2025-02-08T04:25:20,573 Created temporary directory: /tmp/pip-build-tracker-47ls6uu2 2025-02-08T04:25:20,574 Initialized build tracking at /tmp/pip-build-tracker-47ls6uu2 2025-02-08T04:25:20,575 Created build tracker: /tmp/pip-build-tracker-47ls6uu2 2025-02-08T04:25:20,575 Entered build tracker: /tmp/pip-build-tracker-47ls6uu2 2025-02-08T04:25:20,576 Created temporary directory: /tmp/pip-wheel-t9vjrqk2 2025-02-08T04:25:20,580 Created temporary directory: /tmp/pip-ephem-wheel-cache-rkvid2nu 2025-02-08T04:25:20,623 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-02-08T04:25:20,626 2 location(s) to search for versions of protenix: 2025-02-08T04:25:20,626 * https://pypi.org/simple/protenix/ 2025-02-08T04:25:20,626 * https://www.piwheels.org/simple/protenix/ 2025-02-08T04:25:20,627 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2025-02-08T04:25:20,627 Getting page https://pypi.org/simple/protenix/ 2025-02-08T04:25:20,629 Found index url https://pypi.org/simple/ 2025-02-08T04:25:20,880 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2025-02-08T04:25:20,888 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/a8/ea/bbe375d1a89b5e3cbe5e07e56184e29a7b779f964a8ea910337a0746af5e/Protenix-0.0.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) 2025-02-08T04:25:20,889 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/35/f6/105b3517490c13d23880689ef3b4477d072d117ca4cc6f805bad9ee16391/protenix-0.0.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) 2025-02-08T04:25:20,890 Found link https://files.pythonhosted.org/packages/63/d5/22a2098752b2b8c95f2ced18d38918883aa9a5ac8cee9df5174aadfee19c/protenix-0.0.1.tar.gz (from https://pypi.org/simple/protenix/), version: 0.0.1 2025-02-08T04:25:20,890 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/85/33/10bb83edcf222b7cd05cc94d453ac7edfa86f09c7100db8c62fcc894745c/protenix-0.1.0-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,891 Found link https://files.pythonhosted.org/packages/d5/61/cdea4397a181ca2b108c6df0aa4c30e7a6fc34c5b75ad69557569c44b61d/protenix-0.1.0.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.1.0 2025-02-08T04:25:20,892 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/28/00/2206a6a3a02d45eeb6e16c6ffcacff6789f11489238acd07ad5127219741/protenix-0.1.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,893 Found link https://files.pythonhosted.org/packages/2b/7b/20fe2818e890f5d25a892ba31a24b910d0cf34e9f86b990c042c3f91fd05/protenix-0.1.1.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.1.1 2025-02-08T04:25:20,894 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/f5/3f/993181bd5478dccf62a5265df701cc9762d257ac04ea6aec26f2e0ec6b0e/protenix-0.1.2-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:<3.12,>=3.10) 2025-02-08T04:25:20,895 Found link https://files.pythonhosted.org/packages/18/ff/8a30b1df6d1bc731a8b4075a077421e306d85976cae82e758a5f15cef4fd/protenix-0.1.2.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:<3.12,>=3.10), version: 0.1.2 2025-02-08T04:25:20,896 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/c3/31/3b2b20aafa4471bcda6389257ad5348c7762374fe725b0552f836dc13ef6/protenix-0.1.3-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,897 Found link https://files.pythonhosted.org/packages/2c/1c/0788760bb4cd6bae9edc74ef1341e9cc74ad6190b8b5dbd972a361184b97/protenix-0.1.3.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.1.3 2025-02-08T04:25:20,898 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/09/b7/15a72afe3d229492604e5ca7ebed72cd1402068f2d5518e26ebef3f2bb5c/protenix-0.2.0-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,899 Found link https://files.pythonhosted.org/packages/0f/17/fdc141be77d735ddf3bfba80a660873fa13732b6c77847434b969aa66f51/protenix-0.2.0.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.2.0 2025-02-08T04:25:20,900 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/99/56/de0a35a125cc0247a366608c8598bdd949ba6068c02fb8d13e8147f65d9c/protenix-0.3.0-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,901 Found link https://files.pythonhosted.org/packages/b6/96/8d6d036dcaff9c1884fcbaa2c752fed65e24320fab2a0a8b128a615da89d/protenix-0.3.0.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.0 2025-02-08T04:25:20,902 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/bf/6b/1cb9d8eea4be4973f97bd1f138f6da0711fad309b76b5c977b316c6bc511/protenix-0.3.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,903 Found link https://files.pythonhosted.org/packages/9a/85/b1ec219c8b8a3ba735742164561a917f53e81f11d2a3a9544a206f9ac21b/protenix-0.3.1.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.1 2025-02-08T04:25:20,903 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/6d/11/4c2946b935b56d995c7418cfc783c16e9e647de72a34380c42e573d4b28d/protenix-0.3.2-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,904 Found link https://files.pythonhosted.org/packages/65/48/25fdef4629cd5ce68c65f733fc49388378cacd3658cd76b5e88893ca5227/protenix-0.3.2.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.2 2025-02-08T04:25:20,905 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/c7/93/f19c14b2b49405f326fab9594ffd7252ef0e231cc348d61b5e406408c8cf/protenix-0.3.3-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,906 Found link https://files.pythonhosted.org/packages/83/67/8697c13e89ed881756f1d188346b4e241decea92545f611778baa9273a49/protenix-0.3.3.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.3 2025-02-08T04:25:20,906 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/49/29/b5b7a2e6e0802ba1d6256d774aafcce43d86773202697a4d1ebb7ff3a95a/protenix-0.3.4-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,907 Found link https://files.pythonhosted.org/packages/67/bf/6ccce5f88c48f27559d138e5b4e65170e318a0d97c803c655ba3734f9efd/protenix-0.3.4.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.4 2025-02-08T04:25:20,908 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/22/4e/6387baad87ace43b71024601db621c8adb12645ee898bfdf653ffe0067d5/protenix-0.3.5-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,909 Found link https://files.pythonhosted.org/packages/8e/75/ba5a8e3b5e13eab23909185b11b044e4e3db04ade55485e9d7fe09b6e95e/protenix-0.3.5.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.5 2025-02-08T04:25:20,910 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/13/c0/5653f9f3db2450d9c2508c32bccf1503610ef34da8d8d10921db6a750635/protenix-0.3.6-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,911 Found link https://files.pythonhosted.org/packages/02/16/6482a30fa395df9360f808fe44260a9513abff61efdd75f671a7556028eb/protenix-0.3.6.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.6 2025-02-08T04:25:20,911 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/01/68/a09d38d3fc22f34ba7a914f9863ae9b7f2c77f4bfb8fe275aabd477cffa6/protenix-0.3.7-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,913 Found link https://files.pythonhosted.org/packages/fe/58/241e5813c71a2f8d427f579892c69507b4b132537f332faf24f64ebddbc1/protenix-0.3.7.