2025-09-08T09:02:59,811 Created temporary directory: /tmp/pip-build-tracker-u1w8jfvd 2025-09-08T09:02:59,812 Initialized build tracking at /tmp/pip-build-tracker-u1w8jfvd 2025-09-08T09:02:59,812 Created build tracker: /tmp/pip-build-tracker-u1w8jfvd 2025-09-08T09:02:59,812 Entered build tracker: /tmp/pip-build-tracker-u1w8jfvd 2025-09-08T09:02:59,813 Created temporary directory: /tmp/pip-wheel-24zp1dgu 2025-09-08T09:02:59,816 Created temporary directory: /tmp/pip-ephem-wheel-cache-s0j25uym 2025-09-08T09:02:59,874 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T09:02:59,876 2 location(s) to search for versions of molmod: 2025-09-08T09:02:59,876 * https://pypi.org/simple/molmod/ 2025-09-08T09:02:59,876 * https://www.piwheels.org/simple/molmod/ 2025-09-08T09:02:59,876 Fetching project page and analyzing links: https://pypi.org/simple/molmod/ 2025-09-08T09:02:59,877 Getting page https://pypi.org/simple/molmod/ 2025-09-08T09:02:59,878 Found index url https://pypi.org/simple/ 2025-09-08T09:03:00,023 Fetched page https://pypi.org/simple/molmod/ as application/vnd.pypi.simple.v1+json 2025-09-08T09:03:00,028 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 2025-09-08T09:03:00,028 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 2025-09-08T09:03:00,028 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 2025-09-08T09:03:00,029 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 2025-09-08T09:03:00,029 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 2025-09-08T09:03:00,029 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 2025-09-08T09:03:00,030 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 2025-09-08T09:03:00,030 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 2025-09-08T09:03:00,030 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 2025-09-08T09:03:00,031 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 2025-09-08T09:03:00,031 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 2025-09-08T09:03:00,031 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 2025-09-08T09:03:00,031 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 2025-09-08T09:03:00,032 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 2025-09-08T09:03:00,032 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 2025-09-08T09:03:00,032 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 2025-09-08T09:03:00,033 Fetching project page and analyzing links: https://www.piwheels.org/simple/molmod/ 2025-09-08T09:03:00,033 Getting page https://www.piwheels.org/simple/molmod/ 2025-09-08T09:03:00,035 Found index url https://www.piwheels.org/simple/ 2025-09-08T09:03:00,127 Fetched page https://www.piwheels.org/simple/molmod/ as text/html 2025-09-08T09:03:00,144 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/) 2025-09-08T09:03:00,144 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/) 2025-09-08T09:03:00,144 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/) 2025-09-08T09:03:00,144 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/) 2025-09-08T09:03:00,145 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/) 2025-09-08T09:03:00,145 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/) 2025-09-08T09:03:00,145 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/) 2025-09-08T09:03:00,145 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/) 2025-09-08T09:03:00,145 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/) 2025-09-08T09:03:00,145 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/) 2025-09-08T09:03:00,145 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/) 2025-09-08T09:03:00,146 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/) 2025-09-08T09:03:00,146 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/) 2025-09-08T09:03:00,146 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/) 2025-09-08T09:03:00,146 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/) 2025-09-08T09:03:00,146 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/) 2025-09-08T09:03:00,146 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/) 2025-09-08T09:03:00,146 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/) 2025-09-08T09:03:00,147 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/) 2025-09-08T09:03:00,147 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/) 2025-09-08T09:03:00,147 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/) 2025-09-08T09:03:00,147 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/) 2025-09-08T09:03:00,147 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/) 2025-09-08T09:03:00,147 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/) 2025-09-08T09:03:00,147 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/) 2025-09-08T09:03:00,148 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/) 2025-09-08T09:03:00,148 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/) 2025-09-08T09:03:00,148 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/) 2025-09-08T09:03:00,148 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/) 2025-09-08T09:03:00,148 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/) 2025-09-08T09:03:00,148 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/) 2025-09-08T09:03:00,148 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/) 2025-09-08T09:03:00,149 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/) 2025-09-08T09:03:00,150 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/) 2025-09-08T09:03:00,150 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 https://www.piwheels.org/simple/molmod/) 2025-09-08T09:03:00,150 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.1-cp35-cp35m-linux_armv6l.whl#sha256=0c239c573227a354b7c04a18a921402be117d3e4dc14c085133cf1294365c358 (from https://www.piwheels.org/simple/molmod/) 2025-09-08T09:03:00,150 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.1-cp35-cp35m-linux_armv7l.whl#sha256=0c239c573227a354b7c04a18a921402be117d3e4dc14c085133cf1294365c358 (from https://www.piwheels.org/simple/molmod/) 2025-09-08T09:03:00,150 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.1-cp39-cp39-linux_armv6l.whl#sha256=bbd8feed144952e1cd8b1b94792b77ad2b9811a4ea61531fb89024ef9f6c9516 (from https://www.piwheels.org/simple/molmod/) 2025-09-08T09:03:00,150 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.1-cp39-cp39-linux_armv7l.whl#sha256=bbd8feed144952e1cd8b1b94792b77ad2b9811a4ea61531fb89024ef9f6c9516 (from https://www.piwheels.org/simple/molmod/) 2025-09-08T09:03:00,150 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/) 2025-09-08T09:03:00,151 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/) 2025-09-08T09:03:00,151 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/) 2025-09-08T09:03:00,151 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/) 2025-09-08T09:03:00,151 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/) 2025-09-08T09:03:00,151 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/) 2025-09-08T09:03:00,151 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/) 2025-09-08T09:03:00,151 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/) 2025-09-08T09:03:00,151 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/) 2025-09-08T09:03:00,152 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/) 2025-09-08T09:03:00,152 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/) 2025-09-08T09:03:00,152 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/) 2025-09-08T09:03:00,152 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/) 2025-09-08T09:03:00,152 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/) 2025-09-08T09:03:00,152 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/) 2025-09-08T09:03:00,152 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/) 2025-09-08T09:03:00,153 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/) 2025-09-08T09:03:00,153 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/) 2025-09-08T09:03:00,153 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/) 2025-09-08T09:03:00,153 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/) 2025-09-08T09:03:00,153 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/) 2025-09-08T09:03:00,153 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/) 2025-09-08T09:03:00,153 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/) 