2025-02-26T09:16:08,770 Created temporary directory: /tmp/pip-build-tracker-7dg0_3_g 2025-02-26T09:16:08,772 Initialized build tracking at /tmp/pip-build-tracker-7dg0_3_g 2025-02-26T09:16:08,772 Created build tracker: /tmp/pip-build-tracker-7dg0_3_g 2025-02-26T09:16:08,773 Entered build tracker: /tmp/pip-build-tracker-7dg0_3_g 2025-02-26T09:16:08,773 Created temporary directory: /tmp/pip-wheel-j4k7gyhi 2025-02-26T09:16:08,777 Created temporary directory: /tmp/pip-ephem-wheel-cache-_czrlrbi 2025-02-26T09:16:08,821 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-02-26T09:16:08,824 2 location(s) to search for versions of protenix: 2025-02-26T09:16:08,824 * https://pypi.org/simple/protenix/ 2025-02-26T09:16:08,824 * https://www.piwheels.org/simple/protenix/ 2025-02-26T09:16:08,825 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2025-02-26T09:16:08,825 Getting page https://pypi.org/simple/protenix/ 2025-02-26T09:16:08,827 Found index url https://pypi.org/simple/ 2025-02-26T09:16:09,045 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2025-02-26T09:16:09,054 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/a8/ea/bbe375d1a89b5e3cbe5e07e56184e29a7b779f964a8ea910337a0746af5e/Protenix-0.0.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) 2025-02-26T09:16:09,055 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/35/f6/105b3517490c13d23880689ef3b4477d072d117ca4cc6f805bad9ee16391/protenix-0.0.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) 2025-02-26T09:16:09,056 Found link https://files.pythonhosted.org/packages/63/d5/22a2098752b2b8c95f2ced18d38918883aa9a5ac8cee9df5174aadfee19c/protenix-0.0.1.tar.gz (from https://pypi.org/simple/protenix/), version: 0.0.1 2025-02-26T09:16:09,056 Skipping link: No binaries permitted for protenix: 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Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/f5/3f/993181bd5478dccf62a5265df701cc9762d257ac04ea6aec26f2e0ec6b0e/protenix-0.1.2-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:<3.12,>=3.10) 2025-02-26T09:16:09,061 Found link https://files.pythonhosted.org/packages/18/ff/8a30b1df6d1bc731a8b4075a077421e306d85976cae82e758a5f15cef4fd/protenix-0.1.2.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:<3.12,>=3.10), version: 0.1.2 2025-02-26T09:16:09,062 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/c3/31/3b2b20aafa4471bcda6389257ad5348c7762374fe725b0552f836dc13ef6/protenix-0.1.3-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,063 Found link https://files.pythonhosted.org/packages/2c/1c/0788760bb4cd6bae9edc74ef1341e9cc74ad6190b8b5dbd972a361184b97/protenix-0.1.3.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.1.3 2025-02-26T09:16:09,063 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/09/b7/15a72afe3d229492604e5ca7ebed72cd1402068f2d5518e26ebef3f2bb5c/protenix-0.2.0-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,064 Found link https://files.pythonhosted.org/packages/0f/17/fdc141be77d735ddf3bfba80a660873fa13732b6c77847434b969aa66f51/protenix-0.2.0.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.2.0 2025-02-26T09:16:09,065 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/99/56/de0a35a125cc0247a366608c8598bdd949ba6068c02fb8d13e8147f65d9c/protenix-0.3.0-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,066 Found link 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(requires-python:>=3.10) 2025-02-26T09:16:09,069 Found link https://files.pythonhosted.org/packages/65/48/25fdef4629cd5ce68c65f733fc49388378cacd3658cd76b5e88893ca5227/protenix-0.3.2.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.2 2025-02-26T09:16:09,069 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/c7/93/f19c14b2b49405f326fab9594ffd7252ef0e231cc348d61b5e406408c8cf/protenix-0.3.3-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,070 Found link https://files.pythonhosted.org/packages/83/67/8697c13e89ed881756f1d188346b4e241decea92545f611778baa9273a49/protenix-0.3.3.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.3 2025-02-26T09:16:09,071 Skipping link: No binaries permitted for protenix: 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(requires-python:>=3.10), version: 0.3.7 2025-02-26T09:16:09,078 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/be/4d/3a2a007bfb6bab07c98ec53180368db69bd656a3ee277a6a962068da3b06/protenix-0.3.8-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,078 Found link https://files.pythonhosted.org/packages/1f/aa/2445a83be220fc2a24fd269f34dfbfa2e5c9d025103712070bfc85d9bb3f/protenix-0.3.8.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.8 2025-02-26T09:16:09,079 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/2e/8c/93ac8551d47bd1189977231ce255647b3b86d727d67c9ed7e756215aea3a/protenix-0.3.9-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,080 Found link 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(requires-python:>=3.10) 2025-02-26T09:16:09,083 Found link https://files.pythonhosted.org/packages/2e/41/41bfd68e1612028242ccc5834bc1aea70140078d7d99b112ad7ed6e1bb51/protenix-0.4.1.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.4.1 2025-02-26T09:16:09,083 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/95/c9/45ab254d0873d33b90dda3bb852e72c7198c043200800a3a8c20a51516ad/protenix-0.4.2-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,084 Found link https://files.pythonhosted.org/packages/20/53/57bdd33d8c1ac5706bdb210d3347db01fe954085eb79004a29d355a22685/protenix-0.4.2.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.4.2 2025-02-26T09:16:09,085 Skipping link: No binaries permitted for protenix: 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Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2025-02-26T09:16:09,089 Getting page https://www.piwheels.org/simple/protenix/ 2025-02-26T09:16:09,091 Found index url https://www.piwheels.org/simple/ 2025-02-26T09:16:09,274 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2025-02-26T09:16:09,281 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) 2025-02-26T09:16:09,281 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) 2025-02-26T09:16:09,282 Skipping link: No binaries permitted for protenix: 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https://www.piwheels.org/simple/protenix/protenix-0.3.2-py3-none-any.whl#sha256=0255f130567cda78b0dd7e9e1efee966d489a4302df91f47c2ce7d7c5f9b3400 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,288 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.1-py3-none-any.whl#sha256=624b9eaf9450baa3748fbe7d038a393ab59d36d7b191a70d676d592c81f46d1f (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,289 