2025-09-08T09:03:41,654 Created temporary directory: /tmp/pip-build-tracker-y0bdonvr 2025-09-08T09:03:41,654 Initialized build tracking at /tmp/pip-build-tracker-y0bdonvr 2025-09-08T09:03:41,654 Created build tracker: /tmp/pip-build-tracker-y0bdonvr 2025-09-08T09:03:41,654 Entered build tracker: /tmp/pip-build-tracker-y0bdonvr 2025-09-08T09:03:41,655 Created temporary directory: /tmp/pip-wheel-sy_jguvz 2025-09-08T09:03:41,658 Created temporary directory: /tmp/pip-ephem-wheel-cache-n6e2a_la 2025-09-08T09:03:41,719 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T09:03:41,722 2 location(s) to search for versions of molmod: 2025-09-08T09:03:41,722 * https://pypi.org/simple/molmod/ 2025-09-08T09:03:41,722 * https://www.piwheels.org/simple/molmod/ 2025-09-08T09:03:41,722 Fetching project page and analyzing links: https://pypi.org/simple/molmod/ 2025-09-08T09:03:41,722 Getting page https://pypi.org/simple/molmod/ 2025-09-08T09:03:41,723 Found index url https://pypi.org/simple/ 2025-09-08T09:03:41,793 Fetched page https://pypi.org/simple/molmod/ as application/vnd.pypi.simple.v1+json 2025-09-08T09:03:41,796 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 2025-09-08T09:03:41,796 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 2025-09-08T09:03:41,796 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 2025-09-08T09:03:41,797 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 2025-09-08T09:03:41,797 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 2025-09-08T09:03:41,797 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 2025-09-08T09:03:41,797 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 2025-09-08T09:03:41,797 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 2025-09-08T09:03:41,798 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 2025-09-08T09:03:41,798 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 2025-09-08T09:03:41,798 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 2025-09-08T09:03:41,798 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 2025-09-08T09:03:41,799 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 2025-09-08T09:03:41,799 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 2025-09-08T09:03:41,799 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 2025-09-08T09:03:41,799 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 2025-09-08T09:03:41,800 Fetching project page and analyzing links: https://www.piwheels.org/simple/molmod/ 2025-09-08T09:03:41,800 Getting page https://www.piwheels.org/simple/molmod/ 2025-09-08T09:03:41,801 Found index url https://www.piwheels.org/simple/ 2025-09-08T09:03:41,897 Fetched page https://www.piwheels.org/simple/molmod/ as text/html 2025-09-08T09:03:41,916 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/) 2025-09-08T09:03:41,917 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/) 2025-09-08T09:03:41,917 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/) 2025-09-08T09:03:41,917 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/) 2025-09-08T09:03:41,917 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/) 2025-09-08T09:03:41,917 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/) 2025-09-08T09:03:41,917 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/) 2025-09-08T09:03:41,918 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/) 2025-09-08T09:03:41,918 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/) 2025-09-08T09:03:41,918 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/) 2025-09-08T09:03:41,918 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/) 2025-09-08T09:03:41,918 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/) 2025-09-08T09:03:41,918 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/) 2025-09-08T09:03:41,919 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/) 2025-09-08T09:03:41,919 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/) 2025-09-08T09:03:41,919 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/) 2025-09-08T09:03:41,919 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/) 2025-09-08T09:03:41,919 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/) 2025-09-08T09:03:41,919 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/) 2025-09-08T09:03:41,919 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/) 2025-09-08T09:03:41,920 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/) 2025-09-08T09:03:41,920 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/) 2025-09-08T09:03:41,920 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/) 2025-09-08T09:03:41,920 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/) 2025-09-08T09:03:41,920 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/) 2025-09-08T09:03:41,920 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/) 2025-09-08T09:03:41,920 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/) 2025-09-08T09:03:41,921 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/) 2025-09-08T09:03:41,921 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/) 2025-09-08T09:03:41,922 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/) 2025-09-08T09:03:41,922 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/) 2025-09-08T09:03:41,922 Skipping link: No binaries permitted for molmod: 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https://www.piwheels.org/simple/molmod/) 2025-09-08T09:03:41,923 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.2-cp37-cp37m-linux_armv7l.whl#sha256=26ae5048c9b8d810170b4687f20f0db3f9e73ac80ec25294ab9c06457df5693b (from https://www.piwheels.org/simple/molmod/) 2025-09-08T09:03:41,923 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.2-cp35-cp35m-linux_armv7l.whl#sha256=9a3abca443da42da2e0a2e12e84b53573ef4e35511a3761db4d12c3d66197acc (from https://www.piwheels.org/simple/molmod/) 2025-09-08T09:03:41,923 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.2-cp35-cp35m-linux_armv6l.whl#sha256=9a3abca443da42da2e0a2e12e84b53573ef4e35511a3761db4d12c3d66197acc (from https://www.piwheels.org/simple/molmod/) 2025-09-08T09:03:41,923 Skipping link: No binaries permitted for molmod: https://archive1.piwheels.org/simple/molmod/molmod-1.4.2-cp39-cp39-linux_armv6l.whl#sha256=2a63c98cfa820171218e3e0fab5ce769a2bd26e3d4ddc9319878bd448e0f9d48 (from https://www.piwheels.org/simple/molmod/) 2025-09-08T09:03:41,923 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/) 2025-09-08T09:03:41,923 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/) 2025-09-08T09:03:41,923 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/) 2025-09-08T09:03:41,924 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/) 2025-09-08T09:03:41,924 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/) 2025-09-08T09:03:41,924 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/) 2025-09-08T09:03:41,924 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/) 2025-09-08T09:03:41,924 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/) 2025-09-08T09:03:41,924 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/) 2025-09-08T09:03:41,924 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/) 2025-09-08T09:03:41,925 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/) 2025-09-08T09:03:41,925 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/) 2025-09-08T09:03:41,925 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/) 2025-09-08T09:03:41,925 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/) 2025-09-08T09:03:41,925 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/) 2025-09-08T09:03:41,925 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/) 2025-09-08T09:03:41,925 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/) 2025-09-08T09:03:41,926 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/) 2025-09-08T09:03:41,926 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/) 2025-09-08T09:03:41,926 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/) 2025-09-08T09:03:41,926 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/) 2025-09-08T09:03:41,926 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/) 2025-09-08T09:03:41,926 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/) 2025-09-08T09:03:41,926 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/) 2025-09-08T09:03:41,927 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/) 2025-09-08T09:03:41,927 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/) 