2025-09-08T09:03:00,153 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/) 2025-09-08T09:03:00,154 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/) 2025-09-08T09:03:00,154 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/) 2025-09-08T09:03:00,154 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/) 2025-09-08T09:03:00,154 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/) 2025-09-08T09:03:00,154 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/) 2025-09-08T09:03:00,154 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/) 2025-09-08T09:03:00,154 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/) 2025-09-08T09:03:00,155 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/) 2025-09-08T09:03:00,155 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/) 2025-09-08T09:03:00,155 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/) 2025-09-08T09:03:00,155 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/) 2025-09-08T09:03:00,155 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/) 2025-09-08T09:03:00,155 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/) 2025-09-08T09:03:00,155 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/) 2025-09-08T09:03:00,155 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/) 2025-09-08T09:03:00,156 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/) 2025-09-08T09:03:00,156 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/) 2025-09-08T09:03:00,156 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/) 2025-09-08T09:03:00,156 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/) 2025-09-08T09:03:00,156 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/) 2025-09-08T09:03:00,156 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/) 2025-09-08T09:03:00,156 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/) 2025-09-08T09:03:00,157 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/) 2025-09-08T09:03:00,157 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/) 2025-09-08T09:03:00,157 Skipping link: not a file: https://www.piwheels.org/simple/molmod/ 2025-09-08T09:03:00,157 Skipping link: not a file: https://pypi.org/simple/molmod/ 2025-09-08T09:03:00,181 Given no hashes to check 1 links for project 'molmod': discarding no candidates 2025-09-08T09:03:00,182 Collecting molmod==1.2.1 2025-09-08T09:03:00,183 Created temporary directory: /tmp/pip-unpack-n15dmep3 2025-09-08T09:03:00,327 Downloading molmod-1.2.1.tar.gz (1.7 MB) 2025-09-08T09:03:00,771 Added molmod==1.2.1 from https://files.pythonhosted.org/packages/d8/b1/d7cf3645e70ddf22e3c93225a0f963debc4be6276148cbaed46e973d2064/molmod-1.2.1.tar.gz to build tracker '/tmp/pip-build-tracker-u1w8jfvd' 2025-09-08T09:03:00,772 Running setup.py (path:/tmp/pip-wheel-24zp1dgu/molmod_e0122c8ca53345fc891720aa96f2d234/setup.py) egg_info for package molmod 2025-09-08T09:03:00,772 Created temporary directory: /tmp/pip-pip-egg-info-hqaaah9_ 2025-09-08T09:03:00,772 Preparing metadata (setup.py): started 2025-09-08T09:03:00,773 Running command python setup.py egg_info 2025-09-08T09:03:01,684 fatal: not a git repository (or any parent up to mount point /) 2025-09-08T09:03:01,684 Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). 2025-09-08T09:03:01,981 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:03:01,982 !! 2025-09-08T09:03:01,982 ******************************************************************************** 2025-09-08T09:03:01,982 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:03:01,982 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-08T09:03:01,982 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:03:01,982 ******************************************************************************** 2025-09-08T09:03:01,983 !! 2025-09-08T09:03:01,983 self._finalize_license_expression() 2025-09-08T09:03:02,064 running egg_info 2025-09-08T09:03:02,133 creating /tmp/pip-pip-egg-info-hqaaah9_/molmod.egg-info 2025-09-08T09:03:02,133 writing /tmp/pip-pip-egg-info-hqaaah9_/molmod.egg-info/PKG-INFO 2025-09-08T09:03:02,134 writing dependency_links to /tmp/pip-pip-egg-info-hqaaah9_/molmod.egg-info/dependency_links.txt 2025-09-08T09:03:02,135 writing requirements to /tmp/pip-pip-egg-info-hqaaah9_/molmod.egg-info/requires.txt 2025-09-08T09:03:02,135 writing top-level names to /tmp/pip-pip-egg-info-hqaaah9_/molmod.egg-info/top_level.txt 2025-09-08T09:03:02,135 writing manifest file '/tmp/pip-pip-egg-info-hqaaah9_/molmod.egg-info/SOURCES.txt' 2025-09-08T09:03:02,349 reading manifest file '/tmp/pip-pip-egg-info-hqaaah9_/molmod.egg-info/SOURCES.txt' 2025-09-08T09:03:02,350 reading manifest template 'MANIFEST.in' 2025-09-08T09:03:02,386 warning: no previously-included files matching 'ext.c' found under directory 'molmod' 2025-09-08T09:03:02,397 adding license file 'LICENSE.txt' 2025-09-08T09:03:02,405 writing manifest file '/tmp/pip-pip-egg-info-hqaaah9_/molmod.egg-info/SOURCES.txt' 2025-09-08T09:03:02,540 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T09:03:02,544 Source in /tmp/pip-wheel-24zp1dgu/molmod_e0122c8ca53345fc891720aa96f2d234 has version 1.2.1, which satisfies requirement molmod==1.2.1 from https://files.pythonhosted.org/packages/d8/b1/d7cf3645e70ddf22e3c93225a0f963debc4be6276148cbaed46e973d2064/molmod-1.2.1.tar.gz 2025-09-08T09:03:02,545 Removed molmod==1.2.1 from https://files.pythonhosted.org/packages/d8/b1/d7cf3645e70ddf22e3c93225a0f963debc4be6276148cbaed46e973d2064/molmod-1.2.1.tar.gz from build tracker '/tmp/pip-build-tracker-u1w8jfvd' 2025-09-08T09:03:02,548 Created temporary directory: /tmp/pip-unpack-f_2o8ysq 2025-09-08T09:03:02,548 Created temporary directory: /tmp/pip-unpack-nnqinb7f 2025-09-08T09:03:02,549 Building wheels for collected packages: molmod 2025-09-08T09:03:02,550 Created temporary directory: /tmp/pip-wheel-ngho3u0d 2025-09-08T09:03:02,550 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 2025-09-08T09:03:02,551 Building wheel for molmod (setup.py): started 2025-09-08T09:03:02,552 Destination directory: /tmp/pip-wheel-ngho3u0d 2025-09-08T09:03:02,552 Running command python setup.py bdist_wheel 2025-09-08T09:03:03,476 fatal: not a git repository (or any parent up to mount point /) 2025-09-08T09:03:03,477 Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). 2025-09-08T09:03:03,777 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:03:03,777 !! 2025-09-08T09:03:03,777 ******************************************************************************** 2025-09-08T09:03:03,777 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:03:03,778 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-08T09:03:03,778 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:03:03,778 ******************************************************************************** 2025-09-08T09:03:03,778 !! 2025-09-08T09:03:03,778 self._finalize_license_expression() 2025-09-08T09:03:03,802 running bdist_wheel 2025-09-08T09:03:04,088 running build 2025-09-08T09:03:04,088 running build_py 2025-09-08T09:03:04,176 creating build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,176 copying molmod/zmatrix.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,177 copying molmod/version.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,177 copying molmod/vectors.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,178 copying molmod/utils.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,179 copying molmod/units.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,179 copying molmod/unit_cells.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,180 copying molmod/transformations.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,181 copying molmod/toyff.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,181 copying molmod/symmetry.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,182 copying molmod/similarity.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,182 copying molmod/randomize.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,183 copying molmod/quaternions.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,184 copying molmod/periodic.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,184 copying molmod/pairff.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,185 copying molmod/molecules.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,185 copying molmod/molecular_graphs.