2025-02-19T08:52:22,051 Created temporary directory: /tmp/pip-build-tracker-d4x05n8x 2025-02-19T08:52:22,053 Initialized build tracking at /tmp/pip-build-tracker-d4x05n8x 2025-02-19T08:52:22,053 Created build tracker: /tmp/pip-build-tracker-d4x05n8x 2025-02-19T08:52:22,053 Entered build tracker: /tmp/pip-build-tracker-d4x05n8x 2025-02-19T08:52:22,054 Created temporary directory: /tmp/pip-wheel-c6eoxdy4 2025-02-19T08:52:22,058 Created temporary directory: /tmp/pip-ephem-wheel-cache-46dez6zd 2025-02-19T08:52:22,103 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-02-19T08:52:22,105 2 location(s) to search for versions of protenix: 2025-02-19T08:52:22,105 * https://pypi.org/simple/protenix/ 2025-02-19T08:52:22,105 * https://www.piwheels.org/simple/protenix/ 2025-02-19T08:52:22,106 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2025-02-19T08:52:22,107 Getting page https://pypi.org/simple/protenix/ 2025-02-19T08:52:22,108 Found index url https://pypi.org/simple/ 2025-02-19T08:52:22,331 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2025-02-19T08:52:22,339 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/) 2025-02-19T08:52:22,340 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/) 2025-02-19T08:52:22,341 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 2025-02-19T08:52:22,341 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/85/33/10bb83edcf222b7cd05cc94d453ac7edfa86f09c7100db8c62fcc894745c/protenix-0.1.0-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-19T08:52:22,342 Found link https://files.pythonhosted.org/packages/d5/61/cdea4397a181ca2b108c6df0aa4c30e7a6fc34c5b75ad69557569c44b61d/protenix-0.1.0.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.1.0 2025-02-19T08:52:22,343 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/28/00/2206a6a3a02d45eeb6e16c6ffcacff6789f11489238acd07ad5127219741/protenix-0.1.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-19T08:52:22,344 Found link https://files.pythonhosted.org/packages/2b/7b/20fe2818e890f5d25a892ba31a24b910d0cf34e9f86b990c042c3f91fd05/protenix-0.1.1.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.1.1 2025-02-19T08:52:22,345 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) 2025-02-19T08:52:22,346 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 2025-02-19T08:52:22,347 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) 2025-02-19T08:52:22,348 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 2025-02-19T08:52:22,349 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) 2025-02-19T08:52:22,350 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 2025-02-19T08:52:22,351 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) 2025-02-19T08:52:22,352 Found link 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(requires-python:>=3.10) 2025-02-19T08:52:22,355 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 2025-02-19T08:52:22,355 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) 2025-02-19T08:52:22,357 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 2025-02-19T08:52:22,358 Skipping link: No binaries permitted for protenix: 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(requires-python:>=3.10), version: 0.3.7 2025-02-19T08:52:22,365 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) 2025-02-19T08:52:22,365 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 2025-02-19T08:52:22,366 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) 2025-02-19T08:52:22,367 Found link 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(requires-python:>=3.10) 2025-02-19T08:52:22,370 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 2025-02-19T08:52:22,371 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) 2025-02-19T08:52:22,372 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 2025-02-19T08:52:22,373 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/ed/a9/12f54849afefaa671eda0dd50dbfad1205273e643047858b462983506f75/protenix-0.4.3-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-02-19T08:52:22,373 Found link https://files.pythonhosted.org/packages/d7/1b/de4a2a08930efad46ac93230e6a7cd2a3eb55bdf2f30aa1a1c624015ce03/protenix-0.4.3.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.4.3 2025-02-19T08:52:22,374 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2025-02-19T08:52:22,375 Getting page https://www.piwheels.org/simple/protenix/ 2025-02-19T08:52:22,376 Found index url https://www.piwheels.org/simple/ 2025-02-19T08:52:22,537 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2025-02-19T08:52:22,544 Skipping link: No binaries permitted for protenix: 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https://www.piwheels.org/simple/protenix/protenix-0.3.0-py3-none-any.whl#sha256=c2af82dfdebc9606f320eb2d0ae308e644cd77922b443dcd59e7f778e756ac45 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-02-19T08:52:22,552 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) 2025-02-19T08:52:22,552 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) 2025-02-19T08:52:22,553 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) 2025-02-19T08:52:22,554 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) 2025-02-19T08:52:22,554 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) 2025-02-19T08:52:22,555 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/) 2025-02-19T08:52:22,555 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2025-02-19T08:52:22,556 Skipping link: not a file: https://pypi.org/simple/protenix/ 2025-02-19T08:52:22,578 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2025-02-19T08:52:22,580 Collecting protenix==0.4.3 2025-02-19T08:52:22,582 Created temporary directory: /tmp/pip-unpack-49tqntt4 2025-02-19T08:52:22,806 Downloading protenix-0.4.3.tar.gz (345 kB) 2025-02-19T08:52:23,505 Added protenix==0.4.3 from https://files.pythonhosted.org/packages/d7/1b/de4a2a08930efad46ac93230e6a7cd2a3eb55bdf2f30aa1a1c624015ce03/protenix-0.4.3.tar.gz to build tracker '/tmp/pip-build-tracker-d4x05n8x' 2025-02-19T08:52:23,507 Running setup.py (path:/tmp/pip-wheel-c6eoxdy4/protenix_4de3d7c5e5894c61bfe06bd50a908229/setup.py) egg_info for package protenix 2025-02-19T08:52:23,508 Created temporary directory: /tmp/pip-pip-egg-info-1375gyam 2025-02-19T08:52:23,509 Preparing metadata (setup.py): started 2025-02-19T08:52:23,511 