2025-09-08T09:03:41,927 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/) 2025-09-08T09:03:41,927 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/) 2025-09-08T09:03:41,927 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/) 2025-09-08T09:03:41,927 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/) 2025-09-08T09:03:41,927 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/) 2025-09-08T09:03:41,928 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/) 2025-09-08T09:03:41,928 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/) 2025-09-08T09:03:41,928 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/) 2025-09-08T09:03:41,928 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/) 2025-09-08T09:03:41,928 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/) 2025-09-08T09:03:41,928 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/) 2025-09-08T09:03:41,928 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/) 2025-09-08T09:03:41,929 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/) 2025-09-08T09:03:41,929 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/) 2025-09-08T09:03:41,929 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/) 2025-09-08T09:03:41,929 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/) 2025-09-08T09:03:41,929 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/) 2025-09-08T09:03:41,929 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/) 2025-09-08T09:03:41,930 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/) 2025-09-08T09:03:41,930 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/) 2025-09-08T09:03:41,930 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/) 2025-09-08T09:03:41,930 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/) 2025-09-08T09:03:41,930 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/) 2025-09-08T09:03:41,930 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/) 2025-09-08T09:03:41,931 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/) 2025-09-08T09:03:41,931 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/) 2025-09-08T09:03:41,931 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/) 2025-09-08T09:03:41,931 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/) 2025-09-08T09:03:41,931 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/) 2025-09-08T09:03:41,931 Skipping link: not a file: https://www.piwheels.org/simple/molmod/ 2025-09-08T09:03:41,932 Skipping link: not a file: https://pypi.org/simple/molmod/ 2025-09-08T09:03:41,954 Given no hashes to check 1 links for project 'molmod': discarding no candidates 2025-09-08T09:03:41,955 Collecting molmod==1.3.0 2025-09-08T09:03:41,957 Created temporary directory: /tmp/pip-unpack-e11b575r 2025-09-08T09:03:42,099 Downloading molmod-1.3.0.tar.gz (1.7 MB) 2025-09-08T09:03:42,545 Added molmod==1.3.0 from https://files.pythonhosted.org/packages/03/2d/4457e38b0e8245af76b37000ccee228d12b029023b0711954bc495494fd0/molmod-1.3.0.tar.gz to build tracker '/tmp/pip-build-tracker-y0bdonvr' 2025-09-08T09:03:42,546 Running setup.py (path:/tmp/pip-wheel-sy_jguvz/molmod_2419afeae1724a848a66bd4cc56c0061/setup.py) egg_info for package molmod 2025-09-08T09:03:42,546 Created temporary directory: /tmp/pip-pip-egg-info-vrguvnca 2025-09-08T09:03:42,547 Preparing metadata (setup.py): started 2025-09-08T09:03:42,547 Running command python setup.py egg_info 2025-09-08T09:03:43,468 fatal: not a git repository (or any parent up to mount point /) 2025-09-08T09:03:43,468 Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). 2025-09-08T09:03:43,856 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:03:43,856 !! 2025-09-08T09:03:43,856 ******************************************************************************** 2025-09-08T09:03:43,856 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:03:43,856 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-08T09:03:43,857 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:03:43,857 ******************************************************************************** 2025-09-08T09:03:43,857 !! 2025-09-08T09:03:43,857 self._finalize_license_expression() 2025-09-08T09:03:43,930 running egg_info 2025-09-08T09:03:44,003 creating /tmp/pip-pip-egg-info-vrguvnca/molmod.egg-info 2025-09-08T09:03:44,004 writing /tmp/pip-pip-egg-info-vrguvnca/molmod.egg-info/PKG-INFO 2025-09-08T09:03:44,005 writing dependency_links to /tmp/pip-pip-egg-info-vrguvnca/molmod.egg-info/dependency_links.txt 2025-09-08T09:03:44,005 writing requirements to /tmp/pip-pip-egg-info-vrguvnca/molmod.egg-info/requires.txt 2025-09-08T09:03:44,006 writing top-level names to /tmp/pip-pip-egg-info-vrguvnca/molmod.egg-info/top_level.txt 2025-09-08T09:03:44,006 writing manifest file '/tmp/pip-pip-egg-info-vrguvnca/molmod.egg-info/SOURCES.txt' 2025-09-08T09:03:44,233 reading manifest file '/tmp/pip-pip-egg-info-vrguvnca/molmod.egg-info/SOURCES.txt' 2025-09-08T09:03:44,234 reading manifest template 'MANIFEST.in' 2025-09-08T09:03:44,270 warning: no previously-included files matching 'ext.c' found under directory 'molmod' 2025-09-08T09:03:44,281 adding license file 'LICENSE.txt' 2025-09-08T09:03:44,288 writing manifest file '/tmp/pip-pip-egg-info-vrguvnca/molmod.egg-info/SOURCES.txt' 2025-09-08T09:03:44,430 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T09:03:44,434 Source in /tmp/pip-wheel-sy_jguvz/molmod_2419afeae1724a848a66bd4cc56c0061 has version 1.3.0, which satisfies requirement molmod==1.3.0 from https://files.pythonhosted.org/packages/03/2d/4457e38b0e8245af76b37000ccee228d12b029023b0711954bc495494fd0/molmod-1.3.0.tar.gz 2025-09-08T09:03:44,435 Removed molmod==1.3.0 from https://files.pythonhosted.org/packages/03/2d/4457e38b0e8245af76b37000ccee228d12b029023b0711954bc495494fd0/molmod-1.3.0.tar.gz from build tracker '/tmp/pip-build-tracker-y0bdonvr' 2025-09-08T09:03:44,438 Created temporary directory: /tmp/pip-unpack-ahra2tj6 2025-09-08T09:03:44,438 Created temporary directory: /tmp/pip-unpack-5r5e7_nh 2025-09-08T09:03:44,439 Building wheels for collected packages: molmod 2025-09-08T09:03:44,440 Created temporary directory: /tmp/pip-wheel-1f0kfm8a 2025-09-08T09:03:44,440 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 2025-09-08T09:03:44,441 Building wheel for molmod (setup.py): started 2025-09-08T09:03:44,442 Destination directory: /tmp/pip-wheel-1f0kfm8a 2025-09-08T09:03:44,442 Running command python setup.py bdist_wheel 2025-09-08T09:03:45,350 fatal: not a git repository (or any parent up to mount point /) 2025-09-08T09:03:45,350 Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). 2025-09-08T09:03:45,729 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:03:45,729 !! 2025-09-08T09:03:45,729 ******************************************************************************** 2025-09-08T09:03:45,729 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:03:45,729 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-08T09:03:45,730 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:03:45,730 ******************************************************************************** 2025-09-08T09:03:45,730 !! 2025-09-08T09:03:45,730 self._finalize_license_expression() 2025-09-08T09:03:45,730 running bdist_wheel 2025-09-08T09:03:46,014 running build 2025-09-08T09:03:46,015 running build_py 2025-09-08T09:03:46,090 creating build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,090 copying molmod/zmatrix.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,091 copying molmod/version.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,091 copying molmod/vectors.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,092 copying molmod/utils.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,092 copying molmod/units.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,093 copying molmod/unit_cells.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,093 copying molmod/transformations.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,094 copying molmod/toyff.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,095 copying molmod/symmetry.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,095 copying molmod/similarity.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,096 copying molmod/randomize.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,096 copying molmod/quaternions.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,097 copying molmod/periodic.