.piwheels.org/simple/molmod/ 2025-09-09T02:44:25,238 Fetching project page and analyzing links: https://pypi.org/simple/molmod/ 2025-09-09T02:44:25,238 Getting page https://pypi.org/simple/molmod/ 2025-09-09T02:44:25,239 Found index url https://pypi.org/simple/ 2025-09-09T02:44:25,309 Fetched page https://pypi.org/simple/molmod/ as application/vnd.pypi.simple.v1+json 2025-09-09T02:44:25,311 Found link https://files.pythonhosted.org/packages/d8/b1/d7cf3645e70ddf22e3c93225a0f963debc4be6276148cbaed46e973d2064/molmod-1.2.1.tar.gz (from https://pypi.org/simple/molmod/), version: 1.2.1 2025-09-09T02:44:25,311 Found link https://files.pythonhosted.org/packages/03/2d/4457e38b0e8245af76b37000ccee228d12b029023b0711954bc495494fd0/molmod-1.3.0.tar.gz (from https://pypi.org/simple/molmod/), version: 1.3.0 2025-09-09T02:44:25,312 Found link https://files.pythonhosted.org/packages/2c/3d/dd9c32cebc2ee7f29a16a778d775ce074c7c1c7b083f83b0dd63e350927e/molmod-1.3.1.tar.gz (from https://pypi.org/simple/molmod/), version: 1.3.1 2025-09-09T02:44:25,312 Found link https://files.pythonhosted.org/packages/79/fd/9f4282bf37b3ee38242dc4c6883b0923d450331f491ab5942702b791e84a/molmod-1.3.2.tar.gz (from https://pypi.org/simple/molmod/), version: 1.3.2 2025-09-09T02:44:25,312 Found link https://files.pythonhosted.org/packages/8c/b1/a243fe8d060c2ccb643e70504b0a727fe4a3420b2c790e3718865b6ffc8c/molmod-1.3.3.tar.gz (from https://pypi.org/simple/molmod/), version: 1.3.3 2025-09-09T02:44:25,312 Found link https://files.pythonhosted.org/packages/0d/d2/5df39f43e2f91f5a13376ef2c34aa30de3fd9be11fb6e9e5c18a9e15c9f8/molmod-1.3.4.tar.gz (from https://pypi.org/simple/molmod/), version: 1.3.4 2025-09-09T02:44:25,312 Found link https://files.pythonhosted.org/packages/5f/dc/39d3239d5d8d54bfc49378235b7c20f010ba98f3c4552b841617884d3646/molmod-1.3.5.tar.gz (from https://pypi.org/simple/molmod/), version: 1.3.5 2025-09-09T02:44:25,313 Found link https://files.pythonhosted.org/packages/da/f3/41c1c6830eae57a2b96b0d0d9d1853de31119ab7db44136ef69d3690f21a/molmod-1.4.0.tar.gz (from https://pypi.org/simple/molmod/), version: 1.4.0 2025-09-09T02:44:25,313 Found link https://files.pythonhosted.org/packages/03/bc/ca927944923a5de71f19c2390ab0b5f99f5e4723a1661c5917ab2cfe9919/molmod-1.4.1.tar.gz (from https://pypi.org/simple/molmod/), version: 1.4.1 2025-09-09T02:44:25,313 Found link https://files.pythonhosted.org/packages/8a/b8/0edf642e6a0bcb411523f5a25f87f1db08b590a073cb3e21dc332407a663/molmod-1.4.2.tar.gz (from https://pypi.org/simple/molmod/), version: 1.4.2 2025-09-09T02:44:25,313 Found link https://files.pythonhosted.org/packages/0b/85/bb75ec4376a612f3e5300712c5e1abab63894ec1bbf7be249a42a90b2c66/molmod-1.4.3.tar.gz (from https://pypi.org/simple/molmod/), version: 1.4.3 2025-09-09T02:44:25,313 Found link https://files.pythonhosted.org/packages/89/80/6a23f730196ed3ffb478dc3f9ea047913c99091d301cc82f4820ecee095d/molmod-1.4.4.tar.gz (from https://pypi.org/simple/molmod/), version: 1.4.4 2025-09-09T02:44:25,314 Found link https://files.pythonhosted.org/packages/98/08/f84c490fe1a2d0e3ff55dddd1079eeb77b2742ed3c8ad49b392444031d2f/molmod-1.4.5.tar.gz (from https://pypi.org/simple/molmod/), version: 1.4.5 2025-09-09T02:44:25,314 Found link https://files.pythonhosted.org/packages/e0/ce/a5df4a468f492baf8cce68318fd74eac947ff7f0947afc5bb14ac85fdccb/molmod-1.4.6.tar.gz (from https://pypi.org/simple/molmod/), version: 1.4.6 2025-09-09T02:44:25,314 Found link https://files.pythonhosted.org/packages/31/e6/4d8fe5e1fdf2077fdcee631d56aaaf8efaa331d823c4edc870fb30d701d8/molmod-1.4.7.tar.gz (from https://pypi.org/simple/molmod/), version: 1.4.7 2025-09-09T02:44:25,314 Found link https://files.pythonhosted.org/packages/23/77/814f9302b6df72ef3aa6944edd8b9b0f5e983aed07027828a4e0666c4ef3/molmod-1.4.8.tar.gz (from https://pypi.org/simple/molmod/), version: 1.4.8 2025-09-09T02:44:25,315 Fetching project page and analyzing links: https://www.piwheels.org/simple/molmod/ 2025-09-09T02:44:25,315 Getting page https://www.piwheels.org/simple/molmod/ 2025-09-09T02:44:25,316 Found index url https://www.piwheels.org/simple/ 2025-09-09T02:44:25,425 Fetched page https://www.piwheels.org/simple/molmod/ as text/html 2025-09-09T02:44:25,441 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.8-cp35-cp35m-linux_armv7l.whl#sha256=0c62dd6215c7d1ab1b9e5cfec2a58a924cc730a1d5f7ebcbf691e38032f897d8 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,441 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.8-cp35-cp35m-linux_armv6l.whl#sha256=0c62dd6215c7d1ab1b9e5cfec2a58a924cc730a1d5f7ebcbf691e38032f897d8 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,441 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.8-cp37-cp37m-linux_armv6l.whl#sha256=e5afa2214c1c5dd242f09e6f27db350ec7c46402d7e70f2764fab8e313737c35 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,441 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.8-cp37-cp37m-linux_armv7l.whl#sha256=e5afa2214c1c5dd242f09e6f27db350ec7c46402d7e70f2764fab8e313737c35 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,441 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.8-cp39-cp39-linux_armv6l.whl#sha256=25dee3ba29f379934e072bb16b631c5058f90f9cd4a0fdc06423430487e49e27 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,442 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.8-cp39-cp39-linux_armv7l.whl#sha256=25dee3ba29f379934e072bb16b631c5058f90f9cd4a0fdc06423430487e49e27 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,442 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.7-cp37-cp37m-linux_armv7l.whl#sha256=506838770510a3222b384a95dd5e5c3de8ce97b8eaeaf2ffade5dd3793971181 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,442 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.7-cp37-cp37m-linux_armv6l.whl#sha256=506838770510a3222b384a95dd5e5c3de8ce97b8eaeaf2ffade5dd3793971181 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,442 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.7-cp39-cp39-linux_armv6l.whl#sha256=e0eb81d9d34852306f94917e7b0d7d3f58da56125bead7d4a84e300445b8cd60 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,442 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.7-cp39-cp39-linux_armv7l.whl#sha256=e0eb81d9d34852306f94917e7b0d7d3f58da56125bead7d4a84e300445b8cd60 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,442 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.6-cp35-cp35m-linux_armv6l.whl#sha256=387627f9b6f6cca80131ea1038496beae8237f67dc05e75ea10797e321635552 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,443 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.6-cp35-cp35m-linux_armv7l.whl#sha256=387627f9b6f6cca80131ea1038496beae8237f67dc05e75ea10797e321635552 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,443 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.6-cp37-cp37m-linux_armv7l.whl#sha256=8e883987d1801a995bb2ecdd6f0a5a26d0bd988967d4470ae9c9ce7d31f65f33 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,443 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.6-cp37-cp37m-linux_armv6l.whl#sha256=8e883987d1801a995bb2ecdd6f0a5a26d0bd988967d4470ae9c9ce7d31f65f33 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,443 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.6-cp39-cp39-linux_armv6l.whl#sha256=b0a7018d75d184d3e6dca5fe56f23e1762af1d574e72c9d2df83cae4fae3c642 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,443 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.6-cp39-cp39-linux_armv7l.whl#sha256=b0a7018d75d184d3e6dca5fe56f23e1762af1d574e72c9d2df83cae4fae3c642 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,443 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.5-cp39-cp39-linux_armv6l.whl#sha256=b3a04bb54a7150cf1bf2dd273e9b3a11d847dce18242622f153a9a2c3a1ad2b7 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,443 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.5-cp39-cp39-linux_armv7l.whl#sha256=b3a04bb54a7150cf1bf2dd273e9b3a11d847dce18242622f153a9a2c3a1ad2b7 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,444 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.5-cp35-cp35m-linux_armv6l.whl#sha256=d4aa099f64504cfa8200e2bceba123cf86846e6b6dc752fb24dcce3408f5615c (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,444 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.5-cp35-cp35m-linux_armv7l.whl#sha256=d4aa099f64504cfa8200e2bceba123cf86846e6b6dc752fb24dcce3408f5615c (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,444 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.5-cp37-cp37m-linux_armv7l.whl#sha256=a485f1850e1810aa894facb319620ef0d57dc97ae3a8f0b17c6d19662078957f (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,444 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.5-cp37-cp37m-linux_armv6l.whl#sha256=a485f1850e1810aa894facb319620ef0d57dc97ae3a8f0b17c6d19662078957f (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,444 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.4-cp37-cp37m-linux_armv7l.whl#sha256=4b54456a955724201aaedcd50958ad1240f14c1448d75cc979c486bfb2d94422 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,444 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.4-cp37-cp37m-linux_armv6l.whl#sha256=4b54456a955724201aaedcd50958ad1240f14c1448d75cc979c486bfb2d94422 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,445 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.4-cp35-cp35m-linux_armv6l.whl#sha256=16188eb17c722ec601a3b35975b7e6a0f15e571006bef25c5235ab315b30b648 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,445 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.4-cp35-cp35m-linux_armv7l.whl#sha256=16188eb17c722ec601a3b35975b7e6a0f15e571006bef25c5235ab315b30b648 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,445 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.4-cp39-cp39-linux_armv6l.whl#sha256=bd4b288baaa4928f4f237d0b50f638669e5104cd5646298600e6b626d420c0d0 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,445 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.4-cp39-cp39-linux_armv7l.whl#sha256=bd4b288baaa4928f4f237d0b50f638669e5104cd5646298600e6b626d420c0d0 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,445 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.3-cp37-cp37m-linux_armv6l.whl#sha256=68419daf0b5ebd5f63c69ee9995a10f7d4d438c032bee3d7803452d957194b96 