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.7 2025-02-08T04:25:20,913 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/be/4d/3a2a007bfb6bab07c98ec53180368db69bd656a3ee277a6a962068da3b06/protenix-0.3.8-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,914 Found link https://files.pythonhosted.org/packages/1f/aa/2445a83be220fc2a24fd269f34dfbfa2e5c9d025103712070bfc85d9bb3f/protenix-0.3.8.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.8 2025-02-08T04:25:20,915 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/2e/8c/93ac8551d47bd1189977231ce255647b3b86d727d67c9ed7e756215aea3a/protenix-0.3.9-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,915 Found link https://files.pythonhosted.org/packages/57/c4/d9f0a75ae91d1d017c3a3375a9f65ea08165b9123647f085c9d3f8835e36/protenix-0.3.9.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.9 2025-02-08T04:25:20,916 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/53/b4/bc84d60b3c57955f15cb920f570b1f0a0b3248325099a3b4fc4db7c574b3/protenix-0.4.0-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,917 Found link https://files.pythonhosted.org/packages/e9/82/57b5b8cdcfc8221b69016228934083fc0ea2174dbe398e364069b28d88c7/protenix-0.4.0.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.4.0 2025-02-08T04:25:20,918 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/68/b4/6fda3a1c6524a40ae0a928f6c3409b611123a5b4cfce4567da1f3d03d081/protenix-0.4.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,919 Found link https://files.pythonhosted.org/packages/2e/41/41bfd68e1612028242ccc5834bc1aea70140078d7d99b112ad7ed6e1bb51/protenix-0.4.1.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.4.1 2025-02-08T04:25:20,919 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/95/c9/45ab254d0873d33b90dda3bb852e72c7198c043200800a3a8c20a51516ad/protenix-0.4.2-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:20,920 Found link https://files.pythonhosted.org/packages/20/53/57bdd33d8c1ac5706bdb210d3347db01fe954085eb79004a29d355a22685/protenix-0.4.2.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.4.2 2025-02-08T04:25:20,922 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2025-02-08T04:25:20,922 Getting page https://www.piwheels.org/simple/protenix/ 2025-02-08T04:25:20,924 Found index url https://www.piwheels.org/simple/ 2025-02-08T04:25:21,331 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2025-02-08T04:25:21,338 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.4.1-py3-none-any.whl#sha256=48167a0412f33e55e3024ca9598c093e9e60eb96f2815fa11dba8b75a26c8147 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:21,338 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.4.0-py3-none-any.whl#sha256=0ed805ac2fa5dd681d530b84f093142316ea67bd9fba6b63f374d7ec3490756f (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:21,339 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.9-py3-none-any.whl#sha256=86574af5793f00ee12318cfba832f84252f41b928767e598c3a817a9f1c85ae3 (from 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permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.5-py3-none-any.whl#sha256=3719630079eefd5a0ef318cdb45dae22c0b16dd3c6b29bbfcd3b175aa939770b (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:21,342 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.4-py3-none-any.whl#sha256=d375e6e6506082ba1ef1e01d816c701e9287af557cb0852c45aea426702f052f (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:21,342 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.3-py3-none-any.whl#sha256=bce00ef75c8d8f408dca3bd0105c8bc555da5e34c8998748544be1bb5f763c02 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:21,343 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.2-py3-none-any.whl#sha256=0255f130567cda78b0dd7e9e1efee966d489a4302df91f47c2ce7d7c5f9b3400 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:21,344 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.1-py3-none-any.whl#sha256=624b9eaf9450baa3748fbe7d038a393ab59d36d7b191a70d676d592c81f46d1f (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:21,344 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.0-py3-none-any.whl#sha256=c2af82dfdebc9606f320eb2d0ae308e644cd77922b443dcd59e7f778e756ac45 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:21,345 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.2.0-py3-none-any.whl#sha256=0de87030b4ba1d9e3c2b67265493001f00eca096d862816f65f818b739c96c6f (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:21,345 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.3-py3-none-any.whl#sha256=be21c60c572799c5562933a71a3087ae1441533805771913e77578fc6280e314 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:21,346 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.2-py3-none-any.whl#sha256=10909020be81638dbfe8da0ff0bc107ad732dc3dc8e420d09aa3e346c53ac527 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10,<3.12) 2025-02-08T04:25:21,347 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.1-py3-none-any.whl#sha256=aa7a8c0ad8f38f5430cb145bb56675e2b0deb861589bbb05ec6eb09dd95c5f57 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:21,347 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.0-py3-none-any.whl#sha256=95dd14c125ff66c76135ed8525ede80d6be803880749ec813036bb317ca23e6e (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-08T04:25:21,348 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/Protenix-0.0.1-py3-none-any.whl#sha256=5b251c54ef00f26ee302a294be031208ca73350e41e88d05368f4146cdb01794 (from https://www.piwheels.org/simple/protenix/) 2025-02-08T04:25:21,348 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2025-02-08T04:25:21,349 Skipping link: not a file: https://pypi.org/simple/protenix/ 2025-02-08T04:25:21,368 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2025-02-08T04:25:21,370 Collecting protenix==0.4.2 2025-02-08T04:25:21,372 Created temporary directory: /tmp/pip-unpack-uazi9ovg 2025-02-08T04:25:21,589 Downloading protenix-0.4.2.tar.gz (340 kB) 2025-02-08T04:25:22,062 Added protenix==0.4.2 from https://files.pythonhosted.org/packages/20/53/57bdd33d8c1ac5706bdb210d3347db01fe954085eb79004a29d355a22685/protenix-0.4.2.tar.gz to build tracker '/tmp/pip-build-tracker-47ls6uu2' 2025-02-08T04:25:22,064 Running setup.py (path:/tmp/pip-wheel-t9vjrqk2/protenix_630ac64f1cd04d60a65b8f3888647c42/setup.py) egg_info for package protenix 2025-02-08T04:25:22,065 Created temporary directory: /tmp/pip-pip-egg-info-oyl560p9 2025-02-08T04:25:22,065 Preparing metadata (setup.py): started 2025-02-08T04:25:22,067 Running command python setup.py egg_info 2025-02-08T04:25:23,213 running egg_info 2025-02-08T04:25:23,241 creating /tmp/pip-pip-egg-info-oyl560p9/protenix.egg-info 2025-02-08T04:25:23,242 writing /tmp/pip-pip-egg-info-oyl560p9/protenix.egg-info/PKG-INFO 2025-02-08T04:25:23,245 