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,186 copying molmod/minimizer.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,187 copying molmod/log.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,188 copying molmod/isotopes.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,188 copying molmod/ic.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,189 copying molmod/graphs.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,190 copying molmod/constants.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,190 copying molmod/clusters.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,191 copying molmod/bonds.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,192 copying molmod/binning.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,192 copying molmod/__init__.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,194 creating build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,194 copying molmod/test/test_zmatrix.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,195 copying molmod/test/test_vectors.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,195 copying molmod/test/test_utils.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,196 copying molmod/test/test_units.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,196 copying molmod/test/test_unit_cells.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,197 copying molmod/test/test_transformations.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,198 copying molmod/test/test_toyff.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,198 copying molmod/test/test_symmetry.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,199 copying molmod/test/test_similarity.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,199 copying molmod/test/test_randomize.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,200 copying molmod/test/test_quaternions.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,200 copying molmod/test/test_pairff.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,201 copying molmod/test/test_molecules.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,202 copying molmod/test/test_molecular_graphs.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,202 copying molmod/test/test_minimizer.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,203 copying molmod/test/test_meta.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,204 copying molmod/test/test_log.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,204 copying molmod/test/test_ic.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,205 copying molmod/test/test_graphs.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,206 copying molmod/test/test_data.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,206 copying molmod/test/test_clusters.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,207 copying molmod/test/test_binning.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,207 copying molmod/test/common.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,208 copying molmod/test/__init__.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:04,209 creating build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,209 copying molmod/io/xyz.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,210 copying molmod/io/sdf.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,211 copying molmod/io/psf.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,211 copying molmod/io/pdb.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,212 copying molmod/io/number_state.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,212 copying molmod/io/lammps.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,213 copying molmod/io/gromacs.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,213 copying molmod/io/gamess.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,214 copying molmod/io/fchk.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,215 copying molmod/io/dlpoly.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,216 copying molmod/io/cube.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,216 copying molmod/io/crystal.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,217 copying molmod/io/cpmd.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,217 copying molmod/io/cp2k.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,218 copying molmod/io/common.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,218 copying molmod/io/cml.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,219 copying molmod/io/chk.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,219 copying molmod/io/atrj.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,220 copying molmod/io/__init__.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:04,221 creating build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,221 copying molmod/io/test/test_xyz.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,222 copying molmod/io/test/test_sdf.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,223 copying molmod/io/test/test_psf.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,223 copying molmod/io/test/test_pdb.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,224 copying molmod/io/test/test_number_state.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,224 copying molmod/io/test/test_lammps.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,225 copying molmod/io/test/test_gromacs.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,225 copying molmod/io/test/test_gamess.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,226 copying molmod/io/test/test_fchk.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,226 copying molmod/io/test/test_dlpoly.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,227 copying molmod/io/test/test_cube.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,227 copying molmod/io/test/test_crystal.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,228 copying molmod/io/test/test_cpmd.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,229 copying molmod/io/test/test_cp2k.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,230 copying molmod/io/test/test_cml.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,230 copying molmod/io/test/test_atrj.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,231 copying molmod/io/test/__init__.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:04,231 running egg_info 2025-09-08T09:03:04,299 writing molmod.egg-info/PKG-INFO 2025-09-08T09:03:04,301 writing dependency_links to molmod.egg-info/dependency_links.txt 2025-09-08T09:03:04,301 writing requirements to molmod.egg-info/requires.txt 2025-09-08T09:03:04,301 writing top-level names to molmod.egg-info/top_level.txt 2025-09-08T09:03:04,374 reading manifest file 'molmod.egg-info/SOURCES.txt' 2025-09-08T09:03:04,387 reading manifest template 'MANIFEST.in' 2025-09-08T09:03:04,422 warning: no previously-included files matching 'ext.c' found under directory 'molmod' 2025-09-08T09:03:04,433 adding license file 'LICENSE.txt' 2025-09-08T09:03:04,443 writing manifest file 'molmod.egg-info/SOURCES.txt' 2025-09-08T09:03:04,446 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'molmod.data' is absent from the `packages` configuration. 2025-09-08T09:03:04,446 !! 2025-09-08T09:03:04,446 ******************************************************************************** 2025-09-08T09:03:04,446 ############################ 2025-09-08T09:03:04,446 # Package would be ignored # 2025-09-08T09:03:04,446 ############################ 2025-09-08T09:03:04,446 Python recognizes 'molmod.data' as an importable package[^1], 2025-09-08T09:03:04,446 but it is absent from setuptools' `packages` configuration. 2025-09-08T09:03:04,447 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T09:03:04,447 package, please make sure that 'molmod.data' is explicitly added 2025-09-08T09:03:04,447 to the `packages` configuration field. 2025-09-08T09:03:04,447 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T09:03:04,447 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T09:03:04,447 instead of `find_packages(...)`/`find:`). 