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,445 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.3-cp37-cp37m-linux_armv7l.whl#sha256=68419daf0b5ebd5f63c69ee9995a10f7d4d438c032bee3d7803452d957194b96 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,445 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.3-cp35-cp35m-linux_armv7l.whl#sha256=0207b9e905054da5b5dbda3a76eb3f951cf2177d3ece6761bd688e0a6ed350d2 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,446 Skipping link: No binaries permitted for molmod: 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https://archive1.piwheels.org/simple/molmod/molmod-1.4.2-cp39-cp39-linux_armv6l.whl#sha256=2a63c98cfa820171218e3e0fab5ce769a2bd26e3d4ddc9319878bd448e0f9d48 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,447 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.2-cp39-cp39-linux_armv7l.whl#sha256=2a63c98cfa820171218e3e0fab5ce769a2bd26e3d4ddc9319878bd448e0f9d48 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,447 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.1-cp37-cp37m-linux_armv6l.whl#sha256=7e09a91121f6fe4be52b080ba3957116797aaac57bc0662874b650ec2136349f (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,447 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.1-cp37-cp37m-linux_armv7l.whl#sha256=7e09a91121f6fe4be52b080ba3957116797aaac57bc0662874b650ec2136349f (from 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https://archive1.piwheels.org/simple/molmod/molmod-1.4.1-cp39-cp39-linux_armv7l.whl#sha256=bbd8feed144952e1cd8b1b94792b77ad2b9811a4ea61531fb89024ef9f6c9516 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,448 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.0-cp37-cp37m-linux_armv7l.whl#sha256=e9f6cfb88e385e2140f4a3d51654247321cdbf0ee2e788c4f42c797bf97c129d (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,448 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.0-cp37-cp37m-linux_armv6l.whl#sha256=e9f6cfb88e385e2140f4a3d51654247321cdbf0ee2e788c4f42c797bf97c129d (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,448 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.0-cp35-cp35m-linux_armv7l.whl#sha256=832ba3f726aaa608301aed7171497cb95d67d9cdbb67b51c313c85a843e134ed (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,448 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.0-cp35-cp35m-linux_armv6l.whl#sha256=832ba3f726aaa608301aed7171497cb95d67d9cdbb67b51c313c85a843e134ed (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,448 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.0-cp39-cp39-linux_armv6l.whl#sha256=94d51724484330f780e66851f0b3d5a04a572d624186dd184e5df63f93055fde (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,449 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.0-cp39-cp39-linux_armv7l.whl#sha256=94d51724484330f780e66851f0b3d5a04a572d624186dd184e5df63f93055fde (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,449 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.5-cp35-cp35m-linux_armv6l.whl#sha256=1c9efe5602f12d1c3cd1fd51923b91b8ad9c1f60c6dbf2ce2946108a07b35136 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,449 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.5-cp35-cp35m-linux_armv7l.whl#sha256=1c9efe5602f12d1c3cd1fd51923b91b8ad9c1f60c6dbf2ce2946108a07b35136 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,449 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.5-cp37-cp37m-linux_armv6l.whl#sha256=f026b5a093b68e3c8a0587a892770f350cb1370a01da18f17a32b40abc8c51c1 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,449 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.5-cp37-cp37m-linux_armv7l.whl#sha256=f026b5a093b68e3c8a0587a892770f350cb1370a01da18f17a32b40abc8c51c1 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,449 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.5-cp39-cp39-linux_armv6l.whl#sha256=c64f8298ab6a4cb4e41bb0df0c25ff04aaea2e7372ede4d8861624abe42d79ee (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,449 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.5-cp39-cp39-linux_armv7l.whl#sha256=c64f8298ab6a4cb4e41bb0df0c25ff04aaea2e7372ede4d8861624abe42d79ee (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,450 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.4-cp35-cp35m-linux_armv7l.whl#sha256=a5bc6f980651b4e0fb99c6e3f0c34db6b3b6db670455588851299c43f35eae31 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,450 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.4-cp35-cp35m-linux_armv6l.whl#sha256=a5bc6f980651b4e0fb99c6e3f0c34db6b3b6db670455588851299c43f35eae31 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,450 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.4-cp37-cp37m-linux_armv7l.whl#sha256=a9abac891fcb73c81b73f4facfdee4dceaae8e2860204858861a64d3da5951e7 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,450 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.4-cp37-cp37m-linux_armv6l.whl#sha256=a9abac891fcb73c81b73f4facfdee4dceaae8e2860204858861a64d3da5951e7 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,450 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.4-cp39-cp39-linux_armv6l.whl#sha256=b8268442b07783fb4cd0165ef1c9f4acb29db4ac8515594777e839f630810453 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,450 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.4-cp39-cp39-linux_armv7l.whl#sha256=b8268442b07783fb4cd0165ef1c9f4acb29db4ac8515594777e839f630810453 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,450 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.3-cp35-cp35m-linux_armv7l.whl#sha256=e9614b32a08939d91e8445e0358f08b40479a3e4f2c82bf8d9ef17ec4e4a45c3 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,451 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.3-cp35-cp35m-linux_armv6l.whl#sha256=e9614b32a08939d91e8445e0358f08b40479a3e4f2c82bf8d9ef17ec4e4a45c3 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,451 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.3-cp37-cp37m-linux_armv7l.whl#sha256=b5d76906e2ab76734766a497f21e625c75094053d0746ced1e1b15c77442e087 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,451 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.3-cp37-cp37m-linux_armv6l.whl#sha256=b5d76906e2ab76734766a497f21e625c75094053d0746ced1e1b15c77442e087 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,451 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.3-cp39-cp39-linux_armv6l.whl#sha256=c955105191874f6641662739e86d8ce23f438ab2f28a36a36cb8943a4ce21ea0 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,451 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.3-cp39-cp39-linux_armv7l.whl#sha256=c955105191874f6641662739e86d8ce23f438ab2f28a36a36cb8943a4ce21ea0 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,451 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.2-cp35-cp35m-linux_armv6l.whl#sha256=326e064f7a42df9fe34bf61b2b8d250c2075fb13f8a83d3f731d04afa4458495 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,451 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.2-cp35-cp35m-linux_armv7l.whl#sha256=326e064f7a42df9fe34bf61b2b8d250c2075fb13f8a83d3f731d04afa4458495 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,452 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.2-cp37-cp37m-linux_armv7l.whl#sha256=58c6b548ea700185894e6696d7eace87b9570d3f080529e7e91614530de065f0 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,452 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.2-cp37-cp37m-linux_armv6l.whl#sha256=58c6b548ea700185894e6696d7eace87b9570d3f080529e7e91614530de065f0 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,452 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.2-cp39-cp39-linux_armv6l.whl#sha256=f37c6d241bdfee045f443a9d55f9509d86d894a0c11e09ad4c38c91d235649c7 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,452 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.2-cp39-cp39-linux_armv7l.whl#sha256=f37c6d241bdfee045f443a9d55f9509d86d894a0c11e09ad4c38c91d235649c7 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,452 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.1-cp35-cp35m-linux_armv6l.whl#sha256=910b16bfc8b57c90f49cadaf67dded89cbb8cc764fe5e7e3a42fd523ee6448db (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,452 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.1-cp35-cp35m-linux_armv7l.whl#sha256=910b16bfc8b57c90f49cadaf67dded89cbb8cc764fe5e7e3a42fd523ee6448db (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,452 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.1-cp37-cp37m-linux_armv6l.whl#sha256=f82cc58ce559d1ab63e07886aa4cdfb9b92dd6f543da3adb0e1a2951b4e79587 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,453 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.1-cp37-cp37m-linux_armv7l.whl#sha256=f82cc58ce559d1ab63e07886aa4cdfb9b92dd6f543da3adb0e1a2951b4e79587 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,453 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.1-cp39-cp39-linux_armv6l.whl#sha256=babaff03785142a5537ba54c3eaf8ed85f176f9b3fa8d91003fc4020eb8dd525 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,453 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.1-cp39-cp39-linux_armv7l.whl#sha256=babaff03785142a5537ba54c3eaf8ed85f176f9b3fa8d91003fc4020eb8dd525 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,453 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.0-cp35-cp35m-linux_armv6l.whl#sha256=e07bb2f2c7d2cb940aedb4a5878680e828ef4f6e7b7093313c17831627695463 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,453 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.0-cp35-cp35m-linux_armv7l.whl#sha256=e07bb2f2c7d2cb940aedb4a5878680e828ef4f6e7b7093313c17831627695463 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,453 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.0-cp37-cp37m-linux_armv6l.whl#sha256=352896bf80d98d2d145c64078962110d5c4102d64ceb95eafaec29cf2f78fdfe (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,453 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.0-cp37-cp37m-linux_armv7l.whl#sha256=352896bf80d98d2d145c64078962110d5c4102d64ceb95eafaec29cf2f78fdfe (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,454 