writing dependency_links to /tmp/pip-pip-egg-info-oyl560p9/protenix.egg-info/dependency_links.txt 2025-02-08T04:25:23,246 writing entry points to /tmp/pip-pip-egg-info-oyl560p9/protenix.egg-info/entry_points.txt 2025-02-08T04:25:23,248 writing requirements to /tmp/pip-pip-egg-info-oyl560p9/protenix.egg-info/requires.txt 2025-02-08T04:25:23,249 writing top-level names to /tmp/pip-pip-egg-info-oyl560p9/protenix.egg-info/top_level.txt 2025-02-08T04:25:23,250 writing manifest file '/tmp/pip-pip-egg-info-oyl560p9/protenix.egg-info/SOURCES.txt' 2025-02-08T04:25:23,376 reading manifest file '/tmp/pip-pip-egg-info-oyl560p9/protenix.egg-info/SOURCES.txt' 2025-02-08T04:25:23,378 adding license file 'LICENSE' 2025-02-08T04:25:23,384 writing manifest file '/tmp/pip-pip-egg-info-oyl560p9/protenix.egg-info/SOURCES.txt' 2025-02-08T04:25:23,492 Preparing metadata (setup.py): finished with status 'done' 2025-02-08T04:25:23,496 Source in /tmp/pip-wheel-t9vjrqk2/protenix_630ac64f1cd04d60a65b8f3888647c42 has version 0.4.2, which satisfies requirement protenix==0.4.2 from https://files.pythonhosted.org/packages/20/53/57bdd33d8c1ac5706bdb210d3347db01fe954085eb79004a29d355a22685/protenix-0.4.2.tar.gz 2025-02-08T04:25:23,498 Removed protenix==0.4.2 from https://files.pythonhosted.org/packages/20/53/57bdd33d8c1ac5706bdb210d3347db01fe954085eb79004a29d355a22685/protenix-0.4.2.tar.gz from build tracker '/tmp/pip-build-tracker-47ls6uu2' 2025-02-08T04:25:23,507 Created temporary directory: /tmp/pip-unpack-xbblb5fz 2025-02-08T04:25:23,508 Created temporary directory: /tmp/pip-unpack-bfcuzb5h 2025-02-08T04:25:23,508 Building wheels for collected packages: protenix 2025-02-08T04:25:23,512 Created temporary directory: /tmp/pip-wheel-r9ckc66s 2025-02-08T04:25:23,513 Building wheel for protenix (setup.py): started 2025-02-08T04:25:23,514 Destination directory: /tmp/pip-wheel-r9ckc66s 2025-02-08T04:25:23,515 Running command python setup.py bdist_wheel 2025-02-08T04:25:24,557 running bdist_wheel 2025-02-08T04:25:24,693 running build 2025-02-08T04:25:24,693 running build_py 2025-02-08T04:25:24,726 creating build/lib/scripts 2025-02-08T04:25:24,728 copying scripts/gen_ccd_cache.py -> build/lib/scripts 2025-02-08T04:25:24,730 copying scripts/colabfold_msa.py -> build/lib/scripts 2025-02-08T04:25:24,732 copying scripts/prepare_training_data.py -> build/lib/scripts 2025-02-08T04:25:24,735 copying scripts/__init__.py -> build/lib/scripts 2025-02-08T04:25:24,737 creating build/lib/configs 2025-02-08T04:25:24,739 copying configs/configs_data.py -> build/lib/configs 2025-02-08T04:25:24,741 copying configs/configs_inference.py -> build/lib/configs 2025-02-08T04:25:24,743 copying configs/configs_base.py -> build/lib/configs 2025-02-08T04:25:24,745 copying configs/__init__.py -> build/lib/configs 2025-02-08T04:25:24,747 creating build/lib/runner 2025-02-08T04:25:24,748 copying runner/batch_inference.py -> build/lib/runner 2025-02-08T04:25:24,750 copying runner/msa_search.py -> build/lib/runner 2025-02-08T04:25:24,752 copying runner/ema.py -> build/lib/runner 2025-02-08T04:25:24,755 copying runner/train.py -> build/lib/runner 2025-02-08T04:25:24,757 copying runner/dumper.py -> build/lib/runner 2025-02-08T04:25:24,760 copying runner/__init__.py -> build/lib/runner 2025-02-08T04:25:24,761 copying runner/inference.py -> build/lib/runner 2025-02-08T04:25:24,764 creating build/lib/protenix 2025-02-08T04:25:24,765 copying protenix/__init__.py -> build/lib/protenix 2025-02-08T04:25:24,768 creating build/lib/protenix/metrics 2025-02-08T04:25:24,769 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2025-02-08T04:25:24,772 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2025-02-08T04:25:24,774 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2025-02-08T04:25:24,776 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2025-02-08T04:25:24,778 creating build/lib/protenix/config 2025-02-08T04:25:24,779 copying protenix/config/extend_types.py -> build/lib/protenix/config 2025-02-08T04:25:24,781 copying protenix/config/config.py -> build/lib/protenix/config 2025-02-08T04:25:24,784 copying protenix/config/__init__.py -> build/lib/protenix/config 2025-02-08T04:25:24,787 creating build/lib/protenix/openfold_local 2025-02-08T04:25:24,788 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2025-02-08T04:25:24,791 creating build/lib/protenix/utils 2025-02-08T04:25:24,792 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2025-02-08T04:25:24,794 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2025-02-08T04:25:24,796 copying protenix/utils/training.py -> build/lib/protenix/utils 2025-02-08T04:25:24,799 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2025-02-08T04:25:24,801 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2025-02-08T04:25:24,804 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2025-02-08T04:25:24,807 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2025-02-08T04:25:24,809 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2025-02-08T04:25:24,811 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2025-02-08T04:25:24,813 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2025-02-08T04:25:24,815 copying protenix/utils/seed.py -> build/lib/protenix/utils 2025-02-08T04:25:24,817 copying protenix/utils/logger.py -> build/lib/protenix/utils 2025-02-08T04:25:24,820 creating build/lib/protenix/data 2025-02-08T04:25:24,821 copying protenix/data/featurizer.py -> build/lib/protenix/data 2025-02-08T04:25:24,824 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2025-02-08T04:25:24,827 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2025-02-08T04:25:24,830 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2025-02-08T04:25:24,833 copying protenix/data/json_parser.py -> build/lib/protenix/data 2025-02-08T04:25:24,836 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2025-02-08T04:25:24,840 copying protenix/data/dataset.py -> build/lib/protenix/data 2025-02-08T04:25:24,843 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2025-02-08T04:25:24,847 copying protenix/data/dataloader.py -> build/lib/protenix/data 2025-02-08T04:25:24,851 copying protenix/data/constants.py -> build/lib/protenix/data 2025-02-08T04:25:24,854 copying protenix/data/json_maker.py -> build/lib/protenix/data 2025-02-08T04:25:24,857 copying protenix/data/parser.py -> build/lib/protenix/data 2025-02-08T04:25:24,861 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2025-02-08T04:25:24,864 copying protenix/data/filter.py -> build/lib/protenix/data 2025-02-08T04:25:24,867 copying protenix/data/utils.py -> build/lib/protenix/data 2025-02-08T04:25:24,869 copying protenix/data/ccd.py -> build/lib/protenix/data 2025-02-08T04:25:24,872 copying protenix/data/__init__.py -> build/lib/protenix/data 2025-02-08T04:25:24,874 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2025-02-08T04:25:24,877 creating build/lib/protenix/model 2025-02-08T04:25:24,878 