2025-01-21T07:03:17,188 Created temporary directory: /tmp/pip-build-tracker-x8zzkyrb 2025-01-21T07:03:17,189 Initialized build tracking at /tmp/pip-build-tracker-x8zzkyrb 2025-01-21T07:03:17,190 Created build tracker: /tmp/pip-build-tracker-x8zzkyrb 2025-01-21T07:03:17,190 Entered build tracker: /tmp/pip-build-tracker-x8zzkyrb 2025-01-21T07:03:17,191 Created temporary directory: /tmp/pip-wheel-3qescmhb 2025-01-21T07:03:17,195 Created temporary directory: /tmp/pip-ephem-wheel-cache-5ilpg49v 2025-01-21T07:03:17,241 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-01-21T07:03:17,244 2 location(s) to search for versions of protenix: 2025-01-21T07:03:17,244 * https://pypi.org/simple/protenix/ 2025-01-21T07:03:17,244 * https://www.piwheels.org/simple/protenix/ 2025-01-21T07:03:17,245 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2025-01-21T07:03:17,246 Getting page https://pypi.org/simple/protenix/ 2025-01-21T07:03:17,247 Found index url https://pypi.org/simple/ 2025-01-21T07:03:17,465 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2025-01-21T07:03:17,473 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/) 2025-01-21T07:03:17,473 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/) 2025-01-21T07:03:17,474 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 2025-01-21T07:03:17,475 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) 2025-01-21T07:03:17,476 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 2025-01-21T07:03:17,477 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) 2025-01-21T07:03:17,478 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 2025-01-21T07:03:17,478 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) 2025-01-21T07:03:17,480 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 2025-01-21T07:03:17,480 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) 2025-01-21T07:03:17,481 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 2025-01-21T07:03:17,482 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) 2025-01-21T07:03:17,483 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 2025-01-21T07:03:17,484 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) 2025-01-21T07:03:17,485 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 2025-01-21T07:03:17,485 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) 2025-01-21T07:03:17,486 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 2025-01-21T07:03:17,487 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) 2025-01-21T07:03:17,487 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 2025-01-21T07:03:17,488 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) 2025-01-21T07:03:17,489 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 2025-01-21T07:03:17,490 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) 2025-01-21T07:03:17,491 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 2025-01-21T07:03:17,491 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) 2025-01-21T07:03:17,492 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 2025-01-21T07:03:17,493 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) 2025-01-21T07:03:17,494 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 2025-01-21T07:03:17,494 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) 2025-01-21T07:03:17,496 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 2025-01-21T07:03:17,496 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) 2025-01-21T07:03:17,497 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 2025-01-21T07:03:17,497 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) 2025-01-21T07:03:17,498 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 2025-01-21T07:03:17,499 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) 2025-01-21T07:03:17,500 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 2025-01-21T07:03:17,501 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) 2025-01-21T07:03:17,501 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 2025-01-21T07:03:17,502 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2025-01-21T07:03:17,503 Getting page https://www.piwheels.org/simple/protenix/ 2025-01-21T07:03:17,504 Found index url https://www.piwheels.org/simple/ 2025-01-21T07:03:17,681 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2025-01-21T07:03:17,687 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) 2025-01-21T07:03:17,688 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.9-py3-none-any.whl#sha256=86574af5793f00ee12318cfba832f84252f41b928767e598c3a817a9f1c85ae3 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-21T07:03:17,689 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.8-py3-none-any.whl#sha256=f48473ae65c65269825258d1076bd926d822c91535ffc1016ec1b6aa051d6c12 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-21T07:03:17,689 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.7-py3-none-any.whl#sha256=879dd062411f30d5ec9abcb895ee06a2acd7c7435135ea457af7d665e7351ed5 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-21T07:03:17,690 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.6-py3-none-any.whl#sha256=a740708421da6bea03c22fc527e96ec0ce27329a9cfb8adb213d0ad1ec66d031 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-21T07:03:17,691 Skipping link: No binaries 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) 2025-01-21T07:03:17,691 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) 2025-01-21T07:03:17,692 Skipping link: No binaries permitted for protenix: 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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) 2025-01-21T07:03:17,694 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) 2025-01-21T07:03:17,694 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) 2025-01-21T07:03:17,695 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) 2025-01-21T07:03:17,696 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) 2025-01-21T07:03:17,696 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) 2025-01-21T07:03:17,697 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/) 2025-01-21T07:03:17,698 