2025-03-28T17:19:28,148 Created temporary directory: /tmp/pip-build-tracker-avdbfwyz 2025-03-28T17:19:28,149 Initialized build tracking at /tmp/pip-build-tracker-avdbfwyz 2025-03-28T17:19:28,150 Created build tracker: /tmp/pip-build-tracker-avdbfwyz 2025-03-28T17:19:28,150 Entered build tracker: /tmp/pip-build-tracker-avdbfwyz 2025-03-28T17:19:28,151 Created temporary directory: /tmp/pip-wheel-9xh8rhhx 2025-03-28T17:19:28,155 Created temporary directory: /tmp/pip-ephem-wheel-cache-nuve_ywe 2025-03-28T17:19:28,199 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-03-28T17:19:28,202 2 location(s) to search for versions of protenix: 2025-03-28T17:19:28,202 * https://pypi.org/simple/protenix/ 2025-03-28T17:19:28,202 * https://www.piwheels.org/simple/protenix/ 2025-03-28T17:19:28,203 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2025-03-28T17:19:28,204 Getting page https://pypi.org/simple/protenix/ 2025-03-28T17:19:28,205 Found index url https://pypi.org/simple/ 2025-03-28T17:19:28,427 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2025-03-28T17:19:28,437 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/) 2025-03-28T17:19:28,438 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/) 2025-03-28T17:19:28,438 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 2025-03-28T17:19:28,439 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) 2025-03-28T17:19:28,440 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 2025-03-28T17:19:28,441 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) 2025-03-28T17:19:28,442 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 2025-03-28T17:19:28,443 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) 2025-03-28T17:19:28,444 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 2025-03-28T17:19:28,445 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) 2025-03-28T17:19:28,446 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 2025-03-28T17:19:28,446 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) 2025-03-28T17:19:28,447 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 2025-03-28T17:19:28,448 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) 2025-03-28T17:19:28,449 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 2025-03-28T17:19:28,450 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) 2025-03-28T17:19:28,451 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 2025-03-28T17:19:28,451 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) 2025-03-28T17:19:28,452 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 2025-03-28T17:19:28,453 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) 2025-03-28T17:19:28,454 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 2025-03-28T17:19:28,454 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) 2025-03-28T17:19:28,455 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 2025-03-28T17:19:28,456 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) 2025-03-28T17:19:28,457 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 2025-03-28T17:19:28,457 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) 2025-03-28T17:19:28,458 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 2025-03-28T17:19:28,459 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) 2025-03-28T17:19:28,460 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 2025-03-28T17:19:28,461 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) 2025-03-28T17:19:28,462 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 2025-03-28T17:19:28,462 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) 2025-03-28T17:19:28,463 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 2025-03-28T17:19:28,464 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) 2025-03-28T17:19:28,464 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 2025-03-28T17:19:28,465 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) 2025-03-28T17:19:28,466 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 2025-03-28T17:19:28,467 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) 2025-03-28T17:19:28,468 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 2025-03-28T17:19:28,469 Skipping link: No binaries permitted for protenix: 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Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/30/52/45a9a904069e5da45cae9e7fc95f73154cbd146f1ea05d6a8c63ee6db696/protenix-0.4.5-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-03-28T17:19:28,473 Found link https://files.pythonhosted.org/packages/a5/cd/6439c99301c4040d7c72745a5cdaae8fc629c854d4b0d6c701745e2e5b7c/protenix-0.4.5.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.4.5 2025-03-28T17:19:28,474 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/1c/08/ab6182a1b1d6e1b5928e628cb9e8d30eeeaf519aa4d8e2033c2b3784db82/protenix-0.4.6-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-03-28T17:19:28,474 Found link https://files.pythonhosted.org/packages/f5/d4/711ecaa04b8568e2fb6cde5cf70bea4252683a84fbdf48044f34f8222beb/protenix-0.4.6.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.4.6 2025-03-28T17:19:28,475 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2025-03-28T17:19:28,476 Getting page https://www.piwheels.org/simple/protenix/ 2025-03-28T17:19:28,477 Found index url https://www.piwheels.org/simple/ 2025-03-28T17:19:28,641 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2025-03-28T17:19:28,648 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.4.4-py3-none-any.whl#sha256=bfd049b21ac0835a40d8b1cc0d793a4a0aff67c9d86abcb2df51a154d9704ce4 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-03-28T17:19:28,648 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.4.3-py3-none-any.whl#sha256=c78607fb1ac4479a523461b2d153e0bf8dcd142d25461d698b8dcc2a17e78b19 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-03-28T17:19:28,649 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.4.2-py3-none-any.whl#sha256=ce76bd46d2b3f3681ef6f581b036accd18133efea630b4765f0c4ce74521d049 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-03-28T17:19:28,649 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) 2025-03-28T17:19:28,650 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) 2025-03-28T17:19:28,651 Skipping link: No binaries permitted for protenix: 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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) 2025-03-28T17:19:28,654 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) 2025-03-28T17:19:28,654 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) 2025-03-28T17:19:28,655 