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2025-02-08T04:25:24,881 copying protenix/model/loss.py -> build/lib/protenix/model 2025-02-08T04:25:24,885 copying protenix/model/protenix.py -> build/lib/protenix/model 2025-02-08T04:25:24,888 copying protenix/model/utils.py -> build/lib/protenix/model 2025-02-08T04:25:24,891 copying protenix/model/__init__.py -> build/lib/protenix/model 2025-02-08T04:25:24,892 copying protenix/model/generator.py -> build/lib/protenix/model 2025-02-08T04:25:24,895 creating build/lib/protenix/web_service 2025-02-08T04:25:24,896 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2025-02-08T04:25:24,898 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2025-02-08T04:25:24,901 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2025-02-08T04:25:24,903 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2025-02-08T04:25:24,906 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2025-02-08T04:25:24,907 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2025-02-08T04:25:24,910 creating build/lib/protenix/openfold_local/np 2025-02-08T04:25:24,911 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2025-02-08T04:25:24,913 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2025-02-08T04:25:24,916 creating build/lib/protenix/openfold_local/utils 2025-02-08T04:25:24,918 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2025-02-08T04:25:24,920 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2025-02-08T04:25:24,923 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2025-02-08T04:25:24,924 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2025-02-08T04:25:24,926 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2025-02-08T04:25:24,930 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2025-02-08T04:25:24,932 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2025-02-08T04:25:24,934 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2025-02-08T04:25:24,938 creating build/lib/protenix/openfold_local/data 2025-02-08T04:25:24,939 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2025-02-08T04:25:24,942 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2025-02-08T04:25:24,944 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2025-02-08T04:25:24,946 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2025-02-08T04:25:24,949 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2025-02-08T04:25:24,952 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2025-02-08T04:25:24,954 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2025-02-08T04:25:24,955 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2025-02-08T04:25:24,958 creating build/lib/protenix/openfold_local/model 2025-02-08T04:25:24,959 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2025-02-08T04:25:24,961 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2025-02-08T04:25:24,964 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2025-02-08T04:25:24,967 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2025-02-08T04:25:24,969 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2025-02-08T04:25:24,971 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2025-02-08T04:25:24,974 creating build/lib/protenix/openfold_local/utils/kernel 2025-02-08T04:25:24,975 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2025-02-08T04:25:24,977 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2025-02-08T04:25:24,979 creating build/lib/protenix/openfold_local/utils/geometry 2025-02-08T04:25:24,980 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-08T04:25:24,983 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-08T04:25:24,985 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-08T04:25:24,987 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-08T04:25:24,989 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-08T04:25:24,991 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-08T04:25:24,993 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-08T04:25:24,996 creating build/lib/protenix/openfold_local/data/tools 2025-02-08T04:25:24,997 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2025-02-08T04:25:25,000 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2025-02-08T04:25:25,001 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2025-02-08T04:25:25,003 creating build/lib/protenix/utils/permutation 2025-02-08T04:25:25,005 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2025-02-08T04:25:25,008 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2025-02-08T04:25:25,010 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2025-02-08T04:25:25,013 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2025-02-08T04:25:25,015 creating build/lib/protenix/utils/permutation/chain_permutation 2025-02-08T04:25:25,016 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-02-08T04:25:25,018 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-02-08T04:25:25,020 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-02-08T04:25:25,022 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-02-08T04:25:25,026 creating build/lib/protenix/model/layer_norm 2025-02-08T04:25:25,027 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2025-02-08T04:25:25,028 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2025-02-08T04:25:25,031 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2025-02-08T04:25:25,033 creating build/lib/protenix/model/modules 2025-02-08T04:25:25,034 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2025-02-08T04:25:25,036 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2025-02-08T04:25:25,039 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2025-02-08T04:25:25,042 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2025-02-08T04:25:25,045 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2025-02-08T04:25:25,047 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2025-02-08T04:25:25,049 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2025-02-08T04:25:25,051 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2025-02-08T04:25:25,052 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2025-02-08T04:25:25,055 running egg_info 2025-02-08T04:25:25,085 writing protenix.egg-info/PKG-INFO 2025-02-08T04:25:25,088 writing dependency_links to protenix.egg-info/dependency_links.txt 2025-02-08T04:25:25,090 writing entry points to protenix.egg-info/entry_points.txt 2025-02-08T04:25:25,091 writing requirements to protenix.egg-info/requires.txt 2025-02-08T04:25:25,093 writing top-level names to protenix.egg-info/top_level.txt 2025-02-08T04:25:25,142 reading manifest file 'protenix.egg-info/SOURCES.txt' 2025-02-08T04:25:25,151 adding license file 'LICENSE' 2025-02-08T04:25:25,159 writing manifest file 'protenix.egg-info/SOURCES.txt' 2025-02-08T04:25:25,162 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'protenix.model.layer_norm.kernel' is absent from the `packages` configuration. 2025-02-08T04:25:25,162 !! 