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2025-01-21T07:03:17,698 Skipping link: not a file: https://pypi.org/simple/protenix/ 2025-01-21T07:03:17,719 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2025-01-21T07:03:17,721 Collecting protenix==0.4.1 2025-01-21T07:03:17,724 Created temporary directory: /tmp/pip-unpack-c7vcsqwf 2025-01-21T07:03:18,108 Downloading protenix-0.4.1.tar.gz (340 kB) 2025-01-21T07:03:22,410 Added protenix==0.4.1 from https://files.pythonhosted.org/packages/2e/41/41bfd68e1612028242ccc5834bc1aea70140078d7d99b112ad7ed6e1bb51/protenix-0.4.1.tar.gz to build tracker '/tmp/pip-build-tracker-x8zzkyrb' 2025-01-21T07:03:22,413 Running setup.py (path:/tmp/pip-wheel-3qescmhb/protenix_2c72393bcf7e4be793ac5a18d24001cd/setup.py) egg_info for package protenix 2025-01-21T07:03:22,414 Created temporary directory: /tmp/pip-pip-egg-info-t82sqgyf 2025-01-21T07:03:22,414 Preparing metadata (setup.py): started 2025-01-21T07:03:22,416 Running command python setup.py egg_info 2025-01-21T07:03:23,700 running egg_info 2025-01-21T07:03:23,728 creating /tmp/pip-pip-egg-info-t82sqgyf/protenix.egg-info 2025-01-21T07:03:23,730 writing /tmp/pip-pip-egg-info-t82sqgyf/protenix.egg-info/PKG-INFO 2025-01-21T07:03:23,733 writing dependency_links to /tmp/pip-pip-egg-info-t82sqgyf/protenix.egg-info/dependency_links.txt 2025-01-21T07:03:23,735 writing entry points to /tmp/pip-pip-egg-info-t82sqgyf/protenix.egg-info/entry_points.txt 2025-01-21T07:03:23,736 writing requirements to /tmp/pip-pip-egg-info-t82sqgyf/protenix.egg-info/requires.txt 2025-01-21T07:03:23,738 writing top-level names to /tmp/pip-pip-egg-info-t82sqgyf/protenix.egg-info/top_level.txt 2025-01-21T07:03:23,739 writing manifest file '/tmp/pip-pip-egg-info-t82sqgyf/protenix.egg-info/SOURCES.txt' 2025-01-21T07:03:23,857 reading manifest file '/tmp/pip-pip-egg-info-t82sqgyf/protenix.egg-info/SOURCES.txt' 2025-01-21T07:03:23,859 adding license file 'LICENSE' 2025-01-21T07:03:23,865 writing manifest file '/tmp/pip-pip-egg-info-t82sqgyf/protenix.egg-info/SOURCES.txt' 2025-01-21T07:03:23,975 Preparing metadata (setup.py): finished with status 'done' 2025-01-21T07:03:23,979 Source in /tmp/pip-wheel-3qescmhb/protenix_2c72393bcf7e4be793ac5a18d24001cd has version 0.4.1, which satisfies requirement protenix==0.4.1 from https://files.pythonhosted.org/packages/2e/41/41bfd68e1612028242ccc5834bc1aea70140078d7d99b112ad7ed6e1bb51/protenix-0.4.1.tar.gz 2025-01-21T07:03:23,980 Removed protenix==0.4.1 from https://files.pythonhosted.org/packages/2e/41/41bfd68e1612028242ccc5834bc1aea70140078d7d99b112ad7ed6e1bb51/protenix-0.4.1.tar.gz from build tracker '/tmp/pip-build-tracker-x8zzkyrb' 2025-01-21T07:03:23,989 Created temporary directory: /tmp/pip-unpack-lgq2lr6p 2025-01-21T07:03:23,990 Created temporary directory: /tmp/pip-unpack-rn57_kae 2025-01-21T07:03:23,991 Building wheels for collected packages: protenix 2025-01-21T07:03:23,995 Created temporary directory: /tmp/pip-wheel-gu8e2h8e 2025-01-21T07:03:23,996 Building wheel for protenix (setup.py): started 2025-01-21T07:03:23,997 Destination directory: /tmp/pip-wheel-gu8e2h8e 2025-01-21T07:03:23,998 Running command python setup.py bdist_wheel 2025-01-21T07:03:25,025 running bdist_wheel 2025-01-21T07:03:25,158 running build 2025-01-21T07:03:25,158 running build_py 2025-01-21T07:03:25,188 creating build/lib/scripts 2025-01-21T07:03:25,190 copying scripts/prepare_training_data.py -> build/lib/scripts 2025-01-21T07:03:25,193 copying scripts/gen_ccd_cache.py -> build/lib/scripts 2025-01-21T07:03:25,195 copying scripts/colabfold_msa.py -> build/lib/scripts 2025-01-21T07:03:25,198 copying scripts/__init__.py -> build/lib/scripts 2025-01-21T07:03:25,200 creating build/lib/runner 2025-01-21T07:03:25,202 copying runner/train.py -> build/lib/runner 2025-01-21T07:03:25,204 copying runner/inference.py -> build/lib/runner 2025-01-21T07:03:25,207 copying runner/dumper.py -> build/lib/runner 2025-01-21T07:03:25,210 copying runner/batch_inference.py -> build/lib/runner 2025-01-21T07:03:25,212 copying runner/ema.py -> build/lib/runner 2025-01-21T07:03:25,214 copying runner/__init__.py -> build/lib/runner 2025-01-21T07:03:25,215 copying runner/msa_search.py -> build/lib/runner 2025-01-21T07:03:25,218 creating build/lib/protenix 2025-01-21T07:03:25,219 copying protenix/__init__.py -> build/lib/protenix 2025-01-21T07:03:25,221 creating build/lib/configs 2025-01-21T07:03:25,222 copying configs/configs_base.py -> build/lib/configs 2025-01-21T07:03:25,224 copying configs/configs_inference.py -> build/lib/configs 2025-01-21T07:03:25,226 copying configs/configs_data.py -> build/lib/configs 2025-01-21T07:03:25,228 copying configs/__init__.py -> build/lib/configs 2025-01-21T07:03:25,230 creating build/lib/protenix/config 2025-01-21T07:03:25,231 copying protenix/config/config.py -> build/lib/protenix/config 2025-01-21T07:03:25,234 copying protenix/config/extend_types.py -> build/lib/protenix/config 2025-01-21T07:03:25,236 copying protenix/config/__init__.py -> build/lib/protenix/config 2025-01-21T07:03:25,239 creating build/lib/protenix/model 2025-01-21T07:03:25,240 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2025-01-21T07:03:25,243 copying protenix/model/loss.py -> build/lib/protenix/model 2025-01-21T07:03:25,246 copying protenix/model/generator.py -> build/lib/protenix/model 2025-01-21T07:03:25,248 copying protenix/model/protenix.py -> build/lib/protenix/model 2025-01-21T07:03:25,251 copying protenix/model/utils.py -> build/lib/protenix/model 2025-01-21T07:03:25,253 copying protenix/model/__init__.py -> build/lib/protenix/model 2025-01-21T07:03:25,255 creating build/lib/protenix/web_service 2025-01-21T07:03:25,257 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2025-01-21T07:03:25,259 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2025-01-21T07:03:25,261 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2025-01-21T07:03:25,264 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2025-01-21T07:03:25,265 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2025-01-21T07:03:25,268 