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) 2025-03-28T17:19:28,655 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) 2025-03-28T17:19:28,656 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) 2025-03-28T17:19:28,656 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) 2025-03-28T17:19:28,657 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) 2025-03-28T17:19:28,657 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) 2025-03-28T17:19:28,658 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) 2025-03-28T17:19:28,659 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) 2025-03-28T17:19:28,659 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) 2025-03-28T17:19:28,660 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/) 2025-03-28T17:19:28,661 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2025-03-28T17:19:28,662 Skipping link: not a file: https://pypi.org/simple/protenix/ 2025-03-28T17:19:28,684 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2025-03-28T17:19:28,686 Collecting protenix==0.4.6 2025-03-28T17:19:28,689 Created temporary directory: /tmp/pip-unpack-b7haf2bu 2025-03-28T17:19:28,829 Downloading protenix-0.4.6.tar.gz (352 kB) 2025-03-28T17:19:29,250 Added protenix==0.4.6 from https://files.pythonhosted.org/packages/f5/d4/711ecaa04b8568e2fb6cde5cf70bea4252683a84fbdf48044f34f8222beb/protenix-0.4.6.tar.gz to build tracker '/tmp/pip-build-tracker-avdbfwyz' 2025-03-28T17:19:29,252 Running setup.py (path:/tmp/pip-wheel-9xh8rhhx/protenix_d67b9c3a634d4cd5869328a01cd7ea00/setup.py) egg_info for package protenix 2025-03-28T17:19:29,254 Created temporary directory: /tmp/pip-pip-egg-info-3h93j874 2025-03-28T17:19:29,254 Preparing metadata (setup.py): started 2025-03-28T17:19:29,256 Running command python setup.py egg_info 2025-03-28T17:19:30,389 running egg_info 2025-03-28T17:19:30,420 creating /tmp/pip-pip-egg-info-3h93j874/protenix.egg-info 2025-03-28T17:19:30,421 writing /tmp/pip-pip-egg-info-3h93j874/protenix.egg-info/PKG-INFO 2025-03-28T17:19:30,424 writing dependency_links to /tmp/pip-pip-egg-info-3h93j874/protenix.egg-info/dependency_links.txt 2025-03-28T17:19:30,426 writing entry points to /tmp/pip-pip-egg-info-3h93j874/protenix.egg-info/entry_points.txt 2025-03-28T17:19:30,428 writing requirements to /tmp/pip-pip-egg-info-3h93j874/protenix.egg-info/requires.txt 2025-03-28T17:19:30,429 writing top-level names to /tmp/pip-pip-egg-info-3h93j874/protenix.egg-info/top_level.txt 2025-03-28T17:19:30,430 writing manifest file '/tmp/pip-pip-egg-info-3h93j874/protenix.egg-info/SOURCES.txt' 2025-03-28T17:19:30,547 reading manifest file '/tmp/pip-pip-egg-info-3h93j874/protenix.egg-info/SOURCES.txt' 2025-03-28T17:19:30,548 adding license file 'LICENSE' 2025-03-28T17:19:30,555 writing manifest file '/tmp/pip-pip-egg-info-3h93j874/protenix.egg-info/SOURCES.txt' 2025-03-28T17:19:30,665 Preparing metadata (setup.py): finished with status 'done' 2025-03-28T17:19:30,669 Source in /tmp/pip-wheel-9xh8rhhx/protenix_d67b9c3a634d4cd5869328a01cd7ea00 has version 0.4.6, which satisfies requirement protenix==0.4.6 from https://files.pythonhosted.org/packages/f5/d4/711ecaa04b8568e2fb6cde5cf70bea4252683a84fbdf48044f34f8222beb/protenix-0.4.6.tar.gz 2025-03-28T17:19:30,670 Removed protenix==0.4.6 from https://files.pythonhosted.org/packages/f5/d4/711ecaa04b8568e2fb6cde5cf70bea4252683a84fbdf48044f34f8222beb/protenix-0.4.6.tar.gz from build tracker '/tmp/pip-build-tracker-avdbfwyz' 2025-03-28T17:19:30,679 Created temporary directory: /tmp/pip-unpack-j8mhvfkq 2025-03-28T17:19:30,680 Created temporary directory: /tmp/pip-unpack-y18bgx63 2025-03-28T17:19:30,681 Building wheels for collected packages: protenix 2025-03-28T17:19:30,686 Created temporary directory: /tmp/pip-wheel-kar1q1_p 2025-03-28T17:19:30,686 Building wheel for protenix (setup.py): started 2025-03-28T17:19:30,688 Destination directory: /tmp/pip-wheel-kar1q1_p 2025-03-28T17:19:30,689 Running command python setup.py bdist_wheel 2025-03-28T17:19:31,821 running bdist_wheel 2025-03-28T17:19:31,959 running build 2025-03-28T17:19:31,960 running build_py 2025-03-28T17:19:31,990 creating build/lib/scripts 2025-03-28T17:19:31,992 copying scripts/prepare_training_data.py -> build/lib/scripts 2025-03-28T17:19:31,995 copying scripts/__init__.py -> build/lib/scripts 2025-03-28T17:19:31,997 copying scripts/gen_ccd_cache.py -> build/lib/scripts 2025-03-28T17:19:32,000 copying scripts/colabfold_msa.py -> build/lib/scripts 2025-03-28T17:19:32,004 creating build/lib/runner 2025-03-28T17:19:32,005 copying runner/__init__.py -> build/lib/runner 2025-03-28T17:19:32,007 copying runner/inference.py -> build/lib/runner 2025-03-28T17:19:32,010 copying runner/batch_inference.py -> build/lib/runner 2025-03-28T17:19:32,012 copying runner/ema.py -> build/lib/runner 2025-03-28T17:19:32,014 copying runner/dumper.py -> build/lib/runner 2025-03-28T17:19:32,017 copying runner/train.py -> build/lib/runner 2025-03-28T17:19:32,019 copying runner/msa_search.py -> build/lib/runner 2025-03-28T17:19:32,022 creating build/lib/tests 2025-03-28T17:19:32,023 copying tests/test_lr_schedule.py -> build/lib/tests 2025-03-28T17:19:32,026 copying tests/test_weighted_rigid_align.py -> build/lib/tests 2025-03-28T17:19:32,028 copying tests/__init__.py -> build/lib/tests 2025-03-28T17:19:32,030 copying tests/test_condition_transition.py -> build/lib/tests 2025-03-28T17:19:32,032 copying tests/test_attention_pair_bias.py -> build/lib/tests 2025-03-28T17:19:32,034 copying tests/test_diffusion_transformer.py -> build/lib/tests 2025-03-28T17:19:32,036 copying tests/test_utils.py -> build/lib/tests 2025-03-28T17:19:32,039 copying tests/test_frame.py -> build/lib/tests 2025-03-28T17:19:32,041 copying tests/test_local_rearrange.py -> build/lib/tests 2025-03-28T17:19:32,043 creating build/lib/protenix 2025-03-28T17:19:32,044 copying protenix/__init__.py -> build/lib/protenix 2025-03-28T17:19:32,046 creating build/lib/configs 2025-03-28T17:19:32,047 copying configs/__init__.py -> build/lib/configs 2025-03-28T17:19:32,049 copying configs/configs_base.py -> build/lib/configs 2025-03-28T17:19:32,051 copying configs/configs_inference.py -> build/lib/configs 2025-03-28T17:19:32,053 copying configs/configs_data.py -> build/lib/configs 2025-03-28T17:19:32,056 creating build/lib/protenix/config 2025-03-28T17:19:32,057 copying protenix/config/__init__.py -> build/lib/protenix/config 2025-03-28T17:19:32,060 copying protenix/config/extend_types.py -> build/lib/protenix/config 2025-03-28T17:19:32,064 copying