2025-02-08T04:25:25,164 ******************************************************************************** 2025-02-08T04:25:25,164 ############################ 2025-02-08T04:25:25,165 # Package would be ignored # 2025-02-08T04:25:25,165 ############################ 2025-02-08T04:25:25,166 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2025-02-08T04:25:25,166 but it is absent from setuptools' `packages` configuration. 2025-02-08T04:25:25,167 This leads to an ambiguous overall configuration. If you want to distribute this 2025-02-08T04:25:25,168 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2025-02-08T04:25:25,169 to the `packages` configuration field. 2025-02-08T04:25:25,170 Alternatively, you can also rely on setuptools' discovery methods 2025-02-08T04:25:25,170 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-02-08T04:25:25,171 instead of `find_packages(...)`/`find:`). 2025-02-08T04:25:25,172 You can read more about "package discovery" on setuptools documentation page: 2025-02-08T04:25:25,173 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-02-08T04:25:25,174 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2025-02-08T04:25:25,175 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2025-02-08T04:25:25,175 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-02-08T04:25:25,176 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-02-08T04:25:25,176 combination with a more fine grained `package-data` configuration. 2025-02-08T04:25:25,177 You can read more about "package data files" on setuptools documentation page: 2025-02-08T04:25:25,178 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-02-08T04:25:25,180 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-02-08T04:25:25,180 even if it does not contain any `.py` files. 2025-02-08T04:25:25,180 On the other hand, currently there is no concept of package data 2025-02-08T04:25:25,181 directory, all directories are treated like packages. 2025-02-08T04:25:25,182 ******************************************************************************** 2025-02-08T04:25:25,183 !! 2025-02-08T04:25:25,183 check.warn(importable) 2025-02-08T04:25:25,184 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'scripts.msa' is absent from the `packages` configuration. 2025-02-08T04:25:25,184 !! 2025-02-08T04:25:25,185 ******************************************************************************** 2025-02-08T04:25:25,186 ############################ 2025-02-08T04:25:25,187 # Package would be ignored # 2025-02-08T04:25:25,187 ############################ 2025-02-08T04:25:25,188 Python recognizes 'scripts.msa' as an importable package[^1], 2025-02-08T04:25:25,188 but it is absent from setuptools' `packages` configuration. 2025-02-08T04:25:25,189 This leads to an ambiguous overall configuration. If you want to distribute this 2025-02-08T04:25:25,190 package, please make sure that 'scripts.msa' is explicitly added 2025-02-08T04:25:25,190 to the `packages` configuration field. 2025-02-08T04:25:25,191 Alternatively, you can also rely on setuptools' discovery methods 2025-02-08T04:25:25,192 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-02-08T04:25:25,192 instead of `find_packages(...)`/`find:`). 2025-02-08T04:25:25,194 You can read more about "package discovery" on setuptools documentation page: 2025-02-08T04:25:25,195 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-02-08T04:25:25,196 If you don't want 'scripts.msa' to be distributed and are 2025-02-08T04:25:25,197 already explicitly excluding 'scripts.msa' via 2025-02-08T04:25:25,197 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-02-08T04:25:25,198 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-02-08T04:25:25,199 combination with a more fine grained `package-data` configuration. 2025-02-08T04:25:25,200 You can read more about "package data files" on setuptools documentation page: 2025-02-08T04:25:25,201 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-02-08T04:25:25,203 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-02-08T04:25:25,204 even if it does not contain any `.py` files. 2025-02-08T04:25:25,204 On the other hand, currently there is no concept of package data 2025-02-08T04:25:25,205 directory, all directories are treated like packages. 2025-02-08T04:25:25,205 ******************************************************************************** 2025-02-08T04:25:25,207 !! 2025-02-08T04:25:25,207 check.warn(importable) 2025-02-08T04:25:25,208 creating build/lib/scripts/msa 2025-02-08T04:25:25,208 copying scripts/msa/step1-get_prot_seq.py -> build/lib/scripts/msa 2025-02-08T04:25:25,209 copying scripts/msa/step2-get_msa.ipynb -> build/lib/scripts/msa 2025-02-08T04:25:25,209 copying scripts/msa/step3-uniref_add_taxid.py -> build/lib/scripts/msa 2025-02-08T04:25:25,210 copying scripts/msa/step4-split_msa_to_uniref_and_others.py -> build/lib/scripts/msa 2025-02-08T04:25:25,210 creating build/lib/protenix/model/layer_norm/kernel 2025-02-08T04:25:25,211 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2025-02-08T04:25:25,211 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2025-02-08T04:25:25,212 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2025-02-08T04:25:25,212 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2025-02-08T04:25:25,246 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-02-08T04:25:25,247 !! 2025-02-08T04:25:25,248 ******************************************************************************** 2025-02-08T04:25:25,248 Please avoid running ``setup.py`` directly. 2025-02-08T04:25:25,249 Instead, use pypa/build, pypa/installer or other 2025-02-08T04:25:25,249 standards-based tools. 2025-02-08T04:25:25,250 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-02-08T04:25:25,251 ******************************************************************************** 2025-02-08T04:25:25,252 !! 2025-02-08T04:25:25,252 self.initialize_options() 2025-02-08T04:25:25,274 installing to build/bdist.linux-armv7l/wheel 2025-02-08T04:25:25,274 running install 2025-02-08T04:25:25,299 running install_lib 2025-02-08T04:25:25,328 creating build/bdist.linux-armv7l/wheel 2025-02-08T04:25:25,330 creating build/bdist.linux-armv7l/wheel/scripts 2025-02-08T04:25:25,332 copying build/lib/scripts/gen_ccd_cache.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-02-08T04:25:25,335 creating build/bdist.linux-armv7l/wheel/scripts/msa 2025-02-08T04:25:25,336 copying build/lib/scripts/msa/step4-split_msa_to_uniref_and_others.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-02-08T04:25:25,338 copying build/lib/scripts/msa/step1-get_prot_seq.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-02-08T04:25:25,340 copying build/lib/scripts/msa/step2-get_msa.ipynb -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-02-08T04:25:25,342 copying build/lib/scripts/msa/step3-uniref_add_taxid.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-02-08T04:25:25,344 copying build/lib/scripts/colabfold_msa.