2024-12-13T11:33:34,238 Created temporary directory: /tmp/pip-build-tracker-rg9_zd9c 2024-12-13T11:33:34,240 Initialized build tracking at /tmp/pip-build-tracker-rg9_zd9c 2024-12-13T11:33:34,240 Created build tracker: /tmp/pip-build-tracker-rg9_zd9c 2024-12-13T11:33:34,241 Entered build tracker: /tmp/pip-build-tracker-rg9_zd9c 2024-12-13T11:33:34,241 Created temporary directory: /tmp/pip-wheel-i2eas4vg 2024-12-13T11:33:34,245 Created temporary directory: /tmp/pip-ephem-wheel-cache-be5hgfw3 2024-12-13T11:33:34,289 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-12-13T11:33:34,291 2 location(s) to search for versions of protenix: 2024-12-13T11:33:34,291 * https://pypi.org/simple/protenix/ 2024-12-13T11:33:34,291 * https://www.piwheels.org/simple/protenix/ 2024-12-13T11:33:34,292 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2024-12-13T11:33:34,293 Getting page https://pypi.org/simple/protenix/ 2024-12-13T11:33:34,294 Found index url https://pypi.org/simple/ 2024-12-13T11:33:34,517 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2024-12-13T11:33:34,521 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/) 2024-12-13T11:33:34,522 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/) 2024-12-13T11:33:34,523 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 2024-12-13T11:33:34,523 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) 2024-12-13T11:33:34,524 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 2024-12-13T11:33:34,525 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) 2024-12-13T11:33:34,526 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 2024-12-13T11:33:34,527 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) 2024-12-13T11:33:34,528 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 2024-12-13T11:33:34,529 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) 2024-12-13T11:33:34,530 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 2024-12-13T11:33:34,530 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) 2024-12-13T11:33:34,531 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 2024-12-13T11:33:34,533 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) 2024-12-13T11:33:34,533 Found link https://files.pythonhosted.org/packages/b6/96/8d6d036dcaff9c1884fcbaa2c752fed65e24320fab2a0a8b128a615da89d/protenix-0.3.0.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.0 2024-12-13T11:33:34,534 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2024-12-13T11:33:34,535 Getting page https://www.piwheels.org/simple/protenix/ 2024-12-13T11:33:34,536 Found index url https://www.piwheels.org/simple/ 2024-12-13T11:33:34,750 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2024-12-13T11:33:34,752 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) 2024-12-13T11:33:34,753 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) 2024-12-13T11:33:34,754 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) 2024-12-13T11:33:34,754 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) 2024-12-13T11:33:34,755 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) 2024-12-13T11:33:34,755 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/) 2024-12-13T11:33:34,756 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2024-12-13T11:33:34,757 Skipping link: not a file: https://pypi.org/simple/protenix/ 2024-12-13T11:33:34,776 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2024-12-13T11:33:34,778 Collecting protenix==0.3.0 2024-12-13T11:33:34,780 Created temporary directory: /tmp/pip-unpack-1h0pq71d 2024-12-13T11:33:35,002 Downloading protenix-0.3.0.tar.gz (306 kB) 2024-12-13T11:33:35,375 Added protenix==0.3.0 from https://files.pythonhosted.org/packages/b6/96/8d6d036dcaff9c1884fcbaa2c752fed65e24320fab2a0a8b128a615da89d/protenix-0.3.0.tar.gz to build tracker '/tmp/pip-build-tracker-rg9_zd9c' 2024-12-13T11:33:35,377 Running setup.py (path:/tmp/pip-wheel-i2eas4vg/protenix_8c4e34e2ee93488187d0a47d54f42745/setup.py) egg_info for package protenix 2024-12-13T11:33:35,378 Created temporary directory: /tmp/pip-pip-egg-info-swyva_jd 2024-12-13T11:33:35,379 Preparing metadata (setup.py): started 2024-12-13T11:33:35,380 Running command python setup.py egg_info 2024-12-13T11:33:36,470 running egg_info 2024-12-13T11:33:36,498 creating /tmp/pip-pip-egg-info-swyva_jd/protenix.egg-info 2024-12-13T11:33:36,499 writing /tmp/pip-pip-egg-info-swyva_jd/protenix.egg-info/PKG-INFO 2024-12-13T11:33:36,502 writing dependency_links to /tmp/pip-pip-egg-info-swyva_jd/protenix.egg-info/dependency_links.txt 2024-12-13T11:33:36,504 writing entry points to /tmp/pip-pip-egg-info-swyva_jd/protenix.egg-info/entry_points.txt 2024-12-13T11:33:36,506 writing requirements to /tmp/pip-pip-egg-info-swyva_jd/protenix.egg-info/requires.txt 2024-12-13T11:33:36,507 writing top-level names to /tmp/pip-pip-egg-info-swyva_jd/protenix.egg-info/top_level.txt 2024-12-13T11:33:36,508 writing manifest file '/tmp/pip-pip-egg-info-swyva_jd/protenix.egg-info/SOURCES.txt' 2024-12-13T11:33:36,617 reading manifest file '/tmp/pip-pip-egg-info-swyva_jd/protenix.egg-info/SOURCES.txt' 2024-12-13T11:33:36,619 adding license file 'LICENSE' 2024-12-13T11:33:36,625 writing manifest file '/tmp/pip-pip-egg-info-swyva_jd/protenix.egg-info/SOURCES.txt' 2024-12-13T11:33:36,734 Preparing metadata (setup.py): finished with status 'done' 2024-12-13T11:33:36,738 Source in /tmp/pip-wheel-i2eas4vg/protenix_8c4e34e2ee93488187d0a47d54f42745 has version 0.3.0, which satisfies requirement protenix==0.3.0 from https://files.pythonhosted.org/packages/b6/96/8d6d036dcaff9c1884fcbaa2c752fed65e24320fab2a0a8b128a615da89d/protenix-0.3.0.tar.gz 2024-12-13T11:33:36,739 Removed protenix==0.3.0 from https://files.pythonhosted.org/packages/b6/96/8d6d036dcaff9c1884fcbaa2c752fed65e24320fab2a0a8b128a615da89d/protenix-0.3.0.tar.gz from build tracker '/tmp/pip-build-tracker-rg9_zd9c' 2024-12-13T11:33:36,748 Created temporary directory: /tmp/pip-unpack-jpnfkcz8 2024-12-13T11:33:36,749 Created temporary directory: /tmp/pip-unpack-u8u6e_84 2024-12-13T11:33:36,750 Building wheels for collected packages: protenix 2024-12-13T11:33:36,754 Created temporary directory: /tmp/pip-wheel-vofe9lt3 2024-12-13T11:33:36,755 Building wheel for protenix (setup.py): started 2024-12-13T11:33:36,756 Destination directory: /tmp/pip-wheel-vofe9lt3 2024-12-13T11:33:36,757 Running command python setup.py bdist_wheel 2024-12-13T11:33:37,767 running bdist_wheel 2024-12-13T11:33:37,900 running build 2024-12-13T11:33:37,901 running build_py 2024-12-13T11:33:37,931 creating build/lib/runner 2024-12-13T11:33:37,934 copying runner/__init__.py -> build/lib/runner 2024-12-13T11:33:37,936 copying runner/inference.py -> build/lib/runner 2024-12-13T11:33:37,939 copying runner/batch_inference.py -> build/lib/runner 2024-12-13T11:33:37,942 copying runner/ema.py -> build/lib/runner 2024-12-13T11:33:37,946 copying runner/dumper.py -> build/lib/runner 2024-12-13T11:33:37,950 copying runner/train.py -> build/lib/runner 2024-12-13T11:33:37,955 creating build/lib/protenix 2024-12-13T11:33:37,957 copying protenix/__init__.py -> build/lib/protenix 2024-12-13T11:33:37,961 creating build/lib/configs 2024-12-13T11:33:37,962 copying configs/__init__.py -> build/lib/configs 2024-12-13T11:33:37,963 copying configs/configs_base.py -> build/lib/configs 2024-12-13T11:33:37,966 copying configs/configs_inference.py -> build/lib/configs 2024-12-13T11:33:37,968 copying configs/configs_data.py -> build/lib/configs 2024-12-13T11:33:37,970 creating build/lib/protenix/config 2024-12-13T11:33:37,971 copying protenix/config/__init__.py -> build/lib/protenix/config 2024-12-13T11:33:37,973 copying protenix/config/extend_types.py -> build/lib/protenix/config 2024-12-13T11:33:37,975 copying protenix/config/config.py -> build/lib/protenix/config 2024-12-13T11:33:37,978 creating build/lib/protenix/web_service 2024-12-13T11:33:37,979 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2024-12-13T11:33:37,982 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2024-12-13T11:33:37,983 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2024-12-13T11:33:37,986 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2024-12-13T11:33:37,988 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2024-12-13T11:33:37,990 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2024-12-13T11:33:37,993 creating build/lib/protenix/openfold_local 2024-12-13T11:33:37,994 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2024-12-13T11:33:37,997 creating build/lib/protenix/data 2024-12-13T11:33:37,998 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2024-12-13T11:33:38,001 copying protenix/data/__init__.py -> build/lib/protenix/data 2024-12-13T11:33:38,002 copying protenix/data/json_parser.py -> build/lib/protenix/data 2024-12-13T11:33:38,005 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2024-12-13T11:33:38,007 copying protenix/data/parser.py -> build/lib/protenix/data 2024-12-13T11:33:38,010 copying protenix/data/ccd.py -> build/lib/protenix/data 2024-12-13T11:33:38,012 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2024-12-13T11:33:38,015 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2024-12-13T11:33:38,017 