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.0-cp39-cp39-linux_armv6l.whl#sha256=78777d19e953e61a2176ccc556fc4ab996e0397c3ffed562c95ff7069b3e3baf (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,454 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.3.0-cp39-cp39-linux_armv7l.whl#sha256=78777d19e953e61a2176ccc556fc4ab996e0397c3ffed562c95ff7069b3e3baf (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,454 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.2.1-cp37-cp37m-linux_armv7l.whl#sha256=eefc96a8d630109adedcfcc5ea45151afae595ca5ca6c31e409e18eb0064e886 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,454 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.2.1-cp37-cp37m-linux_armv6l.whl#sha256=eefc96a8d630109adedcfcc5ea45151afae595ca5ca6c31e409e18eb0064e886 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,454 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.2.1-cp35-cp35m-linux_armv7l.whl#sha256=a525d0fa321dd8c725819b40a6ee7a1f188aa804c94ad0372a345bd101e9e559 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,454 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.2.1-cp35-cp35m-linux_armv6l.whl#sha256=a525d0fa321dd8c725819b40a6ee7a1f188aa804c94ad0372a345bd101e9e559 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,455 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.2.1-cp39-cp39-linux_armv6l.whl#sha256=ac836463734c5c9f0baad9f4cd509b9bfec96fa475087a4449ae69c9d553e8c0 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,455 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.2.1-cp39-cp39-linux_armv7l.whl#sha256=ac836463734c5c9f0baad9f4cd509b9bfec96fa475087a4449ae69c9d553e8c0 (from https://www.piwheels.org/simple/molmod/) 2025-09-09T02:44:25,455 Skipping link: not a file: https://www.piwheels.org/simple/molmod/ 2025-09-09T02:44:25,455 Skipping link: not a file: https://pypi.org/simple/molmod/ 2025-09-09T02:44:25,479 Given no hashes to check 1 links for project 'molmod': discarding no candidates 2025-09-09T02:44:25,480 Collecting molmod==1.4.8 2025-09-09T02:44:25,481 Created temporary directory: /tmp/pip-unpack-bvg2ykh_ 2025-09-09T02:44:25,623 Downloading molmod-1.4.8.tar.gz (1.7 MB) 2025-09-09T02:44:26,252 Added molmod==1.4.8 from https://files.pythonhosted.org/packages/23/77/814f9302b6df72ef3aa6944edd8b9b0f5e983aed07027828a4e0666c4ef3/molmod-1.4.8.tar.gz to build tracker '/tmp/pip-build-tracker-l9ea6b2z' 2025-09-09T02:44:26,253 Running setup.py (path:/tmp/pip-wheel-w3bq3vzx/molmod_3971519dc0854ea486673255a15302b7/setup.py) egg_info for package molmod 2025-09-09T02:44:26,253 Created temporary directory: /tmp/pip-pip-egg-info-km9_jfzk 2025-09-09T02:44:26,253 Preparing metadata (setup.py): started 2025-09-09T02:44:26,254 Running command python setup.py egg_info 2025-09-09T02:44:27,193 fatal: not a git repository (or any parent up to mount point /) 2025-09-09T02:44:27,194 Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). 2025-09-09T02:44:27,308 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-09T02:44:27,308 !! 2025-09-09T02:44:27,308 ******************************************************************************** 2025-09-09T02:44:27,309 Requirements should be satisfied by a PEP 517 installer. 2025-09-09T02:44:27,309 If you are using pip, you can try `pip install --use-pep517`. 2025-09-09T02:44:27,309 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-09T02:44:27,309 or your builds will no longer be supported. 2025-09-09T02:44:27,309 ******************************************************************************** 2025-09-09T02:44:27,309 !! 2025-09-09T02:44:27,309 dist.fetch_build_eggs(dist.setup_requires) 2025-09-09T02:44:27,558 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T02:44:27,558 !! 2025-09-09T02:44:27,558 ******************************************************************************** 2025-09-09T02:44:27,558 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T02:44:27,559 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-09T02:44:27,559 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T02:44:27,559 ******************************************************************************** 2025-09-09T02:44:27,559 !! 2025-09-09T02:44:27,559 self._finalize_license_expression() 2025-09-09T02:44:27,625 Trying to get the version from git describe 2025-09-09T02:44:27,625 Trying to get the version from {} /tmp/pip-wheel-w3bq3vzx/molmod_3971519dc0854ea486673255a15302b7/molmod/version.py 2025-09-09T02:44:27,625 Version according to /tmp/pip-wheel-w3bq3vzx/molmod_3971519dc0854ea486673255a15302b7/molmod/version.py: 1.4.8 2025-09-09T02:44:27,625 running egg_info 2025-09-09T02:44:27,691 creating /tmp/pip-pip-egg-info-km9_jfzk/molmod.egg-info 2025-09-09T02:44:27,691 writing /tmp/pip-pip-egg-info-km9_jfzk/molmod.egg-info/PKG-INFO 2025-09-09T02:44:27,692 writing dependency_links to /tmp/pip-pip-egg-info-km9_jfzk/molmod.egg-info/dependency_links.txt 2025-09-09T02:44:27,693 writing requirements to /tmp/pip-pip-egg-info-km9_jfzk/molmod.egg-info/requires.txt 2025-09-09T02:44:27,693 writing top-level names to /tmp/pip-pip-egg-info-km9_jfzk/molmod.egg-info/top_level.txt 2025-09-09T02:44:27,694 writing manifest file '/tmp/pip-pip-egg-info-km9_jfzk/molmod.egg-info/SOURCES.txt' 2025-09-09T02:44:27,904 reading manifest file '/tmp/pip-pip-egg-info-km9_jfzk/molmod.egg-info/SOURCES.txt' 2025-09-09T02:44:27,905 reading manifest template 'MANIFEST.in' 2025-09-09T02:44:27,941 warning: no previously-included files matching 'ext.c' found under directory 'molmod' 2025-09-09T02:44:27,952 adding license file 'LICENSE.txt' 2025-09-09T02:44:27,960 writing manifest file '/tmp/pip-pip-egg-info-km9_jfzk/molmod.egg-info/SOURCES.txt' 2025-09-09T02:44:28,098 Preparing metadata (setup.py): finished with status 'done' 2025-09-09T02:44:28,103 Source in /tmp/pip-wheel-w3bq3vzx/molmod_3971519dc0854ea486673255a15302b7 has version 1.4.8, which satisfies requirement molmod==1.4.8 from https://files.pythonhosted.org/packages/23/77/814f9302b6df72ef3aa6944edd8b9b0f5e983aed07027828a4e0666c4ef3/molmod-1.4.8.tar.gz 2025-09-09T02:44:28,103 Removed molmod==1.4.8 from https://files.pythonhosted.org/packages/23/77/814f9302b6df72ef3aa6944edd8b9b0f5e983aed07027828a4e0666c4ef3/molmod-1.4.8.tar.gz from build tracker '/tmp/pip-build-tracker-l9ea6b2z' 2025-09-09T02:44:28,107 Created temporary directory: /tmp/pip-unpack-vutaoh2e 2025-09-09T02:44:28,107 Created temporary directory: /tmp/pip-unpack-ocbjbiq5 2025-09-09T02:44:28,108 Building wheels for collected packages: molmod 2025-09-09T02:44:28,109 Created temporary directory: /tmp/pip-wheel-xryymgox 2025-09-09T02:44:28,110 DEPRECATION: Building 'molmod' 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 'molmod'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-09T02:44:28,111 Building wheel for molmod (setup.py): started 2025-09-09T02:44:28,112 Destination directory: /tmp/pip-wheel-xryymgox 2025-09-09T02:44:28,112 Running command python setup.py bdist_wheel 2025-09-09T02:44:29,036 Trying to get the version from git describe 2025-09-09T02:44:29,042 fatal: not a git repository (or any parent up to mount point /) 2025-09-09T02:44:29,042 Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). 2025-09-09T02:44:29,043 Trying to get the version from {} /tmp/pip-wheel-w3bq3vzx/molmod_3971519dc0854ea486673255a15302b7/molmod/version.py 2025-09-09T02:44:29,043 Version according to /tmp/pip-wheel-w3bq3vzx/molmod_3971519dc0854ea486673255a15302b7/molmod/version.py: 1.4.8 2025-09-09T02:44:29,160 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-09T02:44:29,160 !! 2025-09-09T02:44:29,160 ******************************************************************************** 2025-09-09T02:44:29,160 Requirements should be satisfied by a PEP 517 installer. 2025-09-09T02:44:29,160 If you are using pip, you can try `pip install --use-pep517`. 2025-09-09T02:44:29,161 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-09T02:44:29,161 or your builds will no longer be supported. 2025-09-09T02:44:29,161 ******************************************************************************** 2025-09-09T02:44:29,161 !! 2025-09-09T02:44:29,161 dist.fetch_build_eggs(dist.setup_requires) 2025-09-09T02:44:29,414 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T02:44:29,414 !! 2025-09-09T02:44:29,414 ******************************************************************************** 2025-09-09T02:44:29,414 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T02:44:29,414 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-09T02:44:29,415 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T02:44:29,415 ******************************************************************************** 2025-09-09T02:44:29,415 !! 2025-09-09T02:44:29,415 self._finalize_license_expression() 2025-09-09T02:44:29,425 running bdist_wheel 2025-09-09T02:44:29,701 running build 2025-09-09T02:44:29,701 running build_py 2025-09-09T02:44:29,772 creating build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,772 copying molmod/log.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,773 copying molmod/bonds.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,774 copying molmod/unit_cells.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,774 copying molmod/__init__.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,775 copying molmod/isotopes.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,775 copying molmod/version.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,776 copying molmod/similarity.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,776 copying molmod/binning.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,777 copying molmod/utils.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,777 copying molmod/vectors.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,778 copying molmod/ic.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,778 copying molmod/graphs.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,779 copying molmod/transformations.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,780 copying molmod/symmetry.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,780 copying molmod/periodic.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,781 copying molmod/constants.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,781 copying molmod/minimizer.