protenix/config/config.py -> build/lib/protenix/config 2025-03-28T17:19:32,067 creating build/lib/protenix/web_service 2025-03-28T17:19:32,068 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2025-03-28T17:19:32,071 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2025-03-28T17:19:32,073 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2025-03-28T17:19:32,075 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2025-03-28T17:19:32,078 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2025-03-28T17:19:32,080 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2025-03-28T17:19:32,083 creating build/lib/protenix/openfold_local 2025-03-28T17:19:32,084 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2025-03-28T17:19:32,087 creating build/lib/protenix/data 2025-03-28T17:19:32,088 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2025-03-28T17:19:32,091 copying protenix/data/__init__.py -> build/lib/protenix/data 2025-03-28T17:19:32,093 copying protenix/data/json_parser.py -> build/lib/protenix/data 2025-03-28T17:19:32,095 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2025-03-28T17:19:32,097 copying protenix/data/parser.py -> build/lib/protenix/data 2025-03-28T17:19:32,102 copying protenix/data/ccd.py -> build/lib/protenix/data 2025-03-28T17:19:32,104 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2025-03-28T17:19:32,107 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2025-03-28T17:19:32,109 copying protenix/data/featurizer.py -> build/lib/protenix/data 2025-03-28T17:19:32,112 copying protenix/data/json_maker.py -> build/lib/protenix/data 2025-03-28T17:19:32,114 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2025-03-28T17:19:32,117 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2025-03-28T17:19:32,119 copying protenix/data/dataset.py -> build/lib/protenix/data 2025-03-28T17:19:32,123 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2025-03-28T17:19:32,126 copying protenix/data/dataloader.py -> build/lib/protenix/data 2025-03-28T17:19:32,129 copying protenix/data/filter.py -> build/lib/protenix/data 2025-03-28T17:19:32,132 copying protenix/data/constants.py -> build/lib/protenix/data 2025-03-28T17:19:32,135 copying protenix/data/utils.py -> build/lib/protenix/data 2025-03-28T17:19:32,139 creating build/lib/protenix/utils 2025-03-28T17:19:32,140 copying protenix/utils/logger.py -> build/lib/protenix/utils 2025-03-28T17:19:32,142 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2025-03-28T17:19:32,145 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2025-03-28T17:19:32,147 copying protenix/utils/training.py -> build/lib/protenix/utils 2025-03-28T17:19:32,149 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2025-03-28T17:19:32,151 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2025-03-28T17:19:32,152 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2025-03-28T17:19:32,154 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2025-03-28T17:19:32,156 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2025-03-28T17:19:32,160 copying protenix/utils/seed.py -> build/lib/protenix/utils 2025-03-28T17:19:32,161 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2025-03-28T17:19:32,164 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2025-03-28T17:19:32,167 creating build/lib/protenix/metrics 2025-03-28T17:19:32,168 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2025-03-28T17:19:32,170 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2025-03-28T17:19:32,172 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2025-03-28T17:19:32,175 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2025-03-28T17:19:32,177 creating build/lib/protenix/model 2025-03-28T17:19:32,178 copying protenix/model/protenix.py -> build/lib/protenix/model 2025-03-28T17:19:32,182 copying protenix/model/__init__.py -> build/lib/protenix/model 2025-03-28T17:19:32,184 copying protenix/model/loss.py -> build/lib/protenix/model 2025-03-28T17:19:32,187 copying protenix/model/generator.py -> build/lib/protenix/model 2025-03-28T17:19:32,190 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2025-03-28T17:19:32,193 copying protenix/model/utils.py -> build/lib/protenix/model 2025-03-28T17:19:32,196 creating build/lib/protenix/openfold_local/data 2025-03-28T17:19:32,197 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2025-03-28T17:19:32,199 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2025-03-28T17:19:32,202 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2025-03-28T17:19:32,203 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2025-03-28T17:19:32,206 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2025-03-28T17:19:32,208 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2025-03-28T17:19:32,211 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2025-03-28T17:19:32,213 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2025-03-28T17:19:32,216 creating build/lib/protenix/openfold_local/utils 2025-03-28T17:19:32,217 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2025-03-28T17:19:32,220 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2025-03-28T17:19:32,222 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2025-03-28T17:19:32,224 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2025-03-28T17:19:32,227 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2025-03-28T17:19:32,229 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2025-03-28T17:19:32,231 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2025-03-28T17:19:32,233 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2025-03-28T17:19:32,237 creating build/lib/protenix/openfold_local/np 2025-03-28T17:19:32,239 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2025-03-28T17:19:32,240 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2025-03-28T17:19:32,244 creating build/lib/protenix/openfold_local/model 2025-03-28T17:19:32,245 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2025-03-28T17:19:32,248 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2025-03-28T17:19:32,250 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2025-03-28T17:19:32,252 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2025-03-28T17:19:32,254 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2025-03-28T17:19:32,257 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2025-03-28T17:19:32,260 creating build/lib/protenix/openfold_local/data/tools 2025-03-28T17:19:32,262 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2025-03-28T17:19:32,263 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2025-03-28T17:19:32,265 