Running command python setup.py egg_info 2025-02-19T08:52:24,609 running egg_info 2025-02-19T08:52:24,641 creating /tmp/pip-pip-egg-info-1375gyam/protenix.egg-info 2025-02-19T08:52:24,642 writing /tmp/pip-pip-egg-info-1375gyam/protenix.egg-info/PKG-INFO 2025-02-19T08:52:24,646 writing dependency_links to /tmp/pip-pip-egg-info-1375gyam/protenix.egg-info/dependency_links.txt 2025-02-19T08:52:24,647 writing entry points to /tmp/pip-pip-egg-info-1375gyam/protenix.egg-info/entry_points.txt 2025-02-19T08:52:24,649 writing requirements to /tmp/pip-pip-egg-info-1375gyam/protenix.egg-info/requires.txt 2025-02-19T08:52:24,650 writing top-level names to /tmp/pip-pip-egg-info-1375gyam/protenix.egg-info/top_level.txt 2025-02-19T08:52:24,651 writing manifest file '/tmp/pip-pip-egg-info-1375gyam/protenix.egg-info/SOURCES.txt' 2025-02-19T08:52:24,772 reading manifest file '/tmp/pip-pip-egg-info-1375gyam/protenix.egg-info/SOURCES.txt' 2025-02-19T08:52:24,774 adding license file 'LICENSE' 2025-02-19T08:52:24,780 writing manifest file '/tmp/pip-pip-egg-info-1375gyam/protenix.egg-info/SOURCES.txt' 2025-02-19T08:52:24,890 Preparing metadata (setup.py): finished with status 'done' 2025-02-19T08:52:24,894 Source in /tmp/pip-wheel-c6eoxdy4/protenix_4de3d7c5e5894c61bfe06bd50a908229 has version 0.4.3, which satisfies requirement protenix==0.4.3 from https://files.pythonhosted.org/packages/d7/1b/de4a2a08930efad46ac93230e6a7cd2a3eb55bdf2f30aa1a1c624015ce03/protenix-0.4.3.tar.gz 2025-02-19T08:52:24,895 Removed protenix==0.4.3 from https://files.pythonhosted.org/packages/d7/1b/de4a2a08930efad46ac93230e6a7cd2a3eb55bdf2f30aa1a1c624015ce03/protenix-0.4.3.tar.gz from build tracker '/tmp/pip-build-tracker-d4x05n8x' 2025-02-19T08:52:24,904 Created temporary directory: /tmp/pip-unpack-tcn6z4ac 2025-02-19T08:52:24,905 Created temporary directory: /tmp/pip-unpack-0osvggmi 2025-02-19T08:52:24,906 Building wheels for collected packages: protenix 2025-02-19T08:52:24,910 Created temporary directory: /tmp/pip-wheel-uyo5bue1 2025-02-19T08:52:24,910 Building wheel for protenix (setup.py): started 2025-02-19T08:52:24,911 Destination directory: /tmp/pip-wheel-uyo5bue1 2025-02-19T08:52:24,912 Running command python setup.py bdist_wheel 2025-02-19T08:52:25,945 running bdist_wheel 2025-02-19T08:52:26,076 running build 2025-02-19T08:52:26,077 running build_py 2025-02-19T08:52:26,112 creating build/lib/tests 2025-02-19T08:52:26,114 copying tests/test_lr_schedule.py -> build/lib/tests 2025-02-19T08:52:26,117 copying tests/test_weighted_rigid_align.py -> build/lib/tests 2025-02-19T08:52:26,119 copying tests/test_condition_transition.py -> build/lib/tests 2025-02-19T08:52:26,121 copying tests/test_utils.py -> build/lib/tests 2025-02-19T08:52:26,123 copying tests/test_local_rearrange.py -> build/lib/tests 2025-02-19T08:52:26,125 copying tests/test_attention_pair_bias.py -> build/lib/tests 2025-02-19T08:52:26,127 copying tests/test_frame.py -> build/lib/tests 2025-02-19T08:52:26,129 copying tests/test_diffusion_transformer.py -> build/lib/tests 2025-02-19T08:52:26,131 copying tests/__init__.py -> build/lib/tests 2025-02-19T08:52:26,133 creating build/lib/runner 2025-02-19T08:52:26,134 copying runner/batch_inference.py -> build/lib/runner 2025-02-19T08:52:26,136 copying runner/inference.py -> build/lib/runner 2025-02-19T08:52:26,139 copying runner/ema.py -> build/lib/runner 2025-02-19T08:52:26,141 copying runner/msa_search.py -> build/lib/runner 2025-02-19T08:52:26,143 copying runner/train.py -> build/lib/runner 2025-02-19T08:52:26,146 copying runner/dumper.py -> build/lib/runner 2025-02-19T08:52:26,148 copying runner/__init__.py -> build/lib/runner 2025-02-19T08:52:26,150 creating build/lib/configs 2025-02-19T08:52:26,151 copying configs/configs_inference.py -> build/lib/configs 2025-02-19T08:52:26,153 copying configs/configs_base.py -> build/lib/configs 2025-02-19T08:52:26,155 copying configs/configs_data.py -> build/lib/configs 2025-02-19T08:52:26,158 copying configs/__init__.py -> build/lib/configs 2025-02-19T08:52:26,159 creating build/lib/protenix 2025-02-19T08:52:26,161 copying protenix/__init__.py -> build/lib/protenix 2025-02-19T08:52:26,163 creating build/lib/scripts 2025-02-19T08:52:26,164 copying scripts/colabfold_msa.py -> build/lib/scripts 2025-02-19T08:52:26,167 copying scripts/__init__.py -> build/lib/scripts 2025-02-19T08:52:26,168 copying scripts/prepare_training_data.py -> build/lib/scripts 2025-02-19T08:52:26,170 copying scripts/gen_ccd_cache.py -> build/lib/scripts 2025-02-19T08:52:26,174 creating build/lib/protenix/data 2025-02-19T08:52:26,175 copying protenix/data/utils.py -> build/lib/protenix/data 2025-02-19T08:52:26,178 copying protenix/data/dataset.py -> build/lib/protenix/data 2025-02-19T08:52:26,180 copying protenix/data/ccd.py -> build/lib/protenix/data 2025-02-19T08:52:26,183 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2025-02-19T08:52:26,186 copying protenix/data/json_maker.py -> build/lib/protenix/data 2025-02-19T08:52:26,189 copying protenix/data/filter.py -> build/lib/protenix/data 2025-02-19T08:52:26,191 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2025-02-19T08:52:26,195 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2025-02-19T08:52:26,197 copying protenix/data/json_parser.py -> build/lib/protenix/data 2025-02-19T08:52:26,200 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2025-02-19T08:52:26,202 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2025-02-19T08:52:26,205 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2025-02-19T08:52:26,207 copying protenix/data/dataloader.py -> build/lib/protenix/data 2025-02-19T08:52:26,210 copying protenix/data/featurizer.py -> build/lib/protenix/data 2025-02-19T08:52:26,214 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2025-02-19T08:52:26,216 copying protenix/data/__init__.py -> build/lib/protenix/data 2025-02-19T08:52:26,217 copying protenix/data/constants.py -> build/lib/protenix/data 2025-02-19T08:52:26,220 copying protenix/data/parser.py -> build/lib/protenix/data 2025-02-19T08:52:26,225 creating build/lib/protenix/web_service 2025-02-19T08:52:26,226 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2025-02-19T08:52:26,229 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2025-02-19T08:52:26,231 