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.0-py3-none-any.whl#sha256=c2af82dfdebc9606f320eb2d0ae308e644cd77922b443dcd59e7f778e756ac45 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,289 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.2.0-py3-none-any.whl#sha256=0de87030b4ba1d9e3c2b67265493001f00eca096d862816f65f818b739c96c6f (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,290 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.3-py3-none-any.whl#sha256=be21c60c572799c5562933a71a3087ae1441533805771913e77578fc6280e314 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,290 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.2-py3-none-any.whl#sha256=10909020be81638dbfe8da0ff0bc107ad732dc3dc8e420d09aa3e346c53ac527 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10,<3.12) 2025-02-26T09:16:09,291 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.1-py3-none-any.whl#sha256=aa7a8c0ad8f38f5430cb145bb56675e2b0deb861589bbb05ec6eb09dd95c5f57 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,291 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.0-py3-none-any.whl#sha256=95dd14c125ff66c76135ed8525ede80d6be803880749ec813036bb317ca23e6e (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-26T09:16:09,291 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/Protenix-0.0.1-py3-none-any.whl#sha256=5b251c54ef00f26ee302a294be031208ca73350e41e88d05368f4146cdb01794 (from https://www.piwheels.org/simple/protenix/) 2025-02-26T09:16:09,292 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2025-02-26T09:16:09,293 Skipping link: not a file: https://pypi.org/simple/protenix/ 2025-02-26T09:16:09,314 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2025-02-26T09:16:09,316 Collecting protenix==0.4.4 2025-02-26T09:16:09,319 Created temporary directory: /tmp/pip-unpack-t0v67nx8 2025-02-26T09:16:09,534 Downloading protenix-0.4.4.tar.gz (345 kB) 2025-02-26T09:16:09,975 Added protenix==0.4.4 from https://files.pythonhosted.org/packages/1f/93/f325299d24f446ba8aa5c25f31bb6efe61790f5ce10d6746e1e3028bd496/protenix-0.4.4.tar.gz to build tracker '/tmp/pip-build-tracker-7dg0_3_g' 2025-02-26T09:16:09,977 Running setup.py (path:/tmp/pip-wheel-j4k7gyhi/protenix_d239b92d7c23458ca6348ad0d80ba020/setup.py) egg_info for package protenix 2025-02-26T09:16:09,978 Created temporary directory: /tmp/pip-pip-egg-info-cuo4pnvz 2025-02-26T09:16:09,979 Preparing metadata (setup.py): started 2025-02-26T09:16:09,980 Running command python setup.py egg_info 2025-02-26T09:16:11,109 running egg_info 2025-02-26T09:16:11,137 creating /tmp/pip-pip-egg-info-cuo4pnvz/protenix.egg-info 2025-02-26T09:16:11,138 writing /tmp/pip-pip-egg-info-cuo4pnvz/protenix.egg-info/PKG-INFO 2025-02-26T09:16:11,142 writing dependency_links to /tmp/pip-pip-egg-info-cuo4pnvz/protenix.egg-info/dependency_links.txt 2025-02-26T09:16:11,143 writing entry points to /tmp/pip-pip-egg-info-cuo4pnvz/protenix.egg-info/entry_points.txt 2025-02-26T09:16:11,145 writing requirements to /tmp/pip-pip-egg-info-cuo4pnvz/protenix.egg-info/requires.txt 2025-02-26T09:16:11,146 writing top-level names to /tmp/pip-pip-egg-info-cuo4pnvz/protenix.egg-info/top_level.txt 2025-02-26T09:16:11,148 writing manifest file '/tmp/pip-pip-egg-info-cuo4pnvz/protenix.egg-info/SOURCES.txt' 2025-02-26T09:16:11,261 reading manifest file '/tmp/pip-pip-egg-info-cuo4pnvz/protenix.egg-info/SOURCES.txt' 2025-02-26T09:16:11,263 adding license file 'LICENSE' 2025-02-26T09:16:11,270 writing manifest file '/tmp/pip-pip-egg-info-cuo4pnvz/protenix.egg-info/SOURCES.txt' 2025-02-26T09:16:11,379 Preparing metadata (setup.py): finished with status 'done' 2025-02-26T09:16:11,383 Source in /tmp/pip-wheel-j4k7gyhi/protenix_d239b92d7c23458ca6348ad0d80ba020 has version 0.4.4, which satisfies requirement protenix==0.4.4 from https://files.pythonhosted.org/packages/1f/93/f325299d24f446ba8aa5c25f31bb6efe61790f5ce10d6746e1e3028bd496/protenix-0.4.4.tar.gz 2025-02-26T09:16:11,384 Removed protenix==0.4.4 from https://files.pythonhosted.org/packages/1f/93/f325299d24f446ba8aa5c25f31bb6efe61790f5ce10d6746e1e3028bd496/protenix-0.4.4.tar.gz from build tracker '/tmp/pip-build-tracker-7dg0_3_g' 2025-02-26T09:16:11,393 Created temporary directory: /tmp/pip-unpack-j9yi8qve 2025-02-26T09:16:11,394 Created temporary directory: /tmp/pip-unpack-xbgf_n1l 2025-02-26T09:16:11,394 Building wheels for collected packages: protenix 2025-02-26T09:16:11,399 Created temporary directory: /tmp/pip-wheel-h_d1nqga 2025-02-26T09:16:11,399 Building wheel for protenix (setup.py): started 2025-02-26T09:16:11,400 Destination directory: /tmp/pip-wheel-h_d1nqga 2025-02-26T09:16:11,401 Running command python setup.py bdist_wheel 2025-02-26T09:16:12,576 running bdist_wheel 2025-02-26T09:16:12,708 running build 2025-02-26T09:16:12,709 running build_py 2025-02-26T09:16:12,738 creating build/lib/configs 2025-02-26T09:16:12,740 copying configs/configs_inference.py -> build/lib/configs 2025-02-26T09:16:12,742 copying configs/configs_data.py -> build/lib/configs 2025-02-26T09:16:12,745 copying configs/__init__.py -> build/lib/configs 2025-02-26T09:16:12,746 copying configs/configs_base.py -> build/lib/configs 2025-02-26T09:16:12,749 creating build/lib/scripts 2025-02-26T09:16:12,750 copying scripts/__init__.py -> build/lib/scripts 2025-02-26T09:16:12,752 copying scripts/colabfold_msa.py -> build/lib/scripts 2025-02-26T09:16:12,754 copying scripts/gen_ccd_cache.py -> build/lib/scripts 2025-02-26T09:16:12,757 copying scripts/prepare_training_data.py -> build/lib/scripts 2025-02-26T09:16:12,759 creating build/lib/protenix 2025-02-26T09:16:12,761 copying protenix/__init__.py -> build/lib/protenix 2025-02-26T09:16:12,763 creating build/lib/tests 2025-02-26T09:16:12,764 copying tests/test_utils.py -> build/lib/tests 2025-02-26T09:16:12,766 copying tests/test_frame.py -> build/lib/tests 2025-02-26T09:16:12,768 copying tests/test_weighted_rigid_align.py -> build/lib/tests 2025-02-26T09:16:12,770 copying tests/test_local_rearrange.py -> build/lib/tests 2025-02-26T09:16:12,772 copying tests/__init__.py -> build/lib/tests 2025-02-26T09:16:12,774 copying tests/test_lr_schedule.py -> build/lib/tests 2025-02-26T09:16:12,776 copying tests/test_condition_transition.py -> build/lib/tests 2025-02-26T09:16:12,778 copying tests/test_attention_pair_bias.py -> build/lib/tests 2025-02-26T09:16:12,780 copying tests/test_diffusion_transformer.py -> build/lib/tests 2025-02-26T09:16:12,783 creating build/lib/runner 2025-02-26T09:16:12,784 copying runner/dumper.py -> build/lib/runner 2025-02-26T09:16:12,786 copying runner/__init__.py -> build/lib/runner 2025-02-26T09:16:12,788 copying