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2025-03-28T17:19:32,268 creating build/lib/protenix/openfold_local/utils/kernel 2025-03-28T17:19:32,269 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2025-03-28T17:19:32,271 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2025-03-28T17:19:32,274 creating build/lib/protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,275 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,277 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,279 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,281 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,283 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,285 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,288 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,290 creating build/lib/protenix/utils/permutation 2025-03-28T17:19:32,292 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2025-03-28T17:19:32,294 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2025-03-28T17:19:32,296 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2025-03-28T17:19:32,299 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2025-03-28T17:19:32,302 creating build/lib/protenix/utils/permutation/chain_permutation 2025-03-28T17:19:32,303 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-03-28T17:19:32,306 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-03-28T17:19:32,309 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-03-28T17:19:32,312 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-03-28T17:19:32,315 creating build/lib/protenix/model/modules 2025-03-28T17:19:32,316 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2025-03-28T17:19:32,319 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2025-03-28T17:19:32,322 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2025-03-28T17:19:32,324 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2025-03-28T17:19:32,326 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2025-03-28T17:19:32,328 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2025-03-28T17:19:32,331 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2025-03-28T17:19:32,333 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2025-03-28T17:19:32,335 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2025-03-28T17:19:32,338 creating build/lib/protenix/model/layer_norm 2025-03-28T17:19:32,339 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2025-03-28T17:19:32,341 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2025-03-28T17:19:32,343 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2025-03-28T17:19:32,346 running egg_info 2025-03-28T17:19:32,375 writing protenix.egg-info/PKG-INFO 2025-03-28T17:19:32,378 writing dependency_links to protenix.egg-info/dependency_links.txt 2025-03-28T17:19:32,380 writing entry points to protenix.egg-info/entry_points.txt 2025-03-28T17:19:32,381 writing requirements to protenix.egg-info/requires.txt 2025-03-28T17:19:32,383 writing top-level names to protenix.egg-info/top_level.txt 2025-03-28T17:19:32,436 reading manifest file 'protenix.egg-info/SOURCES.txt' 2025-03-28T17:19:32,449 adding license file 'LICENSE' 2025-03-28T17:19:32,458 writing manifest file 'protenix.egg-info/SOURCES.txt' 2025-03-28T17:19:32,461 /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. 2025-03-28T17:19:32,461 !! 2025-03-28T17:19:32,463 ******************************************************************************** 2025-03-28T17:19:32,463 ############################ 2025-03-28T17:19:32,464 # Package would be ignored # 2025-03-28T17:19:32,465 ############################ 2025-03-28T17:19:32,466 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2025-03-28T17:19:32,466 but it is absent from setuptools' `packages` configuration. 2025-03-28T17:19:32,467 This leads to an ambiguous overall configuration. If you want to distribute this 2025-03-28T17:19:32,468 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2025-03-28T17:19:32,468 to the `packages` configuration field. 2025-03-28T17:19:32,469 Alternatively, you can also rely on setuptools' discovery methods 2025-03-28T17:19:32,470 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-03-28T17:19:32,471 instead of `find_packages(...)`/`find:`). 2025-03-28T17:19:32,472 You can read more about "package discovery" on setuptools documentation page: 2025-03-28T17:19:32,473 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-03-28T17:19:32,475 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2025-03-28T17:19:32,475 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2025-03-28T17:19:32,476 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-03-28T17:19:32,477 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-03-28T17:19:32,477 combination with a more fine grained `package-data` configuration. 2025-03-28T17:19:32,478 You can read more about "package data files" on setuptools documentation page: 2025-03-28T17:19:32,479 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-03-28T17:19:32,481 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-03-28T17:19:32,481 even if it does not contain any `.py` files. 2025-03-28T17:19:32,482 On the other hand, currently there is no concept of package data 2025-03-28T17:19:32,482 directory, all directories are treated like packages. 2025-03-28T17:19:32,483 ******************************************************************************** 2025-03-28T17:19:32,484 !! 2025-03-28T17:19:32,485 check.warn(importable) 2025-03-28T17:19:32,485 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'scripts.msa' is absent from the `packages` configuration. 2025-03-28T17:19:32,486 !! 2025-03-28T17:19:32,487 ******************************************************************************** 2025-03-28T17:19:32,488 ############################ 2025-03-28T17:19:32,488 # Package would be ignored # 2025-03-28T17:19:32,489 ############################ 2025-03-28T17:19:32,490 Python recognizes 'scripts.msa' as an importable package[^1], 2025-03-28T17:19:32,490 but it is absent from setuptools' `packages` configuration. 2025-03-28T17:19:32,492 This leads to an ambiguous overall configuration. If you want to distribute this 2025-03-28T17:19:32,493 package, please make sure that 'scripts.msa' is explicitly added 2025-03-28T17:19:32,493 to the `packages` configuration field. 2025-03-28T17:19:32,494 Alternatively, you can also rely on setuptools' discovery methods 2025-03-28T17:19:32,495 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-03-28T17:19:32,495 instead of `find_packages(...)