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2025-02-19T08:52:26,233 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2025-02-19T08:52:26,236 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2025-02-19T08:52:26,238 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2025-02-19T08:52:26,240 creating build/lib/protenix/model 2025-02-19T08:52:26,241 copying protenix/model/utils.py -> build/lib/protenix/model 2025-02-19T08:52:26,244 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2025-02-19T08:52:26,247 copying protenix/model/loss.py -> build/lib/protenix/model 2025-02-19T08:52:26,251 copying protenix/model/generator.py -> build/lib/protenix/model 2025-02-19T08:52:26,254 copying protenix/model/protenix.py -> build/lib/protenix/model 2025-02-19T08:52:26,258 copying protenix/model/__init__.py -> build/lib/protenix/model 2025-02-19T08:52:26,260 creating build/lib/protenix/config 2025-02-19T08:52:26,261 copying protenix/config/config.py -> build/lib/protenix/config 2025-02-19T08:52:26,264 copying protenix/config/extend_types.py -> build/lib/protenix/config 2025-02-19T08:52:26,266 copying protenix/config/__init__.py -> build/lib/protenix/config 2025-02-19T08:52:26,269 creating build/lib/protenix/utils 2025-02-19T08:52:26,270 copying protenix/utils/logger.py -> build/lib/protenix/utils 2025-02-19T08:52:26,273 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2025-02-19T08:52:26,275 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2025-02-19T08:52:26,278 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2025-02-19T08:52:26,280 copying protenix/utils/seed.py -> build/lib/protenix/utils 2025-02-19T08:52:26,282 copying protenix/utils/training.py -> build/lib/protenix/utils 2025-02-19T08:52:26,285 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2025-02-19T08:52:26,288 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2025-02-19T08:52:26,291 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2025-02-19T08:52:26,293 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2025-02-19T08:52:26,295 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2025-02-19T08:52:26,297 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2025-02-19T08:52:26,300 creating build/lib/protenix/openfold_local 2025-02-19T08:52:26,302 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2025-02-19T08:52:26,305 creating build/lib/protenix/metrics 2025-02-19T08:52:26,306 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2025-02-19T08:52:26,309 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2025-02-19T08:52:26,312 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2025-02-19T08:52:26,315 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2025-02-19T08:52:26,317 creating build/lib/protenix/model/modules 2025-02-19T08:52:26,319 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2025-02-19T08:52:26,321 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2025-02-19T08:52:26,324 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2025-02-19T08:52:26,327 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2025-02-19T08:52:26,329 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2025-02-19T08:52:26,333 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2025-02-19T08:52:26,335 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2025-02-19T08:52:26,339 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2025-02-19T08:52:26,342 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2025-02-19T08:52:26,344 creating build/lib/protenix/model/layer_norm 2025-02-19T08:52:26,345 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2025-02-19T08:52:26,348 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2025-02-19T08:52:26,350 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2025-02-19T08:52:26,353 creating build/lib/protenix/utils/permutation 2025-02-19T08:52:26,355 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2025-02-19T08:52:26,357 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2025-02-19T08:52:26,360 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2025-02-19T08:52:26,363 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2025-02-19T08:52:26,366 creating build/lib/protenix/utils/permutation/chain_permutation 2025-02-19T08:52:26,367 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-02-19T08:52:26,370 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-02-19T08:52:26,373 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-02-19T08:52:26,377 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-02-19T08:52:26,380 creating build/lib/protenix/openfold_local/np 2025-02-19T08:52:26,382 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2025-02-19T08:52:26,385 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2025-02-19T08:52:26,387 creating build/lib/protenix/openfold_local/data 2025-02-19T08:52:26,388 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2025-02-19T08:52:26,391 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2025-02-19T08:52:26,394 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2025-02-19T08:52:26,396 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2025-02-19T08:52:26,398 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2025-02-19T08:52:26,402 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2025-02-19T08:52:26,405 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2025-02-19T08:52:26,407 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2025-02-19T08:52:26,409 creating build/lib/protenix/openfold_local/model 2025-02-19T08:52:26,410 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2025-02-19T08:52:26,412 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2025-02-19T08:52:26,415 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2025-02-19T08:52:26,418 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2025-02-19T08:52:26,420 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2025-02-19T08:52:26,422 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2025-02-19T08:52:26,425 creating build/lib/protenix/openfold_local/utils 2025-02-19T08:52:26,426 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2025-02-19T08:52:26,429 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2025-02-19T08:52:26,431 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2025-02-19T08:52:26,433 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2025-02-19T08:52:26,436 