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-02-08T04:25:25,346 copying build/lib/scripts/prepare_training_data.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-02-08T04:25:25,349 copying build/lib/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-02-08T04:25:25,351 creating build/bdist.linux-armv7l/wheel/configs 2025-02-08T04:25:25,352 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2025-02-08T04:25:25,355 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2025-02-08T04:25:25,357 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2025-02-08T04:25:25,361 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2025-02-08T04:25:25,364 creating build/bdist.linux-armv7l/wheel/runner 2025-02-08T04:25:25,365 copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-08T04:25:25,368 copying build/lib/runner/msa_search.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-08T04:25:25,371 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-08T04:25:25,373 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-08T04:25:25,376 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-08T04:25:25,379 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-08T04:25:25,381 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-08T04:25:25,385 creating build/bdist.linux-armv7l/wheel/protenix 2025-02-08T04:25:25,387 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2025-02-08T04:25:25,389 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-02-08T04:25:25,392 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-02-08T04:25:25,395 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-02-08T04:25:25,397 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-02-08T04:25:25,400 creating build/bdist.linux-armv7l/wheel/protenix/config 2025-02-08T04:25:25,402 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-02-08T04:25:25,404 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-02-08T04:25:25,408 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-02-08T04:25:25,411 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2025-02-08T04:25:25,413 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2025-02-08T04:25:25,414 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2025-02-08T04:25:25,416 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2025-02-08T04:25:25,421 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2025-02-08T04:25:25,423 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2025-02-08T04:25:25,425 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2025-02-08T04:25:25,427 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2025-02-08T04:25:25,430 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2025-02-08T04:25:25,431 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-08T04:25:25,434 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-08T04:25:25,437 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-08T04:25:25,439 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-08T04:25:25,442 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-08T04:25:25,444 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-08T04:25:25,447 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-08T04:25:25,449 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-08T04:25:25,452 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-08T04:25:25,456 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-08T04:25:25,458 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-08T04:25:25,460 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-08T04:25:25,464 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-08T04:25:25,466 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-08T04:25:25,469 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-08T04:25:25,473 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2025-02-08T04:25:25,475 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-08T04:25:25,478 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-08T04:25:25,480 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-08T04:25:25,484 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2025-02-08T04:25:25,485 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-02-08T04:25:25,488 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-02-08T04:25:25,491 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-02-08T04:25:25,493 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-08T04:25:25,496 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-08T04:25:25,499 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-08T04:25:25,502 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-08T04:25:25,503 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-08T04:25:25,507 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2025-02-08T04:25:25,509 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-08T04:25:25,512 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-08T04:25:25,516 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-08T04:25:25,519 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-08T04:25:25,521 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-08T04:25:25,523 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-08T04:25:25,526 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2025-02-08T04:25:25,530 creating build/bdist.linux-armv7l/wheel/protenix/utils 2025-02-08T04:25:25,531 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-08T04:25:25,534 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-08T04:25:25,536 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-08T04:25:25,539 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-08T04:25:25,541 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-08T04:25:25,544 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-08T04:25:25,548 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-08T04:25:25,551 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2025-02-08T04:25:25,553 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2025-02-08T04:25:25,554 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-02-08T04:25:25,557 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-02-08T04:25:25,559 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-02-08T04:25:25,561 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-02-08T04:25:25,564 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-02-08T04:25:25,567 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-02-08T04:25:25,570 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-02-08T04:25:25,572 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-02-08T04:25:25,574 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-08T04:25:25,575 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-08T04:25:25,578 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-08T04:25:25,579 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-08T04:25:25,581 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-08T04:25:25,583 