2025-09-08T09:03:04,447 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T09:03:04,447 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T09:03:04,448 If you don't want 'molmod.data' to be distributed and are 2025-09-08T09:03:04,448 already explicitly excluding 'molmod.data' via 2025-09-08T09:03:04,448 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T09:03:04,448 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T09:03:04,448 combination with a more fine grained `package-data` configuration. 2025-09-08T09:03:04,448 You can read more about "package data files" on setuptools documentation page: 2025-09-08T09:03:04,448 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T09:03:04,449 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T09:03:04,449 even if it does not contain any `.py` files. 2025-09-08T09:03:04,449 On the other hand, currently there is no concept of package data 2025-09-08T09:03:04,449 directory, all directories are treated like packages. 2025-09-08T09:03:04,449 ******************************************************************************** 2025-09-08T09:03:04,449 !! 2025-09-08T09:03:04,449 check.warn(importable) 2025-09-08T09:03:04,449 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'molmod.data.test' is absent from the `packages` configuration. 2025-09-08T09:03:04,449 !! 2025-09-08T09:03:04,450 ******************************************************************************** 2025-09-08T09:03:04,450 ############################ 2025-09-08T09:03:04,450 # Package would be ignored # 2025-09-08T09:03:04,450 ############################ 2025-09-08T09:03:04,450 Python recognizes 'molmod.data.test' as an importable package[^1], 2025-09-08T09:03:04,450 but it is absent from setuptools' `packages` configuration. 2025-09-08T09:03:04,450 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T09:03:04,450 package, please make sure that 'molmod.data.test' is explicitly added 2025-09-08T09:03:04,450 to the `packages` configuration field. 2025-09-08T09:03:04,450 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T09:03:04,451 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T09:03:04,451 instead of `find_packages(...)`/`find:`). 2025-09-08T09:03:04,451 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T09:03:04,451 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T09:03:04,451 If you don't want 'molmod.data.test' to be distributed and are 2025-09-08T09:03:04,451 already explicitly excluding 'molmod.data.test' via 2025-09-08T09:03:04,451 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T09:03:04,451 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T09:03:04,452 combination with a more fine grained `package-data` configuration. 2025-09-08T09:03:04,452 You can read more about "package data files" on setuptools documentation page: 2025-09-08T09:03:04,452 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T09:03:04,452 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T09:03:04,452 even if it does not contain any `.py` files. 2025-09-08T09:03:04,452 On the other hand, currently there is no concept of package data 2025-09-08T09:03:04,452 directory, all directories are treated like packages. 2025-09-08T09:03:04,452 ******************************************************************************** 2025-09-08T09:03:04,453 !! 2025-09-08T09:03:04,453 check.warn(importable) 2025-09-08T09:03:04,453 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'molmod.examples' is absent from the `packages` configuration. 2025-09-08T09:03:04,453 !! 2025-09-08T09:03:04,453 ******************************************************************************** 2025-09-08T09:03:04,453 ############################ 2025-09-08T09:03:04,453 # Package would be ignored # 2025-09-08T09:03:04,453 ############################ 2025-09-08T09:03:04,453 Python recognizes 'molmod.examples' as an importable package[^1], 2025-09-08T09:03:04,453 but it is absent from setuptools' `packages` configuration. 2025-09-08T09:03:04,454 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T09:03:04,454 package, please make sure that 'molmod.examples' is explicitly added 2025-09-08T09:03:04,454 to the `packages` configuration field. 2025-09-08T09:03:04,454 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T09:03:04,454 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T09:03:04,454 instead of `find_packages(...)`/`find:`). 2025-09-08T09:03:04,454 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T09:03:04,455 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T09:03:04,455 If you don't want 'molmod.examples' to be distributed and are 2025-09-08T09:03:04,455 already explicitly excluding 'molmod.examples' via 2025-09-08T09:03:04,455 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T09:03:04,455 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T09:03:04,455 combination with a more fine grained `package-data` configuration. 2025-09-08T09:03:04,455 You can read more about "package data files" on setuptools documentation page: 2025-09-08T09:03:04,455 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T09:03:04,456 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T09:03:04,456 even if it does not contain any `.py` files. 2025-09-08T09:03:04,456 On the other hand, currently there is no concept of package data 2025-09-08T09:03:04,456 directory, all directories are treated like packages. 2025-09-08T09:03:04,456 ******************************************************************************** 2025-09-08T09:03:04,456 !! 2025-09-08T09:03:04,456 check.warn(importable) 2025-09-08T09:03:04,460 copying molmod/common.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,460 copying molmod/common.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,461 copying molmod/ext.pyx -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,462 copying molmod/ff.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,462 copying molmod/ff.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,463 copying molmod/ff.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,463 copying molmod/graphs.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,464 copying molmod/graphs.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,464 copying molmod/graphs.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,465 copying molmod/molecules.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,465 copying molmod/molecules.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,466 copying molmod/molecules.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,466 copying molmod/similarity.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,467 copying molmod/similarity.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,467 copying molmod/similarity.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,468 copying molmod/unit_cells.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,468 copying molmod/unit_cells.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,469 copying molmod/unit_cells.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:04,469 creating build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:04,470 copying molmod/data/bonds.csv -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:04,470 copying molmod/data/bonds.ods -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:04,471 copying molmod/data/mass.mas03 -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:04,473 copying molmod/data/nubtab03.asc -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:04,476 copying molmod/data/periodic.csv -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:04,476 copying molmod/data/periodic.ods -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:04,477 copying molmod/data/toyff_angles.txt -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:04,478 creating build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,478 copying molmod/data/test/1LJL_Cys10.cml -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,479 copying molmod/data/test/1TOH.b3lyp.fchk -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,481 copying molmod/data/test/1TOH.b3lyp.trim.fchk -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,482 copying molmod/data/test/5ringOH.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,482 copying molmod/data/test/CID_22898828.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,483 copying molmod/data/test/PCGamess_PUNCH -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,487 copying molmod/data/test/SID_31646545.