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,782 copying molmod/molecular_graphs.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,783 copying molmod/units.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,783 copying molmod/randomize.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,784 copying molmod/clusters.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,784 copying molmod/pairff.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,785 copying molmod/toyff.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,785 copying molmod/quaternions.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,786 copying molmod/molecules.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,787 copying molmod/zmatrix.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:29,788 creating build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,788 copying molmod/test/test_randomize.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,789 copying molmod/test/test_molecules.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,789 copying molmod/test/test_utils.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,790 copying molmod/test/test_transformations.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,790 copying molmod/test/test_log.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,791 copying molmod/test/__init__.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,791 copying molmod/test/test_quaternions.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,792 copying molmod/test/test_unit_cells.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,792 copying molmod/test/test_binning.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,793 copying molmod/test/test_minimizer.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,793 copying molmod/test/test_toyff.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,794 copying molmod/test/test_molecular_graphs.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,794 copying molmod/test/test_pairff.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,795 copying molmod/test/common.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,796 copying molmod/test/test_zmatrix.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,796 copying molmod/test/test_clusters.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,797 copying molmod/test/test_graphs.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,797 copying molmod/test/test_vectors.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,798 copying molmod/test/test_data.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,798 copying molmod/test/test_similarity.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,799 copying molmod/test/test_ic.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,799 copying molmod/test/test_symmetry.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,800 copying molmod/test/test_examples.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,800 copying molmod/test/test_units.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-09T02:44:29,801 creating build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,802 copying molmod/io/pdb.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,802 copying molmod/io/__init__.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,803 copying molmod/io/cpmd.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,803 copying molmod/io/gamess.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,804 copying molmod/io/lammps.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,804 copying molmod/io/chk.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,805 copying molmod/io/cp2k.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,805 copying molmod/io/fchk.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,806 copying molmod/io/psf.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,806 copying molmod/io/gromacs.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,807 copying molmod/io/number_state.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,807 copying molmod/io/atrj.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,808 copying molmod/io/sdf.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,808 copying molmod/io/common.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,809 copying molmod/io/dlpoly.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,809 copying molmod/io/xyz.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,810 copying molmod/io/cml.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,810 copying molmod/io/crystal.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,811 copying molmod/io/cube.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-09T02:44:29,812 creating build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,812 copying molmod/io/test/test_cml.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,813 copying molmod/io/test/test_fchk.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,813 copying molmod/io/test/test_crystal.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,814 copying molmod/io/test/test_xyz.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,814 copying molmod/io/test/test_sdf.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,815 copying molmod/io/test/__init__.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,815 copying molmod/io/test/test_number_state.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,816 copying molmod/io/test/test_pdb.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,816 copying molmod/io/test/test_lammps.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,817 copying molmod/io/test/test_chk.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,817 copying molmod/io/test/test_cube.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,818 copying molmod/io/test/test_cpmd.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,818 copying molmod/io/test/test_gamess.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,819 copying molmod/io/test/test_dlpoly.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,819 copying molmod/io/test/test_gromacs.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,820 copying molmod/io/test/test_cp2k.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,821 copying molmod/io/test/test_atrj.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,821 copying molmod/io/test/test_psf.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-09T02:44:29,821 running egg_info 2025-09-09T02:44:29,888 writing molmod.egg-info/PKG-INFO 2025-09-09T02:44:29,889 writing dependency_links to molmod.egg-info/dependency_links.txt 2025-09-09T02:44:29,890 writing requirements to molmod.egg-info/requires.txt 2025-09-09T02:44:29,890 writing top-level names to molmod.egg-info/top_level.txt 2025-09-09T02:44:29,964 reading manifest file 'molmod.egg-info/SOURCES.txt' 2025-09-09T02:44:29,977 reading manifest template 'MANIFEST.in' 2025-09-09T02:44:30,014 warning: no previously-included files matching 'ext.c' found under directory 'molmod' 2025-09-09T02:44:30,024 adding license file 'LICENSE.txt' 2025-09-09T02:44:30,035 writing manifest file 'molmod.egg-info/SOURCES.txt' 2025-09-09T02:44:30,037 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'molmod.data' is absent from the `packages` configuration. 2025-09-09T02:44:30,037 !! 2025-09-09T02:44:30,038 ******************************************************************************** 2025-09-09T02:44:30,038 ############################ 2025-09-09T02:44:30,038 # Package would be ignored # 2025-09-09T02:44:30,038 ############################ 2025-09-09T02:44:30,038 Python recognizes 'molmod.data' as an importable package[^1], 2025-09-09T02:44:30,038 but it is absent from setuptools' `packages` configuration. 2025-09-09T02:44:30,038 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-09T02:44:30,038 package, please make sure that 'molmod.data' is explicitly added 2025-09-09T02:44:30,038 to the `packages` configuration field. 2025-09-09T02:44:30,039 Alternatively, you can also rely on setuptools' discovery methods 2025-09-09T02:44:30,039 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-09T02:44:30,039 instead of `find_packages(...)`/`find:`). 2025-09-09T02:44:30,039 You can read more about "package discovery" on setuptools documentation page: 2025-09-09T02:44:30,039 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-09T02:44:30,039 If you don't want 'molmod.data' to be distributed and are 2025-09-09T02:44:30,039 already explicitly excluding 'molmod.data' via 2025-09-09T02:44:30,039 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-09T02:44:30,039 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-09T02:44:30,040 combination with a more fine grained `package-data` configuration. 2025-09-09T02:44:30,040 You can read more about "package data files" on setuptools documentation page: 2025-09-09T02:44:30,040 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-09T02:44:30,040 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-09T02:44:30,040 even if it does not contain any `.py` files. 2025-09-09T02:44:30,040 On the other hand, currently there is no concept of package data 2025-09-09T02:44:30,040 directory, all directories are treated like packages. 2025-09-09T02:44:30,040 ******************************************************************************** 2025-09-09T02:44:30,041 !! 2025-09-09T02:44:30,041 check.warn(importable) 2025-09-09T02:44:30,041 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'molmod.data.test' is absent from the `packages` configuration. 2025-09-09T02:44:30,041 !! 2025-09-09T02:44:30,041 ******************************************************************************** 2025-09-09T02:44:30,041 ############################ 2025-09-09T02:44:30,041 # Package would be ignored # 2025-09-09T02:44:30,041 ############################ 2025-09-09T02:44:30,041 Python recognizes 'molmod.data.test' as an importable package[^1], 2025-09-09T02:44:30,042 but it is absent from setuptools' `packages` configuration. 2025-09-09T02:44:30,042 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-09T02:44:30,042 package, please make sure that 'molmod.data.test' is explicitly added 2025-09-09T02:44:30,042 to the `packages` configuration field. 