creating build/bdist.linux-armv7l/wheel/protenix/data 2025-02-08T04:25:25,584 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,587 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,590 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,592 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,595 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,598 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,600 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,603 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,606 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,608 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,611 copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,613 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,617 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,619 copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,622 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,624 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,627 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,628 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-08T04:25:25,632 creating build/bdist.linux-armv7l/wheel/protenix/model 2025-02-08T04:25:25,633 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-08T04:25:25,636 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2025-02-08T04:25:25,637 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-02-08T04:25:25,640 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2025-02-08T04:25:25,641 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-02-08T04:25:25,644 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-02-08T04:25:25,646 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-02-08T04:25:25,648 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-02-08T04:25:25,650 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-02-08T04:25:25,652 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-02-08T04:25:25,654 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-08T04:25:25,658 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-08T04:25:25,661 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-08T04:25:25,663 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-08T04:25:25,666 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2025-02-08T04:25:25,667 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-08T04:25:25,669 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-08T04:25:25,672 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-08T04:25:25,675 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-08T04:25:25,678 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-08T04:25:25,680 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-08T04:25:25,682 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-08T04:25:25,684 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-08T04:25:25,686 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-08T04:25:25,688 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-08T04:25:25,691 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2025-02-08T04:25:25,693 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2025-02-08T04:25:25,694 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-08T04:25:25,696 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-08T04:25:25,698 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-08T04:25:25,701 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-08T04:25:25,703 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-08T04:25:25,705 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-08T04:25:25,707 running install_egg_info 2025-02-08T04:25:25,740 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.4.2-py3.11.egg-info 2025-02-08T04:25:25,752 running install_scripts 2025-02-08T04:25:25,772 creating build/bdist.linux-armv7l/wheel/protenix-0.4.2.dist-info/WHEEL 2025-02-08T04:25:25,774 creating '/tmp/pip-wheel-r9ckc66s/protenix-0.4.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-02-08T04:25:25,776 adding 'configs/__init__.py' 2025-02-08T04:25:25,779 adding 'configs/configs_base.py' 2025-02-08T04:25:25,781 adding 'configs/configs_data.py' 2025-02-08T04:25:25,782 adding 'configs/configs_inference.py' 2025-02-08T04:25:25,784 adding 'protenix/__init__.py' 2025-02-08T04:25:25,786 adding 'protenix/config/__init__.py' 2025-02-08T04:25:25,788 adding 'protenix/config/config.py' 2025-02-08T04:25:25,789 adding 'protenix/config/extend_types.py' 2025-02-08T04:25:25,802 adding 'protenix/data/__init__.py' 2025-02-08T04:25:25,804 adding 'protenix/data/ccd.py' 2025-02-08T04:25:25,809 adding 'protenix/data/constants.py' 2025-02-08T04:25:25,811 adding 'protenix/data/data_pipeline.py' 2025-02-08T04:25:25,813 adding 'protenix/data/dataloader.py' 2025-02-08T04:25:25,818 adding 'protenix/data/dataset.py' 2025-02-08T04:25:25,822 adding 'protenix/data/featurizer.py' 2025-02-08T04:25:25,825 adding 'protenix/data/filter.py' 2025-02-08T04:25:25,827 adding 'protenix/data/infer_data_pipeline.py' 2025-02-08T04:25:25,829 adding 'protenix/data/json_maker.py' 2025-02-08T04:25:25,832 adding 'protenix/data/json_parser.py' 2025-02-08T04:25:25,834 adding 'protenix/data/json_to_feature.py' 2025-02-08T04:25:25,838 adding 'protenix/data/msa_featurizer.py' 2025-02-08T04:25:25,844 adding 'protenix/data/msa_utils.py' 2025-02-08T04:25:25,856 adding 'protenix/data/parser.py' 2025-02-08T04:25:25,858 adding 'protenix/data/substructure_perms.py' 2025-02-08T04:25:25,860 adding 'protenix/data/tokenizer.py' 2025-02-08T04:25:25,863 adding 'protenix/data/utils.py' 2025-02-08T04:25:25,865 adding 'protenix/metrics/__init__.py' 2025-02-08T04:25:25,867 adding 'protenix/metrics/clash.py' 2025-02-08T04:25:25,869 adding 'protenix/metrics/lddt_metrics.py' 2025-02-08T04:25:25,871 adding 'protenix/metrics/rmsd.py' 2025-02-08T04:25:25,872 adding 'protenix/model/__init__.py' 2025-02-08T04:25:25,874 adding 'protenix/model/generator.py' 2025-02-08T04:25:25,880 adding 'protenix/model/loss.py' 2025-02-08T04:25:25,883 adding 'protenix/model/protenix.py' 2025-02-08T04:25:25,886 adding 'protenix/model/sample_confidence.py' 2025-02-08T04:25:25,888 adding 'protenix/model/utils.py' 2025-02-08T04:25:25,891 adding 'protenix/model/layer_norm/__init__.py' 2025-02-08T04:25:25,892 adding 'protenix/model/layer_norm/layer_norm.py' 2025-02-08T04:25:25,893 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2025-02-08T04:25:25,895 adding 'protenix/model/layer_norm/kernel/compat.h' 2025-02-08T04:25:25,896 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2025-02-08T04:25:25,898 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2025-02-08T04:25:25,900 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2025-02-08T04:25:25,902 adding 'protenix/model/modules/__init__.py' 2025-02-08T04:25:25,904 adding 'protenix/model/modules/confidence.py' 2025-02-08T04:25:25,906 adding 'protenix/model/modules/diffusion.py' 2025-02-08T04:25:25,908 adding 