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,487 copying molmod/data/test/SID_31646548.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,488 copying molmod/data/test/SID_40363570.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,488 copying molmod/data/test/SID_40363571.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,489 copying molmod/data/test/SID_41893278.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,489 copying molmod/data/test/SID_41893280.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,490 copying molmod/data/test/SID_54258192.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,490 copying molmod/data/test/SID_55127927.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,491 copying molmod/data/test/SID_55488598.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,491 copying molmod/data/test/SID_56274343.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,492 copying molmod/data/test/TRAJECTORY_H2_CPMD -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,492 copying molmod/data/test/alanine.cube -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,493 copying molmod/data/test/argon.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,494 copying molmod/data/test/bartek.atrj -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,495 copying molmod/data/test/benzene.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,496 copying molmod/data/test/butane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,497 copying molmod/data/test/caplayer.cml -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,497 copying molmod/data/test/crystal_api.out -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,499 copying molmod/data/test/cyclopentane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,500 copying molmod/data/test/dinitrogen.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,500 copying molmod/data/test/dlpoly_HISTORY -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,501 copying molmod/data/test/dlpoly_HISTORY_an2 -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,502 copying molmod/data/test/dlpoly_OUTPUT -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,502 copying molmod/data/test/dopamine.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,503 copying molmod/data/test/ethane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,503 copying molmod/data/test/ethene.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,504 copying molmod/data/test/ethene_ethyl_trans.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,504 copying molmod/data/test/example.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,505 copying molmod/data/test/formol.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,505 copying molmod/data/test/funny.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,506 copying molmod/data/test/h3zrosihohosioh3.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,506 copying molmod/data/test/il2.pdb -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,508 copying molmod/data/test/lammps_dump.txt -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,508 copying molmod/data/test/lau.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,509 copying molmod/data/test/octane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,509 copying molmod/data/test/oh3siozroh3.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,510 copying molmod/data/test/opt_5ring10T.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,510 copying molmod/data/test/opt_5ring12T.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,511 copying molmod/data/test/opt_6_6ring.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,511 copying molmod/data/test/opt_6ring.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,512 copying molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,512 copying molmod/data/test/pentapeptide.psf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,513 copying molmod/data/test/precursor.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,513 copying molmod/data/test/probes.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,514 copying molmod/data/test/tea.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,514 copying molmod/data/test/tetra.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,515 copying molmod/data/test/thf.psf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,516 copying molmod/data/test/thf.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,517 copying molmod/data/test/thf_64.cell -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,517 copying molmod/data/test/thf_single.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,518 copying molmod/data/test/tpa.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,518 copying molmod/data/test/water.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,519 copying molmod/data/test/water2.gro -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,519 copying molmod/data/test/water_md.inp -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,520 copying molmod/data/test/zr4o8-3.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:04,520 creating build/lib.linux-armv7l-cpython-313/molmod/examples/000_units 2025-09-08T09:03:04,521 copying molmod/examples/000_units/a_reaction.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/000_units 2025-09-08T09:03:04,521 copying molmod/examples/000_units/b_chbond.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/000_units 2025-09-08T09:03:04,522 copying molmod/examples/000_units/c_h2rot.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/000_units 2025-09-08T09:03:04,522 creating build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:04,522 copying molmod/examples/001_molecules/a_convert.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:04,523 copying molmod/examples/001_molecules/b_com.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:04,524 copying molmod/examples/001_molecules/c_carbon.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:04,524 copying molmod/examples/001_molecules/d_size.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:04,525 copying molmod/examples/001_molecules/e_shape.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:04,525 copying molmod/examples/001_molecules/ibuprofen.sdf -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:04,526 creating build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:04,526 copying molmod/examples/002_graphs/a_graphs.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:04,526 copying molmod/examples/002_graphs/b_neighbors.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:04,527 copying molmod/examples/002_graphs/c_distances.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:04,527 copying molmod/examples/002_graphs/caffeine.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:04,528 copying molmod/examples/002_graphs/d_symmetries.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:04,528 copying molmod/examples/002_graphs/ethanol.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:04,529 creating build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:04,529 copying molmod/examples/003_internal_coordinates/a_bond_length.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:04,530 copying molmod/examples/003_internal_coordinates/b_bending_angles.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:04,530 copying molmod/examples/003_internal_coordinates/c_ff_hessian.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:04,531 copying molmod/examples/003_internal_coordinates/d_dft_hessian.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:04,531 copying molmod/examples/003_internal_coordinates/dopamine.fchk -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:04,532 copying molmod/examples/003_internal_coordinates/dopamine.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:04,533 copying molmod/examples/003_internal_coordinates/propane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:04,533 creating build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-08T09:03:04,533 copying molmod/examples/004_patterns/a_propane_types.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-08T09:03:04,534 copying molmod/examples/004_patterns/b_dopamine_types.