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2025-02-19T08:52:26,438 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2025-02-19T08:52:26,441 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2025-02-19T08:52:26,442 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2025-02-19T08:52:26,444 creating build/lib/protenix/openfold_local/data/tools 2025-02-19T08:52:26,446 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2025-02-19T08:52:26,448 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2025-02-19T08:52:26,450 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2025-02-19T08:52:26,452 creating build/lib/protenix/openfold_local/utils/kernel 2025-02-19T08:52:26,453 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2025-02-19T08:52:26,455 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2025-02-19T08:52:26,457 creating build/lib/protenix/openfold_local/utils/geometry 2025-02-19T08:52:26,458 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-19T08:52:26,460 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-19T08:52:26,463 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-19T08:52:26,464 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-19T08:52:26,466 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-19T08:52:26,469 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-19T08:52:26,471 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2025-02-19T08:52:26,473 running egg_info 2025-02-19T08:52:26,505 writing protenix.egg-info/PKG-INFO 2025-02-19T08:52:26,509 writing dependency_links to protenix.egg-info/dependency_links.txt 2025-02-19T08:52:26,510 writing entry points to protenix.egg-info/entry_points.txt 2025-02-19T08:52:26,512 writing requirements to protenix.egg-info/requires.txt 2025-02-19T08:52:26,513 writing top-level names to protenix.egg-info/top_level.txt 2025-02-19T08:52:26,565 reading manifest file 'protenix.egg-info/SOURCES.txt' 2025-02-19T08:52:26,575 adding license file 'LICENSE' 2025-02-19T08:52:26,583 writing manifest file 'protenix.egg-info/SOURCES.txt' 2025-02-19T08:52:26,586 /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. 2025-02-19T08:52:26,587 !! 2025-02-19T08:52:26,588 ******************************************************************************** 2025-02-19T08:52:26,588 ############################ 2025-02-19T08:52:26,588 # Package would be ignored # 2025-02-19T08:52:26,589 ############################ 2025-02-19T08:52:26,589 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2025-02-19T08:52:26,590 but it is absent from setuptools' `packages` configuration. 2025-02-19T08:52:26,591 This leads to an ambiguous overall configuration. If you want to distribute this 2025-02-19T08:52:26,591 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2025-02-19T08:52:26,591 to the `packages` configuration field. 2025-02-19T08:52:26,593 Alternatively, you can also rely on setuptools' discovery methods 2025-02-19T08:52:26,593 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-02-19T08:52:26,594 instead of `find_packages(...)`/`find:`). 2025-02-19T08:52:26,595 You can read more about "package discovery" on setuptools documentation page: 2025-02-19T08:52:26,595 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-02-19T08:52:26,596 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2025-02-19T08:52:26,597 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2025-02-19T08:52:26,597 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-02-19T08:52:26,598 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-02-19T08:52:26,599 combination with a more fine grained `package-data` configuration. 2025-02-19T08:52:26,600 You can read more about "package data files" on setuptools documentation page: 2025-02-19T08:52:26,601 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-02-19T08:52:26,602 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-02-19T08:52:26,603 even if it does not contain any `.py` files. 2025-02-19T08:52:26,604 On the other hand, currently there is no concept of package data 2025-02-19T08:52:26,604 directory, all directories are treated like packages. 2025-02-19T08:52:26,605 ******************************************************************************** 2025-02-19T08:52:26,606 !! 2025-02-19T08:52:26,606 check.warn(importable) 2025-02-19T08:52:26,607 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'scripts.msa' is absent from the `packages` configuration. 2025-02-19T08:52:26,607 !! 2025-02-19T08:52:26,609 ******************************************************************************** 2025-02-19T08:52:26,609 ############################ 2025-02-19T08:52:26,610 # Package would be ignored # 2025-02-19T08:52:26,610 ############################ 2025-02-19T08:52:26,611 Python recognizes 'scripts.msa' as an importable package[^1], 2025-02-19T08:52:26,611 but it is absent from setuptools' `packages` configuration. 2025-02-19T08:52:26,612 This leads to an ambiguous overall configuration. If you want to distribute this 2025-02-19T08:52:26,613 package, please make sure that 'scripts.msa' is explicitly added 2025-02-19T08:52:26,613 to the `packages` configuration field. 2025-02-19T08:52:26,615 Alternatively, you can also rely on setuptools' discovery methods 2025-02-19T08:52:26,615 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-02-19T08:52:26,615 instead of `find_packages(...)`/`find:`). 2025-02-19T08:52:26,616 You can read more about "package discovery" on setuptools documentation page: 2025-02-19T08:52:26,617 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-02-19T08:52:26,618 If you don't want 'scripts.msa' to be distributed and are 2025-02-19T08:52:26,618 already explicitly excluding 'scripts.msa' via 2025-02-19T08:52:26,619 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-02-19T08:52:26,619 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-02-19T08:52:26,620 combination with a more fine grained `package-data` configuration. 2025-02-19T08:52:26,621 You can read more about "package data files" on setuptools documentation page: 2025-02-19T08:52:26,622 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-02-19T08:52:26,623 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-02-19T08:52:26,624 even if it does not contain any `.py` files. 