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2025-01-21T07:03:25,271 creating build/lib/protenix/utils 2025-01-21T07:03:25,273 copying protenix/utils/training.py -> build/lib/protenix/utils 2025-01-21T07:03:25,275 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2025-01-21T07:03:25,277 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2025-01-21T07:03:25,279 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2025-01-21T07:03:25,281 copying protenix/utils/seed.py -> build/lib/protenix/utils 2025-01-21T07:03:25,283 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2025-01-21T07:03:25,285 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2025-01-21T07:03:25,287 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2025-01-21T07:03:25,290 copying protenix/utils/logger.py -> build/lib/protenix/utils 2025-01-21T07:03:25,292 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2025-01-21T07:03:25,294 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2025-01-21T07:03:25,296 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2025-01-21T07:03:25,298 creating build/lib/protenix/data 2025-01-21T07:03:25,300 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2025-01-21T07:03:25,302 copying protenix/data/json_maker.py -> build/lib/protenix/data 2025-01-21T07:03:25,305 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2025-01-21T07:03:25,307 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2025-01-21T07:03:25,310 copying protenix/data/json_parser.py -> build/lib/protenix/data 2025-01-21T07:03:25,313 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2025-01-21T07:03:25,315 copying protenix/data/dataloader.py -> build/lib/protenix/data 2025-01-21T07:03:25,317 copying protenix/data/constants.py -> build/lib/protenix/data 2025-01-21T07:03:25,320 copying protenix/data/featurizer.py -> build/lib/protenix/data 2025-01-21T07:03:25,323 copying protenix/data/parser.py -> build/lib/protenix/data 2025-01-21T07:03:25,327 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2025-01-21T07:03:25,329 copying protenix/data/ccd.py -> build/lib/protenix/data 2025-01-21T07:03:25,332 copying protenix/data/utils.py -> build/lib/protenix/data 2025-01-21T07:03:25,335 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2025-01-21T07:03:25,337 copying protenix/data/__init__.py -> build/lib/protenix/data 2025-01-21T07:03:25,338 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2025-01-21T07:03:25,341 copying protenix/data/filter.py -> build/lib/protenix/data 2025-01-21T07:03:25,344 copying protenix/data/dataset.py -> build/lib/protenix/data 2025-01-21T07:03:25,347 creating build/lib/protenix/openfold_local 2025-01-21T07:03:25,348 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2025-01-21T07:03:25,351 creating build/lib/protenix/metrics 2025-01-21T07:03:25,352 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2025-01-21T07:03:25,354 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2025-01-21T07:03:25,357 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2025-01-21T07:03:25,359 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2025-01-21T07:03:25,361 creating build/lib/protenix/model/layer_norm 2025-01-21T07:03:25,363 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2025-01-21T07:03:25,365 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2025-01-21T07:03:25,367 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2025-01-21T07:03:25,370 creating build/lib/protenix/model/modules 2025-01-21T07:03:25,371 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2025-01-21T07:03:25,374 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2025-01-21T07:03:25,377 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2025-01-21T07:03:25,379 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2025-01-21T07:03:25,382 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2025-01-21T07:03:25,385 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2025-01-21T07:03:25,389 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2025-01-21T07:03:25,391 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2025-01-21T07:03:25,394 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2025-01-21T07:03:25,397 creating build/lib/protenix/utils/permutation 2025-01-21T07:03:25,398 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2025-01-21T07:03:25,401 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2025-01-21T07:03:25,404 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2025-01-21T07:03:25,406 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2025-01-21T07:03:25,410 creating build/lib/protenix/utils/permutation/chain_permutation 2025-01-21T07:03:25,412 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-01-21T07:03:25,415 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-01-21T07:03:25,417 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-01-21T07:03:25,421 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-01-21T07:03:25,424 creating build/lib/protenix/openfold_local/np 2025-01-21T07:03:25,426 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2025-01-21T07:03:25,429 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2025-01-21T07:03:25,432 creating build/lib/protenix/openfold_local/model 2025-01-21T07:03:25,433 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2025-01-21T07:03:25,436 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2025-01-21T07:03:25,438 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2025-01-21T07:03:25,440 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2025-01-21T07:03:25,443 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2025-01-21T07:03:25,445 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2025-01-21T07:03:25,449 creating build/lib/protenix/openfold_local/utils 2025-01-21T07:03:25,450 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2025-01-21T07:03:25,453 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2025-01-21T07:03:25,455 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2025-01-21T07:03:25,459 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2025-01-21T07:03:25,462 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2025-01-21T07:03:25,464 