runner/ema.py -> build/lib/runner 2025-02-26T09:16:12,790 copying runner/train.py -> build/lib/runner 2025-02-26T09:16:12,792 copying runner/msa_search.py -> build/lib/runner 2025-02-26T09:16:12,794 copying runner/inference.py -> build/lib/runner 2025-02-26T09:16:12,802 copying runner/batch_inference.py -> build/lib/runner 2025-02-26T09:16:12,806 creating build/lib/protenix/data 2025-02-26T09:16:12,807 copying protenix/data/constants.py -> build/lib/protenix/data 2025-02-26T09:16:12,809 copying protenix/data/ccd.py -> build/lib/protenix/data 2025-02-26T09:16:12,812 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2025-02-26T09:16:12,814 copying protenix/data/json_maker.py -> build/lib/protenix/data 2025-02-26T09:16:12,817 copying protenix/data/utils.py -> build/lib/protenix/data 2025-02-26T09:16:12,819 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2025-02-26T09:16:12,822 copying protenix/data/parser.py -> build/lib/protenix/data 2025-02-26T09:16:12,825 copying protenix/data/dataloader.py -> build/lib/protenix/data 2025-02-26T09:16:12,828 copying protenix/data/dataset.py -> build/lib/protenix/data 2025-02-26T09:16:12,831 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2025-02-26T09:16:12,834 copying protenix/data/__init__.py -> build/lib/protenix/data 2025-02-26T09:16:12,835 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2025-02-26T09:16:12,837 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2025-02-26T09:16:12,840 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2025-02-26T09:16:12,842 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2025-02-26T09:16:12,845 copying protenix/data/filter.py -> build/lib/protenix/data 2025-02-26T09:16:12,847 copying protenix/data/featurizer.py -> build/lib/protenix/data 2025-02-26T09:16:12,850 copying protenix/data/json_parser.py -> build/lib/protenix/data 2025-02-26T09:16:12,853 creating build/lib/protenix/metrics 2025-02-26T09:16:12,854 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2025-02-26T09:16:12,857 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2025-02-26T09:16:12,858 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2025-02-26T09:16:12,861 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2025-02-26T09:16:12,864 creating build/lib/protenix/utils 2025-02-26T09:16:12,865 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2025-02-26T09:16:12,867 copying protenix/utils/logger.py -> build/lib/protenix/utils 2025-02-26T09:16:12,870 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2025-02-26T09:16:12,872 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2025-02-26T09:16:12,874 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2025-02-26T09:16:12,877 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2025-02-26T09:16:12,878 copying protenix/utils/training.py -> build/lib/protenix/utils 2025-02-26T09:16:12,880 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2025-02-26T09:16:12,882 copying protenix/utils/seed.py -> build/lib/protenix/utils 2025-02-26T09:16:12,884 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2025-02-26T09:16:12,887 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2025-02-26T09:16:12,889 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2025-02-26T09:16:12,891 creating build/lib/protenix/config 2025-02-26T09:16:12,892 copying protenix/config/extend_types.py -> build/lib/protenix/config 2025-02-26T09:16:12,894 copying protenix/config/config.py -> build/lib/protenix/config 2025-02-26T09:16:12,897 copying protenix/config/__init__.py -> build/lib/protenix/config 2025-02-26T09:16:12,899 creating build/lib/protenix/web_service 2025-02-26T09:16:12,900 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2025-02-26T09:16:12,902 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2025-02-26T09:16:12,905 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2025-02-26T09:16:12,907 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2025-02-26T09:16:12,910 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2025-02-26T09:16:12,911 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2025-02-26T09:16:12,914 creating build/lib/protenix/model 2025-02-26T09:16:12,916 copying protenix/model/utils.py -> build/lib/protenix/model 2025-02-26T09:16:12,918 copying protenix/model/__init__.py -> build/lib/protenix/model 2025-02-26T09:16:12,920 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2025-02-26T09:16:12,922 copying protenix/model/protenix.py -> build/lib/protenix/model 2025-02-26T09:16:12,925 copying protenix/model/loss.py -> build/lib/protenix/model 2025-02-26T09:16:12,929 copying protenix/model/generator.py -> build/lib/protenix/model 2025-02-26T09:16:12,931 creating build/lib/protenix/openfold_local 2025-02-26T09:16:12,932 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2025-02-26T09:16:12,935 creating build/lib/protenix/utils/permutation 2025-02-26T09:16:12,936 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2025-02-26T09:16:12,938 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2025-02-26T09:16:12,939 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2025-02-26T09:16:12,942 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2025-02-26T09:16:12,945 creating build/lib/protenix/utils/permutation/chain_permutation 2025-02-26T09:16:12,946 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-02-26T09:16:12,948 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-02-26T09:16:12,950 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-02-26T09:16:12,953 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-02-26T09:16:12,957 creating build/lib/protenix/model/layer_norm 2025-02-26T09:16:12,958 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2025-02-26T09:16:12,960 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2025-02-26T09:16:12,962 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2025-02-26T09:16:12,965 creating build/lib/protenix/model/modules 2025-02-26T09:16:12,966 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2025-02-26T09:16:12,968 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2025-02-26T09:16:12,971 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2025-02-26T09:16:12,972 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2025-02-26T09:16:12,974 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2025-02-26T09:16:12,976 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2025-02-26T09:16:12,979 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2025-02-26T09:16:12,982 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2025-02-26T09:16:12,985 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2025-02-26T09:16:12,988 creating