`/`find:`). 2025-03-28T17:19:32,497 You can read more about "package discovery" on setuptools documentation page: 2025-03-28T17:19:32,498 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-03-28T17:19:32,499 If you don't want 'scripts.msa' to be distributed and are 2025-03-28T17:19:32,500 already explicitly excluding 'scripts.msa' via 2025-03-28T17:19:32,500 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-03-28T17:19:32,501 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-03-28T17:19:32,501 combination with a more fine grained `package-data` configuration. 2025-03-28T17:19:32,503 You can read more about "package data files" on setuptools documentation page: 2025-03-28T17:19:32,504 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-03-28T17:19:32,506 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-03-28T17:19:32,507 even if it does not contain any `.py` files. 2025-03-28T17:19:32,508 On the other hand, currently there is no concept of package data 2025-03-28T17:19:32,508 directory, all directories are treated like packages. 2025-03-28T17:19:32,509 ******************************************************************************** 2025-03-28T17:19:32,510 !! 2025-03-28T17:19:32,510 check.warn(importable) 2025-03-28T17:19:32,511 creating build/lib/scripts/msa 2025-03-28T17:19:32,511 copying scripts/msa/step1-get_prot_seq.py -> build/lib/scripts/msa 2025-03-28T17:19:32,512 copying scripts/msa/step2-get_msa.ipynb -> build/lib/scripts/msa 2025-03-28T17:19:32,513 copying scripts/msa/step3-uniref_add_taxid.py -> build/lib/scripts/msa 2025-03-28T17:19:32,514 copying scripts/msa/step4-split_msa_to_uniref_and_others.py -> build/lib/scripts/msa 2025-03-28T17:19:32,514 creating build/lib/protenix/model/layer_norm/kernel 2025-03-28T17:19:32,514 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2025-03-28T17:19:32,515 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2025-03-28T17:19:32,515 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2025-03-28T17:19:32,516 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2025-03-28T17:19:32,549 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-03-28T17:19:32,550 !! 2025-03-28T17:19:32,551 ******************************************************************************** 2025-03-28T17:19:32,551 Please avoid running ``setup.py`` directly. 2025-03-28T17:19:32,552 Instead, use pypa/build, pypa/installer or other 2025-03-28T17:19:32,552 standards-based tools. 2025-03-28T17:19:32,553 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-03-28T17:19:32,554 ******************************************************************************** 2025-03-28T17:19:32,555 !! 2025-03-28T17:19:32,555 self.initialize_options() 2025-03-28T17:19:32,577 installing to build/bdist.linux-armv7l/wheel 2025-03-28T17:19:32,578 running install 2025-03-28T17:19:32,601 running install_lib 2025-03-28T17:19:32,629 creating build/bdist.linux-armv7l/wheel 2025-03-28T17:19:32,631 creating build/bdist.linux-armv7l/wheel/scripts 2025-03-28T17:19:32,633 copying build/lib/scripts/prepare_training_data.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-03-28T17:19:32,635 copying build/lib/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-03-28T17:19:32,636 copying build/lib/scripts/gen_ccd_cache.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-03-28T17:19:32,639 copying build/lib/scripts/colabfold_msa.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-03-28T17:19:32,641 creating build/bdist.linux-armv7l/wheel/scripts/msa 2025-03-28T17:19:32,642 copying build/lib/scripts/msa/step3-uniref_add_taxid.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-03-28T17:19:32,645 copying build/lib/scripts/msa/step2-get_msa.ipynb -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-03-28T17:19:32,647 copying build/lib/scripts/msa/step1-get_prot_seq.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-03-28T17:19:32,650 copying build/lib/scripts/msa/step4-split_msa_to_uniref_and_others.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-03-28T17:19:32,653 creating build/bdist.linux-armv7l/wheel/runner 2025-03-28T17:19:32,654 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2025-03-28T17:19:32,655 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2025-03-28T17:19:32,658 copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner 2025-03-28T17:19:32,660 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2025-03-28T17:19:32,663 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2025-03-28T17:19:32,666 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2025-03-28T17:19:32,668 copying build/lib/runner/msa_search.py -> build/bdist.linux-armv7l/wheel/./runner 2025-03-28T17:19:32,671 creating build/bdist.linux-armv7l/wheel/tests 2025-03-28T17:19:32,672 copying build/lib/tests/test_lr_schedule.py -> build/bdist.linux-armv7l/wheel/./tests 2025-03-28T17:19:32,675 copying build/lib/tests/test_weighted_rigid_align.py -> build/bdist.linux-armv7l/wheel/./tests 2025-03-28T17:19:32,677 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2025-03-28T17:19:32,679 copying build/lib/tests/test_condition_transition.py -> build/bdist.linux-armv7l/wheel/./tests 2025-03-28T17:19:32,680 copying build/lib/tests/test_attention_pair_bias.py -> build/bdist.linux-armv7l/wheel/./tests 2025-03-28T17:19:32,682 copying build/lib/tests/test_diffusion_transformer.py -> build/bdist.linux-armv7l/wheel/./tests 2025-03-28T17:19:32,684 copying build/lib/tests/test_utils.py -> build/bdist.linux-armv7l/wheel/./tests 2025-03-28T17:19:32,686 copying build/lib/tests/test_frame.py -> build/bdist.linux-armv7l/wheel/./tests 2025-03-28T17:19:32,688 copying build/lib/tests/test_local_rearrange.py -> build/bdist.linux-armv7l/wheel/./tests 2025-03-28T17:19:32,691 creating build/bdist.linux-armv7l/wheel/protenix 2025-03-28T17:19:32,693 creating build/bdist.linux-armv7l/wheel/protenix/config 2025-03-28T17:19:32,694 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-03-28T17:19:32,696 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-03-28T17:19:32,697 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-03-28T17:19:32,700 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2025-03-28T17:19:32,701 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-03-28T17:19:32,704 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-03-28T17:19:32,705 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-03-28T17:19:32,708 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-03-28T17:19:32,710 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-03-28T17:19:32,712 