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,097 copying molmod/pairff.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,098 copying molmod/molecules.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,098 copying molmod/molecular_graphs.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,099 copying molmod/minimizer.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,100 copying molmod/log.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,100 copying molmod/isotopes.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,101 copying molmod/ic.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,102 copying molmod/graphs.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,102 copying molmod/constants.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,103 copying molmod/clusters.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,103 copying molmod/bonds.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,104 copying molmod/binning.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,104 copying molmod/__init__.py -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,106 creating build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,106 copying molmod/test/test_zmatrix.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,106 copying molmod/test/test_vectors.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,107 copying molmod/test/test_utils.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,107 copying molmod/test/test_units.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,108 copying molmod/test/test_unit_cells.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,108 copying molmod/test/test_transformations.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,109 copying molmod/test/test_toyff.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,110 copying molmod/test/test_symmetry.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,110 copying molmod/test/test_similarity.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,111 copying molmod/test/test_randomize.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,111 copying molmod/test/test_quaternions.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,112 copying molmod/test/test_pairff.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,112 copying molmod/test/test_molecules.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,113 copying molmod/test/test_molecular_graphs.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,113 copying molmod/test/test_minimizer.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,114 copying molmod/test/test_log.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,114 copying molmod/test/test_ic.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,115 copying molmod/test/test_graphs.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,115 copying molmod/test/test_examples.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,116 copying molmod/test/test_data.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,116 copying molmod/test/test_clusters.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,117 copying molmod/test/test_binning.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,117 copying molmod/test/common.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,118 copying molmod/test/__init__.py -> build/lib.linux-armv7l-cpython-313/molmod/test 2025-09-08T09:03:46,119 creating build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,119 copying molmod/io/xyz.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,120 copying molmod/io/sdf.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,120 copying molmod/io/psf.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,121 copying molmod/io/pdb.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,122 copying molmod/io/number_state.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,122 copying molmod/io/lammps.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,123 copying molmod/io/gromacs.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,123 copying molmod/io/gamess.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,124 copying molmod/io/fchk.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,125 copying molmod/io/dlpoly.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,125 copying molmod/io/cube.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,126 copying molmod/io/crystal.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,127 copying molmod/io/cpmd.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,127 copying molmod/io/cp2k.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,128 copying molmod/io/common.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,128 copying molmod/io/cml.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,129 copying molmod/io/chk.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,129 copying molmod/io/atrj.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,130 copying molmod/io/__init__.py -> build/lib.linux-armv7l-cpython-313/molmod/io 2025-09-08T09:03:46,131 creating build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,131 copying molmod/io/test/test_xyz.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,132 copying molmod/io/test/test_sdf.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,132 copying molmod/io/test/test_psf.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,133 copying molmod/io/test/test_pdb.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,133 copying molmod/io/test/test_number_state.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,134 copying molmod/io/test/test_lammps.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,134 copying molmod/io/test/test_gromacs.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,135 copying molmod/io/test/test_gamess.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,135 copying molmod/io/test/test_fchk.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,136 copying molmod/io/test/test_dlpoly.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,136 copying molmod/io/test/test_cube.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,137 copying molmod/io/test/test_crystal.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,137 copying molmod/io/test/test_cpmd.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,138 copying molmod/io/test/test_cp2k.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,138 copying molmod/io/test/test_cml.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,139 copying molmod/io/test/test_atrj.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,140 copying molmod/io/test/__init__.py -> build/lib.linux-armv7l-cpython-313/molmod/io/test 2025-09-08T09:03:46,140 running egg_info 2025-09-08T09:03:46,212 writing molmod.egg-info/PKG-INFO 2025-09-08T09:03:46,213 writing dependency_links to molmod.egg-info/dependency_links.txt 2025-09-08T09:03:46,214 writing requirements to molmod.egg-info/requires.txt 2025-09-08T09:03:46,214 writing top-level names to molmod.egg-info/top_level.txt 2025-09-08T09:03:46,292 reading manifest file 'molmod.egg-info/SOURCES.txt' 2025-09-08T09:03:46,304 reading manifest template 'MANIFEST.in' 2025-09-08T09:03:46,341 warning: no previously-included files matching 'ext.c' found under directory 'molmod' 2025-09-08T09:03:46,351 adding license file 'LICENSE.txt' 2025-09-08T09:03:46,363 writing manifest file 'molmod.egg-info/SOURCES.txt' 2025-09-08T09:03:46,365 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'molmod.data' is absent from the `packages` configuration. 2025-09-08T09:03:46,365 !! 2025-09-08T09:03:46,365 ******************************************************************************** 2025-09-08T09:03:46,365 ############################ 2025-09-08T09:03:46,366 # Package would be ignored # 2025-09-08T09:03:46,366 ############################ 2025-09-08T09:03:46,366 Python recognizes 'molmod.data' as an importable package[^1], 2025-09-08T09:03:46,366 but it is absent from setuptools' `packages` configuration. 2025-09-08T09:03:46,366 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T09:03:46,366 package, please make sure that 'molmod.data' is explicitly added 2025-09-08T09:03:46,366 to the `packages` configuration field. 2025-09-08T09:03:46,366 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T09:03:46,366 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T09:03:46,367 instead of `find_packages(...)