2025-09-09T02:44:30,042 Alternatively, you can also rely on setuptools' discovery methods 2025-09-09T02:44:30,042 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-09T02:44:30,042 instead of `find_packages(...)`/`find:`). 2025-09-09T02:44:30,042 You can read more about "package discovery" on setuptools documentation page: 2025-09-09T02:44:30,043 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-09T02:44:30,043 If you don't want 'molmod.data.test' to be distributed and are 2025-09-09T02:44:30,043 already explicitly excluding 'molmod.data.test' via 2025-09-09T02:44:30,043 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-09T02:44:30,043 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-09T02:44:30,043 combination with a more fine grained `package-data` configuration. 2025-09-09T02:44:30,043 You can read more about "package data files" on setuptools documentation page: 2025-09-09T02:44:30,043 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-09T02:44:30,044 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-09T02:44:30,044 even if it does not contain any `.py` files. 2025-09-09T02:44:30,044 On the other hand, currently there is no concept of package data 2025-09-09T02:44:30,044 directory, all directories are treated like packages. 2025-09-09T02:44:30,044 ******************************************************************************** 2025-09-09T02:44:30,044 !! 2025-09-09T02:44:30,044 check.warn(importable) 2025-09-09T02:44:30,044 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'molmod.examples' is absent from the `packages` configuration. 2025-09-09T02:44:30,045 !! 2025-09-09T02:44:30,045 ******************************************************************************** 2025-09-09T02:44:30,045 ############################ 2025-09-09T02:44:30,045 # Package would be ignored # 2025-09-09T02:44:30,045 ############################ 2025-09-09T02:44:30,045 Python recognizes 'molmod.examples' as an importable package[^1], 2025-09-09T02:44:30,045 but it is absent from setuptools' `packages` configuration. 2025-09-09T02:44:30,045 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-09T02:44:30,045 package, please make sure that 'molmod.examples' is explicitly added 2025-09-09T02:44:30,045 to the `packages` configuration field. 2025-09-09T02:44:30,046 Alternatively, you can also rely on setuptools' discovery methods 2025-09-09T02:44:30,046 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-09T02:44:30,046 instead of `find_packages(...)`/`find:`). 2025-09-09T02:44:30,046 You can read more about "package discovery" on setuptools documentation page: 2025-09-09T02:44:30,046 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-09T02:44:30,046 If you don't want 'molmod.examples' to be distributed and are 2025-09-09T02:44:30,046 already explicitly excluding 'molmod.examples' via 2025-09-09T02:44:30,046 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-09T02:44:30,047 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-09T02:44:30,047 combination with a more fine grained `package-data` configuration. 2025-09-09T02:44:30,047 You can read more about "package data files" on setuptools documentation page: 2025-09-09T02:44:30,047 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-09T02:44:30,047 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-09T02:44:30,047 even if it does not contain any `.py` files. 2025-09-09T02:44:30,047 On the other hand, currently there is no concept of package data 2025-09-09T02:44:30,047 directory, all directories are treated like packages. 2025-09-09T02:44:30,048 ******************************************************************************** 2025-09-09T02:44:30,048 !! 2025-09-09T02:44:30,048 check.warn(importable) 2025-09-09T02:44:30,050 copying molmod/common.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,051 copying molmod/common.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,051 copying molmod/ext.pyx -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,052 copying molmod/ff.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,052 copying molmod/ff.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,053 copying molmod/ff.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,053 copying molmod/graphs.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,054 copying molmod/graphs.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,054 copying molmod/graphs.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,055 copying molmod/molecules.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,055 copying molmod/molecules.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,056 copying molmod/molecules.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,056 copying molmod/similarity.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,057 copying molmod/similarity.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,057 copying molmod/similarity.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,058 copying molmod/unit_cells.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,058 copying molmod/unit_cells.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,059 copying molmod/unit_cells.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-09T02:44:30,059 creating build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-09T02:44:30,060 copying molmod/data/bonds.csv -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-09T02:44:30,060 copying molmod/data/bonds.ods -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-09T02:44:30,061 copying molmod/data/mass.mas03 -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-09T02:44:30,063 copying molmod/data/nubtab03.asc -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-09T02:44:30,067 copying molmod/data/periodic.csv -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-09T02:44:30,067 copying molmod/data/periodic.ods -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-09T02:44:30,068 copying molmod/data/toyff_angles.txt -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-09T02:44:30,069 creating build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,069 copying molmod/data/test/1LJL_Cys10.cml -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,070 copying molmod/data/test/1TOH.b3lyp.fchk -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,072 copying molmod/data/test/1TOH.b3lyp.trim.fchk -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,073 copying molmod/data/test/5ringOH.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,073 copying molmod/data/test/CID_22898828.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,074 copying molmod/data/test/PCGamess_PUNCH -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,078 copying molmod/data/test/SID_31646545.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,078 copying molmod/data/test/SID_31646548.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,079 copying molmod/data/test/SID_40363570.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,079 copying molmod/data/test/SID_40363571.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,080 copying molmod/data/test/SID_41893278.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,080 copying molmod/data/test/SID_41893280.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,081 copying molmod/data/test/SID_54258192.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,081 copying molmod/data/test/SID_55127927.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,082 copying molmod/data/test/SID_55488598.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,082 copying molmod/data/test/SID_56274343.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,083 copying molmod/data/test/TRAJECTORY_H2_CPMD -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,083 copying molmod/data/test/alanine.cube -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,084 copying molmod/data/test/argon.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,085 copying molmod/data/test/bartek.atrj -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,086 copying molmod/data/test/benzene.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,087 copying molmod/data/test/butane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,088 copying molmod/data/test/caplayer.cml -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,088 copying molmod/data/test/crystal_api.out -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,090 copying molmod/data/test/cyclopentane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,091 copying molmod/data/test/dinitrogen.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,091 copying molmod/data/test/dlpoly_HISTORY -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,092 copying molmod/data/test/dlpoly_HISTORY_an2 -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,092 copying molmod/data/test/dlpoly_OUTPUT -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,093 copying molmod/data/test/dopamine.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,094 copying molmod/data/test/ethane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,094 copying molmod/data/test/ethene.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,095 copying molmod/data/test/ethene_ethyl_trans.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,095 copying molmod/data/test/example.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,096 copying molmod/data/test/formol.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,096 copying molmod/data/test/funny.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,097 copying molmod/data/test/h3zrosihohosioh3.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,097 copying molmod/data/test/il2.pdb -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,099 copying molmod/data/test/lammps_dump.txt -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,099 copying molmod/data/test/lau.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,100 copying molmod/data/test/octane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,100 copying molmod/data/test/oh3siozroh3.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,101 copying molmod/data/test/opt_5ring10T.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,101 copying molmod/data/test/opt_5ring12T.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,102 copying molmod/data/test/opt_6_6ring.