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-08T09:03:04,535 copying molmod/examples/004_patterns/dopamine.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-08T09:03:04,535 copying molmod/examples/004_patterns/mfi_fragment.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-08T09:03:04,536 copying molmod/examples/004_patterns/propane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-08T09:03:04,539 running build_ext 2025-09-08T09:03:04,975 Compiling molmod/ext.pyx because it changed. 2025-09-08T09:03:04,975 [1/1] Cythonizing molmod/ext.pyx 2025-09-08T09:03:06,483 Error compiling Cython file: 2025-09-08T09:03:06,483 ------------------------------------------------------------ 2025-09-08T09:03:06,483 ... 2025-09-08T09:03:06,483 """C extensions for molmod.""" 2025-09-08T09:03:06,483 import numpy as np 2025-09-08T09:03:06,483 cimport numpy as np 2025-09-08T09:03:06,483 cimport ff 2025-09-08T09:03:06,484 ^ 2025-09-08T09:03:06,484 ------------------------------------------------------------ 2025-09-08T09:03:06,484 molmod/ext.pyx:28:8: 'ff.pxd' not found 2025-09-08T09:03:06,515 Error compiling Cython file: 2025-09-08T09:03:06,515 ------------------------------------------------------------ 2025-09-08T09:03:06,515 ... 2025-09-08T09:03:06,516 import numpy as np 2025-09-08T09:03:06,516 cimport numpy as np 2025-09-08T09:03:06,516 cimport ff 2025-09-08T09:03:06,516 cimport graphs 2025-09-08T09:03:06,516 ^ 2025-09-08T09:03:06,516 ------------------------------------------------------------ 2025-09-08T09:03:06,516 molmod/ext.pyx:29:8: 'graphs.pxd' not found 2025-09-08T09:03:06,545 Error compiling Cython file: 2025-09-08T09:03:06,545 ------------------------------------------------------------ 2025-09-08T09:03:06,545 ... 2025-09-08T09:03:06,545 import numpy as np 2025-09-08T09:03:06,545 cimport numpy as np 2025-09-08T09:03:06,546 cimport ff 2025-09-08T09:03:06,546 cimport graphs 2025-09-08T09:03:06,546 cimport molecules 2025-09-08T09:03:06,546 ^ 2025-09-08T09:03:06,546 ------------------------------------------------------------ 2025-09-08T09:03:06,546 molmod/ext.pyx:30:8: 'molecules.pxd' not found 2025-09-08T09:03:06,574 Error compiling Cython file: 2025-09-08T09:03:06,574 ------------------------------------------------------------ 2025-09-08T09:03:06,574 ... 2025-09-08T09:03:06,574 cimport numpy as np 2025-09-08T09:03:06,574 cimport ff 2025-09-08T09:03:06,575 cimport graphs 2025-09-08T09:03:06,575 cimport molecules 2025-09-08T09:03:06,575 cimport similarity 2025-09-08T09:03:06,575 ^ 2025-09-08T09:03:06,575 ------------------------------------------------------------ 2025-09-08T09:03:06,575 molmod/ext.pyx:31:8: 'similarity.pxd' not found 2025-09-08T09:03:06,603 Error compiling Cython file: 2025-09-08T09:03:06,603 ------------------------------------------------------------ 2025-09-08T09:03:06,603 ... 2025-09-08T09:03:06,603 cimport ff 2025-09-08T09:03:06,603 cimport graphs 2025-09-08T09:03:06,603 cimport molecules 2025-09-08T09:03:06,603 cimport similarity 2025-09-08T09:03:06,603 cimport unit_cells 2025-09-08T09:03:06,603 ^ 2025-09-08T09:03:06,604 ------------------------------------------------------------ 2025-09-08T09:03:06,604 molmod/ext.pyx:32:8: 'unit_cells.pxd' not found 2025-09-08T09:03:07,113 Error compiling Cython file: 2025-09-08T09:03:07,113 ------------------------------------------------------------ 2025-09-08T09:03:07,113 ... 2025-09-08T09:03:07,113 if matrix is not None and matrix.shape[0] != 3 and matrix.shape[1] != 3: 2025-09-08T09:03:07,113 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-08T09:03:07,113 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-08T09:03:07,113 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-08T09:03:07,113 if matrix is None: 2025-09-08T09:03:07,113 return ff.ff_dm_quad( 2025-09-08T09:03:07,114 ^ 2025-09-08T09:03:07,114 ------------------------------------------------------------ 2025-09-08T09:03:07,114 molmod/ext.pyx:58:17: cimported module has no attribute 'ff_dm_quad' 2025-09-08T09:03:07,114 Error compiling Cython file: 2025-09-08T09:03:07,114 ------------------------------------------------------------ 2025-09-08T09:03:07,114 ... 2025-09-08T09:03:07,114 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-08T09:03:07,114 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-08T09:03:07,115 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-08T09:03:07,115 if matrix is None: 2025-09-08T09:03:07,115 return ff.ff_dm_quad( 2025-09-08T09:03:07,115 natom, long(matrix is not None), &cor[0, 0], &dm0[0, 0], &dmk[0, 0], amp, 2025-09-08T09:03:07,115 ^ 2025-09-08T09:03:07,115 ------------------------------------------------------------ 2025-09-08T09:03:07,115 molmod/ext.pyx:59:19: undeclared name not builtin: long 2025-09-08T09:03:07,115 Error compiling Cython file: 2025-09-08T09:03:07,115 ------------------------------------------------------------ 2025-09-08T09:03:07,116 ... 2025-09-08T09:03:07,116 if matrix is None: 2025-09-08T09:03:07,116 return ff.ff_dm_quad( 2025-09-08T09:03:07,116 natom, long(matrix is not None), &cor[0, 0], &dm0[0, 0], &dmk[0, 0], amp, 2025-09-08T09:03:07,116 &gradient[0, 0], NULL, NULL) 2025-09-08T09:03:07,116 else: 2025-09-08T09:03:07,116 return ff.ff_dm_quad( 2025-09-08T09:03:07,116 ^ 2025-09-08T09:03:07,116 ------------------------------------------------------------ 2025-09-08T09:03:07,116 molmod/ext.pyx:62:17: cimported module has no attribute 'ff_dm_quad' 2025-09-08T09:03:07,123 Error compiling Cython file: 2025-09-08T09:03:07,123 ------------------------------------------------------------ 2025-09-08T09:03:07,123 ... 2025-09-08T09:03:07,123 if matrix is not None and matrix.shape[0] != 3 and matrix.shape[1] != 3: 2025-09-08T09:03:07,123 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-08T09:03:07,123 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-08T09:03:07,123 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-08T09:03:07,123 if matrix is None: 2025-09-08T09:03:07,123 return ff.ff_dm_reci( 2025-09-08T09:03:07,123 ^ 2025-09-08T09:03:07,123 ------------------------------------------------------------ 2025-09-08T09:03:07,124 molmod/ext.pyx:86:17: cimported module has no attribute 'ff_dm_reci' 2025-09-08T09:03:07,124 Error compiling Cython file: 2025-09-08T09:03:07,124 ------------------------------------------------------------ 2025-09-08T09:03:07,124 ... 2025-09-08T09:03:07,124 if matrix is None: 2025-09-08T09:03:07,124 return ff.ff_dm_reci( 2025-09-08T09:03:07,124 natom, long(matrix is not None), &cor[0, 0], &radii[0], &dm0[0, 0], amp, 2025-09-08T09:03:07,124 &gradient[0, 0], NULL, NULL) 2025-09-08T09:03:07,125 else: 2025-09-08T09:03:07,125 return ff.ff_dm_reci( 2025-09-08T09:03:07,125 ^ 2025-09-08T09:03:07,125 ------------------------------------------------------------ 2025-09-08T09:03:07,125 molmod/ext.pyx:90:17: cimported module has no attribute 'ff_dm_reci' 2025-09-08T09:03:07,143 Error compiling Cython file: 2025-09-08T09:03:07,144 ------------------------------------------------------------ 2025-09-08T09:03:07,144 ... 2025-09-08T09:03:07,144 if matrix is not None and matrix.shape[0] != 3 and matrix.shape[1] != 3: 2025-09-08T09:03:07,144 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-08T09:03:07,144 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-08T09:03:07,144 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-08T09:03:07,144 if matrix is None: 2025-09-08T09:03:07,144 return ff.ff_bond_quad( 2025-09-08T09:03:07,144 ^ 2025-09-08T09:03:07,144 ------------------------------------------------------------ 2025-09-08T09:03:07,145 molmod/ext.pyx:117:17: cimported module has no attribute 'ff_bond_quad' 2025-09-08T09:03:07,145 Error compiling Cython file: 2025-09-08T09:03:07,145 ------------------------------------------------------------ 2025-09-08T09:03:07,145 ... 2025-09-08T09:03:07,145 if matrix is None: 2025-09-08T09:03:07,145 return ff.ff_bond_quad( 2025-09-08T09:03:07,145 npair, long(matrix is not None), &cor[0, 0], &pairs[0, 0], &lengths[0], amp, 2025-09-08T09:03:07,145 &gradient[0, 0], NULL, NULL) 2025-09-08T09:03:07,145 else: 2025-09-08T09:03:07,146 return ff.ff_bond_quad( 2025-09-08T09:03:07,146 ^ 2025-09-08T09:03:07,146 ------------------------------------------------------------ 2025-09-08T09:03:07,146 molmod/ext.pyx:121:17: cimported module has no attribute 'ff_bond_quad' 2025-09-08T09:03:07,152 Error compiling Cython file: 2025-09-08T09:03:07,152 ------------------------------------------------------------ 2025-09-08T09:03:07,152 ... 