`/`find:`). 2025-09-08T09:03:46,367 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T09:03:46,367 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T09:03:46,367 If you don't want 'molmod.data' to be distributed and are 2025-09-08T09:03:46,367 already explicitly excluding 'molmod.data' via 2025-09-08T09:03:46,367 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T09:03:46,367 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T09:03:46,367 combination with a more fine grained `package-data` configuration. 2025-09-08T09:03:46,368 You can read more about "package data files" on setuptools documentation page: 2025-09-08T09:03:46,368 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T09:03:46,368 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T09:03:46,368 even if it does not contain any `.py` files. 2025-09-08T09:03:46,368 On the other hand, currently there is no concept of package data 2025-09-08T09:03:46,368 directory, all directories are treated like packages. 2025-09-08T09:03:46,368 ******************************************************************************** 2025-09-08T09:03:46,368 !! 2025-09-08T09:03:46,369 check.warn(importable) 2025-09-08T09:03:46,369 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'molmod.data.test' is absent from the `packages` configuration. 2025-09-08T09:03:46,369 !! 2025-09-08T09:03:46,369 ******************************************************************************** 2025-09-08T09:03:46,369 ############################ 2025-09-08T09:03:46,369 # Package would be ignored # 2025-09-08T09:03:46,369 ############################ 2025-09-08T09:03:46,369 Python recognizes 'molmod.data.test' as an importable package[^1], 2025-09-08T09:03:46,369 but it is absent from setuptools' `packages` configuration. 2025-09-08T09:03:46,370 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T09:03:46,370 package, please make sure that 'molmod.data.test' is explicitly added 2025-09-08T09:03:46,370 to the `packages` configuration field. 2025-09-08T09:03:46,370 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T09:03:46,370 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T09:03:46,370 instead of `find_packages(...)`/`find:`). 2025-09-08T09:03:46,371 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T09:03:46,371 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T09:03:46,371 If you don't want 'molmod.data.test' to be distributed and are 2025-09-08T09:03:46,371 already explicitly excluding 'molmod.data.test' via 2025-09-08T09:03:46,371 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T09:03:46,371 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T09:03:46,371 combination with a more fine grained `package-data` configuration. 2025-09-08T09:03:46,371 You can read more about "package data files" on setuptools documentation page: 2025-09-08T09:03:46,372 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T09:03:46,372 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T09:03:46,372 even if it does not contain any `.py` files. 2025-09-08T09:03:46,372 On the other hand, currently there is no concept of package data 2025-09-08T09:03:46,372 directory, all directories are treated like packages. 2025-09-08T09:03:46,372 ******************************************************************************** 2025-09-08T09:03:46,372 !! 2025-09-08T09:03:46,373 check.warn(importable) 2025-09-08T09:03:46,373 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'molmod.examples' is absent from the `packages` configuration. 2025-09-08T09:03:46,373 !! 2025-09-08T09:03:46,373 ******************************************************************************** 2025-09-08T09:03:46,373 ############################ 2025-09-08T09:03:46,373 # Package would be ignored # 2025-09-08T09:03:46,373 ############################ 2025-09-08T09:03:46,373 Python recognizes 'molmod.examples' as an importable package[^1], 2025-09-08T09:03:46,374 but it is absent from setuptools' `packages` configuration. 2025-09-08T09:03:46,374 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T09:03:46,374 package, please make sure that 'molmod.examples' is explicitly added 2025-09-08T09:03:46,374 to the `packages` configuration field. 2025-09-08T09:03:46,374 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T09:03:46,374 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T09:03:46,374 instead of `find_packages(...)`/`find:`). 2025-09-08T09:03:46,374 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T09:03:46,375 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T09:03:46,375 If you don't want 'molmod.examples' to be distributed and are 2025-09-08T09:03:46,375 already explicitly excluding 'molmod.examples' via 2025-09-08T09:03:46,375 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T09:03:46,375 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T09:03:46,375 combination with a more fine grained `package-data` configuration. 2025-09-08T09:03:46,375 You can read more about "package data files" on setuptools documentation page: 2025-09-08T09:03:46,376 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T09:03:46,376 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T09:03:46,376 even if it does not contain any `.py` files. 2025-09-08T09:03:46,376 On the other hand, currently there is no concept of package data 2025-09-08T09:03:46,376 directory, all directories are treated like packages. 2025-09-08T09:03:46,376 ******************************************************************************** 2025-09-08T09:03:46,376 !! 2025-09-08T09:03:46,377 check.warn(importable) 2025-09-08T09:03:46,378 copying molmod/common.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,378 copying molmod/common.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,379 copying molmod/ext.pyx -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,380 copying molmod/ff.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,380 copying molmod/ff.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,381 copying molmod/ff.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,381 copying molmod/graphs.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,382 copying molmod/graphs.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,382 copying molmod/graphs.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,383 copying molmod/molecules.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,383 copying molmod/molecules.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,384 copying molmod/molecules.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,384 copying molmod/similarity.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,385 copying molmod/similarity.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,385 copying molmod/similarity.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,386 copying molmod/unit_cells.c -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,386 copying molmod/unit_cells.h -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,387 copying molmod/unit_cells.pxd -> build/lib.linux-armv7l-cpython-313/molmod 2025-09-08T09:03:46,387 creating build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:46,388 copying molmod/data/bonds.csv -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:46,388 copying molmod/data/bonds.ods -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:46,389 copying molmod/data/mass.mas03 -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:46,391 copying molmod/data/nubtab03.asc -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:46,393 copying molmod/data/periodic.csv -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:46,394 copying molmod/data/periodic.ods -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:46,395 copying molmod/data/toyff_angles.txt -> build/lib.linux-armv7l-cpython-313/molmod/data 2025-09-08T09:03:46,395 creating build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,396 copying molmod/data/test/1LJL_Cys10.cml -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,396 copying molmod/data/test/1TOH.b3lyp.fchk -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,399 copying molmod/data/test/1TOH.b3lyp.trim.fchk -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,399 copying molmod/data/test/5ringOH.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,401 copying molmod/data/test/CID_22898828.