2025-02-19T08:52:26,624 On the other hand, currently there is no concept of package data 2025-02-19T08:52:26,625 directory, all directories are treated like packages. 2025-02-19T08:52:26,625 ******************************************************************************** 2025-02-19T08:52:26,626 !! 2025-02-19T08:52:26,626 check.warn(importable) 2025-02-19T08:52:26,627 creating build/lib/protenix/model/layer_norm/kernel 2025-02-19T08:52:26,627 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2025-02-19T08:52:26,628 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2025-02-19T08:52:26,628 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2025-02-19T08:52:26,629 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2025-02-19T08:52:26,630 creating build/lib/scripts/msa 2025-02-19T08:52:26,630 copying scripts/msa/step1-get_prot_seq.py -> build/lib/scripts/msa 2025-02-19T08:52:26,631 copying scripts/msa/step2-get_msa.ipynb -> build/lib/scripts/msa 2025-02-19T08:52:26,631 copying scripts/msa/step3-uniref_add_taxid.py -> build/lib/scripts/msa 2025-02-19T08:52:26,632 copying scripts/msa/step4-split_msa_to_uniref_and_others.py -> build/lib/scripts/msa 2025-02-19T08:52:26,671 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-02-19T08:52:26,671 !! 2025-02-19T08:52:26,673 ******************************************************************************** 2025-02-19T08:52:26,673 Please avoid running ``setup.py`` directly. 2025-02-19T08:52:26,674 Instead, use pypa/build, pypa/installer or other 2025-02-19T08:52:26,674 standards-based tools. 2025-02-19T08:52:26,676 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-02-19T08:52:26,676 ******************************************************************************** 2025-02-19T08:52:26,677 !! 2025-02-19T08:52:26,678 self.initialize_options() 2025-02-19T08:52:26,699 installing to build/bdist.linux-armv7l/wheel 2025-02-19T08:52:26,699 running install 2025-02-19T08:52:26,723 running install_lib 2025-02-19T08:52:26,750 creating build/bdist.linux-armv7l/wheel 2025-02-19T08:52:26,753 creating build/bdist.linux-armv7l/wheel/tests 2025-02-19T08:52:26,754 copying build/lib/tests/test_lr_schedule.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-19T08:52:26,757 copying build/lib/tests/test_weighted_rigid_align.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-19T08:52:26,759 copying build/lib/tests/test_condition_transition.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-19T08:52:26,761 copying build/lib/tests/test_utils.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-19T08:52:26,763 copying build/lib/tests/test_local_rearrange.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-19T08:52:26,765 copying build/lib/tests/test_attention_pair_bias.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-19T08:52:26,768 copying build/lib/tests/test_frame.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-19T08:52:26,770 copying build/lib/tests/test_diffusion_transformer.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-19T08:52:26,773 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2025-02-19T08:52:26,776 creating build/bdist.linux-armv7l/wheel/runner 2025-02-19T08:52:26,778 copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-19T08:52:26,781 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-19T08:52:26,785 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-19T08:52:27,005 copying build/lib/runner/msa_search.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-19T08:52:27,009 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-19T08:52:27,014 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-19T08:52:27,018 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2025-02-19T08:52:27,022 creating build/bdist.linux-armv7l/wheel/configs 2025-02-19T08:52:27,023 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2025-02-19T08:52:27,027 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2025-02-19T08:52:27,030 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2025-02-19T08:52:27,033 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2025-02-19T08:52:27,036 creating build/bdist.linux-armv7l/wheel/protenix 2025-02-19T08:52:27,039 creating build/bdist.linux-armv7l/wheel/protenix/data 2025-02-19T08:52:27,041 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,045 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,050 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,053 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,058 copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,062 copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,066 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,071 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,075 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,079 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,084 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,088 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,093 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,097 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,103 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,107 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,110 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,115 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-02-19T08:52:27,125 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2025-02-19T08:52:27,127 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-19T08:52:27,130 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-19T08:52:27,132 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-19T08:52:27,135 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-19T08:52:27,138 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-19T08:52:27,141 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-02-19T08:52:27,143 creating build/bdist.linux-armv7l/wheel/protenix/model 2025-02-19T08:52:27,145 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-19T08:52:27,148 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-19T08:52:27,150 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-19T08:52:27,155 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2025-02-19T08:52:27,157 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-19T08:52:27,159 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-19T08:52:27,162 