build/lib/protenix/openfold_local/data 2025-02-26T09:16:12,993 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2025-02-26T09:16:12,996 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2025-02-26T09:16:12,999 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2025-02-26T09:16:13,002 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2025-02-26T09:16:13,003 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2025-02-26T09:16:13,005 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2025-02-26T09:16:13,007 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2025-02-26T09:16:13,010 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2025-02-26T09:16:13,012 creating build/lib/protenix/openfold_local/utils 2025-02-26T09:16:13,013 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2025-02-26T09:16:13,016 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2025-02-26T09:16:13,019 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2025-02-26T09:16:13,020 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2025-02-26T09:16:13,022 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2025-02-26T09:16:13,024 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2025-02-26T09:16:13,026 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2025-02-26T09:16:13,028 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2025-02-26T09:16:13,031 creating build/lib/protenix/openfold_local/np 2025-02-26T09:16:13,032 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2025-02-26T09:16:13,034 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2025-02-26T09:16:13,038 creating build/lib/protenix/openfold_local/model 2025-02-26T09:16:13,039 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2025-02-26T09:16:13,041 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2025-02-26T09:16:13,044 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2025-02-26T09:16:13,045 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2025-02-26T09:16:13,048 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2025-02-26T09:16:13,051 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2025-02-26T09:16:13,053 creating build/lib/protenix/openfold_local/data/tools 2025-02-26T09:16:13,054 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2025-02-26T09:16:13,056 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2025-02-26T09:16:13,058 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2025-02-26T09:16:13,060 creating build/lib/protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,062 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,064 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,066 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,069 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,070 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,072 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,074 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,077 creating build/lib/protenix/openfold_local/utils/kernel 2025-02-26T09:16:13,078 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2025-02-26T09:16:13,080 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2025-02-26T09:16:13,082 running egg_info 2025-02-26T09:16:13,111 writing protenix.egg-info/PKG-INFO 2025-02-26T09:16:13,115 writing dependency_links to protenix.egg-info/dependency_links.txt 2025-02-26T09:16:13,116 writing entry points to protenix.egg-info/entry_points.txt 2025-02-26T09:16:13,118 writing requirements to protenix.egg-info/requires.txt 2025-02-26T09:16:13,119 writing top-level names to protenix.egg-info/top_level.txt 2025-02-26T09:16:13,169 reading manifest file 'protenix.egg-info/SOURCES.txt' 2025-02-26T09:16:13,178 adding license file 'LICENSE' 2025-02-26T09:16:13,187 writing manifest file 'protenix.egg-info/SOURCES.txt' 2025-02-26T09:16:13,190 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'protenix.model.layer_norm.kernel' is absent from the `packages` configuration. 2025-02-26T09:16:13,191 !! 2025-02-26T09:16:13,191 ******************************************************************************** 2025-02-26T09:16:13,192 ############################ 2025-02-26T09:16:13,192 # Package would be ignored # 2025-02-26T09:16:13,193 ############################ 2025-02-26T09:16:13,193 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2025-02-26T09:16:13,194 but it is absent from setuptools' `packages` configuration. 2025-02-26T09:16:13,195 This leads to an ambiguous overall configuration. If you want to distribute this 2025-02-26T09:16:13,195 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2025-02-26T09:16:13,196 to the `packages` configuration field. 2025-02-26T09:16:13,197 Alternatively, you can also rely on setuptools' discovery methods 2025-02-26T09:16:13,198 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-02-26T09:16:13,198 instead of `find_packages(...)`/`find:`). 2025-02-26T09:16:13,199 You can read more about "package discovery" on setuptools documentation page: 2025-02-26T09:16:13,201 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-02-26T09:16:13,202 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2025-02-26T09:16:13,202 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2025-02-26T09:16:13,203 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-02-26T09:16:13,203 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-02-26T09:16:13,204 combination with a more fine grained `package-data` configuration. 2025-02-26T09:16:13,205 You can read more about "package data files" on setuptools documentation page: 2025-02-26T09:16:13,206 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-02-26T09:16:13,208 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-02-26T09:16:13,208 even if it does not contain any `.py` files. 2025-02-26T09:16:13,209 On the other hand, currently there is no concept of package data 2025-02-26T09:16:13,210 directory, all directories are treated like packages. 2025-02-26T09:16:13,210 ******************************************************************************** 2025-02-26T09:16:13,211 !! 2025-02-26T09:16:13,212 check.warn(importable) 2025-02-26T09:16:13,213 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'scripts.msa' is absent from the `packages` configuration. 2025-02-26T09:16:13,213 !! 2025-02-26T09:16:13,214 ******************************************************************************** 2025-02-26T09:16:13,215 ############################ 2025-02-26T09:16:13,215 # Package would be ignored # 2025-02-26T09:16:13,215 ############################ 2025-02-26T09:16:13,216 Python recognizes 'scripts.msa' as an importable package[^1], 2025-02-26T09:16:13,216 but it is absent from setuptools' `packages` configuration. 