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,401 copying molmod/data/test/PCGamess_PUNCH -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,405 copying molmod/data/test/SID_31646545.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,406 copying molmod/data/test/SID_31646548.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,406 copying molmod/data/test/SID_40363570.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,407 copying molmod/data/test/SID_40363571.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,407 copying molmod/data/test/SID_41893278.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,408 copying molmod/data/test/SID_41893280.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,408 copying molmod/data/test/SID_54258192.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,409 copying molmod/data/test/SID_55127927.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,409 copying molmod/data/test/SID_55488598.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,410 copying molmod/data/test/SID_56274343.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,410 copying molmod/data/test/TRAJECTORY_H2_CPMD -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,411 copying molmod/data/test/alanine.cube -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,411 copying molmod/data/test/argon.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,412 copying molmod/data/test/bartek.atrj -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,414 copying molmod/data/test/benzene.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,414 copying molmod/data/test/butane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,415 copying molmod/data/test/caplayer.cml -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,415 copying molmod/data/test/crystal_api.out -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,418 copying molmod/data/test/cyclopentane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,418 copying molmod/data/test/dinitrogen.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,419 copying molmod/data/test/dlpoly_HISTORY -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,419 copying molmod/data/test/dlpoly_HISTORY_an2 -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,420 copying molmod/data/test/dlpoly_OUTPUT -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,421 copying molmod/data/test/dopamine.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,421 copying molmod/data/test/ethane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,422 copying molmod/data/test/ethene.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,422 copying molmod/data/test/ethene_ethyl_trans.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,423 copying molmod/data/test/example.sdf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,423 copying molmod/data/test/formol.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,424 copying molmod/data/test/funny.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,424 copying molmod/data/test/h3zrosihohosioh3.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,425 copying molmod/data/test/il2.pdb -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,426 copying molmod/data/test/lammps_dump.txt -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,427 copying molmod/data/test/lau.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,427 copying molmod/data/test/octane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,428 copying molmod/data/test/oh3siozroh3.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,428 copying molmod/data/test/opt_5ring10T.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,429 copying molmod/data/test/opt_5ring12T.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,429 copying molmod/data/test/opt_6_6ring.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,430 copying molmod/data/test/opt_6ring.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,430 copying molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,431 copying molmod/data/test/pentapeptide.psf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,431 copying molmod/data/test/precursor.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,432 copying molmod/data/test/probes.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,433 copying molmod/data/test/tea.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,433 copying molmod/data/test/tetra.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,434 copying molmod/data/test/thf.psf -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,435 copying molmod/data/test/thf.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,435 copying molmod/data/test/thf_64.cell -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,436 copying molmod/data/test/thf_single.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,436 copying molmod/data/test/tpa.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,437 copying molmod/data/test/water.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,437 copying molmod/data/test/water2.gro -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,438 copying molmod/data/test/water_md.inp -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,439 copying molmod/data/test/zr4o8-3.xyz -> build/lib.linux-armv7l-cpython-313/molmod/data/test 2025-09-08T09:03:46,439 creating build/lib.linux-armv7l-cpython-313/molmod/examples/000_units 2025-09-08T09:03:46,439 copying molmod/examples/000_units/a_reaction.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/000_units 2025-09-08T09:03:46,440 copying molmod/examples/000_units/b_chbond.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/000_units 2025-09-08T09:03:46,440 copying molmod/examples/000_units/c_h2rot.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/000_units 2025-09-08T09:03:46,441 creating build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:46,441 copying molmod/examples/001_molecules/a_convert.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:46,442 copying molmod/examples/001_molecules/b_com.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:46,442 copying molmod/examples/001_molecules/c_carbon.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:46,443 copying molmod/examples/001_molecules/d_size.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:46,443 copying molmod/examples/001_molecules/e_shape.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:46,444 copying molmod/examples/001_molecules/ibuprofen.sdf -> build/lib.linux-armv7l-cpython-313/molmod/examples/001_molecules 2025-09-08T09:03:46,444 creating build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:46,444 copying molmod/examples/002_graphs/a_graphs.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:46,445 copying molmod/examples/002_graphs/b_neighbors.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:46,446 copying molmod/examples/002_graphs/c_distances.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:46,446 copying molmod/examples/002_graphs/caffeine.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:46,447 copying molmod/examples/002_graphs/d_symmetries.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:46,447 copying molmod/examples/002_graphs/ethanol.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/002_graphs 2025-09-08T09:03:46,448 creating build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:46,448 copying molmod/examples/003_internal_coordinates/a_bond_length.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:46,448 copying molmod/examples/003_internal_coordinates/b_bending_angles.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:46,449 copying molmod/examples/003_internal_coordinates/c_ff_hessian.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:46,449 copying molmod/examples/003_internal_coordinates/d_dft_hessian.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:46,450 copying molmod/examples/003_internal_coordinates/dopamine.fchk -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:46,451 copying molmod/examples/003_internal_coordinates/dopamine.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:46,451 copying molmod/examples/003_internal_coordinates/propane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/003_internal_coordinates 2025-09-08T09:03:46,452 creating build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-08T09:03:46,452 copying molmod/examples/004_patterns/a_propane_types.