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-03-28T17:19:32,716 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2025-03-28T17:19:32,717 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2025-03-28T17:19:32,719 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2025-03-28T17:19:32,721 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-03-28T17:19:32,723 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-03-28T17:19:32,726 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2025-03-28T17:19:32,727 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-03-28T17:19:32,729 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-03-28T17:19:32,731 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-03-28T17:19:32,733 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-03-28T17:19:32,735 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-03-28T17:19:32,738 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-03-28T17:19:32,739 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-03-28T17:19:32,742 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-03-28T17:19:32,744 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-03-28T17:19:32,747 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2025-03-28T17:19:32,749 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-03-28T17:19:32,751 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-03-28T17:19:32,753 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-03-28T17:19:32,755 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-03-28T17:19:32,757 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-03-28T17:19:32,759 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-03-28T17:19:32,762 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2025-03-28T17:19:32,763 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2025-03-28T17:19:32,765 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2025-03-28T17:19:32,774 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,775 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,777 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,779 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,781 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,783 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,785 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,788 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-03-28T17:19:32,790 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-03-28T17:19:32,792 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-03-28T17:19:32,797 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2025-03-28T17:19:32,799 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2025-03-28T17:19:32,801 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2025-03-28T17:19:32,806 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2025-03-28T17:19:32,807 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-03-28T17:19:32,811 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-03-28T17:19:32,814 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-03-28T17:19:32,816 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-03-28T17:19:32,818 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-03-28T17:19:32,822 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-03-28T17:19:32,826 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2025-03-28T17:19:32,828 creating build/bdist.linux-armv7l/wheel/protenix/data 2025-03-28T17:19:32,830 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,834 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,838 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,842 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,845 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,851 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,855 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,859 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,863 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,867 copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,871 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,874 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,877 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,882 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,887 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,890 copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,894 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,897 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-03-28T17:19:32,900 creating build/bdist.linux-armv7l/wheel/protenix/utils 2025-03-28T17:19:32,901 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-03-28T17:19:32,903 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-03-28T17:19:32,906 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-03-28T17:19:32,907 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-03-28T17:19:32,910 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-03-28T17:19:32,912 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2025-03-28T17:19:32,913 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-03-28T17:19:32,915 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2025-03-28T17:19:32,917 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-03-28T17:19:32,919 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-03-28T17:19:32,921 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-03-28T17:19:32,924 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-03-28T17:19:32,926 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-03-28T17:19:32,929 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-03-28T17:19:32,933 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-03-28T17:19:32,935 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-03-28T17:19:32,936 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-03-28T17:19:32,938 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-03-28T17:19:32,940 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-03-28T17:19:32,943 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-03-28T17:19:32,945 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-03-28T17:19:32,947 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-03-28T17:19:32,950 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2025-03-28T17:19:32,951 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-03-28T17:19:32,952 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-03-28T17:19:32,955 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-03-28T17:19:32,957 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-03-28T17:19:32,960 