2025-09-08T09:03:07,152 if matrix is not None and matrix.shape[0] != 3 and matrix.shape[1] != 3: 2025-09-08T09:03:07,152 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-08T09:03:07,152 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-08T09:03:07,152 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-08T09:03:07,152 if matrix is None: 2025-09-08T09:03:07,152 return ff.ff_bond_hyper( 2025-09-08T09:03:07,153 ^ 2025-09-08T09:03:07,153 ------------------------------------------------------------ 2025-09-08T09:03:07,153 molmod/ext.pyx:148:17: cimported module has no attribute 'ff_bond_hyper' 2025-09-08T09:03:07,153 Error compiling Cython file: 2025-09-08T09:03:07,153 ------------------------------------------------------------ 2025-09-08T09:03:07,153 ... 2025-09-08T09:03:07,153 if matrix is None: 2025-09-08T09:03:07,153 return ff.ff_bond_hyper( 2025-09-08T09:03:07,153 npair, long(matrix is not None), &cor[0, 0], &pairs[0, 0], &lengths[0], scale, 2025-09-08T09:03:07,154 amp, &gradient[0, 0], NULL, NULL) 2025-09-08T09:03:07,154 else: 2025-09-08T09:03:07,154 return ff.ff_bond_hyper( 2025-09-08T09:03:07,154 ^ 2025-09-08T09:03:07,154 ------------------------------------------------------------ 2025-09-08T09:03:07,154 molmod/ext.pyx:152:17: cimported module has no attribute 'ff_bond_hyper' 2025-09-08T09:03:07,156 Error compiling Cython file: 2025-09-08T09:03:07,156 ------------------------------------------------------------ 2025-09-08T09:03:07,156 ... 2025-09-08T09:03:07,156 def graphs_floyd_warshall(long[:, ::1] dm): 2025-09-08T09:03:07,156 cdef size_t nvertex = dm.shape[0] 2025-09-08T09:03:07,156 if dm.shape[1] != nvertex: 2025-09-08T09:03:07,157 raise TypeError('dm must be a square matrix.') 2025-09-08T09:03:07,157 graphs.graphs_floyd_warshall(nvertex, &dm[0, 0]) 2025-09-08T09:03:07,157 ^ 2025-09-08T09:03:07,157 ------------------------------------------------------------ 2025-09-08T09:03:07,157 molmod/ext.pyx:166:10: cimported module has no attribute 'graphs_floyd_warshall' 2025-09-08T09:03:07,160 Error compiling Cython file: 2025-09-08T09:03:07,160 ------------------------------------------------------------ 2025-09-08T09:03:07,160 ... 2025-09-08T09:03:07,160 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-08T09:03:07,161 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-08T09:03:07,161 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-08T09:03:07,161 cdef np.ndarray[double, ndim=2] dm = np.zeros((natom, natom), float) 2025-09-08T09:03:07,161 if matrix is None: 2025-09-08T09:03:07,161 molecules.molecules_distance_matrix( 2025-09-08T09:03:07,161 ^ 2025-09-08T09:03:07,161 ------------------------------------------------------------ 2025-09-08T09:03:07,161 molmod/ext.pyx:186:17: cimported module has no attribute 'molecules_distance_matrix' 2025-09-08T09:03:07,161 Error compiling Cython file: 2025-09-08T09:03:07,162 ------------------------------------------------------------ 2025-09-08T09:03:07,162 ... 2025-09-08T09:03:07,162 cdef np.ndarray[double, ndim=2] dm = np.zeros((natom, natom), float) 2025-09-08T09:03:07,162 if matrix is None: 2025-09-08T09:03:07,162 molecules.molecules_distance_matrix( 2025-09-08T09:03:07,162 natom, &cor[0, 0], long(matrix is not None), NULL, NULL, &dm[0, 0]) 2025-09-08T09:03:07,162 else: 2025-09-08T09:03:07,162 molecules.molecules_distance_matrix( 2025-09-08T09:03:07,162 ^ 2025-09-08T09:03:07,162 ------------------------------------------------------------ 2025-09-08T09:03:07,162 molmod/ext.pyx:189:17: cimported module has no attribute 'molecules_distance_matrix' 2025-09-08T09:03:07,165 Error compiling Cython file: 2025-09-08T09:03:07,165 ------------------------------------------------------------ 2025-09-08T09:03:07,165 ... 2025-09-08T09:03:07,165 def similarity_table_labels(const long[::1] labels not None): 2025-09-08T09:03:07,165 cdef size_t n = labels.shape[0] 2025-09-08T09:03:07,165 cdef np.ndarray[long, ndim=2] labels_table = np.zeros(((n*(n-1))/2, 2), dtype=int) 2025-09-08T09:03:07,165 similarity.similarity_table_labels(n, &labels[0], &labels_table[0, 0]) 2025-09-08T09:03:07,165 ^ 2025-09-08T09:03:07,165 ------------------------------------------------------------ 2025-09-08T09:03:07,166 molmod/ext.pyx:203:14: cimported module has no attribute 'similarity_table_labels' 2025-09-08T09:03:07,167 Error compiling Cython file: 2025-09-08T09:03:07,167 ------------------------------------------------------------ 2025-09-08T09:03:07,167 ... 2025-09-08T09:03:07,167 def similarity_table_distances(const double[:, ::1] distance_matrix not None): 2025-09-08T09:03:07,168 cdef size_t n = distance_matrix.shape[0] 2025-09-08T09:03:07,168 if distance_matrix.shape[1] != n: 2025-09-08T09:03:07,168 raise TypeError('distance_matrix must be sqaure') 2025-09-08T09:03:07,168 cdef np.ndarray[double] distances_table = np.zeros(((n*(n-1))/2), dtype=float) 2025-09-08T09:03:07,168 similarity.similarity_table_distances(n, &distance_matrix[0, 0], &distances_table[0]) 2025-09-08T09:03:07,168 ^ 2025-09-08T09:03:07,168 ------------------------------------------------------------ 2025-09-08T09:03:07,168 molmod/ext.pyx:212:14: cimported module has no attribute 'similarity_table_distances' 2025-09-08T09:03:07,171 Error compiling Cython file: 2025-09-08T09:03:07,171 ------------------------------------------------------------ 2025-09-08T09:03:07,171 ... 2025-09-08T09:03:07,172 raise TypeError('labels1 and distances1 must have the same numbers of rows.') 2025-09-08T09:03:07,172 if labels2.shape[1] != 2: 2025-09-08T09:03:07,172 raise TypeError('labels1 must have two columns.') 2025-09-08T09:03:07,172 if distances2.shape[0] != n2: 2025-09-08T09:03:07,172 raise TypeError('labels2 and distances2 must have the same numbers of rows.') 2025-09-08T09:03:07,172 return similarity.similarity_measure(n1, &labels1[0, 0], &distances1[0], 2025-09-08T09:03:07,172 ^ 2025-09-08T09:03:07,172 ------------------------------------------------------------ 2025-09-08T09:03:07,172 molmod/ext.pyx:229:21: cimported module has no attribute 'similarity_measure' 2025-09-08T09:03:07,176 Error compiling Cython file: 2025-09-08T09:03:07,176 ------------------------------------------------------------ 2025-09-08T09:03:07,176 ... 2025-09-08T09:03:07,176 raise ValueError('Radius must be positive.') 2025-09-08T09:03:07,176 if max_ranges.shape[0] != 3: 2025-09-08T09:03:07,176 raise TypeError('max_ranges must have shape (3, ).') 2025-09-08T09:03:07,176 if indexes.shape[1] != 3: 2025-09-08T09:03:07,176 raise TypeError('indexes must have three columns.') 2025-09-08T09:03:07,176 return unit_cells.unit_cell_get_radius_indexes(&matrix[0, 0], &reciprocal[0, 0], radius, 2025-09-08T09:03:07,176 ^ 2025-09-08T09:03:07,177 ------------------------------------------------------------ 2025-09-08T09:03:07,177 molmod/ext.pyx:253:21: cimported module has no attribute 'unit_cell_get_radius_indexes' 2025-09-08T09:03:08,026 Traceback (most recent call last): 2025-09-08T09:03:08,035 File "", line 2, in 2025-09-08T09:03:08,035 exec(compile(''' 2025-09-08T09:03:08,035 ~~~~^^^^^^^^^^^^ 2025-09-08T09:03:08,035 # This is -- a caller that pip uses to run setup.py 2025-09-08T09:03:08,035 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:03:08,035 ...<32 lines>... 2025-09-08T09:03:08,035 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T09:03:08,035 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:03:08,036 ''' % ('/tmp/pip-wheel-24zp1dgu/molmod_e0122c8ca53345fc891720aa96f2d234/setup.py',), "", "exec")) 2025-09-08T09:03:08,036 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:03:08,036 File "", line 35, in 2025-09-08T09:03:08,036 File "/tmp/pip-wheel-24zp1dgu/molmod_e0122c8ca53345fc891720aa96f2d234/setup.py", line 67, in 2025-09-08T09:03:08,036 setup( 2025-09-08T09:03:08,036 ~~~~~^ 2025-09-08T09:03:08,036 name='molmod', 2025-09-08T09:03:08,036 ^^^^^^^^^^^^^^ 2025-09-08T09:03:08,036 ...<30 lines>... 