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-08T09:03:46,453 copying molmod/examples/004_patterns/b_dopamine_types.py -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-08T09:03:46,453 copying molmod/examples/004_patterns/dopamine.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-08T09:03:46,454 copying molmod/examples/004_patterns/mfi_fragment.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-08T09:03:46,454 copying molmod/examples/004_patterns/propane.xyz -> build/lib.linux-armv7l-cpython-313/molmod/examples/004_patterns 2025-09-08T09:03:46,458 running build_ext 2025-09-08T09:03:46,907 Compiling molmod/ext.pyx because it changed. 2025-09-08T09:03:46,907 [1/1] Cythonizing molmod/ext.pyx 2025-09-08T09:03:48,410 Error compiling Cython file: 2025-09-08T09:03:48,410 ------------------------------------------------------------ 2025-09-08T09:03:48,411 ... 2025-09-08T09:03:48,411 """C extensions for molmod.""" 2025-09-08T09:03:48,411 import numpy as np 2025-09-08T09:03:48,411 cimport numpy as np 2025-09-08T09:03:48,411 cimport ff 2025-09-08T09:03:48,411 ^ 2025-09-08T09:03:48,411 ------------------------------------------------------------ 2025-09-08T09:03:48,412 molmod/ext.pyx:28:8: 'ff.pxd' not found 2025-09-08T09:03:48,440 Error compiling Cython file: 2025-09-08T09:03:48,440 ------------------------------------------------------------ 2025-09-08T09:03:48,440 ... 2025-09-08T09:03:48,441 import numpy as np 2025-09-08T09:03:48,441 cimport numpy as np 2025-09-08T09:03:48,441 cimport ff 2025-09-08T09:03:48,441 cimport graphs 2025-09-08T09:03:48,441 ^ 2025-09-08T09:03:48,441 ------------------------------------------------------------ 2025-09-08T09:03:48,441 molmod/ext.pyx:29:8: 'graphs.pxd' not found 2025-09-08T09:03:48,470 Error compiling Cython file: 2025-09-08T09:03:48,470 ------------------------------------------------------------ 2025-09-08T09:03:48,470 ... 2025-09-08T09:03:48,470 import numpy as np 2025-09-08T09:03:48,470 cimport numpy as np 2025-09-08T09:03:48,470 cimport ff 2025-09-08T09:03:48,471 cimport graphs 2025-09-08T09:03:48,471 cimport molecules 2025-09-08T09:03:48,471 ^ 2025-09-08T09:03:48,471 ------------------------------------------------------------ 2025-09-08T09:03:48,471 molmod/ext.pyx:30:8: 'molecules.pxd' not found 2025-09-08T09:03:48,499 Error compiling Cython file: 2025-09-08T09:03:48,499 ------------------------------------------------------------ 2025-09-08T09:03:48,499 ... 2025-09-08T09:03:48,499 cimport numpy as np 2025-09-08T09:03:48,500 cimport ff 2025-09-08T09:03:48,500 cimport graphs 2025-09-08T09:03:48,500 cimport molecules 2025-09-08T09:03:48,500 cimport similarity 2025-09-08T09:03:48,500 ^ 2025-09-08T09:03:48,500 ------------------------------------------------------------ 2025-09-08T09:03:48,500 molmod/ext.pyx:31:8: 'similarity.pxd' not found 2025-09-08T09:03:48,529 Error compiling Cython file: 2025-09-08T09:03:48,529 ------------------------------------------------------------ 2025-09-08T09:03:48,529 ... 2025-09-08T09:03:48,529 cimport ff 2025-09-08T09:03:48,529 cimport graphs 2025-09-08T09:03:48,529 cimport molecules 2025-09-08T09:03:48,529 cimport similarity 2025-09-08T09:03:48,529 cimport unit_cells 2025-09-08T09:03:48,529 ^ 2025-09-08T09:03:48,530 ------------------------------------------------------------ 2025-09-08T09:03:48,530 molmod/ext.pyx:32:8: 'unit_cells.pxd' not found 2025-09-08T09:03:49,042 Error compiling Cython file: 2025-09-08T09:03:49,042 ------------------------------------------------------------ 2025-09-08T09:03:49,042 ... 2025-09-08T09:03:49,042 if matrix is not None and matrix.shape[0] != 3 and matrix.shape[1] != 3: 2025-09-08T09:03:49,042 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-08T09:03:49,042 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-08T09:03:49,043 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-08T09:03:49,043 if matrix is None: 2025-09-08T09:03:49,043 return ff.ff_dm_quad( 2025-09-08T09:03:49,043 ^ 2025-09-08T09:03:49,043 ------------------------------------------------------------ 2025-09-08T09:03:49,043 molmod/ext.pyx:58:17: cimported module has no attribute 'ff_dm_quad' 2025-09-08T09:03:49,043 Error compiling Cython file: 2025-09-08T09:03:49,043 ------------------------------------------------------------ 2025-09-08T09:03:49,043 ... 2025-09-08T09:03:49,044 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-08T09:03:49,044 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-08T09:03:49,044 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-08T09:03:49,044 if matrix is None: 2025-09-08T09:03:49,044 return ff.ff_dm_quad( 2025-09-08T09:03:49,044 natom, long(matrix is not None), &cor[0, 0], &dm0[0, 0], &dmk[0, 0], amp, 2025-09-08T09:03:49,044 ^ 2025-09-08T09:03:49,044 ------------------------------------------------------------ 2025-09-08T09:03:49,044 molmod/ext.pyx:59:19: undeclared name not builtin: long 2025-09-08T09:03:49,045 Error compiling Cython file: 2025-09-08T09:03:49,045 ------------------------------------------------------------ 2025-09-08T09:03:49,045 ... 2025-09-08T09:03:49,045 if matrix is None: 2025-09-08T09:03:49,045 return ff.ff_dm_quad( 2025-09-08T09:03:49,045 natom, long(matrix is not None), &cor[0, 0], &dm0[0, 0], &dmk[0, 0], amp, 2025-09-08T09:03:49,045 &gradient[0, 0], NULL, NULL) 2025-09-08T09:03:49,045 else: 2025-09-08T09:03:49,045 return ff.ff_dm_quad( 2025-09-08T09:03:49,045 ^ 2025-09-08T09:03:49,045 ------------------------------------------------------------ 2025-09-08T09:03:49,046 molmod/ext.pyx:62:17: cimported module has no attribute 'ff_dm_quad' 2025-09-08T09:03:49,052 Error compiling Cython file: 2025-09-08T09:03:49,052 ------------------------------------------------------------ 2025-09-08T09:03:49,052 ... 2025-09-08T09:03:49,052 if matrix is not None and matrix.shape[0] != 3 and matrix.shape[1] != 3: 2025-09-08T09:03:49,052 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-08T09:03:49,052 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-08T09:03:49,053 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-08T09:03:49,053 if matrix is None: 2025-09-08T09:03:49,053 return ff.ff_dm_reci( 2025-09-08T09:03:49,053 ^ 2025-09-08T09:03:49,053 ------------------------------------------------------------ 2025-09-08T09:03:49,053 molmod/ext.pyx:86:17: cimported module has no attribute 'ff_dm_reci' 2025-09-08T09:03:49,053 Error compiling Cython file: 2025-09-08T09:03:49,053 ------------------------------------------------------------ 2025-09-08T09:03:49,053 ... 2025-09-08T09:03:49,054 if matrix is None: 2025-09-08T09:03:49,054 return ff.ff_dm_reci( 2025-09-08T09:03:49,054 natom, long(matrix is not None), &cor[0, 0], &radii[0], &dm0[0, 0], amp, 2025-09-08T09:03:49,054 &gradient[0, 0], NULL, NULL) 2025-09-08T09:03:49,054 else: 2025-09-08T09:03:49,054 return ff.ff_dm_reci( 2025-09-08T09:03:49,054 ^ 2025-09-08T09:03:49,054 ------------------------------------------------------------ 2025-09-08T09:03:49,054 molmod/ext.pyx:90:17: cimported module has no attribute 'ff_dm_reci' 2025-09-08T09:03:49,072 Error compiling Cython file: 2025-09-08T09:03:49,072 ------------------------------------------------------------ 2025-09-08T09:03:49,072 ... 2025-09-08T09:03:49,073 if matrix is not None and matrix.shape[0] != 3 and matrix.shape[1] != 3: 2025-09-08T09:03:49,073 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-08T09:03:49,073 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-08T09:03:49,073 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-08T09:03:49,073 if matrix is None: 2025-09-08T09:03:49,073 return ff.ff_bond_quad( 2025-09-08T09:03:49,073 ^ 2025-09-08T09:03:49,073 ------------------------------------------------------------ 2025-09-08T09:03:49,073 molmod/ext.pyx:117:17: cimported module has no attribute 'ff_bond_quad' 2025-09-08T09:03:49,074 Error compiling Cython file: 2025-09-08T09:03:49,074 ------------------------------------------------------------ 2025-09-08T09:03:49,074 ... 