2025-02-26T09:16:13,217 This leads to an ambiguous overall configuration. If you want to distribute this 2025-02-26T09:16:13,218 package, please make sure that 'scripts.msa' is explicitly added 2025-02-26T09:16:13,218 to the `packages` configuration field. 2025-02-26T09:16:13,219 Alternatively, you can also rely on setuptools' discovery methods 2025-02-26T09:16:13,219 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-02-26T09:16:13,220 instead of `find_packages(...)`/`find:`). 2025-02-26T09:16:13,221 You can read more about "package discovery" on setuptools documentation page: 2025-02-26T09:16:13,222 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-02-26T09:16:13,223 If you don't want 'scripts.msa' to be distributed and are 2025-02-26T09:16:13,223 already explicitly excluding 'scripts.msa' via 2025-02-26T09:16:13,224 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-02-26T09:16:13,225 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-02-26T09:16:13,225 combination with a more fine grained `package-data` configuration. 2025-02-26T09:16:13,226 You can read more about "package data files" on setuptools documentation page: 2025-02-26T09:16:13,227 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-02-26T09:16:13,228 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-02-26T09:16:13,229 even if it does not contain any `.py` files. 2025-02-26T09:16:13,229 On the other hand, currently there is no concept of package data 2025-02-26T09:16:13,230 directory, all directories are treated like packages. 2025-02-26T09:16:13,230 ******************************************************************************** 2025-02-26T09:16:13,232 !! 2025-02-26T09:16:13,232 check.warn(importable) 2025-02-26T09:16:13,233 creating build/lib/scripts/msa 2025-02-26T09:16:13,233 copying scripts/msa/step1-get_prot_seq.py -> build/lib/scripts/msa 2025-02-26T09:16:13,233 copying scripts/msa/step2-get_msa.ipynb -> build/lib/scripts/msa 2025-02-26T09:16:13,234 copying scripts/msa/step3-uniref_add_taxid.py -> build/lib/scripts/msa 2025-02-26T09:16:13,235 copying scripts/msa/step4-split_msa_to_uniref_and_others.py -> build/lib/scripts/msa 2025-02-26T09:16:13,235 creating build/lib/protenix/model/layer_norm/kernel 2025-02-26T09:16:13,236 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2025-02-26T09:16:13,237 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2025-02-26T09:16:13,237 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2025-02-26T09:16:13,238 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2025-02-26T09:16:13,276 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-02-26T09:16:13,277 !! 2025-02-26T09:16:13,278 ******************************************************************************** 2025-02-26T09:16:13,279 Please avoid running ``setup.py`` directly. 2025-02-26T09:16:13,279 Instead, use pypa/build, pypa/installer or other 2025-02-26T09:16:13,280 standards-based tools. 2025-02-26T09:16:13,281 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-02-26T09:16:13,282 ******************************************************************************** 2025-02-26T09:16:13,282 !! 2025-02-26T09:16:13,283 self.initialize_options() 2025-02-26T09:16:13,305 installing to build/bdist.linux-armv7l/wheel 2025-02-26T09:16:13,305 running install 2025-02-26T09:16:13,330 running install_lib 2025-02-26T09:16:13,358 creating build/bdist.linux-armv7l/wheel 2025-02-26T09:16:13,360 creating build/bdist.linux-armv7l/wheel/configs 2025-02-26T09:16:13,361 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2025-02-26T09:16:13,363 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2025-02-26T09:16:13,365 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2025-02-26T09:16:13,367 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2025-02-26T09:16:13,369 creating build/bdist.linux-armv7l/wheel/scripts 2025-02-26T09:16:13,371 creating build/bdist.linux-armv7l/wheel/scripts/msa 2025-02-26T09:16:13,372 copying build/lib/scripts/msa/step3-uniref_add_taxid.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-02-26T09:16:13,374 copying build/lib/scripts/msa/step1-get_prot_seq.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-02-26T09:16:13,377 copying build/lib/scripts/msa/step2-get_msa.ipynb -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-02-26T09:16:13,378 copying build/lib/scripts/msa/step4-split_msa_to_uniref_and_others.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-02-26T09:16:13,380 copying build/lib/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-02-26T09:16:13,382 copying build/lib/scripts/colabfold_msa.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-02-26T09:16:13,384 copying build/lib/scripts/gen_ccd_cache.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-02-26T09:16:13,386 copying build/lib/scripts/prepare_training_data.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-02-26T09:16:13,389 creating build/bdist.linux-armv7l/wheel/protenix 2025-02-26T09:16:13,391 creating build/bdist.linux-armv7l/wheel/protenix/data 2025-02-26T09:16:13,392 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,396 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,398 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,401 copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,404 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,407 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,409 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,414 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,417 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,421 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,424 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,426 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,428 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,431 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,433 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,436 copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,438 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,441 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-26T09:16:13,444 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2025-02-26T09:16:13,445 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-02-26T09:16:13,447 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-02-26T09:16:13,449 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-02-26T09:16:13,451 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-02-26T09:16:13,454 creating build/bdist.linux-armv7l/wheel/protenix/utils 2025-02-26T09:16:13,455 