'protenix/model/modules/embedders.py' 2025-02-08T04:25:25,909 adding 'protenix/model/modules/frames.py' 2025-02-08T04:25:25,911 adding 'protenix/model/modules/head.py' 2025-02-08T04:25:25,913 adding 'protenix/model/modules/pairformer.py' 2025-02-08T04:25:25,917 adding 'protenix/model/modules/primitives.py' 2025-02-08T04:25:25,921 adding 'protenix/model/modules/transformer.py' 2025-02-08T04:25:25,923 adding 'protenix/openfold_local/__init__.py' 2025-02-08T04:25:25,924 adding 'protenix/openfold_local/data/__init__.py' 2025-02-08T04:25:25,926 adding 'protenix/openfold_local/data/data_transforms.py' 2025-02-08T04:25:25,927 adding 'protenix/openfold_local/data/errors.py' 2025-02-08T04:25:25,930 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2025-02-08T04:25:25,931 adding 'protenix/openfold_local/data/msa_identifiers.py' 2025-02-08T04:25:25,934 adding 'protenix/openfold_local/data/msa_pairing.py' 2025-02-08T04:25:25,937 adding 'protenix/openfold_local/data/parsers.py' 2025-02-08T04:25:25,940 adding 'protenix/openfold_local/data/templates.py' 2025-02-08T04:25:25,941 adding 'protenix/openfold_local/data/tools/__init__.py' 2025-02-08T04:25:25,943 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2025-02-08T04:25:25,945 adding 'protenix/openfold_local/data/tools/utils.py' 2025-02-08T04:25:25,946 adding 'protenix/openfold_local/model/__init__.py' 2025-02-08T04:25:25,948 adding 'protenix/openfold_local/model/dropout.py' 2025-02-08T04:25:25,949 adding 'protenix/openfold_local/model/outer_product_mean.py' 2025-02-08T04:25:25,952 adding 'protenix/openfold_local/model/primitives.py' 2025-02-08T04:25:25,954 adding 'protenix/openfold_local/model/triangular_attention.py' 2025-02-08T04:25:25,957 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2025-02-08T04:25:25,959 adding 'protenix/openfold_local/np/__init__.py' 2025-02-08T04:25:25,964 adding 'protenix/openfold_local/np/residue_constants.py' 2025-02-08T04:25:25,966 adding 'protenix/openfold_local/utils/__init__.py' 2025-02-08T04:25:25,968 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2025-02-08T04:25:25,970 adding 'protenix/openfold_local/utils/checkpointing.py' 2025-02-08T04:25:25,972 adding 'protenix/openfold_local/utils/chunk_utils.py' 2025-02-08T04:25:25,974 adding 'protenix/openfold_local/utils/feats.py' 2025-02-08T04:25:25,976 adding 'protenix/openfold_local/utils/precision_utils.py' 2025-02-08T04:25:25,980 adding 'protenix/openfold_local/utils/rigid_utils.py' 2025-02-08T04:25:25,983 adding 'protenix/openfold_local/utils/tensor_utils.py' 2025-02-08T04:25:25,984 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2025-02-08T04:25:25,986 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2025-02-08T04:25:25,987 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2025-02-08T04:25:25,989 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2025-02-08T04:25:25,990 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2025-02-08T04:25:25,991 adding 'protenix/openfold_local/utils/geometry/utils.py' 2025-02-08T04:25:25,993 adding 'protenix/openfold_local/utils/geometry/vector.py' 2025-02-08T04:25:25,994 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2025-02-08T04:25:25,996 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2025-02-08T04:25:25,997 adding 'protenix/utils/__init__.py' 2025-02-08T04:25:26,000 adding 'protenix/utils/cropping.py' 2025-02-08T04:25:26,002 adding 'protenix/utils/distributed.py' 2025-02-08T04:25:26,003 adding 'protenix/utils/file_io.py' 2025-02-08T04:25:26,004 adding 'protenix/utils/geometry.py' 2025-02-08T04:25:26,006 adding 'protenix/utils/logger.py' 2025-02-08T04:25:26,007 adding 'protenix/utils/lr_scheduler.py' 2025-02-08T04:25:26,009 adding 'protenix/utils/metrics.py' 2025-02-08T04:25:26,010 adding 'protenix/utils/scatter_utils.py' 2025-02-08T04:25:26,012 adding 'protenix/utils/seed.py' 2025-02-08T04:25:26,013 adding 'protenix/utils/torch_utils.py' 2025-02-08T04:25:26,015 adding 'protenix/utils/training.py' 2025-02-08T04:25:26,016 adding 'protenix/utils/permutation/__init__.py' 2025-02-08T04:25:26,020 adding 'protenix/utils/permutation/atom_permutation.py' 2025-02-08T04:25:26,022 adding 'protenix/utils/permutation/permutation.py' 2025-02-08T04:25:26,024 adding 'protenix/utils/permutation/utils.py' 2025-02-08T04:25:26,026 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2025-02-08T04:25:26,030 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2025-02-08T04:25:26,032 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2025-02-08T04:25:26,033 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2025-02-08T04:25:26,035 adding 'protenix/web_service/__init__.py' 2025-02-08T04:25:26,037 adding 'protenix/web_service/colab_request_parser.py' 2025-02-08T04:25:26,039 adding 'protenix/web_service/colab_request_utils.py' 2025-02-08T04:25:26,040 adding 'protenix/web_service/dependency_url.py' 2025-02-08T04:25:26,042 adding 'protenix/web_service/prediction_visualization.py' 2025-02-08T04:25:26,044 adding 'protenix/web_service/viewer.py' 2025-02-08T04:25:26,047 adding 'runner/__init__.py' 2025-02-08T04:25:26,049 adding 'runner/batch_inference.py' 2025-02-08T04:25:26,051 adding 'runner/dumper.py' 2025-02-08T04:25:26,052 adding 'runner/ema.py' 2025-02-08T04:25:26,054 adding 'runner/inference.py' 2025-02-08T04:25:26,056 adding 'runner/msa_search.py' 2025-02-08T04:25:26,059 adding 'runner/train.py' 2025-02-08T04:25:26,060 adding 'scripts/__init__.py' 2025-02-08T04:25:26,062 adding 'scripts/colabfold_msa.py' 2025-02-08T04:25:26,064 adding 'scripts/gen_ccd_cache.py' 2025-02-08T04:25:26,066 adding 'scripts/prepare_training_data.py' 2025-02-08T04:25:26,068 adding 'scripts/msa/step1-get_prot_seq.py' 2025-02-08T04:25:26,069 adding 'scripts/msa/step2-get_msa.ipynb' 2025-02-08T04:25:26,071 adding 'scripts/msa/step3-uniref_add_taxid.py' 2025-02-08T04:25:26,072 adding 'scripts/msa/step4-split_msa_to_uniref_and_others.py' 2025-02-08T04:25:26,074 adding 'protenix-0.4.2.dist-info/LICENSE' 2025-02-08T04:25:26,075 adding 'protenix-0.4.2.dist-info/METADATA' 2025-02-08T04:25:26,076 adding 'protenix-0.4.2.dist-info/WHEEL' 2025-02-08T04:25:26,078 adding 'protenix-0.4.2.dist-info/entry_points.txt' 2025-02-08T04:25:26,079 adding 'protenix-0.4.2.dist-info/top_level.txt' 2025-02-08T04:25:26,081 adding 'protenix-0.4.2.dist-info/RECORD' 2025-02-08T04:25:26,088 removing build/bdist.linux-armv7l/wheel 2025-02-08T04:25:26,236 Building wheel for protenix (setup.py): finished with status 'done' 2025-02-08T04:25:26,243 Created wheel for protenix: filename=protenix-0.4.2-py3-none-any.whl size=418287 sha256=ce76bd46d2b3f3681ef6f581b036accd18133efea630b4765f0c4ce74521d049 2025-02-08T04:25:26,244 Stored in directory: /tmp/pip-ephem-wheel-cache-rkvid2nu/wheels/19/82/5d/caa9044e6d5103704f4ac4c4654b4c11dfbfcbbc85540812ce 2025-02-08T04:25:26,259 Successfully built protenix 2025-02-08T04:25:26,272 Removed build tracker: '/tmp/pip-build-tracker-47ls6uu2'