2025-09-08T09:03:49,074 if matrix is None: 2025-09-08T09:03:49,074 return ff.ff_bond_quad( 2025-09-08T09:03:49,074 npair, long(matrix is not None), &cor[0, 0], &pairs[0, 0], &lengths[0], amp, 2025-09-08T09:03:49,074 &gradient[0, 0], NULL, NULL) 2025-09-08T09:03:49,074 else: 2025-09-08T09:03:49,074 return ff.ff_bond_quad( 2025-09-08T09:03:49,074 ^ 2025-09-08T09:03:49,074 ------------------------------------------------------------ 2025-09-08T09:03:49,075 molmod/ext.pyx:121:17: cimported module has no attribute 'ff_bond_quad' 2025-09-08T09:03:49,081 Error compiling Cython file: 2025-09-08T09:03:49,082 ------------------------------------------------------------ 2025-09-08T09:03:49,082 ... 2025-09-08T09:03:49,082 if matrix is not None and matrix.shape[0] != 3 and matrix.shape[1] != 3: 2025-09-08T09:03:49,082 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-08T09:03:49,082 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-08T09:03:49,082 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-08T09:03:49,082 if matrix is None: 2025-09-08T09:03:49,082 return ff.ff_bond_hyper( 2025-09-08T09:03:49,082 ^ 2025-09-08T09:03:49,082 ------------------------------------------------------------ 2025-09-08T09:03:49,083 molmod/ext.pyx:148:17: cimported module has no attribute 'ff_bond_hyper' 2025-09-08T09:03:49,083 Error compiling Cython file: 2025-09-08T09:03:49,083 ------------------------------------------------------------ 2025-09-08T09:03:49,083 ... 2025-09-08T09:03:49,083 if matrix is None: 2025-09-08T09:03:49,083 return ff.ff_bond_hyper( 2025-09-08T09:03:49,083 npair, long(matrix is not None), &cor[0, 0], &pairs[0, 0], &lengths[0], scale, 2025-09-08T09:03:49,083 amp, &gradient[0, 0], NULL, NULL) 2025-09-08T09:03:49,083 else: 2025-09-08T09:03:49,083 return ff.ff_bond_hyper( 2025-09-08T09:03:49,084 ^ 2025-09-08T09:03:49,084 ------------------------------------------------------------ 2025-09-08T09:03:49,084 molmod/ext.pyx:152:17: cimported module has no attribute 'ff_bond_hyper' 2025-09-08T09:03:49,086 Error compiling Cython file: 2025-09-08T09:03:49,086 ------------------------------------------------------------ 2025-09-08T09:03:49,086 ... 2025-09-08T09:03:49,086 def graphs_floyd_warshall(long[:, ::1] dm): 2025-09-08T09:03:49,086 cdef size_t nvertex = dm.shape[0] 2025-09-08T09:03:49,086 if dm.shape[1] != nvertex: 2025-09-08T09:03:49,086 raise TypeError('dm must be a square matrix.') 2025-09-08T09:03:49,086 graphs.graphs_floyd_warshall(nvertex, &dm[0, 0]) 2025-09-08T09:03:49,087 ^ 2025-09-08T09:03:49,087 ------------------------------------------------------------ 2025-09-08T09:03:49,087 molmod/ext.pyx:166:10: cimported module has no attribute 'graphs_floyd_warshall' 2025-09-08T09:03:49,090 Error compiling Cython file: 2025-09-08T09:03:49,090 ------------------------------------------------------------ 2025-09-08T09:03:49,090 ... 2025-09-08T09:03:49,090 raise TypeError('matrix must be an array with shape (3, 3)') 2025-09-08T09:03:49,091 if reciprocal is not None and reciprocal.shape[0] != 3 and reciprocal.shape[1] != 3: 2025-09-08T09:03:49,091 raise TypeError('reciprocal must be an array with shape (3, 3)') 2025-09-08T09:03:49,091 cdef np.ndarray[double, ndim=2] dm = np.zeros((natom, natom), float) 2025-09-08T09:03:49,091 if matrix is None: 2025-09-08T09:03:49,091 molecules.molecules_distance_matrix( 2025-09-08T09:03:49,091 ^ 2025-09-08T09:03:49,091 ------------------------------------------------------------ 2025-09-08T09:03:49,091 molmod/ext.pyx:186:17: cimported module has no attribute 'molecules_distance_matrix' 2025-09-08T09:03:49,091 Error compiling Cython file: 2025-09-08T09:03:49,092 ------------------------------------------------------------ 2025-09-08T09:03:49,092 ... 2025-09-08T09:03:49,092 cdef np.ndarray[double, ndim=2] dm = np.zeros((natom, natom), float) 2025-09-08T09:03:49,092 if matrix is None: 2025-09-08T09:03:49,092 molecules.molecules_distance_matrix( 2025-09-08T09:03:49,092 natom, &cor[0, 0], long(matrix is not None), NULL, NULL, &dm[0, 0]) 2025-09-08T09:03:49,092 else: 2025-09-08T09:03:49,092 molecules.molecules_distance_matrix( 2025-09-08T09:03:49,092 ^ 2025-09-08T09:03:49,092 ------------------------------------------------------------ 2025-09-08T09:03:49,093 molmod/ext.pyx:189:17: cimported module has no attribute 'molecules_distance_matrix' 2025-09-08T09:03:49,095 Error compiling Cython file: 2025-09-08T09:03:49,095 ------------------------------------------------------------ 2025-09-08T09:03:49,095 ... 2025-09-08T09:03:49,095 def similarity_table_labels(const long[::1] labels not None): 2025-09-08T09:03:49,095 cdef size_t n = labels.shape[0] 2025-09-08T09:03:49,095 cdef np.ndarray[long, ndim=2] labels_table = np.zeros(((n*(n-1))/2, 2), dtype=int) 2025-09-08T09:03:49,095 similarity.similarity_table_labels(n, &labels[0], &labels_table[0, 0]) 2025-09-08T09:03:49,095 ^ 2025-09-08T09:03:49,096 ------------------------------------------------------------ 2025-09-08T09:03:49,096 molmod/ext.pyx:203:14: cimported module has no attribute 'similarity_table_labels' 2025-09-08T09:03:49,097 Error compiling Cython file: 2025-09-08T09:03:49,097 ------------------------------------------------------------ 2025-09-08T09:03:49,097 ... 2025-09-08T09:03:49,098 def similarity_table_distances(const double[:, ::1] distance_matrix not None): 2025-09-08T09:03:49,098 cdef size_t n = distance_matrix.shape[0] 2025-09-08T09:03:49,098 if distance_matrix.shape[1] != n: 2025-09-08T09:03:49,098 raise TypeError('distance_matrix must be sqaure') 2025-09-08T09:03:49,098 cdef np.ndarray[double] distances_table = np.zeros(((n*(n-1))/2), dtype=float) 2025-09-08T09:03:49,098 similarity.similarity_table_distances(n, &distance_matrix[0, 0], &distances_table[0]) 2025-09-08T09:03:49,098 ^ 2025-09-08T09:03:49,098 ------------------------------------------------------------ 2025-09-08T09:03:49,098 molmod/ext.pyx:212:14: cimported module has no attribute 'similarity_table_distances' 2025-09-08T09:03:49,101 Error compiling Cython file: 2025-09-08T09:03:49,101 ------------------------------------------------------------ 2025-09-08T09:03:49,101 ... 2025-09-08T09:03:49,101 raise TypeError('labels1 and distances1 must have the same numbers of rows.') 2025-09-08T09:03:49,101 if labels2.shape[1] != 2: 2025-09-08T09:03:49,101 raise TypeError('labels1 must have two columns.') 2025-09-08T09:03:49,101 if distances2.shape[0] != n2: 2025-09-08T09:03:49,101 raise TypeError('labels2 and distances2 must have the same numbers of rows.') 2025-09-08T09:03:49,101 return similarity.similarity_measure(n1, &labels1[0, 0], &distances1[0], 2025-09-08T09:03:49,102 ^ 2025-09-08T09:03:49,102 ------------------------------------------------------------ 2025-09-08T09:03:49,102 molmod/ext.pyx:229:21: cimported module has no attribute 'similarity_measure' 2025-09-08T09:03:49,106 Error compiling Cython file: 2025-09-08T09:03:49,106 ------------------------------------------------------------ 2025-09-08T09:03:49,106 ... 2025-09-08T09:03:49,106 raise ValueError('Radius must be positive.') 2025-09-08T09:03:49,106 if max_ranges.shape[0] != 3: 2025-09-08T09:03:49,106 raise TypeError('max_ranges must have shape (3, ).') 2025-09-08T09:03:49,106 if indexes.shape[1] != 3: 2025-09-08T09:03:49,106 raise TypeError('indexes must have three columns.') 2025-09-08T09:03:49,107 return unit_cells.unit_cell_get_radius_indexes(&matrix[0, 0], &reciprocal[0, 0], radius, 2025-09-08T09:03:49,107 ^ 2025-09-08T09:03:49,107 ------------------------------------------------------------ 2025-09-08T09:03:49,107 molmod/ext.pyx:253:21: cimported module has no attribute 'unit_cell_get_radius_indexes' 2025-09-08T09:03:49,956 Traceback (most recent call last): 2025-09-08T09:03:49,964 File "", line 2, in 2025-09-08T09:03:49,965 exec(compile(''' 2025-09-08T09:03:49,965 ~~~~^^^^^^^^^^^^ 2025-09-08T09:03:49,965 # This is -- a caller that pip uses to run setup.py 2025-09-08T09:03:49,965 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:03:49,965 ...<32 lines>... 2025-09-08T09:03:49,965 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T09:03:49,965 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:03:49,965 ''' % ('/tmp/pip-wheel-sy_jguvz/molmod_2419afeae1724a848a66bd4cc56c0061/setup.py',), "", "exec")) 2025-09-08T09:03:49,965 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:03:49,966 File "", line 35, in 2025-09-08T09:03:49,966 File "/tmp/pip-wheel-sy_jguvz/molmod_2419afeae1724a848a66bd4cc56c0061/setup.py", line 69, in 2025-09-08T09:03:49,966 setup( 2025-09-08T09:03:49,966 ~~~~~^ 2025-09-08T09:03:49,966 name='molmod', 2025-09-08T09:03:49,966 ^^^^^^^^^^^^^^ 2025-09-08T09:03:49,966 ...<30 lines>... 