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-26T09:16:13,457 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-26T09:16:13,459 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-26T09:16:13,461 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-26T09:16:13,463 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-26T09:16:13,465 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-26T09:16:13,467 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-26T09:16:13,469 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-26T09:16:13,471 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-26T09:16:13,473 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-26T09:16:13,475 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-26T09:16:13,478 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-26T09:16:13,480 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2025-02-26T09:16:13,482 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2025-02-26T09:16:13,483 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-02-26T09:16:13,485 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-02-26T09:16:13,487 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-02-26T09:16:13,490 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-02-26T09:16:13,492 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-02-26T09:16:13,496 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-02-26T09:16:13,498 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-02-26T09:16:13,501 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-02-26T09:16:13,504 creating build/bdist.linux-armv7l/wheel/protenix/config 2025-02-26T09:16:13,505 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-02-26T09:16:13,507 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-02-26T09:16:13,509 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-02-26T09:16:13,511 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2025-02-26T09:16:13,512 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-26T09:16:13,514 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-26T09:16:13,516 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-26T09:16:13,519 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-26T09:16:13,521 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-26T09:16:13,522 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-26T09:16:13,525 creating build/bdist.linux-armv7l/wheel/protenix/model 2025-02-26T09:16:13,526 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-26T09:16:13,529 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-26T09:16:13,530 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-26T09:16:13,534 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2025-02-26T09:16:13,535 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2025-02-26T09:16:13,537 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-02-26T09:16:13,540 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-02-26T09:16:13,542 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-02-26T09:16:13,545 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-02-26T09:16:13,547 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-02-26T09:16:13,549 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-02-26T09:16:13,551 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-02-26T09:16:13,554 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2025-02-26T09:16:13,555 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-26T09:16:13,557 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-26T09:16:13,560 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-26T09:16:13,562 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-26T09:16:13,564 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-26T09:16:13,566 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-26T09:16:13,569 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-26T09:16:13,571 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-26T09:16:13,574 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-26T09:16:13,576 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-26T09:16:13,579 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-26T09:16:13,582 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-26T09:16:13,585 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2025-02-26T09:16:13,587 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2025-02-26T09:16:13,588 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2025-02-26T09:16:13,589 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-26T09:16:13,593 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-26T09:16:13,595 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-26T09:16:13,599 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-26T09:16:13,601 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-26T09:16:13,603 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2025-02-26T09:16:13,605 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-02-26T09:16:13,606 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-02-26T09:16:13,608 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-02-26T09:16:13,611 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-26T09:16:13,613 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-26T09:16:13,615 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-26T09:16:13,618 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2025-02-26T09:16:13,620 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,621 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,624 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,626 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,628 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,630 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,632 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,634 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-26T09:16:13,637 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2025-02-26T09:16:13,638 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2025-02-26T09:16:13,640 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2025-02-26T09:16:13,641 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-26T09:16:13,644 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-26T09:16:13,646 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-26T09:16:13,648 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-26T09:16:13,650 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-26T09:16:13,652 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-26T09:16:13,654 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-26T09:16:13,655 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-26T09:16:13,658 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2025-02-26T09:16:13,659 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2025-02-26T09:16:13,661 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2025-02-26T09:16:13,665 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2025-02-26T09:16:13,666 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-26T09:16:13,668 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-26T09:16:13,670 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-26T09:16:13,672 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-26T09:16:13,675 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-26T09:16:13,677 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-26T09:16:13,679 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2025-02-26T09:16:13,682 creating build/bdist.linux-armv7l/wheel/tests 2025-02-26T09:16:13,683 copying build/lib/tests/test_utils.