copying protenix/data/featurizer.py -> build/lib/protenix/data 2024-12-13T11:33:38,020 copying protenix/data/json_maker.py -> build/lib/protenix/data 2024-12-13T11:33:38,022 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2024-12-13T11:33:38,025 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2024-12-13T11:33:38,027 copying protenix/data/dataset.py -> build/lib/protenix/data 2024-12-13T11:33:38,030 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2024-12-13T11:33:38,033 copying protenix/data/dataloader.py -> build/lib/protenix/data 2024-12-13T11:33:38,036 copying protenix/data/filter.py -> build/lib/protenix/data 2024-12-13T11:33:38,037 copying protenix/data/constants.py -> build/lib/protenix/data 2024-12-13T11:33:38,040 copying protenix/data/utils.py -> build/lib/protenix/data 2024-12-13T11:33:38,044 creating build/lib/protenix/utils 2024-12-13T11:33:38,046 copying protenix/utils/logger.py -> build/lib/protenix/utils 2024-12-13T11:33:38,048 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2024-12-13T11:33:38,051 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2024-12-13T11:33:38,053 copying protenix/utils/training.py -> build/lib/protenix/utils 2024-12-13T11:33:38,056 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2024-12-13T11:33:38,058 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2024-12-13T11:33:38,060 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2024-12-13T11:33:38,063 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2024-12-13T11:33:38,066 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2024-12-13T11:33:38,070 copying protenix/utils/seed.py -> build/lib/protenix/utils 2024-12-13T11:33:38,073 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2024-12-13T11:33:38,078 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2024-12-13T11:33:38,081 creating build/lib/protenix/metrics 2024-12-13T11:33:38,082 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2024-12-13T11:33:38,085 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2024-12-13T11:33:38,088 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2024-12-13T11:33:38,092 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2024-12-13T11:33:38,096 creating build/lib/protenix/model 2024-12-13T11:33:38,098 copying protenix/model/protenix.py -> build/lib/protenix/model 2024-12-13T11:33:38,103 copying protenix/model/__init__.py -> build/lib/protenix/model 2024-12-13T11:33:38,107 copying protenix/model/loss.py -> build/lib/protenix/model 2024-12-13T11:33:38,146 copying protenix/model/generator.py -> build/lib/protenix/model 2024-12-13T11:33:38,150 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2024-12-13T11:33:38,154 copying protenix/model/utils.py -> build/lib/protenix/model 2024-12-13T11:33:38,158 creating build/lib/protenix/openfold_local/data 2024-12-13T11:33:38,160 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2024-12-13T11:33:38,164 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2024-12-13T11:33:38,169 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2024-12-13T11:33:38,171 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2024-12-13T11:33:38,175 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2024-12-13T11:33:38,177 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2024-12-13T11:33:38,180 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2024-12-13T11:33:38,182 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2024-12-13T11:33:38,186 creating build/lib/protenix/openfold_local/utils 2024-12-13T11:33:38,187 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-13T11:33:38,190 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2024-12-13T11:33:38,193 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2024-12-13T11:33:38,195 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2024-12-13T11:33:38,198 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2024-12-13T11:33:38,200 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-13T11:33:38,204 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-13T11:33:38,206 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-13T11:33:38,211 creating build/lib/protenix/openfold_local/np 2024-12-13T11:33:38,213 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2024-12-13T11:33:38,214 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2024-12-13T11:33:38,219 creating build/lib/protenix/openfold_local/model 2024-12-13T11:33:38,221 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2024-12-13T11:33:38,224 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2024-12-13T11:33:38,227 