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,102 copying molmod/data/test/opt_6ring.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,103 copying molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,103 copying molmod/data/test/pentapeptide.psf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,104 copying molmod/data/test/precursor.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,104 copying molmod/data/test/probes.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,105 copying molmod/data/test/tea.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,105 copying molmod/data/test/tetra.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,106 copying molmod/data/test/thf.psf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,107 copying molmod/data/test/thf.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,108 copying molmod/data/test/thf_64.cell -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,108 copying molmod/data/test/thf_single.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,109 copying molmod/data/test/tpa.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,109 copying molmod/data/test/water.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,110 copying molmod/data/test/water2.gro -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,110 copying molmod/data/test/water_md.inp -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,111 copying molmod/data/test/zr4o8-3.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-09T02:44:30,111 creating build/lib.linux-armv7l-cpython-313/molmod/examples/000_units 2025-09-09T02:44:30,112 copying molmod/examples/000_units/a_reaction.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/000_units 2025-09-09T02:44:30,112 copying molmod/examples/000_units/b_chbond.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/000_units 2025-09-09T02:44:30,113 copying molmod/examples/000_units/c_h2rot.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/000_units 2025-09-09T02:44:30,113 creating build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-09T02:44:30,113 copying molmod/examples/001_molecules/a_convert.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-09T02:44:30,114 copying molmod/examples/001_molecules/b_com.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-09T02:44:30,114 copying molmod/examples/001_molecules/c_carbon.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-09T02:44:30,115 copying molmod/examples/001_molecules/d_size.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-09T02:44:30,115 copying molmod/examples/001_molecules/e_shape.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-09T02:44:30,116 copying molmod/examples/001_molecules/ibuprofen.sdf -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-09T02:44:30,117 creating build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-09T02:44:30,117 copying molmod/examples/002_graphs/a_graphs.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-09T02:44:30,117 copying molmod/examples/002_graphs/b_neighbors.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-09T02:44:30,118 copying molmod/examples/002_graphs/c_distances.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-09T02:44:30,118 copying molmod/examples/002_graphs/caffeine.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-09T02:44:30,119 copying molmod/examples/002_graphs/d_symmetries.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-09T02:44:30,119 copying molmod/examples/002_graphs/ethanol.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-09T02:44:30,120 creating build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-09T02:44:30,120 copying molmod/examples/003_internal_coordinates/a_bond_length.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-09T02:44:30,121 copying molmod/examples/003_internal_coordinates/b_bending_angles.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-09T02:44:30,121 copying molmod/examples/003_internal_coordinates/c_ff_hessian.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-09T02:44:30,122 copying molmod/examples/003_internal_coordinates/d_dft_hessian.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-09T02:44:30,122 copying molmod/examples/003_internal_coordinates/dopamine.fchk -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-09T02:44:30,123 copying molmod/examples/003_internal_coordinates/dopamine.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-09T02:44:30,124 copying molmod/examples/003_internal_coordinates/propane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-09T02:44:30,124 creating build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-09T02:44:30,124 copying molmod/examples/004_patterns/a_propane_types.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-09T02:44:30,125 copying molmod/examples/004_patterns/b_dopamine_types.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-09T02:44:30,126 copying molmod/examples/004_patterns/dopamine.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-09T02:44:30,126 copying molmod/examples/004_patterns/mfi_fragment.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-09T02:44:30,127 copying molmod/examples/004_patterns/propane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-09T02:44:30,130 running build_ext 2025-09-09T02:44:30,566 Compiling molmod/ext.pyx because it changed. 2025-09-09T02:44:30,566 [1/1] Cythonizing molmod/ext.pyx 2025-09-09T02:44:32,080 Error compiling Cython file: 2025-09-09T02:44:32,080 ------------------------------------------------------------ 2025-09-09T02:44:32,080 ... 2025-09-09T02:44:32,081 import numpy as np 2025-09-09T02:44:32,081 cimport numpy as np 2025-09-09T02:44:32,081 cimport ff 2025-09-09T02:44:32,081 ^ 2025-09-09T02:44:32,081 ------------------------------------------------------------ 2025-09-09T02:44:32,081 molmod/ext.pyx:32:8: 'ff.pxd' not found 2025-09-09T02:44:32,112 Error compiling Cython file: 2025-09-09T02:44:32,112 ------------------------------------------------------------ 2025-09-09T02:44:32,112 ... 2025-09-09T02:44:32,112 import numpy as np 2025-09-09T02:44:32,112 cimport numpy as np 2025-09-09T02:44:32,113 cimport ff 2025-09-09T02:44:32,113 cimport graphs 2025-09-09T02:44:32,113 ^ 2025-09-09T02:44:32,113 ------------------------------------------------------------ 2025-09-09T02:44:32,113 molmod/ext.pyx:33:8: 'graphs.pxd' not found 2025-09-09T02:44:32,143 Error compiling Cython file: 2025-09-09T02:44:32,143 ------------------------------------------------------------ 2025-09-09T02:44:32,143 ... 2025-09-09T02:44:32,143 import numpy as np 2025-09-09T02:44:32,143 cimport numpy as np 2025-09-09T02:44:32,144 cimport ff 2025-09-09T02:44:32,144 cimport graphs 2025-09-09T02:44:32,144 cimport molecules 2025-09-09T02:44:32,144 ^ 2025-09-09T02:44:32,144 ------------------------------------------------------------ 2025-09-09T02:44:32,144 molmod/ext.pyx:34:8: 'molecules.pxd' not found 2025-09-09T02:44:32,175 Error compiling Cython file: 2025-09-09T02:44:32,175 ------------------------------------------------------------ 2025-09-09T02:44:32,175 ... 2025-09-09T02:44:32,175 cimport numpy as np 2025-09-09T02:44:32,175 cimport ff 2025-09-09T02:44:32,175 cimport graphs 2025-09-09T02:44:32,175 cimport molecules 2025-09-09T02:44:32,176 cimport similarity 2025-09-09T02:44:32,176 ^ 2025-09-09T02:44:32,176 ------------------------------------------------------------ 2025-09-09T02:44:32,176 molmod/ext.pyx:35:8: 'similarity.pxd' not found 2025-09-09T02:44:32,206 Error compiling Cython file: 2025-09-09T02:44:32,206 ------------------------------------------------------------ 2025-09-09T02:44:32,206 ... 2025-09-09T02:44:32,206 cimport ff 2025-09-09T02:44:32,206 cimport graphs 2025-09-09T02:44:32,206 cimport molecules 2025-09-09T02:44:32,206 cimport similarity 2025-09-09T02:44:32,207 cimport unit_cells 2025-09-09T02:44:32,207 ^ 2025-09-09T02:44:32,207 ------------------------------------------------------------ 2025-09-09T02:44:32,207 molmod/ext.pyx:36:8: 'unit_cells.pxd' not found 2025-09-09T02:44:32,721 Error compiling Cython file: 2025-09-09T02:44:32,721 ------------------------------------------------------------ 2025-09-09T02:44:32,722 ... 2025-09-09T02:44:32,722 if matrix is not None and matrix.shape[0] != 3 and matrix.shape[1] != 3: 2025-09-09T02:44:32,722 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-09T02:44:32,722 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-09T02:44:32,722 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-09T02:44:32,722 if matrix is None: 2025-09-09T02:44:32,722 return ff.ff_dm_quad( 2025-09-09T02:44:32,722 ^ 2025-09-09T02:44:32,722 ------------------------------------------------------------ 2025-09-09T02:44:32,722 molmod/ext.pyx:62:17: cimported module has no attribute 'ff_dm_quad' 2025-09-09T02:44:32,723 Error compiling Cython file: 2025-09-09T02:44:32,723 ------------------------------------------------------------ 2025-09-09T02:44:32,723 ... 2025-09-09T02:44:32,723 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-09T02:44:32,723 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-09T02:44:32,723 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-09T02:44:32,723 if matrix is None: 2025-09-09T02:44:32,723 return ff.ff_dm_quad( 2025-09-09T02:44:32,723 natom, long(matrix is not None), &cor[0, 0], &dm0[0, 0], &dmk[0, 0], amp, 2025-09-09T02:44:32,723 ^ 2025-09-09T02:44:32,724 ------------------------------------------------------------ 2025-09-09T02:44:32,724 molmod/ext.pyx:63:19: undeclared name not builtin: long 2025-09-09T02:44:32,724 Error compiling Cython file: 2025-09-09T02:44:32,724 ------------------------------------------------------------ 2025-09-09T02:44:32,724 ... 2025-09-09T02:44:32,724 if matrix is None: 2025-09-09T02:44:32,724 return ff.ff_dm_quad( 2025-09-09T02:44:32,724 natom, long(matrix is not None), &cor[0, 0], &dm0[0, 0], &dmk[0, 0], amp, 2025-09-09T02:44:32,725 &gradient[0, 0], NULL, NULL) 2025-09-09T02:44:32,725 else: 2025-09-09T02:44:32,725 return ff.ff_dm_quad( 2025-09-09T02:44:32,725 ^ 2025-09-09T02:44:32,725 ------------------------------------------------------------ 2025-09-09T02:44:32,725 molmod/ext.pyx:66:17: cimported module has no attribute 'ff_dm_quad' 2025-09-09T02:44:32,731 Error compiling Cython file: 2025-09-09T02:44:32,731 ------------------------------------------------------------ 2025-09-09T02:44:32,732 ... 