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-19T08:52:27,165 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-19T08:52:27,167 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-19T08:52:27,170 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-19T08:52:27,173 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-19T08:52:27,176 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-19T08:52:27,179 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-02-19T08:52:27,182 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2025-02-19T08:52:27,183 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-02-19T08:52:27,186 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-02-19T08:52:27,189 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2025-02-19T08:52:27,191 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-02-19T08:52:27,194 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-02-19T08:52:27,197 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-02-19T08:52:27,199 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-02-19T08:52:27,201 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-02-19T08:52:27,203 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-19T08:52:27,206 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-19T08:52:27,209 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-02-19T08:52:27,211 creating build/bdist.linux-armv7l/wheel/protenix/config 2025-02-19T08:52:27,213 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-02-19T08:52:27,215 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-02-19T08:52:27,218 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-02-19T08:52:27,220 creating build/bdist.linux-armv7l/wheel/protenix/utils 2025-02-19T08:52:27,222 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-19T08:52:27,224 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-19T08:52:27,227 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-19T08:52:27,229 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-19T08:52:27,231 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-19T08:52:27,233 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-19T08:52:27,236 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-19T08:52:27,239 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-19T08:52:27,242 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-19T08:52:27,244 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-19T08:52:27,245 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-19T08:52:27,247 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-02-19T08:52:27,250 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2025-02-19T08:52:27,251 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-02-19T08:52:27,254 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2025-02-19T08:52:27,255 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-02-19T08:52:27,258 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-02-19T08:52:27,260 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-02-19T08:52:27,263 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-02-19T08:52:27,266 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-02-19T08:52:27,268 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-02-19T08:52:27,272 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-02-19T08:52:27,274 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2025-02-19T08:52:27,276 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2025-02-19T08:52:27,278 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2025-02-19T08:52:27,282 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2025-02-19T08:52:27,284 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2025-02-19T08:52:27,286 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-19T08:52:27,289 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-19T08:52:27,291 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-19T08:52:27,294 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-19T08:52:27,296 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-19T08:52:27,299 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2025-02-19T08:52:27,301 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-02-19T08:52:27,303 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-02-19T08:52:27,306 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-02-19T08:52:27,308 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-19T08:52:27,311 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-19T08:52:27,314 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-02-19T08:52:27,316 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2025-02-19T08:52:27,317 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-19T08:52:27,320 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-19T08:52:27,323 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-19T08:52:27,326 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-19T08:52:27,329 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-19T08:52:27,331 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-02-19T08:52:27,334 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2025-02-19T08:52:27,335 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-19T08:52:27,338 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-19T08:52:27,341 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-19T08:52:27,343 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-19T08:52:27,346 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-19T08:52:27,348 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-19T08:52:27,351 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2025-02-19T08:52:27,353 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2025-02-19T08:52:27,355 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2025-02-19T08:52:27,357 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-19T08:52:27,359 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-02-19T08:52:27,362 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2025-02-19T08:52:27,363 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-19T08:52:27,365 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-19T08:52:27,368 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-19T08:52:27,370 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-19T08:52:27,373 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-19T08:52:27,375 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-19T08:52:27,377 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-02-19T08:52:27,380 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2025-02-19T08:52:27,382 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2025-02-19T08:52:27,384 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2025-02-19T08:52:27,386 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-02-19T08:52:27,390 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-02-19T08:52:27,393 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-02-19T08:52:27,395 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-02-19T08:52:27,398 creating build/bdist.linux-armv7l/wheel/scripts 2025-02-19T08:52:27,399 copying build/lib/scripts/colabfold_msa.