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2025-01-21T07:03:25,467 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2025-01-21T07:03:25,469 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2025-01-21T07:03:25,472 creating build/lib/protenix/openfold_local/data 2025-01-21T07:03:25,473 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2025-01-21T07:03:25,477 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2025-01-21T07:03:25,480 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2025-01-21T07:03:25,483 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2025-01-21T07:03:25,485 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2025-01-21T07:03:25,488 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2025-01-21T07:03:25,490 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2025-01-21T07:03:25,493 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2025-01-21T07:03:25,496 creating build/lib/protenix/openfold_local/utils/kernel 2025-01-21T07:03:25,498 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2025-01-21T07:03:25,501 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2025-01-21T07:03:25,504 creating build/lib/protenix/openfold_local/utils/geometry 2025-01-21T07:03:25,506 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-21T07:03:25,508 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-21T07:03:25,510 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-21T07:03:25,513 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-21T07:03:25,515 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-21T07:03:25,518 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-21T07:03:25,520 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-21T07:03:25,523 creating build/lib/protenix/openfold_local/data/tools 2025-01-21T07:03:25,524 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2025-01-21T07:03:25,526 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2025-01-21T07:03:25,528 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2025-01-21T07:03:25,531 running egg_info 2025-01-21T07:03:25,563 writing protenix.egg-info/PKG-INFO 2025-01-21T07:03:25,566 writing dependency_links to protenix.egg-info/dependency_links.txt 2025-01-21T07:03:25,568 writing entry points to protenix.egg-info/entry_points.txt 2025-01-21T07:03:25,570 writing requirements to protenix.egg-info/requires.txt 2025-01-21T07:03:25,571 writing top-level names to protenix.egg-info/top_level.txt 2025-01-21T07:03:25,622 reading manifest file 'protenix.egg-info/SOURCES.txt' 2025-01-21T07:03:25,632 adding license file 'LICENSE' 2025-01-21T07:03:25,640 writing manifest file 'protenix.egg-info/SOURCES.txt' 2025-01-21T07:03:25,644 /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. 2025-01-21T07:03:25,644 !! 2025-01-21T07:03:25,646 ******************************************************************************** 2025-01-21T07:03:25,646 ############################ 2025-01-21T07:03:25,647 # Package would be ignored # 2025-01-21T07:03:25,647 ############################ 2025-01-21T07:03:25,648 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2025-01-21T07:03:25,649 but it is absent from setuptools' `packages` configuration. 2025-01-21T07:03:25,650 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-21T07:03:25,651 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2025-01-21T07:03:25,651 to the `packages` configuration field. 2025-01-21T07:03:25,652 Alternatively, you can also rely on setuptools' discovery methods 2025-01-21T07:03:25,653 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-21T07:03:25,653 instead of `find_packages(...)`/`find:`). 2025-01-21T07:03:25,655 You can read more about "package discovery" on setuptools documentation page: 2025-01-21T07:03:25,656 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-21T07:03:25,657 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2025-01-21T07:03:25,658 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2025-01-21T07:03:25,658 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-21T07:03:25,659 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-21T07:03:25,659 combination with a more fine grained `package-data` configuration. 2025-01-21T07:03:25,661 You can read more about "package data files" on setuptools documentation page: 2025-01-21T07:03:25,662 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-21T07:03:25,664 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-21T07:03:25,664 even if it does not contain any `.py` files. 2025-01-21T07:03:25,664 On the other hand, currently there is no concept of package data 2025-01-21T07:03:25,665 directory, all directories are treated like packages. 2025-01-21T07:03:25,665 ******************************************************************************** 2025-01-21T07:03:25,667 !! 2025-01-21T07:03:25,667 check.warn(importable) 2025-01-21T07:03:25,668 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'scripts.msa' is absent from the `packages` configuration. 2025-01-21T07:03:25,669 !! 2025-01-21T07:03:25,670 ******************************************************************************** 2025-01-21T07:03:25,670 ############################ 2025-01-21T07:03:25,671 # Package would be ignored # 2025-01-21T07:03:25,671 ############################ 2025-01-21T07:03:25,672 Python recognizes 'scripts.msa' as an importable package[^1], 2025-01-21T07:03:25,672 but it is absent from setuptools' `packages` configuration. 2025-01-21T07:03:25,673 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-21T07:03:25,673 package, please make sure that 'scripts.msa' is explicitly added 2025-01-21T07:03:25,674 to the `packages` configuration field. 2025-01-21T07:03:25,675 Alternatively, you can also rely on setuptools' discovery methods 2025-01-21T07:03:25,676 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-21T07:03:25,676 instead of `find_packages(...)`/`find:`). 