2025-09-09T02:44:32,732 if matrix is not None and matrix.shape[0] != 3 and matrix.shape[1] != 3: 2025-09-09T02:44:32,732 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-09T02:44:32,732 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-09T02:44:32,732 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-09T02:44:32,732 if matrix is None: 2025-09-09T02:44:32,732 return ff.ff_dm_reci( 2025-09-09T02:44:32,732 ^ 2025-09-09T02:44:32,732 ------------------------------------------------------------ 2025-09-09T02:44:32,732 molmod/ext.pyx:90:17: cimported module has no attribute 'ff_dm_reci' 2025-09-09T02:44:32,733 Error compiling Cython file: 2025-09-09T02:44:32,733 ------------------------------------------------------------ 2025-09-09T02:44:32,733 ... 2025-09-09T02:44:32,733 if matrix is None: 2025-09-09T02:44:32,733 return ff.ff_dm_reci( 2025-09-09T02:44:32,733 natom, long(matrix is not None), &cor[0, 0], &radii[0], &dm0[0, 0], amp, 2025-09-09T02:44:32,733 &gradient[0, 0], NULL, NULL) 2025-09-09T02:44:32,733 else: 2025-09-09T02:44:32,733 return ff.ff_dm_reci( 2025-09-09T02:44:32,733 ^ 2025-09-09T02:44:32,733 ------------------------------------------------------------ 2025-09-09T02:44:32,734 molmod/ext.pyx:94:17: cimported module has no attribute 'ff_dm_reci' 2025-09-09T02:44:32,753 Error compiling Cython file: 2025-09-09T02:44:32,753 ------------------------------------------------------------ 2025-09-09T02:44:32,753 ... 2025-09-09T02:44:32,753 if matrix is not None and matrix.shape[0] != 3 and matrix.shape[1] != 3: 2025-09-09T02:44:32,753 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-09T02:44:32,753 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-09T02:44:32,753 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-09T02:44:32,753 if matrix is None: 2025-09-09T02:44:32,753 return ff.ff_bond_quad( 2025-09-09T02:44:32,753 ^ 2025-09-09T02:44:32,753 ------------------------------------------------------------ 2025-09-09T02:44:32,754 molmod/ext.pyx:121:17: cimported module has no attribute 'ff_bond_quad' 2025-09-09T02:44:32,754 Error compiling Cython file: 2025-09-09T02:44:32,754 ------------------------------------------------------------ 2025-09-09T02:44:32,754 ... 2025-09-09T02:44:32,754 if matrix is None: 2025-09-09T02:44:32,754 return ff.ff_bond_quad( 2025-09-09T02:44:32,754 npair, long(matrix is not None), &cor[0, 0], &pairs[0, 0], &lengths[0], amp, 2025-09-09T02:44:32,754 &gradient[0, 0], NULL, NULL) 2025-09-09T02:44:32,754 else: 2025-09-09T02:44:32,755 return ff.ff_bond_quad( 2025-09-09T02:44:32,755 ^ 2025-09-09T02:44:32,755 ------------------------------------------------------------ 2025-09-09T02:44:32,755 molmod/ext.pyx:125:17: cimported module has no attribute 'ff_bond_quad' 2025-09-09T02:44:32,761 Error compiling Cython file: 2025-09-09T02:44:32,761 ------------------------------------------------------------ 2025-09-09T02:44:32,761 ... 2025-09-09T02:44:32,761 if matrix is not None and matrix.shape[0] != 3 and matrix.shape[1] != 3: 2025-09-09T02:44:32,761 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-09T02:44:32,761 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-09T02:44:32,761 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-09T02:44:32,761 if matrix is None: 2025-09-09T02:44:32,762 return ff.ff_bond_hyper( 2025-09-09T02:44:32,762 ^ 2025-09-09T02:44:32,762 ------------------------------------------------------------ 2025-09-09T02:44:32,762 molmod/ext.pyx:152:17: cimported module has no attribute 'ff_bond_hyper' 2025-09-09T02:44:32,762 Error compiling Cython file: 2025-09-09T02:44:32,762 ------------------------------------------------------------ 2025-09-09T02:44:32,762 ... 2025-09-09T02:44:32,762 if matrix is None: 2025-09-09T02:44:32,762 return ff.ff_bond_hyper( 2025-09-09T02:44:32,763 npair, long(matrix is not None), &cor[0, 0], &pairs[0, 0], &lengths[0], scale, 2025-09-09T02:44:32,763 amp, &gradient[0, 0], NULL, NULL) 2025-09-09T02:44:32,763 else: 2025-09-09T02:44:32,763 return ff.ff_bond_hyper( 2025-09-09T02:44:32,763 ^ 2025-09-09T02:44:32,763 ------------------------------------------------------------ 2025-09-09T02:44:32,763 molmod/ext.pyx:156:17: cimported module has no attribute 'ff_bond_hyper' 2025-09-09T02:44:32,765 Error compiling Cython file: 2025-09-09T02:44:32,765 ------------------------------------------------------------ 2025-09-09T02:44:32,765 ... 2025-09-09T02:44:32,765 def graphs_floyd_warshall(long[:, ::1] dm): 2025-09-09T02:44:32,766 cdef size_t nvertex = dm.shape[0] 2025-09-09T02:44:32,766 if dm.shape[1] != nvertex: 2025-09-09T02:44:32,766 raise TypeError('dm must be a square matrix.') 2025-09-09T02:44:32,766 graphs.graphs_floyd_warshall(nvertex, &dm[0, 0]) 2025-09-09T02:44:32,766 ^ 2025-09-09T02:44:32,766 ------------------------------------------------------------ 2025-09-09T02:44:32,766 molmod/ext.pyx:170:10: cimported module has no attribute 'graphs_floyd_warshall' 2025-09-09T02:44:32,769 Error compiling Cython file: 2025-09-09T02:44:32,769 ------------------------------------------------------------ 2025-09-09T02:44:32,770 ... 2025-09-09T02:44:32,770 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-09T02:44:32,770 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-09T02:44:32,770 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-09T02:44:32,770 cdef np.ndarray[double, ndim=2] dm = np.zeros((natom, natom), float) 2025-09-09T02:44:32,770 if matrix is None: 2025-09-09T02:44:32,770 molecules.molecules_distance_matrix( 2025-09-09T02:44:32,770 ^ 2025-09-09T02:44:32,770 ------------------------------------------------------------ 2025-09-09T02:44:32,770 molmod/ext.pyx:190:17: cimported module has no attribute 'molecules_distance_matrix' 2025-09-09T02:44:32,771 Error compiling Cython file: 2025-09-09T02:44:32,771 ------------------------------------------------------------ 2025-09-09T02:44:32,771 ... 2025-09-09T02:44:32,771 cdef np.ndarray[double, ndim=2] dm = np.zeros((natom, natom), float) 2025-09-09T02:44:32,771 if matrix is None: 2025-09-09T02:44:32,771 molecules.molecules_distance_matrix( 2025-09-09T02:44:32,771 natom, &cor[0, 0], long(matrix is not None), NULL, NULL, &dm[0, 0]) 2025-09-09T02:44:32,771 else: 2025-09-09T02:44:32,771 molecules.molecules_distance_matrix( 2025-09-09T02:44:32,771 ^ 2025-09-09T02:44:32,772 ------------------------------------------------------------ 2025-09-09T02:44:32,772 molmod/ext.pyx:193:17: cimported module has no attribute 'molecules_distance_matrix' 2025-09-09T02:44:32,774 Error compiling Cython file: 2025-09-09T02:44:32,774 ------------------------------------------------------------ 2025-09-09T02:44:32,774 ... 2025-09-09T02:44:32,774 def similarity_table_labels(const long[::1] labels not None): 2025-09-09T02:44:32,774 cdef size_t n = labels.shape[0] 2025-09-09T02:44:32,774 cdef np.ndarray[long, ndim=2] labels_table = np.zeros(((n*(n-1))//2, 2), dtype=int) 2025-09-09T02:44:32,775 similarity.similarity_table_labels(n, &labels[0], &labels_table[0, 0]) 2025-09-09T02:44:32,775 ^ 2025-09-09T02:44:32,775 ------------------------------------------------------------ 2025-09-09T02:44:32,775 molmod/ext.pyx:207:14: cimported module has no attribute 'similarity_table_labels' 2025-09-09T02:44:32,776 Error compiling Cython file: 2025-09-09T02:44:32,776 ------------------------------------------------------------ 2025-09-09T02:44:32,777 ... 2025-09-09T02:44:32,777 def similarity_table_distances(const double[:, ::1] distance_matrix not None): 2025-09-09T02:44:32,777 cdef size_t n = distance_matrix.shape[0] 2025-09-09T02:44:32,777 if distance_matrix.shape[1] != n: 2025-09-09T02:44:32,777 raise TypeError('distance_matrix must be sqaure') 2025-09-09T02:44:32,777 cdef np.ndarray[double] distances_table = np.zeros(((n*(n-1))//2), dtype=float) 2025-09-09T02:44:32,777 similarity.similarity_table_distances(n, &distance_matrix[0, 0], &distances_table[0]) 2025-09-09T02:44:32,777 ^ 2025-09-09T02:44:32,777 ------------------------------------------------------------ 2025-09-09T02:44:32,777 molmod/ext.pyx:216:14: cimported module has no attribute 'similarity_table_distances' 2025-09-09T02:44:32,781 Error compiling Cython file: 2025-09-09T02:44:32,781 ------------------------------------------------------------ 2025-09-09T02:44:32,781 ... 2025-09-09T02:44:32,781 raise TypeError('labels1 and distances1 must have the same numbers of rows.') 2025-09-09T02:44:32,781 if labels2.shape[1] != 2: 2025-09-09T02:44:32,781 raise TypeError('labels1 must have two columns.') 2025-09-09T02:44:32,781 if distances2.shape[0] != n2: 2025-09-09T02:44:32,781 raise TypeError('labels2 and distances2 must have the same numbers of rows.') 2025-09-09T02:44:32,781 return similarity.similarity_measure(n1, &labels1[0, 0], &distances1[0], 2025-09-09T02:44:32,781 ^ 2025-09-09T02:44:32,781 ------------------------------------------------------------ 2025-09-09T02:44:32,782 molmod/ext.pyx:233:21: cimported module has no attribute 'similarity_measure' 2025-09-09T02:44:32,785 Error compiling Cython file: 2025-09-09T02:44:32,785 ------------------------------------------------------------ 2025-09-09T02:44:32,785 ... 2025-09-09T02:44:32,785 raise ValueError('Radius must be positive.') 2025-09-09T02:44:32,785 if max_ranges.shape[0] != 3: 2025-09-09T02:44:32,786 raise TypeError('max_ranges must have shape (3, ).') 2025-09-09T02:44:32,786 if indexes.shape[1] != 3: 2025-09-09T02:44:32,786 raise TypeError('indexes must have three columns.') 2025-09-09T02:44:32,786 return unit_cells.unit_cell_get_radius_indexes(&matrix[0, 0], &reciprocal[0, 0], radius, 2025-09-09T02:44:32,786 ^ 2025-09-09T02:44:32,786 ------------------------------------------------------------ 2025-09-09T02:44:32,786 molmod/ext.pyx:257:21: cimported module has no attribute 'unit_cell_get_radius_indexes' 2025-09-09T02:44:33,633 Traceback (most recent call last): 2025-09-09T02:44:33,641 File "", line 2, in 2025-09-09T02:44:33,641 exec(compile(''' 2025-09-09T02:44:33,641 ~~~~^^^^^^^^^^^^ 2025-09-09T02:44:33,642 # This is -- a caller that pip uses to run setup.py 2025-09-09T02:44:33,642 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-09T02:44:33,642 ...