creating build/bdist.linux-armv7l/wheel/protenix/model 2025-03-28T17:19:32,962 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-03-28T17:19:32,965 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2025-03-28T17:19:32,966 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-03-28T17:19:32,969 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-03-28T17:19:32,972 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-03-28T17:19:32,974 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-03-28T17:19:32,976 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-03-28T17:19:32,979 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-03-28T17:19:32,982 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-03-28T17:19:32,984 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-03-28T17:19:32,987 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-03-28T17:19:32,991 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2025-03-28T17:19:32,992 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-03-28T17:19:32,994 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-03-28T17:19:32,997 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2025-03-28T17:19:32,998 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-03-28T17:19:33,001 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-03-28T17:19:33,004 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-03-28T17:19:33,006 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-03-28T17:19:33,009 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-03-28T17:19:33,012 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-03-28T17:19:33,013 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-03-28T17:19:33,017 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-03-28T17:19:33,019 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-03-28T17:19:33,022 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-03-28T17:19:33,025 creating build/bdist.linux-armv7l/wheel/configs 2025-03-28T17:19:33,026 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2025-03-28T17:19:33,028 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2025-03-28T17:19:33,031 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2025-03-28T17:19:33,032 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2025-03-28T17:19:33,034 running install_egg_info 2025-03-28T17:19:33,069 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.4.6-py3.11.egg-info 2025-03-28T17:19:33,080 running install_scripts 2025-03-28T17:19:33,100 creating build/bdist.linux-armv7l/wheel/protenix-0.4.6.dist-info/WHEEL 2025-03-28T17:19:33,103 creating '/tmp/pip-wheel-kar1q1_p/protenix-0.4.6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-03-28T17:19:33,105 adding 'configs/__init__.py' 2025-03-28T17:19:33,107 adding 'configs/configs_base.py' 2025-03-28T17:19:33,110 adding 'configs/configs_data.py' 2025-03-28T17:19:33,111 adding 'configs/configs_inference.py' 2025-03-28T17:19:33,113 adding 'protenix/__init__.py' 2025-03-28T17:19:33,115 adding 'protenix/config/__init__.py' 2025-03-28T17:19:33,117 adding 'protenix/config/config.py' 2025-03-28T17:19:33,118 adding 'protenix/config/extend_types.py' 2025-03-28T17:19:33,120 adding 'protenix/data/__init__.py' 2025-03-28T17:19:33,123 adding 'protenix/data/ccd.py' 2025-03-28T17:19:33,127 adding 'protenix/data/constants.py' 2025-03-28T17:19:33,129 adding 'protenix/data/data_pipeline.py' 2025-03-28T17:19:33,131 adding 'protenix/data/dataloader.py' 2025-03-28T17:19:33,136 adding 'protenix/data/dataset.py' 2025-03-28T17:19:33,140 adding 'protenix/data/featurizer.py' 2025-03-28T17:19:33,144 adding 'protenix/data/filter.py' 2025-03-28T17:19:33,146 adding 'protenix/data/infer_data_pipeline.py' 2025-03-28T17:19:33,147 adding 'protenix/data/json_maker.py' 2025-03-28T17:19:33,150 adding 'protenix/data/json_parser.py' 2025-03-28T17:19:33,152 adding 'protenix/data/json_to_feature.py' 2025-03-28T17:19:33,157 adding 'protenix/data/msa_featurizer.py' 2025-03-28T17:19:33,162 adding 'protenix/data/msa_utils.py' 2025-03-28T17:19:33,174 adding 'protenix/data/parser.py' 2025-03-28T17:19:33,176 adding 'protenix/data/substructure_perms.py' 2025-03-28T17:19:33,178 adding 'protenix/data/tokenizer.py' 2025-03-28T17:19:33,181 adding 'protenix/data/utils.py' 2025-03-28T17:19:33,183 adding 'protenix/metrics/__init__.py' 2025-03-28T17:19:33,184 adding 'protenix/metrics/clash.py' 2025-03-28T17:19:33,186 adding 'protenix/metrics/lddt_metrics.py' 2025-03-28T17:19:33,188 adding 'protenix/metrics/rmsd.py' 2025-03-28T17:19:33,190 adding 'protenix/model/__init__.py' 2025-03-28T17:19:33,192 adding 'protenix/model/generator.py' 2025-03-28T17:19:33,198 adding 'protenix/model/loss.py' 2025-03-28T17:19:33,201 adding 'protenix/model/protenix.py' 2025-03-28T17:19:33,204 adding 'protenix/model/sample_confidence.py' 2025-03-28T17:19:33,206 adding 'protenix/model/utils.py' 2025-03-28T17:19:33,208 adding 'protenix/model/layer_norm/__init__.py' 2025-03-28T17:19:33,210 adding 'protenix/model/layer_norm/layer_norm.py' 2025-03-28T17:19:33,211 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2025-03-28T17:19:33,214 adding 'protenix/model/layer_norm/kernel/compat.h' 2025-03-28T17:19:33,215 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2025-03-28T17:19:33,217 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2025-03-28T17:19:33,219 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2025-03-28T17:19:33,221 adding 'protenix/model/modules/__init__.py' 2025-03-28T17:19:33,223 adding 'protenix/model/modules/confidence.py' 2025-03-28T17:19:33,226 adding 'protenix/model/modules/diffusion.py' 2025-03-28T17:19:33,227 adding 'protenix/model/modules/embedders.py' 2025-03-28T17:19:33,229 adding 'protenix/model/modules/frames.py' 2025-03-28T17:19:33,230 adding 'protenix/model/modules/head.py' 2025-03-28T17:19:33,233 adding 'protenix/model/modules/pairformer.py' 2025-03-28T17:19:33,237 adding 'protenix/model/modules/primitives.py' 2025-03-28T17:19:33,240 adding 'protenix/model/modules/transformer.py' 2025-03-28T17:19:33,242 adding 'protenix/openfold_local/__init__.py' 2025-03-28T17:19:33,243 adding 'protenix/openfold_local/data/__init__.py' 2025-03-28T17:19:33,245 adding 'protenix/openfold_local/data/data_transforms.py' 2025-03-28T17:19:33,246 adding 'protenix/openfold_local/data/errors.py' 2025-03-28T17:19:33,249 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2025-03-28T17:19:33,250 adding 'protenix/openfold_local/data/msa_identifiers.py' 2025-03-28T17:19:33,253 adding 'protenix/openfold_local/data/msa_pairing.py' 