2025-01-21T07:03:25,677 You can read more about "package discovery" on setuptools documentation page: 2025-01-21T07:03:25,678 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-21T07:03:25,679 If you don't want 'scripts.msa' to be distributed and are 2025-01-21T07:03:25,680 already explicitly excluding 'scripts.msa' via 2025-01-21T07:03:25,681 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-21T07:03:25,681 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-21T07:03:25,682 combination with a more fine grained `package-data` configuration. 2025-01-21T07:03:25,683 You can read more about "package data files" on setuptools documentation page: 2025-01-21T07:03:25,684 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-21T07:03:25,686 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-21T07:03:25,686 even if it does not contain any `.py` files. 2025-01-21T07:03:25,687 On the other hand, currently there is no concept of package data 2025-01-21T07:03:25,687 directory, all directories are treated like packages. 2025-01-21T07:03:25,688 ******************************************************************************** 2025-01-21T07:03:25,689 !! 2025-01-21T07:03:25,690 check.warn(importable) 2025-01-21T07:03:25,690 creating build/lib/scripts/msa 2025-01-21T07:03:25,691 copying scripts/msa/step1-get_prot_seq.py -> build/lib/scripts/msa 2025-01-21T07:03:25,691 copying scripts/msa/step2-get_msa.ipynb -> build/lib/scripts/msa 2025-01-21T07:03:25,692 copying scripts/msa/step3-uniref_add_taxid.py -> build/lib/scripts/msa 2025-01-21T07:03:25,692 copying scripts/msa/step4-split_msa_to_uniref_and_others.py -> build/lib/scripts/msa 2025-01-21T07:03:25,693 creating build/lib/protenix/model/layer_norm/kernel 2025-01-21T07:03:25,694 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2025-01-21T07:03:25,694 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2025-01-21T07:03:25,695 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2025-01-21T07:03:25,695 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2025-01-21T07:03:25,736 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-01-21T07:03:25,737 !! 2025-01-21T07:03:25,738 ******************************************************************************** 2025-01-21T07:03:25,738 Please avoid running ``setup.py`` directly. 2025-01-21T07:03:25,739 Instead, use pypa/build, pypa/installer or other 2025-01-21T07:03:25,739 standards-based tools. 2025-01-21T07:03:25,740 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-01-21T07:03:25,741 ******************************************************************************** 2025-01-21T07:03:25,742 !! 2025-01-21T07:03:25,742 self.initialize_options() 2025-01-21T07:03:25,764 installing to build/bdist.linux-armv7l/wheel 2025-01-21T07:03:25,764 running install 2025-01-21T07:03:25,788 running install_lib 2025-01-21T07:03:25,815 creating build/bdist.linux-armv7l/wheel 2025-01-21T07:03:25,817 creating build/bdist.linux-armv7l/wheel/scripts 2025-01-21T07:03:25,819 creating build/bdist.linux-armv7l/wheel/scripts/msa 2025-01-21T07:03:25,820 copying build/lib/scripts/msa/step4-split_msa_to_uniref_and_others.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-01-21T07:03:25,822 copying build/lib/scripts/msa/step1-get_prot_seq.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-01-21T07:03:25,825 copying build/lib/scripts/msa/step2-get_msa.ipynb -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-01-21T07:03:25,826 copying build/lib/scripts/msa/step3-uniref_add_taxid.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-01-21T07:03:25,829 copying build/lib/scripts/prepare_training_data.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-01-21T07:03:25,831 copying build/lib/scripts/gen_ccd_cache.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-01-21T07:03:25,833 copying build/lib/scripts/colabfold_msa.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-01-21T07:03:25,835 copying build/lib/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-01-21T07:03:25,837 creating build/bdist.linux-armv7l/wheel/runner 2025-01-21T07:03:25,838 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-21T07:03:25,841 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-21T07:03:25,844 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-21T07:03:25,846 copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-21T07:03:25,848 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-21T07:03:25,850 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-21T07:03:25,852 copying build/lib/runner/msa_search.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-21T07:03:25,855 creating build/bdist.linux-armv7l/wheel/protenix 2025-01-21T07:03:25,857 creating build/bdist.linux-armv7l/wheel/protenix/config 2025-01-21T07:03:25,859 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-01-21T07:03:25,861 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-01-21T07:03:25,863 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-01-21T07:03:25,866 creating build/bdist.linux-armv7l/wheel/protenix/model 2025-01-21T07:03:25,867 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2025-01-21T07:03:25,869 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2025-01-21T07:03:25,870 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-01-21T07:03:25,873 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-01-21T07:03:25,875 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-01-21T07:03:25,877 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-01-21T07:03:25,879 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-01-21T07:03:25,881 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-01-21T07:03:25,883 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-01-21T07:03:25,885 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-01-21T07:03:25,888 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-01-21T07:03:25,891 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-01-21T07:03:25,894 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2025-01-21T07:03:25,895 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-21T07:03:25,898 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-21T07:03:25,900 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-21T07:03:25,902 