<32 lines>... 2025-09-09T02:44:33,642 exec(compile(setup_py_code, filename, "exec")) 2025-09-09T02:44:33,642 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-09T02:44:33,642 ''' % ('/tmp/pip-wheel-w3bq3vzx/molmod_3971519dc0854ea486673255a15302b7/setup.py',), "", "exec")) 2025-09-09T02:44:33,642 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-09T02:44:33,642 File "", line 35, in 2025-09-09T02:44:33,643 File "/tmp/pip-wheel-w3bq3vzx/molmod_3971519dc0854ea486673255a15302b7/setup.py", line 73, in 2025-09-09T02:44:33,643 setup( 2025-09-09T02:44:33,643 ~~~~~^ 2025-09-09T02:44:33,643 name='molmod', 2025-09-09T02:44:33,643 ^^^^^^^^^^^^^^ 2025-09-09T02:44:33,643 ...<31 lines>... 2025-09-09T02:44:33,643 ], 2025-09-09T02:44:33,643 ^^ 2025-09-09T02:44:33,643 ) 2025-09-09T02:44:33,643 ^ 2025-09-09T02:44:33,644 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-09T02:44:33,644 return distutils.core.setup(**attrs) 2025-09-09T02:44:33,644 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T02:44:33,644 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-09T02:44:33,644 return run_commands(dist) 2025-09-09T02:44:33,644 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-09T02:44:33,644 dist.run_commands() 2025-09-09T02:44:33,645 ~~~~~~~~~~~~~~~~~^^ 2025-09-09T02:44:33,645 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-09T02:44:33,645 self.run_command(cmd) 2025-09-09T02:44:33,645 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-09T02:44:33,645 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-09T02:44:33,645 super().run_command(command) 2025-09-09T02:44:33,645 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T02:44:33,645 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-09T02:44:33,645 cmd_obj.run() 2025-09-09T02:44:33,646 ~~~~~~~~~~~^^ 2025-09-09T02:44:33,646 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run 2025-09-09T02:44:33,646 self.run_command("build") 2025-09-09T02:44:33,646 ~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T02:44:33,646 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-09T02:44:33,646 self.distribution.run_command(command) 2025-09-09T02:44:33,646 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T02:44:33,646 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-09T02:44:33,646 super().run_command(command) 2025-09-09T02:44:33,647 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T02:44:33,647 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-09T02:44:33,647 cmd_obj.run() 2025-09-09T02:44:33,647 ~~~~~~~~~~~^^ 2025-09-09T02:44:33,647 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run 2025-09-09T02:44:33,647 self.run_command(cmd_name) 2025-09-09T02:44:33,647 ~~~~~~~~~~~~~~~~^^^^^^^^^^ 2025-09-09T02:44:33,647 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-09T02:44:33,648 self.distribution.run_command(command) 2025-09-09T02:44:33,648 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T02:44:33,648 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-09T02:44:33,648 super().run_command(command) 2025-09-09T02:44:33,648 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-09T02:44:33,648 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-09T02:44:33,648 cmd_obj.run() 2025-09-09T02:44:33,648 ~~~~~~~~~~~^^ 2025-09-09T02:44:33,648 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 368, in run 2025-09-09T02:44:33,649 self.build_extensions() 2025-09-09T02:44:33,649 ~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-09T02:44:33,649 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 484, in build_extensions 2025-09-09T02:44:33,649 self._build_extensions_serial() 2025-09-09T02:44:33,649 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-09T02:44:33,649 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 510, in _build_extensions_serial 2025-09-09T02:44:33,649 self.build_extension(ext) 2025-09-09T02:44:33,649 ~~~~~~~~~~~~~~~~~~~~^^^^^ 2025-09-09T02:44:33,649 File "/usr/local/lib/python3.13/dist-packages/Cython/Distutils/build_ext.py", line 131, in build_extension 2025-09-09T02:44:33,649 new_ext = cythonize( 2025-09-09T02:44:33,650 ~~~~~~~~~^ 2025-09-09T02:44:33,650 ext,force=self.force, quiet=self.verbose == 0, **options 2025-09-09T02:44:33,650 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-09T02:44:33,650 )[0] 2025-09-09T02:44:33,650 ^ 2025-09-09T02:44:33,650 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize 2025-09-09T02:44:33,650 cythonize_one(*args) 2025-09-09T02:44:33,650 ~~~~~~~~~~~~~^^^^^^^ 2025-09-09T02:44:33,650 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one 2025-09-09T02:44:33,651 raise CompileError(None, pyx_file) 2025-09-09T02:44:33,651 Cython.Compiler.Errors.CompileError: molmod/ext.pyx 2025-09-09T02:44:34,173 ERROR: python setup.py bdist_wheel exited with 1 2025-09-09T02:44:34,186 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-09T02:44:34,186 exec(compile('"'"''"'"''"'"' 2025-09-09T02:44:34,186 # This is -- a caller that pip uses to run setup.py 2025-09-09T02:44:34,186 # 2025-09-09T02:44:34,186 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-09T02:44:34,186 # import from `distutils.core` to work with newer packaging standards. 2025-09-09T02:44:34,186 # - It provides a clear error message when setuptools is not installed. 2025-09-09T02:44:34,186 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-09T02:44:34,186 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-09T02:44:34,186 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-09T02:44:34,186 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-09T02:44:34,186 import os, sys, tokenize, traceback 2025-09-09T02:44:34,186 2025-09-09T02:44:34,186 try: 2025-09-09T02:44:34,186 import setuptools 2025-09-09T02:44:34,186 except ImportError: 2025-09-09T02:44:34,186 print( 2025-09-09T02:44:34,186 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-09T02:44:34,186 "the build environment with exception:", 2025-09-09T02:44:34,186 file=sys.stderr, 2025-09-09T02:44:34,186 ) 2025-09-09T02:44:34,186 traceback.print_exc() 2025-09-09T02:44:34,186 sys.exit(1) 2025-09-09T02:44:34,186 2025-09-09T02:44:34,186 __file__ = %r 2025-09-09T02:44:34,186 sys.argv[0] = __file__ 2025-09-09T02:44:34,186 2025-09-09T02:44:34,186 if os.path.exists(__file__): 2025-09-09T02:44:34,186 filename = __file__ 2025-09-09T02:44:34,186 with tokenize.open(__file__) as f: 2025-09-09T02:44:34,186 setup_py_code = f.read() 2025-09-09T02:44:34,186 else: 2025-09-09T02:44:34,186 filename = "" 2025-09-09T02:44:34,186 setup_py_code = "from setuptools import setup; setup()" 2025-09-09T02:44:34,186 2025-09-09T02:44:34,186 exec(compile(setup_py_code, filename, "exec")) 2025-09-09T02:44:34,186 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-w3bq3vzx/molmod_3971519dc0854ea486673255a15302b7/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-xryymgox[/] 2025-09-09T02:44:34,186 [bold magenta]cwd[/]: /tmp/pip-wheel-w3bq3vzx/molmod_3971519dc0854ea486673255a15302b7/ 2025-09-09T02:44:34,186 Building wheel for molmod (setup.py): finished with status 'error' 2025-09-09T02:44:34,187 ERROR: Failed building wheel for molmod 2025-09-09T02:44:34,188 Running setup.py clean for molmod 2025-09-09T02:44:34,189 Running command python setup.py clean 2025-09-09T02:44:35,101 Trying to get the version from git describe 2025-09-09T02:44:35,107 fatal: not a git repository (or any parent up to mount point /) 2025-09-09T02:44:35,107 Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). 2025-09-09T02:44:35,108 Trying to get the version from {} /tmp/pip-wheel-w3bq3vzx/molmod_3971519dc0854ea486673255a15302b7/molmod/version.py 2025-09-09T02:44:35,108 Version according to /tmp/pip-wheel-w3bq3vzx/molmod_3971519dc0854ea486673255a15302b7/molmod/version.py: 1.4.8 2025-09-09T02:44:35,223 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-09T02:44:35,223 !! 2025-09-09T02:44:35,223 ******************************************************************************** 2025-09-09T02:44:35,223 Requirements should be satisfied by a PEP 517 installer. 2025-09-09T02:44:35,223 If you are using pip, you can try `pip install --use-pep517`. 2025-09-09T02:44:35,224 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-09T02:44:35,224 or your builds will no longer be supported. 2025-09-09T02:44:35,224 ******************************************************************************** 2025-09-09T02:44:35,224 !! 2025-09-09T02:44:35,224 dist.fetch_build_eggs(dist.setup_requires) 2025-09-09T02:44:35,474 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T02:44:35,475 !! 2025-09-09T02:44:35,475 ******************************************************************************** 2025-09-09T02:44:35,475 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T02:44:35,475 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-09T02:44:35,475 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T02:44:35,475 ******************************************************************************** 2025-09-09T02:44:35,476 !! 2025-09-09T02:44:35,476 self._finalize_license_expression() 2025-09-09T02:44:35,544 running clean 2025-09-09T02:44:35,681 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-09T02:44:35,689 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-09T02:44:35,689 'build/scripts-3.13' does not exist -- can't clean it 2025-09-09T02:44:35,689 removing 'build' 2025-09-09T02:44:35,826 Failed to build molmod 2025-09-09T02:44:35,827 ERROR: Failed to build one or more wheels 2025-09-09T02:44:35,828 Exception information: 2025-09-09T02:44:35,828 Traceback (most recent call last): 2025-09-09T02:44:35,828 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-09T02:44:35,828 status = _inner_run() 2025-09-09T02:44:35,828 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-09T02:44:35,828 return self.run(options, args) 2025-09-09T02:44:35,828 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-09T02:44:35,828 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-09T02:44:35,828 return func(self, options, args) 2025-09-09T02:44:35,828 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-09T02:44:35,828 raise CommandError("Failed to build one or more wheels") 2025-09-09T02:44:35,828 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-09T02:44:35,832 Removed build tracker: '/tmp/pip-build-tracker-l9ea6b2z'