2025-09-08T09:03:49,966 ], 2025-09-08T09:03:49,967 ^^ 2025-09-08T09:03:49,967 ) 2025-09-08T09:03:49,967 ^ 2025-09-08T09:03:49,967 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-08T09:03:49,967 return distutils.core.setup(**attrs) 2025-09-08T09:03:49,967 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:49,967 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-08T09:03:49,967 return run_commands(dist) 2025-09-08T09:03:49,967 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-08T09:03:49,968 dist.run_commands() 2025-09-08T09:03:49,968 ~~~~~~~~~~~~~~~~~^^ 2025-09-08T09:03:49,968 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-08T09:03:49,968 self.run_command(cmd) 2025-09-08T09:03:49,968 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T09:03:49,968 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T09:03:49,968 super().run_command(command) 2025-09-08T09:03:49,968 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:49,968 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T09:03:49,969 cmd_obj.run() 2025-09-08T09:03:49,969 ~~~~~~~~~~~^^ 2025-09-08T09:03:49,969 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run 2025-09-08T09:03:49,969 self.run_command("build") 2025-09-08T09:03:49,969 ~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:49,969 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T09:03:49,969 self.distribution.run_command(command) 2025-09-08T09:03:49,970 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:49,970 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T09:03:49,970 super().run_command(command) 2025-09-08T09:03:49,970 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:49,970 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T09:03:49,971 cmd_obj.run() 2025-09-08T09:03:49,971 ~~~~~~~~~~~^^ 2025-09-08T09:03:49,971 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run 2025-09-08T09:03:49,971 self.run_command(cmd_name) 2025-09-08T09:03:49,971 ~~~~~~~~~~~~~~~~^^^^^^^^^^ 2025-09-08T09:03:49,971 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T09:03:49,971 self.distribution.run_command(command) 2025-09-08T09:03:49,972 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:49,972 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T09:03:49,972 super().run_command(command) 2025-09-08T09:03:49,972 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:03:49,972 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T09:03:49,972 cmd_obj.run() 2025-09-08T09:03:49,973 ~~~~~~~~~~~^^ 2025-09-08T09:03:49,973 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 368, in run 2025-09-08T09:03:49,973 self.build_extensions() 2025-09-08T09:03:49,973 ~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T09:03:49,973 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 484, in build_extensions 2025-09-08T09:03:49,973 self._build_extensions_serial() 2025-09-08T09:03:49,973 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T09:03:49,974 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 510, in _build_extensions_serial 2025-09-08T09:03:49,974 self.build_extension(ext) 2025-09-08T09:03:49,974 ~~~~~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T09:03:49,974 File "/usr/local/lib/python3.13/dist-packages/Cython/Distutils/build_ext.py", line 131, in build_extension 2025-09-08T09:03:49,974 new_ext = cythonize( 2025-09-08T09:03:49,974 ~~~~~~~~~^ 2025-09-08T09:03:49,974 ext,force=self.force, quiet=self.verbose == 0, **options 2025-09-08T09:03:49,974 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:03:49,974 )[0] 2025-09-08T09:03:49,975 ^ 2025-09-08T09:03:49,975 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize 2025-09-08T09:03:49,975 cythonize_one(*args) 2025-09-08T09:03:49,975 ~~~~~~~~~~~~~^^^^^^^ 2025-09-08T09:03:49,975 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one 2025-09-08T09:03:49,976 raise CompileError(None, pyx_file) 2025-09-08T09:03:49,976 Cython.Compiler.Errors.CompileError: molmod/ext.pyx 2025-09-08T09:03:50,500 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T09:03:50,513 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T09:03:50,513 exec(compile('"'"''"'"''"'"' 2025-09-08T09:03:50,513 # This is -- a caller that pip uses to run setup.py 2025-09-08T09:03:50,513 # 2025-09-08T09:03:50,513 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T09:03:50,513 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T09:03:50,513 # - It provides a clear error message when setuptools is not installed. 2025-09-08T09:03:50,513 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T09:03:50,513 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T09:03:50,513 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T09:03:50,513 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T09:03:50,513 import os, sys, tokenize, traceback 2025-09-08T09:03:50,513 2025-09-08T09:03:50,513 try: 2025-09-08T09:03:50,513 import setuptools 2025-09-08T09:03:50,513 except ImportError: 2025-09-08T09:03:50,513 print( 2025-09-08T09:03:50,513 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T09:03:50,513 "the build environment with exception:", 2025-09-08T09:03:50,513 file=sys.stderr, 2025-09-08T09:03:50,513 ) 2025-09-08T09:03:50,513 traceback.print_exc() 2025-09-08T09:03:50,513 sys.exit(1) 2025-09-08T09:03:50,513 2025-09-08T09:03:50,513 __file__ = %r 2025-09-08T09:03:50,513 sys.argv[0] = __file__ 2025-09-08T09:03:50,513 2025-09-08T09:03:50,513 if os.path.exists(__file__): 2025-09-08T09:03:50,513 filename = __file__ 2025-09-08T09:03:50,513 with tokenize.open(__file__) as f: 2025-09-08T09:03:50,513 setup_py_code = f.read() 2025-09-08T09:03:50,513 else: 2025-09-08T09:03:50,513 filename = "" 2025-09-08T09:03:50,513 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T09:03:50,513 2025-09-08T09:03:50,513 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T09:03:50,513 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-sy_jguvz/molmod_2419afeae1724a848a66bd4cc56c0061/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-1f0kfm8a[/] 2025-09-08T09:03:50,514 [bold magenta]cwd[/]: /tmp/pip-wheel-sy_jguvz/molmod_2419afeae1724a848a66bd4cc56c0061/ 2025-09-08T09:03:50,514 Building wheel for molmod (setup.py): finished with status 'error' 2025-09-08T09:03:50,515 ERROR: Failed building wheel for molmod 2025-09-08T09:03:50,516 Running setup.py clean for molmod 2025-09-08T09:03:50,517 Running command python setup.py clean 2025-09-08T09:03:51,437 fatal: not a git repository (or any parent up to mount point /) 2025-09-08T09:03:51,437 Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). 2025-09-08T09:03:51,825 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:03:51,825 !! 2025-09-08T09:03:51,825 ******************************************************************************** 2025-09-08T09:03:51,825 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:03:51,825 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-08T09:03:51,826 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:03:51,826 ******************************************************************************** 2025-09-08T09:03:51,826 !! 2025-09-08T09:03:51,826 self._finalize_license_expression() 2025-09-08T09:03:51,900 running clean 2025-09-08T09:03:52,046 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T09:03:52,054 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T09:03:52,054 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T09:03:52,054 removing 'build' 2025-09-08T09:03:52,194 Failed to build molmod 2025-09-08T09:03:52,195 ERROR: Failed to build one or more wheels 2025-09-08T09:03:52,196 Exception information: 2025-09-08T09:03:52,196 Traceback (most recent call last): 2025-09-08T09:03:52,196 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T09:03:52,196 status = _inner_run() 2025-09-08T09:03:52,196 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T09:03:52,196 return self.run(options, args) 2025-09-08T09:03:52,196 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T09:03:52,196 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T09:03:52,196 return func(self, options, args) 2025-09-08T09:03:52,196 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T09:03:52,196 raise CommandError("Failed to build one or more wheels") 2025-09-08T09:03:52,196 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T09:03:52,200 Removed build tracker: '/tmp/pip-build-tracker-y0bdonvr'