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-21T07:03:25,904 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-21T07:03:25,907 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-21T07:03:25,910 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-21T07:03:25,912 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-21T07:03:25,914 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-21T07:03:25,916 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-01-21T07:03:25,919 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-01-21T07:03:25,921 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-01-21T07:03:25,923 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2025-01-21T07:03:25,924 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-01-21T07:03:25,926 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-01-21T07:03:25,929 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-01-21T07:03:25,931 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-01-21T07:03:25,933 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-01-21T07:03:25,936 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-01-21T07:03:25,939 creating build/bdist.linux-armv7l/wheel/protenix/utils 2025-01-21T07:03:25,940 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-21T07:03:25,942 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-21T07:03:25,944 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-21T07:03:25,947 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-21T07:03:25,949 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-21T07:03:25,951 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-21T07:03:25,953 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-21T07:03:25,956 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2025-01-21T07:03:25,958 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2025-01-21T07:03:25,959 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-01-21T07:03:25,961 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-01-21T07:03:25,963 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-01-21T07:03:25,966 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-01-21T07:03:25,968 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-01-21T07:03:25,971 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-01-21T07:03:25,973 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-01-21T07:03:25,975 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-01-21T07:03:25,978 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-21T07:03:25,980 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-21T07:03:25,982 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-21T07:03:25,984 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-21T07:03:25,986 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-21T07:03:25,989 creating build/bdist.linux-armv7l/wheel/protenix/data 2025-01-21T07:03:25,990 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:25,992 copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:25,995 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:25,997 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,000 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,003 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,005 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,008 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,010 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,013 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,018 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,021 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,023 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,026 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,029 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,030 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,034 copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,037 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-21T07:03:26,040 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2025-01-21T07:03:26,042 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2025-01-21T07:03:26,043 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2025-01-21T07:03:26,046 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2025-01-21T07:03:26,048 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2025-01-21T07:03:26,049 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-01-21T07:03:26,051 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-01-21T07:03:26,053 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-01-21T07:03:26,056 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-01-21T07:03:26,058 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-01-21T07:03:26,060 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-01-21T07:03:26,063 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2025-01-21T07:03:26,064 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-21T07:03:26,066 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-21T07:03:26,069 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-21T07:03:26,073 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2025-01-21T07:03:26,074 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2025-01-21T07:03:26,076 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2025-01-21T07:03:26,077 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-21T07:03:26,080 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-21T07:03:26,083 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-21T07:03:26,084 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-21T07:03:26,086 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-21T07:03:26,088 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2025-01-21T07:03:26,089 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-21T07:03:26,091 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-21T07:03:26,094 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-21T07:03:26,097 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-21T07:03:26,101 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-21T07:03:26,103 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-21T07:03:26,105 