2025-09-08T09:03:08,037 ], 2025-09-08T09:03:08,037 ^^ 2025-09-08T09:03:08,037 ) 2025-09-08T09:03:08,037 ^ 2025-09-08T09:03:08,037 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-08T09:03:08,037 return distutils.core.setup(**attrs) 2025-09-08T09:03:08,037 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:08,037 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-08T09:03:08,037 return run_commands(dist) 2025-09-08T09:03:08,038 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-08T09:03:08,038 dist.run_commands() 2025-09-08T09:03:08,038 ~~~~~~~~~~~~~~~~~^^ 2025-09-08T09:03:08,038 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-08T09:03:08,038 self.run_command(cmd) 2025-09-08T09:03:08,038 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T09:03:08,038 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T09:03:08,038 super().run_command(command) 2025-09-08T09:03:08,038 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:08,039 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T09:03:08,039 cmd_obj.run() 2025-09-08T09:03:08,039 ~~~~~~~~~~~^^ 2025-09-08T09:03:08,039 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run 2025-09-08T09:03:08,039 self.run_command("build") 2025-09-08T09:03:08,039 ~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:08,039 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T09:03:08,039 self.distribution.run_command(command) 2025-09-08T09:03:08,039 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:08,040 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T09:03:08,040 super().run_command(command) 2025-09-08T09:03:08,040 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:08,040 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T09:03:08,040 cmd_obj.run() 2025-09-08T09:03:08,040 ~~~~~~~~~~~^^ 2025-09-08T09:03:08,040 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run 2025-09-08T09:03:08,040 self.run_command(cmd_name) 2025-09-08T09:03:08,040 ~~~~~~~~~~~~~~~~^^^^^^^^^^ 2025-09-08T09:03:08,041 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T09:03:08,041 self.distribution.run_command(command) 2025-09-08T09:03:08,041 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:08,041 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T09:03:08,041 super().run_command(command) 2025-09-08T09:03:08,041 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:08,041 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T09:03:08,041 cmd_obj.run() 2025-09-08T09:03:08,041 ~~~~~~~~~~~^^ 2025-09-08T09:03:08,042 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 368, in run 2025-09-08T09:03:08,042 self.build_extensions() 2025-09-08T09:03:08,042 ~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T09:03:08,042 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 484, in build_extensions 2025-09-08T09:03:08,042 self._build_extensions_serial() 2025-09-08T09:03:08,042 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T09:03:08,042 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 510, in _build_extensions_serial 2025-09-08T09:03:08,042 self.build_extension(ext) 2025-09-08T09:03:08,042 ~~~~~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T09:03:08,043 File "/usr/local/lib/python3.13/dist-packages/Cython/Distutils/build_ext.py", line 131, in build_extension 2025-09-08T09:03:08,043 new_ext = cythonize( 2025-09-08T09:03:08,043 ~~~~~~~~~^ 2025-09-08T09:03:08,043 ext,force=self.force, quiet=self.verbose == 0, **options 2025-09-08T09:03:08,043 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:03:08,043 )[0] 2025-09-08T09:03:08,043 ^ 2025-09-08T09:03:08,043 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize 2025-09-08T09:03:08,043 cythonize_one(*args) 2025-09-08T09:03:08,043 ~~~~~~~~~~~~~^^^^^^^ 2025-09-08T09:03:08,044 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one 2025-09-08T09:03:08,044 raise CompileError(None, pyx_file) 2025-09-08T09:03:08,044 Cython.Compiler.Errors.CompileError: molmod/ext.pyx 2025-09-08T09:03:08,559 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T09:03:08,573 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T09:03:08,573 exec(compile('"'"''"'"''"'"' 2025-09-08T09:03:08,573 # This is -- a caller that pip uses to run setup.py 2025-09-08T09:03:08,573 # 2025-09-08T09:03:08,573 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T09:03:08,573 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T09:03:08,573 # - It provides a clear error message when setuptools is not installed. 2025-09-08T09:03:08,573 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T09:03:08,573 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T09:03:08,573 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T09:03:08,573 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T09:03:08,573 import os, sys, tokenize, traceback 2025-09-08T09:03:08,573 2025-09-08T09:03:08,573 try: 2025-09-08T09:03:08,573 import setuptools 2025-09-08T09:03:08,573 except ImportError: 2025-09-08T09:03:08,573 print( 2025-09-08T09:03:08,573 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T09:03:08,573 "the build environment with exception:", 2025-09-08T09:03:08,573 file=sys.stderr, 2025-09-08T09:03:08,573 ) 2025-09-08T09:03:08,573 traceback.print_exc() 2025-09-08T09:03:08,573 sys.exit(1) 2025-09-08T09:03:08,573 2025-09-08T09:03:08,573 __file__ = %r 2025-09-08T09:03:08,573 sys.argv[0] = __file__ 2025-09-08T09:03:08,573 2025-09-08T09:03:08,573 if os.path.exists(__file__): 2025-09-08T09:03:08,573 filename = __file__ 2025-09-08T09:03:08,573 with tokenize.open(__file__) as f: 2025-09-08T09:03:08,573 setup_py_code = f.read() 2025-09-08T09:03:08,573 else: 2025-09-08T09:03:08,573 filename = "" 2025-09-08T09:03:08,573 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T09:03:08,573 2025-09-08T09:03:08,573 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T09:03:08,573 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-24zp1dgu/molmod_e0122c8ca53345fc891720aa96f2d234/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-ngho3u0d[/] 2025-09-08T09:03:08,573 [bold magenta]cwd[/]: /tmp/pip-wheel-24zp1dgu/molmod_e0122c8ca53345fc891720aa96f2d234/ 2025-09-08T09:03:08,573 Building wheel for molmod (setup.py): finished with status 'error' 2025-09-08T09:03:08,574 ERROR: Failed building wheel for molmod 2025-09-08T09:03:08,575 Running setup.py clean for molmod 2025-09-08T09:03:08,576 Running command python setup.py clean 2025-09-08T09:03:09,526 fatal: not a git repository (or any parent up to mount point /) 2025-09-08T09:03:09,527 Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). 2025-09-08T09:03:09,830 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:03:09,830 !! 2025-09-08T09:03:09,831 ******************************************************************************** 2025-09-08T09:03:09,831 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:03:09,831 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-08T09:03:09,831 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:03:09,831 ******************************************************************************** 2025-09-08T09:03:09,831 !! 2025-09-08T09:03:09,832 self._finalize_license_expression() 2025-09-08T09:03:09,898 running clean 2025-09-08T09:03:10,037 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T09:03:10,044 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T09:03:10,045 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T09:03:10,045 removing 'build' 2025-09-08T09:03:10,177 Failed to build molmod 2025-09-08T09:03:10,178 ERROR: Failed to build one or more wheels 2025-09-08T09:03:10,179 Exception information: 2025-09-08T09:03:10,179 Traceback (most recent call last): 2025-09-08T09:03:10,179 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T09:03:10,179 status = _inner_run() 2025-09-08T09:03:10,179 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T09:03:10,179 return self.run(options, args) 2025-09-08T09:03:10,179 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T09:03:10,179 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T09:03:10,179 return func(self, options, args) 2025-09-08T09:03:10,179 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T09:03:10,179 raise CommandError("Failed to build one or more wheels") 2025-09-08T09:03:10,179 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T09:03:10,183 Removed build tracker: '/tmp/pip-build-tracker-u1w8jfvd'