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-26T09:16:13,685 copying build/lib/tests/test_frame.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-26T09:16:13,687 copying build/lib/tests/test_weighted_rigid_align.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-26T09:16:13,689 copying build/lib/tests/test_local_rearrange.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-26T09:16:13,691 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-26T09:16:13,693 copying build/lib/tests/test_lr_schedule.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-26T09:16:13,695 copying build/lib/tests/test_condition_transition.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-26T09:16:13,696 copying build/lib/tests/test_attention_pair_bias.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-26T09:16:13,699 copying build/lib/tests/test_diffusion_transformer.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-26T09:16:13,702 creating build/bdist.linux-armv7l/wheel/runner 2025-02-26T09:16:13,703 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-26T09:16:13,706 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-26T09:16:13,708 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-26T09:16:13,710 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-26T09:16:13,713 copying build/lib/runner/msa_search.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-26T09:16:13,715 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-26T09:16:13,717 copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-26T09:16:13,719 running install_egg_info 2025-02-26T09:16:13,752 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.4.4-py3.11.egg-info 2025-02-26T09:16:13,763 running install_scripts 2025-02-26T09:16:13,783 creating build/bdist.linux-armv7l/wheel/protenix-0.4.4.dist-info/WHEEL 2025-02-26T09:16:13,785 creating '/tmp/pip-wheel-h_d1nqga/protenix-0.4.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-02-26T09:16:13,787 adding 'configs/__init__.py' 2025-02-26T09:16:13,790 adding 'configs/configs_base.py' 2025-02-26T09:16:13,792 adding 'configs/configs_data.py' 2025-02-26T09:16:13,793 adding 'configs/configs_inference.py' 2025-02-26T09:16:13,795 adding 'protenix/__init__.py' 2025-02-26T09:16:13,797 adding 'protenix/config/__init__.py' 2025-02-26T09:16:13,799 adding 'protenix/config/config.py' 2025-02-26T09:16:13,801 adding 'protenix/config/extend_types.py' 2025-02-26T09:16:13,802 adding 'protenix/data/__init__.py' 2025-02-26T09:16:13,805 adding 'protenix/data/ccd.py' 2025-02-26T09:16:13,809 adding 'protenix/data/constants.py' 2025-02-26T09:16:13,811 adding 'protenix/data/data_pipeline.py' 2025-02-26T09:16:13,814 adding 'protenix/data/dataloader.py' 2025-02-26T09:16:13,819 adding 'protenix/data/dataset.py' 2025-02-26T09:16:13,823 adding 'protenix/data/featurizer.py' 2025-02-26T09:16:13,826 adding 'protenix/data/filter.py' 2025-02-26T09:16:13,828 adding 'protenix/data/infer_data_pipeline.py' 2025-02-26T09:16:13,830 adding 'protenix/data/json_maker.py' 2025-02-26T09:16:13,833 adding 'protenix/data/json_parser.py' 2025-02-26T09:16:13,835 adding 'protenix/data/json_to_feature.py' 2025-02-26T09:16:13,840 adding 'protenix/data/msa_featurizer.py' 2025-02-26T09:16:13,846 adding 'protenix/data/msa_utils.py' 2025-02-26T09:16:13,857 adding 'protenix/data/parser.py' 2025-02-26T09:16:13,860 adding 'protenix/data/substructure_perms.py' 2025-02-26T09:16:13,862 adding 'protenix/data/tokenizer.py' 2025-02-26T09:16:13,865 adding 'protenix/data/utils.py' 2025-02-26T09:16:13,867 adding 'protenix/metrics/__init__.py' 2025-02-26T09:16:13,869 adding 'protenix/metrics/clash.py' 2025-02-26T09:16:13,871 adding 'protenix/metrics/lddt_metrics.py' 2025-02-26T09:16:13,873 adding 'protenix/metrics/rmsd.py' 2025-02-26T09:16:13,874 adding 'protenix/model/__init__.py' 2025-02-26T09:16:13,876 adding 'protenix/model/generator.py' 2025-02-26T09:16:13,882 adding 'protenix/model/loss.py' 2025-02-26T09:16:13,886 adding 'protenix/model/protenix.py' 2025-02-26T09:16:13,889 adding 'protenix/model/sample_confidence.py' 2025-02-26T09:16:13,892 adding 'protenix/model/utils.py' 2025-02-26T09:16:13,893 adding 'protenix/model/layer_norm/__init__.py' 2025-02-26T09:16:13,895 adding 'protenix/model/layer_norm/layer_norm.py' 2025-02-26T09:16:13,897 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2025-02-26T09:16:13,898 adding 'protenix/model/layer_norm/kernel/compat.h' 2025-02-26T09:16:13,900 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2025-02-26T09:16:13,902 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2025-02-26T09:16:13,904 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2025-02-26T09:16:13,906 adding 'protenix/model/modules/__init__.py' 2025-02-26T09:16:13,908 adding 'protenix/model/modules/confidence.py' 2025-02-26T09:16:13,910 adding 'protenix/model/modules/diffusion.py' 2025-02-26T09:16:13,912 adding 'protenix/model/modules/embedders.py' 2025-02-26T09:16:13,914 adding 'protenix/model/modules/frames.py' 2025-02-26T09:16:13,915 adding 'protenix/model/modules/head.py' 2025-02-26T09:16:13,918 adding 'protenix/model/modules/pairformer.py' 2025-02-26T09:16:13,922 adding 'protenix/model/modules/primitives.py' 2025-02-26T09:16:13,925 adding 'protenix/model/modules/transformer.py' 2025-02-26T09:16:13,927 adding 'protenix/openfold_local/__init__.py' 2025-02-26T09:16:13,929 adding 'protenix/openfold_local/data/__init__.py' 2025-02-26T09:16:13,931 adding 'protenix/openfold_local/data/data_transforms.py' 2025-02-26T09:16:13,932 adding 'protenix/openfold_local/data/errors.py' 2025-02-26T09:16:13,934 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2025-02-26T09:16:13,936 adding 'protenix/openfold_local/data/msa_identifiers.py' 