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-21T07:03:26,108 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2025-01-21T07:03:26,109 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-21T07:03:26,112 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-21T07:03:26,116 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2025-01-21T07:03:26,117 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-01-21T07:03:26,119 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-01-21T07:03:26,121 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-01-21T07:03:26,123 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-21T07:03:26,126 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-21T07:03:26,127 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-21T07:03:26,130 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-21T07:03:26,132 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-21T07:03:26,134 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-21T07:03:26,136 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2025-01-21T07:03:26,138 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2025-01-21T07:03:26,140 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-01-21T07:03:26,142 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-01-21T07:03:26,145 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-01-21T07:03:26,147 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-01-21T07:03:26,149 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2025-01-21T07:03:26,151 creating build/bdist.linux-armv7l/wheel/configs 2025-01-21T07:03:26,152 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2025-01-21T07:03:26,154 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2025-01-21T07:03:26,156 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2025-01-21T07:03:26,158 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2025-01-21T07:03:26,159 running install_egg_info 2025-01-21T07:03:26,193 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.4.1-py3.11.egg-info 2025-01-21T07:03:26,207 running install_scripts 2025-01-21T07:03:26,228 creating build/bdist.linux-armv7l/wheel/protenix-0.4.1.dist-info/WHEEL 2025-01-21T07:03:26,231 creating '/tmp/pip-wheel-gu8e2h8e/protenix-0.4.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-01-21T07:03:26,233 adding 'configs/__init__.py' 2025-01-21T07:03:26,235 adding 'configs/configs_base.py' 2025-01-21T07:03:26,237 adding 'configs/configs_data.py' 2025-01-21T07:03:26,239 adding 'configs/configs_inference.py' 2025-01-21T07:03:26,240 adding 'protenix/__init__.py' 2025-01-21T07:03:26,242 adding 'protenix/config/__init__.py' 2025-01-21T07:03:26,244 adding 'protenix/config/config.py' 2025-01-21T07:03:26,245 adding 'protenix/config/extend_types.py' 2025-01-21T07:03:26,247 adding 'protenix/data/__init__.py' 2025-01-21T07:03:26,250 adding 'protenix/data/ccd.py' 2025-01-21T07:03:26,254 adding 'protenix/data/constants.py' 2025-01-21T07:03:26,256 adding 'protenix/data/data_pipeline.py' 2025-01-21T07:03:26,258 adding 'protenix/data/dataloader.py' 2025-01-21T07:03:26,263 adding 'protenix/data/dataset.py' 2025-01-21T07:03:26,267 adding 'protenix/data/featurizer.py' 2025-01-21T07:03:26,271 adding 'protenix/data/filter.py' 2025-01-21T07:03:26,273 adding 'protenix/data/infer_data_pipeline.py' 2025-01-21T07:03:26,275 adding 'protenix/data/json_maker.py' 2025-01-21T07:03:26,278 adding 'protenix/data/json_parser.py' 2025-01-21T07:03:26,280 adding 'protenix/data/json_to_feature.py' 2025-01-21T07:03:26,285 adding 'protenix/data/msa_featurizer.py' 2025-01-21T07:03:26,290 adding 'protenix/data/msa_utils.py' 2025-01-21T07:03:26,302 adding 'protenix/data/parser.py' 2025-01-21T07:03:26,305 adding 'protenix/data/substructure_perms.py' 2025-01-21T07:03:26,306 adding 'protenix/data/tokenizer.py' 2025-01-21T07:03:26,310 adding 'protenix/data/utils.py' 2025-01-21T07:03:26,311 adding 'protenix/metrics/__init__.py' 2025-01-21T07:03:26,313 adding 'protenix/metrics/clash.py' 2025-01-21T07:03:26,315 adding 'protenix/metrics/lddt_metrics.py' 2025-01-21T07:03:26,317 adding 'protenix/metrics/rmsd.py' 2025-01-21T07:03:26,318 adding 'protenix/model/__init__.py' 2025-01-21T07:03:26,320 adding 'protenix/model/generator.py' 2025-01-21T07:03:26,326 adding 'protenix/model/loss.py' 2025-01-21T07:03:26,330 adding 'protenix/model/protenix.py' 2025-01-21T07:03:26,333 adding 'protenix/model/sample_confidence.py' 2025-01-21T07:03:26,335 adding 'protenix/model/utils.py' 2025-01-21T07:03:26,337 adding 'protenix/model/layer_norm/__init__.py' 2025-01-21T07:03:26,339 adding 'protenix/model/layer_norm/layer_norm.py' 2025-01-21T07:03:26,340 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2025-01-21T07:03:26,342 adding 'protenix/model/layer_norm/kernel/compat.h' 2025-01-21T07:03:26,343 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2025-01-21T07:03:26,346 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2025-01-21T07:03:26,348 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2025-01-21T07:03:26,350 adding 'protenix/model/modules/__init__.py' 2025-01-21T07:03:26,352 adding 'protenix/model/modules/confidence.py' 2025-01-21T07:03:26,355 adding 'protenix/model/modules/diffusion.py' 2025-01-21T07:03:26,357 adding 'protenix/model/modules/embedders.py' 2025-01-21T07:03:26,358 adding 'protenix/model/modules/frames.py' 2025-01-21T07:03:26,359 adding 'protenix/model/modules/head.py' 2025-01-21T07:03:26,362 adding 'protenix/model/modules/pairformer.py' 2025-01-21T07:03:26,366 adding 'protenix/model/modules/primitives.py' 2025-01-21T07:03:26,369 adding 'protenix/model/modules/transformer.py' 2025-01-21T07:03:26,371 adding 'protenix/openfold_local/__init__.py' 2025-01-21T07:03:26,372 adding 'protenix/openfold_local/data/__init__.py' 2025-01-21T07:03:26,374 adding 'protenix/openfold_local/data/data_transforms.py' 2025-01-21T07:03:26,375 adding 'protenix/openfold_local/data/errors.py' 2025-01-21T07:03:26,378 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2025-01-21T07:03:26,380 adding 'protenix/openfold_local/data/msa_identifiers.py' 