2025-03-28T17:19:33,256 adding 'protenix/openfold_local/data/parsers.py' 2025-03-28T17:19:33,259 adding 'protenix/openfold_local/data/templates.py' 2025-03-28T17:19:33,261 adding 'protenix/openfold_local/data/tools/__init__.py' 2025-03-28T17:19:33,263 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2025-03-28T17:19:33,264 adding 'protenix/openfold_local/data/tools/utils.py' 2025-03-28T17:19:33,266 adding 'protenix/openfold_local/model/__init__.py' 2025-03-28T17:19:33,267 adding 'protenix/openfold_local/model/dropout.py' 2025-03-28T17:19:33,268 adding 'protenix/openfold_local/model/outer_product_mean.py' 2025-03-28T17:19:33,271 adding 'protenix/openfold_local/model/primitives.py' 2025-03-28T17:19:33,273 adding 'protenix/openfold_local/model/triangular_attention.py' 2025-03-28T17:19:33,276 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2025-03-28T17:19:33,278 adding 'protenix/openfold_local/np/__init__.py' 2025-03-28T17:19:33,283 adding 'protenix/openfold_local/np/residue_constants.py' 2025-03-28T17:19:33,285 adding 'protenix/openfold_local/utils/__init__.py' 2025-03-28T17:19:33,287 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2025-03-28T17:19:33,289 adding 'protenix/openfold_local/utils/checkpointing.py' 2025-03-28T17:19:33,291 adding 'protenix/openfold_local/utils/chunk_utils.py' 2025-03-28T17:19:33,292 adding 'protenix/openfold_local/utils/feats.py' 2025-03-28T17:19:33,293 adding 'protenix/openfold_local/utils/precision_utils.py' 2025-03-28T17:19:33,298 adding 'protenix/openfold_local/utils/rigid_utils.py' 2025-03-28T17:19:33,299 adding 'protenix/openfold_local/utils/tensor_utils.py' 2025-03-28T17:19:33,301 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2025-03-28T17:19:33,302 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2025-03-28T17:19:33,304 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2025-03-28T17:19:33,306 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2025-03-28T17:19:33,307 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2025-03-28T17:19:33,308 adding 'protenix/openfold_local/utils/geometry/utils.py' 2025-03-28T17:19:33,310 adding 'protenix/openfold_local/utils/geometry/vector.py' 2025-03-28T17:19:33,311 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2025-03-28T17:19:33,313 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2025-03-28T17:19:33,314 adding 'protenix/utils/__init__.py' 2025-03-28T17:19:33,318 adding 'protenix/utils/cropping.py' 2025-03-28T17:19:33,319 adding 'protenix/utils/distributed.py' 2025-03-28T17:19:33,321 adding 'protenix/utils/file_io.py' 2025-03-28T17:19:33,322 adding 'protenix/utils/geometry.py' 2025-03-28T17:19:33,323 adding 'protenix/utils/logger.py' 2025-03-28T17:19:33,325 adding 'protenix/utils/lr_scheduler.py' 2025-03-28T17:19:33,326 adding 'protenix/utils/metrics.py' 2025-03-28T17:19:33,328 adding 'protenix/utils/scatter_utils.py' 2025-03-28T17:19:33,329 adding 'protenix/utils/seed.py' 2025-03-28T17:19:33,330 adding 'protenix/utils/torch_utils.py' 2025-03-28T17:19:33,332 adding 'protenix/utils/training.py' 2025-03-28T17:19:33,333 adding 'protenix/utils/permutation/__init__.py' 2025-03-28T17:19:33,337 adding 'protenix/utils/permutation/atom_permutation.py' 2025-03-28T17:19:33,340 adding 'protenix/utils/permutation/permutation.py' 2025-03-28T17:19:33,342 adding 'protenix/utils/permutation/utils.py' 2025-03-28T17:19:33,344 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2025-03-28T17:19:33,348 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2025-03-28T17:19:33,350 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2025-03-28T17:19:33,352 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2025-03-28T17:19:33,354 adding 'protenix/web_service/__init__.py' 2025-03-28T17:19:33,356 adding 'protenix/web_service/colab_request_parser.py' 2025-03-28T17:19:33,358 adding 'protenix/web_service/colab_request_utils.py' 2025-03-28T17:19:33,359 adding 'protenix/web_service/dependency_url.py' 2025-03-28T17:19:33,361 adding 'protenix/web_service/prediction_visualization.py' 2025-03-28T17:19:33,364 adding 'protenix/web_service/viewer.py' 2025-03-28T17:19:33,366 adding 'runner/__init__.py' 2025-03-28T17:19:33,368 adding 'runner/batch_inference.py' 2025-03-28T17:19:33,370 adding 'runner/dumper.py' 2025-03-28T17:19:33,371 adding 'runner/ema.py' 2025-03-28T17:19:33,373 adding 'runner/inference.py' 2025-03-28T17:19:33,375 adding 'runner/msa_search.py' 2025-03-28T17:19:33,378 adding 'runner/train.py' 2025-03-28T17:19:33,380 adding 'scripts/__init__.py' 2025-03-28T17:19:33,382 adding 'scripts/colabfold_msa.py' 2025-03-28T17:19:33,384 adding 'scripts/gen_ccd_cache.py' 2025-03-28T17:19:33,386 adding 'scripts/prepare_training_data.py' 2025-03-28T17:19:33,388 adding 'scripts/msa/step1-get_prot_seq.py' 2025-03-28T17:19:33,390 adding 'scripts/msa/step2-get_msa.ipynb' 2025-03-28T17:19:33,392 adding 'scripts/msa/step3-uniref_add_taxid.py' 2025-03-28T17:19:33,394 adding 'scripts/msa/step4-split_msa_to_uniref_and_others.py' 2025-03-28T17:19:33,396 adding 'tests/__init__.py' 2025-03-28T17:19:33,397 adding 'tests/test_attention_pair_bias.py' 2025-03-28T17:19:33,399 adding 'tests/test_condition_transition.py' 2025-03-28T17:19:33,400 adding 'tests/test_diffusion_transformer.py' 2025-03-28T17:19:33,401 adding 'tests/test_frame.py' 2025-03-28T17:19:33,402 adding 'tests/test_local_rearrange.py' 2025-03-28T17:19:33,404 adding 'tests/test_lr_schedule.py' 2025-03-28T17:19:33,405 adding 'tests/test_utils.py' 2025-03-28T17:19:33,406 adding 'tests/test_weighted_rigid_align.py' 2025-03-28T17:19:33,408 adding 'protenix-0.4.6.dist-info/LICENSE' 2025-03-28T17:19:33,410 adding 'protenix-0.4.6.dist-info/METADATA' 2025-03-28T17:19:33,410 adding 'protenix-0.4.6.dist-info/WHEEL' 2025-03-28T17:19:33,411 adding 'protenix-0.4.6.dist-info/entry_points.txt' 2025-03-28T17:19:33,412 adding 'protenix-0.4.6.dist-info/top_level.txt' 2025-03-28T17:19:33,415 adding 'protenix-0.4.6.dist-info/RECORD' 2025-03-28T17:19:33,422 removing build/bdist.linux-armv7l/wheel 2025-03-28T17:19:33,574 Building wheel for protenix (setup.py): finished with status 'done' 2025-03-28T17:19:33,581 Created wheel for protenix: filename=protenix-0.4.6-py3-none-any.whl size=435613 sha256=d49c1fb72f7c765f413bc3e7761ac13be9e33c2730ad189e1c3ee4a20f9540a3 2025-03-28T17:19:33,583 Stored in directory: /tmp/pip-ephem-wheel-cache-nuve_ywe/wheels/5e/5d/5f/4ff1f66e4529e009fe67c53a450210630fa12a955547f02fd0 2025-03-28T17:19:33,597 Successfully built protenix 2025-03-28T17:19:33,613 Removed build tracker: '/tmp/pip-build-tracker-avdbfwyz'