2025-02-26T09:16:13,938 adding 'protenix/openfold_local/data/msa_pairing.py' 2025-02-26T09:16:13,942 adding 'protenix/openfold_local/data/parsers.py' 2025-02-26T09:16:13,945 adding 'protenix/openfold_local/data/templates.py' 2025-02-26T09:16:13,946 adding 'protenix/openfold_local/data/tools/__init__.py' 2025-02-26T09:16:13,948 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2025-02-26T09:16:13,949 adding 'protenix/openfold_local/data/tools/utils.py' 2025-02-26T09:16:13,951 adding 'protenix/openfold_local/model/__init__.py' 2025-02-26T09:16:13,952 adding 'protenix/openfold_local/model/dropout.py' 2025-02-26T09:16:13,954 adding 'protenix/openfold_local/model/outer_product_mean.py' 2025-02-26T09:16:13,957 adding 'protenix/openfold_local/model/primitives.py' 2025-02-26T09:16:13,958 adding 'protenix/openfold_local/model/triangular_attention.py' 2025-02-26T09:16:13,961 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2025-02-26T09:16:13,963 adding 'protenix/openfold_local/np/__init__.py' 2025-02-26T09:16:13,967 adding 'protenix/openfold_local/np/residue_constants.py' 2025-02-26T09:16:13,970 adding 'protenix/openfold_local/utils/__init__.py' 2025-02-26T09:16:13,972 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2025-02-26T09:16:13,974 adding 'protenix/openfold_local/utils/checkpointing.py' 2025-02-26T09:16:13,976 adding 'protenix/openfold_local/utils/chunk_utils.py' 2025-02-26T09:16:13,978 adding 'protenix/openfold_local/utils/feats.py' 2025-02-26T09:16:13,979 adding 'protenix/openfold_local/utils/precision_utils.py' 2025-02-26T09:16:13,983 adding 'protenix/openfold_local/utils/rigid_utils.py' 2025-02-26T09:16:13,985 adding 'protenix/openfold_local/utils/tensor_utils.py' 2025-02-26T09:16:13,987 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2025-02-26T09:16:13,988 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2025-02-26T09:16:13,990 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2025-02-26T09:16:13,991 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2025-02-26T09:16:13,993 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2025-02-26T09:16:13,994 adding 'protenix/openfold_local/utils/geometry/utils.py' 2025-02-26T09:16:13,996 adding 'protenix/openfold_local/utils/geometry/vector.py' 2025-02-26T09:16:13,997 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2025-02-26T09:16:13,999 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2025-02-26T09:16:14,000 adding 'protenix/utils/__init__.py' 2025-02-26T09:16:14,004 adding 'protenix/utils/cropping.py' 2025-02-26T09:16:14,005 adding 'protenix/utils/distributed.py' 2025-02-26T09:16:14,006 adding 'protenix/utils/file_io.py' 2025-02-26T09:16:14,008 adding 'protenix/utils/geometry.py' 2025-02-26T09:16:14,009 adding 'protenix/utils/logger.py' 2025-02-26T09:16:14,010 adding 'protenix/utils/lr_scheduler.py' 2025-02-26T09:16:14,012 adding 'protenix/utils/metrics.py' 2025-02-26T09:16:14,014 adding 'protenix/utils/scatter_utils.py' 2025-02-26T09:16:14,016 adding 'protenix/utils/seed.py' 2025-02-26T09:16:14,017 adding 'protenix/utils/torch_utils.py' 2025-02-26T09:16:14,018 adding 'protenix/utils/training.py' 2025-02-26T09:16:14,020 adding 'protenix/utils/permutation/__init__.py' 2025-02-26T09:16:14,024 adding 'protenix/utils/permutation/atom_permutation.py' 2025-02-26T09:16:14,026 adding 'protenix/utils/permutation/permutation.py' 2025-02-26T09:16:14,028 adding 'protenix/utils/permutation/utils.py' 2025-02-26T09:16:14,030 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2025-02-26T09:16:14,034 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2025-02-26T09:16:14,036 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2025-02-26T09:16:14,037 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2025-02-26T09:16:14,039 adding 'protenix/web_service/__init__.py' 2025-02-26T09:16:14,041 adding 'protenix/web_service/colab_request_parser.py' 2025-02-26T09:16:14,043 adding 'protenix/web_service/colab_request_utils.py' 2025-02-26T09:16:14,044 adding 'protenix/web_service/dependency_url.py' 2025-02-26T09:16:14,046 adding 'protenix/web_service/prediction_visualization.py' 2025-02-26T09:16:14,048 adding 'protenix/web_service/viewer.py' 2025-02-26T09:16:14,051 adding 'runner/__init__.py' 2025-02-26T09:16:14,053 adding 'runner/batch_inference.py' 2025-02-26T09:16:14,055 adding 'runner/dumper.py' 2025-02-26T09:16:14,056 adding 'runner/ema.py' 2025-02-26T09:16:14,058 adding 'runner/inference.py' 2025-02-26T09:16:14,059 adding 'runner/msa_search.py' 2025-02-26T09:16:14,062 adding 'runner/train.py' 2025-02-26T09:16:14,064 adding 'scripts/__init__.py' 2025-02-26T09:16:14,066 adding 'scripts/colabfold_msa.py' 2025-02-26T09:16:14,068 adding 'scripts/gen_ccd_cache.py' 2025-02-26T09:16:14,069 adding 'scripts/prepare_training_data.py' 2025-02-26T09:16:14,072 adding 'scripts/msa/step1-get_prot_seq.py' 2025-02-26T09:16:14,073 adding 'scripts/msa/step2-get_msa.ipynb' 2025-02-26T09:16:14,075 adding 'scripts/msa/step3-uniref_add_taxid.py' 2025-02-26T09:16:14,076 adding 'scripts/msa/step4-split_msa_to_uniref_and_others.py' 2025-02-26T09:16:14,078 adding 'tests/__init__.py' 2025-02-26T09:16:14,079 adding 'tests/test_attention_pair_bias.py' 2025-02-26T09:16:14,080 adding 'tests/test_condition_transition.py' 2025-02-26T09:16:14,082 adding 'tests/test_diffusion_transformer.py' 2025-02-26T09:16:14,083 adding 'tests/test_frame.py' 2025-02-26T09:16:14,084 adding 'tests/test_local_rearrange.py' 2025-02-26T09:16:14,086 adding 'tests/test_lr_schedule.py' 2025-02-26T09:16:14,087 adding 'tests/test_utils.py' 2025-02-26T09:16:14,089 adding 'tests/test_weighted_rigid_align.py' 2025-02-26T09:16:14,091 adding 'protenix-0.4.4.dist-info/LICENSE' 2025-02-26T09:16:14,092 adding 'protenix-0.4.4.dist-info/METADATA' 2025-02-26T09:16:14,093 adding 'protenix-0.4.4.dist-info/WHEEL' 2025-02-26T09:16:14,094 adding 'protenix-0.4.4.dist-info/entry_points.txt' 2025-02-26T09:16:14,095 adding 'protenix-0.4.4.dist-info/top_level.txt' 2025-02-26T09:16:14,097 adding 'protenix-0.4.4.dist-info/RECORD' 2025-02-26T09:16:14,104 removing build/bdist.linux-armv7l/wheel 2025-02-26T09:16:14,254 Building wheel for protenix (setup.py): finished with status 'done' 2025-02-26T09:16:14,261 Created wheel for protenix: filename=protenix-0.4.4-py3-none-any.whl size=428461 sha256=bfd049b21ac0835a40d8b1cc0d793a4a0aff67c9d86abcb2df51a154d9704ce4 2025-02-26T09:16:14,263 Stored in directory: /tmp/pip-ephem-wheel-cache-_czrlrbi/wheels/91/7f/fa/d27ad5533d5b050d868eb7c26bb5057c745814ab44871b23b1 2025-02-26T09:16:14,280 Successfully built protenix 2025-02-26T09:16:14,293 Removed build tracker: '/tmp/pip-build-tracker-7dg0_3_g'