2025-01-21T07:03:26,383 adding 'protenix/openfold_local/data/msa_pairing.py' 2025-01-21T07:03:26,386 adding 'protenix/openfold_local/data/parsers.py' 2025-01-21T07:03:26,389 adding 'protenix/openfold_local/data/templates.py' 2025-01-21T07:03:26,391 adding 'protenix/openfold_local/data/tools/__init__.py' 2025-01-21T07:03:26,393 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2025-01-21T07:03:26,394 adding 'protenix/openfold_local/data/tools/utils.py' 2025-01-21T07:03:26,395 adding 'protenix/openfold_local/model/__init__.py' 2025-01-21T07:03:26,397 adding 'protenix/openfold_local/model/dropout.py' 2025-01-21T07:03:26,398 adding 'protenix/openfold_local/model/outer_product_mean.py' 2025-01-21T07:03:26,402 adding 'protenix/openfold_local/model/primitives.py' 2025-01-21T07:03:26,403 adding 'protenix/openfold_local/model/triangular_attention.py' 2025-01-21T07:03:26,406 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2025-01-21T07:03:26,407 adding 'protenix/openfold_local/np/__init__.py' 2025-01-21T07:03:26,412 adding 'protenix/openfold_local/np/residue_constants.py' 2025-01-21T07:03:26,414 adding 'protenix/openfold_local/utils/__init__.py' 2025-01-21T07:03:26,417 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2025-01-21T07:03:26,418 adding 'protenix/openfold_local/utils/checkpointing.py' 2025-01-21T07:03:26,420 adding 'protenix/openfold_local/utils/chunk_utils.py' 2025-01-21T07:03:26,422 adding 'protenix/openfold_local/utils/feats.py' 2025-01-21T07:03:26,423 adding 'protenix/openfold_local/utils/precision_utils.py' 2025-01-21T07:03:26,428 adding 'protenix/openfold_local/utils/rigid_utils.py' 2025-01-21T07:03:26,429 adding 'protenix/openfold_local/utils/tensor_utils.py' 2025-01-21T07:03:26,431 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2025-01-21T07:03:26,432 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2025-01-21T07:03:26,434 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2025-01-21T07:03:26,436 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2025-01-21T07:03:26,437 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2025-01-21T07:03:26,438 adding 'protenix/openfold_local/utils/geometry/utils.py' 2025-01-21T07:03:26,440 adding 'protenix/openfold_local/utils/geometry/vector.py' 2025-01-21T07:03:26,442 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2025-01-21T07:03:26,443 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2025-01-21T07:03:26,445 adding 'protenix/utils/__init__.py' 2025-01-21T07:03:26,449 adding 'protenix/utils/cropping.py' 2025-01-21T07:03:26,450 adding 'protenix/utils/distributed.py' 2025-01-21T07:03:26,451 adding 'protenix/utils/file_io.py' 2025-01-21T07:03:26,453 adding 'protenix/utils/geometry.py' 2025-01-21T07:03:26,454 adding 'protenix/utils/logger.py' 2025-01-21T07:03:26,455 adding 'protenix/utils/lr_scheduler.py' 2025-01-21T07:03:26,457 adding 'protenix/utils/metrics.py' 2025-01-21T07:03:26,458 adding 'protenix/utils/scatter_utils.py' 2025-01-21T07:03:26,459 adding 'protenix/utils/seed.py' 2025-01-21T07:03:26,461 adding 'protenix/utils/torch_utils.py' 2025-01-21T07:03:26,462 adding 'protenix/utils/training.py' 2025-01-21T07:03:26,463 adding 'protenix/utils/permutation/__init__.py' 2025-01-21T07:03:26,467 adding 'protenix/utils/permutation/atom_permutation.py' 2025-01-21T07:03:26,470 adding 'protenix/utils/permutation/permutation.py' 2025-01-21T07:03:26,471 adding 'protenix/utils/permutation/utils.py' 2025-01-21T07:03:26,473 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2025-01-21T07:03:26,477 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2025-01-21T07:03:26,479 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2025-01-21T07:03:26,481 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2025-01-21T07:03:26,482 adding 'protenix/web_service/__init__.py' 2025-01-21T07:03:26,484 adding 'protenix/web_service/colab_request_parser.py' 2025-01-21T07:03:26,486 adding 'protenix/web_service/colab_request_utils.py' 2025-01-21T07:03:26,487 adding 'protenix/web_service/dependency_url.py' 2025-01-21T07:03:26,489 adding 'protenix/web_service/prediction_visualization.py' 2025-01-21T07:03:26,491 adding 'protenix/web_service/viewer.py' 2025-01-21T07:03:26,493 adding 'runner/__init__.py' 2025-01-21T07:03:26,496 adding 'runner/batch_inference.py' 2025-01-21T07:03:26,497 adding 'runner/dumper.py' 2025-01-21T07:03:26,499 adding 'runner/ema.py' 2025-01-21T07:03:26,501 adding 'runner/inference.py' 2025-01-21T07:03:26,502 adding 'runner/msa_search.py' 2025-01-21T07:03:26,505 adding 'runner/train.py' 2025-01-21T07:03:26,507 adding 'scripts/__init__.py' 2025-01-21T07:03:26,508 adding 'scripts/colabfold_msa.py' 2025-01-21T07:03:26,510 adding 'scripts/gen_ccd_cache.py' 2025-01-21T07:03:26,512 adding 'scripts/prepare_training_data.py' 2025-01-21T07:03:26,515 adding 'scripts/msa/step1-get_prot_seq.py' 2025-01-21T07:03:26,516 adding 'scripts/msa/step2-get_msa.ipynb' 2025-01-21T07:03:26,518 adding 'scripts/msa/step3-uniref_add_taxid.py' 2025-01-21T07:03:26,519 adding 'scripts/msa/step4-split_msa_to_uniref_and_others.py' 2025-01-21T07:03:26,521 adding 'protenix-0.4.1.dist-info/LICENSE' 2025-01-21T07:03:26,523 adding 'protenix-0.4.1.dist-info/METADATA' 2025-01-21T07:03:26,524 adding 'protenix-0.4.1.dist-info/WHEEL' 2025-01-21T07:03:26,525 adding 'protenix-0.4.1.dist-info/entry_points.txt' 2025-01-21T07:03:26,526 adding 'protenix-0.4.1.dist-info/top_level.txt' 2025-01-21T07:03:26,528 adding 'protenix-0.4.1.dist-info/RECORD' 2025-01-21T07:03:26,535 removing build/bdist.linux-armv7l/wheel 2025-01-21T07:03:26,686 Building wheel for protenix (setup.py): finished with status 'done' 2025-01-21T07:03:26,693 Created wheel for protenix: filename=protenix-0.4.1-py3-none-any.whl size=418285 sha256=48167a0412f33e55e3024ca9598c093e9e60eb96f2815fa11dba8b75a26c8147 2025-01-21T07:03:26,700 Stored in directory: /tmp/pip-ephem-wheel-cache-5ilpg49v/wheels/b2/80/3e/ebc78075fb1fd965c1729604a58fc97ddfdb274cddcd92d2a5 2025-01-21T07:03:26,717 Successfully built protenix 2025-01-21T07:03:26,731 Removed build tracker: '/tmp/pip-build-tracker-x8zzkyrb'