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-02-19T08:52:27,402 creating build/bdist.linux-armv7l/wheel/scripts/msa 2025-02-19T08:52:27,404 copying build/lib/scripts/msa/step3-uniref_add_taxid.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-02-19T08:52:27,407 copying build/lib/scripts/msa/step2-get_msa.ipynb -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-02-19T08:52:27,409 copying build/lib/scripts/msa/step4-split_msa_to_uniref_and_others.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-02-19T08:52:27,412 copying build/lib/scripts/msa/step1-get_prot_seq.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-02-19T08:52:27,415 copying build/lib/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-02-19T08:52:27,417 copying build/lib/scripts/prepare_training_data.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-02-19T08:52:27,419 copying build/lib/scripts/gen_ccd_cache.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-02-19T08:52:27,422 running install_egg_info 2025-02-19T08:52:27,458 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.4.3-py3.11.egg-info 2025-02-19T08:52:27,470 running install_scripts 2025-02-19T08:52:27,491 creating build/bdist.linux-armv7l/wheel/protenix-0.4.3.dist-info/WHEEL 2025-02-19T08:52:27,494 creating '/tmp/pip-wheel-uyo5bue1/protenix-0.4.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-02-19T08:52:27,496 adding 'configs/__init__.py' 2025-02-19T08:52:27,499 adding 'configs/configs_base.py' 2025-02-19T08:52:27,501 adding 'configs/configs_data.py' 2025-02-19T08:52:27,503 adding 'configs/configs_inference.py' 2025-02-19T08:52:27,505 adding 'protenix/__init__.py' 2025-02-19T08:52:27,507 adding 'protenix/config/__init__.py' 2025-02-19T08:52:27,509 adding 'protenix/config/config.py' 2025-02-19T08:52:27,511 adding 'protenix/config/extend_types.py' 2025-02-19T08:52:27,513 adding 'protenix/data/__init__.py' 2025-02-19T08:52:27,516 adding 'protenix/data/ccd.py' 2025-02-19T08:52:27,520 adding 'protenix/data/constants.py' 2025-02-19T08:52:27,523 adding 'protenix/data/data_pipeline.py' 2025-02-19T08:52:27,526 adding 'protenix/data/dataloader.py' 2025-02-19T08:52:27,531 adding 'protenix/data/dataset.py' 2025-02-19T08:52:27,536 adding 'protenix/data/featurizer.py' 2025-02-19T08:52:27,539 adding 'protenix/data/filter.py' 2025-02-19T08:52:27,542 adding 'protenix/data/infer_data_pipeline.py' 2025-02-19T08:52:27,544 adding 'protenix/data/json_maker.py' 2025-02-19T08:52:27,547 adding 'protenix/data/json_parser.py' 2025-02-19T08:52:27,550 adding 'protenix/data/json_to_feature.py' 2025-02-19T08:52:27,555 adding 'protenix/data/msa_featurizer.py' 2025-02-19T08:52:27,561 adding 'protenix/data/msa_utils.py' 2025-02-19T08:52:27,573 adding 'protenix/data/parser.py' 2025-02-19T08:52:27,576 adding 'protenix/data/substructure_perms.py' 2025-02-19T08:52:27,578 adding 'protenix/data/tokenizer.py' 2025-02-19T08:52:27,582 adding 'protenix/data/utils.py' 2025-02-19T08:52:27,584 adding 'protenix/metrics/__init__.py' 2025-02-19T08:52:27,586 adding 'protenix/metrics/clash.py' 2025-02-19T08:52:27,588 adding 'protenix/metrics/lddt_metrics.py' 2025-02-19T08:52:27,591 adding 'protenix/metrics/rmsd.py' 2025-02-19T08:52:27,593 adding 'protenix/model/__init__.py' 2025-02-19T08:52:27,595 adding 'protenix/model/generator.py' 2025-02-19T08:52:27,602 adding 'protenix/model/loss.py' 2025-02-19T08:52:27,606 adding 'protenix/model/protenix.py' 2025-02-19T08:52:27,609 adding 'protenix/model/sample_confidence.py' 2025-02-19T08:52:27,612 adding 'protenix/model/utils.py' 2025-02-19T08:52:27,614 adding 'protenix/model/layer_norm/__init__.py' 2025-02-19T08:52:27,616 adding 'protenix/model/layer_norm/layer_norm.py' 2025-02-19T08:52:27,618 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2025-02-19T08:52:27,620 adding 'protenix/model/layer_norm/kernel/compat.h' 2025-02-19T08:52:27,622 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2025-02-19T08:52:27,624 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2025-02-19T08:52:27,626 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2025-02-19T08:52:27,629 adding 'protenix/model/modules/__init__.py' 2025-02-19T08:52:27,631 adding 'protenix/model/modules/confidence.py' 2025-02-19T08:52:27,634 adding 'protenix/model/modules/diffusion.py' 2025-02-19T08:52:27,636 adding 'protenix/model/modules/embedders.py' 2025-02-19T08:52:27,637 adding 'protenix/model/modules/frames.py' 2025-02-19T08:52:27,639 adding 'protenix/model/modules/head.py' 2025-02-19T08:52:27,641 adding 'protenix/model/modules/pairformer.py' 2025-02-19T08:52:27,645 adding 'protenix/model/modules/primitives.py' 2025-02-19T08:52:27,648 adding 'protenix/model/modules/transformer.py' 2025-02-19T08:52:27,650 adding 'protenix/openfold_local/__init__.py' 2025-02-19T08:52:27,652 adding 'protenix/openfold_local/data/__init__.py' 2025-02-19T08:52:27,653 adding 'protenix/openfold_local/data/data_transforms.py' 2025-02-19T08:52:27,655 adding 'protenix/openfold_local/data/errors.py' 2025-02-19T08:52:27,657 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2025-02-19T08:52:27,658 adding 'protenix/openfold_local/data/msa_identifiers.py' 2025-02-19T08:52:27,661 adding 'protenix/openfold_local/data/msa_pairing.py' 2025-02-19T08:52:27,664 adding 'protenix/openfold_local/data/parsers.py' 2025-02-19T08:52:27,667 adding 'protenix/openfold_local/data/templates.py' 2025-02-19T08:52:27,669 adding 'protenix/openfold_local/data/tools/__init__.py' 2025-02-19T08:52:27,671 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2025-02-19T08:52:27,672 adding 'protenix/openfold_local/data/tools/utils.py' 2025-02-19T08:52:27,674 adding 'protenix/openfold_local/model/__init__.py' 2025-02-19T08:52:27,675 adding 'protenix/openfold_local/model/dropout.py' 2025-02-19T08:52:27,676 adding 'protenix/openfold_local/model/outer_product_mean.py' 2025-02-19T08:52:27,679 adding 'protenix/openfold_local/model/primitives.py' 2025-02-19T08:52:27,681 adding 'protenix/openfold_local/model/triangular_attention.py' 2025-02-19T08:52:27,684 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2025-02-19T08:52:27,685 adding 'protenix/openfold_local/np/__init__.py' 2025-02-19T08:52:27,690 adding 'protenix/openfold_local/np/residue_constants.py' 2025-02-19T08:52:27,692 adding 'protenix/openfold_local/utils/__init__.py' 2025-02-19T08:52:27,694 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2025-02-19T08:52:27,696 adding 'protenix/openfold_local/utils/checkpointing.py' 2025-02-19T08:52:27,698 adding 'protenix/openfold_local/utils/chunk_utils.py' 2025-02-19T08:52:27,700 adding 'protenix/openfold_local/utils/feats.py' 2025-02-19T08:52:27,701 adding 'protenix/openfold_local/utils/precision_utils.py' 2025-02-19T08:52:27,706 adding 'protenix/openfold_local/utils/rigid_utils.py' 2025-02-19T08:52:27,707 adding 'protenix/openfold_local/utils/tensor_utils.py' 2025-02-19T08:52:27,709 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2025-02-19T08:52:27,710 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2025-02-19T08:52:27,712 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2025-02-19T08:52:27,714 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2025-02-19T08:52:27,716 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2025-02-19T08:52:27,936 adding 'protenix/openfold_local/utils/geometry/utils.py' 2025-02-19T08:52:27,940 adding 'protenix/openfold_local/utils/geometry/vector.py' 2025-02-19T08:52:27,946 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2025-02-19T08:52:27,950 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2025-02-19T08:52:27,953 adding 'protenix/utils/__init__.py' 2025-02-19T08:52:27,961 adding 'protenix/utils/cropping.py' 2025-02-19T08:52:27,964 adding 'protenix/utils/distributed.py' 2025-02-19T08:52:27,966 adding 'protenix/utils/file_io.py' 2025-02-19T08:52:27,969 adding 'protenix/utils/geometry.py' 2025-02-19T08:52:27,972 adding 'protenix/utils/logger.py' 2025-02-19T08:52:27,975 adding 'protenix/utils/lr_scheduler.py' 2025-02-19T08:52:27,977 adding 'protenix/utils/metrics.py' 2025-02-19T08:52:27,981 adding 'protenix/utils/scatter_utils.py' 2025-02-19T08:52:27,983 adding 'protenix/utils/seed.py' 2025-02-19T08:52:27,986 adding 'protenix/utils/torch_utils.py' 2025-02-19T08:52:27,989 adding 'protenix/utils/training.py' 2025-02-19T08:52:27,992 adding 'protenix/utils/permutation/__init__.py' 2025-02-19T08:52:28,001 adding 'protenix/utils/permutation/atom_permutation.py' 2025-02-19T08:52:28,006 adding 'protenix/utils/permutation/permutation.py' 2025-02-19T08:52:28,009 adding 'protenix/utils/permutation/utils.py' 2025-02-19T08:52:28,013 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2025-02-19T08:52:28,022 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2025-02-19T08:52:28,026 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2025-02-19T08:52:28,029 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2025-02-19T08:52:28,031 adding 'protenix/web_service/__init__.py' 2025-02-19T08:52:28,036 adding 'protenix/web_service/colab_request_parser.py' 2025-02-19T08:52:28,038 adding 'protenix/web_service/colab_request_utils.py' 2025-02-19T08:52:28,039 adding 'protenix/web_service/dependency_url.py' 2025-02-19T08:52:28,041 adding 'protenix/web_service/prediction_visualization.py' 2025-02-19T08:52:28,043 adding 'protenix/web_service/viewer.py' 2025-02-19T08:52:28,047 adding 'runner/__init__.py' 2025-02-19T08:52:28,049 adding 'runner/batch_inference.py' 2025-02-19T08:52:28,050 adding 'runner/dumper.py' 2025-02-19T08:52:28,052 adding 'runner/ema.py' 2025-02-19T08:52:28,054 adding 'runner/inference.py' 2025-02-19T08:52:28,055 adding 'runner/msa_search.py' 2025-02-19T08:52:28,058 adding 'runner/train.py' 2025-02-19T08:52:28,060 adding 'scripts/__init__.py' 2025-02-19T08:52:28,062 adding 'scripts/colabfold_msa.py' 2025-02-19T08:52:28,064 adding 'scripts/gen_ccd_cache.py' 2025-02-19T08:52:28,066 adding 'scripts/prepare_training_data.py' 2025-02-19T08:52:28,068 adding 'scripts/msa/step1-get_prot_seq.py' 2025-02-19T08:52:28,070 adding 'scripts/msa/step2-get_msa.ipynb' 2025-02-19T08:52:28,072 adding 'scripts/msa/step3-uniref_add_taxid.py' 2025-02-19T08:52:28,073 adding 'scripts/msa/step4-split_msa_to_uniref_and_others.py' 2025-02-19T08:52:28,075 adding 'tests/__init__.py' 2025-02-19T08:52:28,077 adding 'tests/test_attention_pair_bias.py' 2025-02-19T08:52:28,079 adding 'tests/test_condition_transition.py' 2025-02-19T08:52:28,080 adding 'tests/test_diffusion_transformer.py' 2025-02-19T08:52:28,082 adding 'tests/test_frame.py' 2025-02-19T08:52:28,083 adding 'tests/test_local_rearrange.py' 2025-02-19T08:52:28,085 adding 'tests/test_lr_schedule.py' 2025-02-19T08:52:28,087 adding 'tests/test_utils.py' 2025-02-19T08:52:28,088 adding 'tests/test_weighted_rigid_align.py' 2025-02-19T08:52:28,091 adding 'protenix-0.4.3.dist-info/LICENSE' 2025-02-19T08:52:28,092 adding 'protenix-0.4.3.dist-info/METADATA' 2025-02-19T08:52:28,094 adding 'protenix-0.4.3.dist-info/WHEEL' 2025-02-19T08:52:28,095 adding 'protenix-0.4.3.dist-info/entry_points.txt' 2025-02-19T08:52:28,096 adding 'protenix-0.4.3.dist-info/top_level.txt' 2025-02-19T08:52:28,099 adding 'protenix-0.4.3.dist-info/RECORD' 2025-02-19T08:52:28,108 removing build/bdist.linux-armv7l/wheel 2025-02-19T08:52:28,259 Building wheel for protenix (setup.py): finished with status 'done' 2025-02-19T08:52:28,266 Created wheel for protenix: filename=protenix-0.4.3-py3-none-any.whl size=428380 sha256=c78607fb1ac4479a523461b2d153e0bf8dcd142d25461d698b8dcc2a17e78b19 2025-02-19T08:52:28,267 Stored in directory: /tmp/pip-ephem-wheel-cache-46dez6zd/wheels/e8/85/b7/45c730a841d70bc973d09bf35e3d0b8ac5e0cc3453c1c852fe 2025-02-19T08:52:28,284 Successfully built protenix 2025-02-19T08:52:28,303 Removed build tracker: '/tmp/pip-build-tracker-d4x05n8x'