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2024-12-13T11:33:38,229 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2024-12-13T11:33:38,232 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2024-12-13T11:33:38,236 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2024-12-13T11:33:38,239 creating build/lib/protenix/openfold_local/data/tools 2024-12-13T11:33:38,240 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2024-12-13T11:33:38,242 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2024-12-13T11:33:38,244 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2024-12-13T11:33:38,247 creating build/lib/protenix/openfold_local/utils/kernel 2024-12-13T11:33:38,248 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2024-12-13T11:33:38,250 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2024-12-13T11:33:38,253 creating build/lib/protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,254 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,257 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,259 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,262 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,264 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,267 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,270 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,273 creating build/lib/protenix/utils/permutation 2024-12-13T11:33:38,274 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2024-12-13T11:33:38,276 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2024-12-13T11:33:38,281 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2024-12-13T11:33:38,286 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2024-12-13T11:33:38,293 creating build/lib/protenix/utils/permutation/chain_permutation 2024-12-13T11:33:38,296 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-13T11:33:38,301 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-13T11:33:38,303 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-13T11:33:38,307 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-13T11:33:38,309 creating build/lib/protenix/model/modules 2024-12-13T11:33:38,311 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2024-12-13T11:33:38,314 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2024-12-13T11:33:38,318 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2024-12-13T11:33:38,320 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2024-12-13T11:33:38,321 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2024-12-13T11:33:38,324 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2024-12-13T11:33:38,327 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2024-12-13T11:33:38,329 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2024-12-13T11:33:38,330 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2024-12-13T11:33:38,334 creating build/lib/protenix/model/layer_norm 2024-12-13T11:33:38,335 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2024-12-13T11:33:38,337 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2024-12-13T11:33:38,339 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2024-12-13T11:33:38,341 running egg_info 2024-12-13T11:33:38,371 writing protenix.egg-info/PKG-INFO 2024-12-13T11:33:38,375 writing dependency_links to protenix.egg-info/dependency_links.txt 2024-12-13T11:33:38,376 writing entry points to protenix.egg-info/entry_points.txt 2024-12-13T11:33:38,378 writing requirements to protenix.egg-info/requires.txt 2024-12-13T11:33:38,379 writing top-level names to protenix.egg-info/top_level.txt 2024-12-13T11:33:38,428 reading manifest file 'protenix.egg-info/SOURCES.txt' 2024-12-13T11:33:38,436 adding license file 'LICENSE' 2024-12-13T11:33:38,443 writing manifest file 'protenix.egg-info/SOURCES.txt' 2024-12-13T11:33:38,446 /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. 2024-12-13T11:33:38,447 !! 2024-12-13T11:33:38,447 ******************************************************************************** 2024-12-13T11:33:38,448 ############################ 2024-12-13T11:33:38,449 # Package would be ignored # 2024-12-13T11:33:38,449 ############################ 2024-12-13T11:33:38,449 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2024-12-13T11:33:38,450 but it is absent from setuptools' `packages` configuration. 2024-12-13T11:33:38,451 This leads to an ambiguous overall configuration. If you want to distribute this 2024-12-13T11:33:38,451 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2024-12-13T11:33:38,452 to the `packages` configuration field. 2024-12-13T11:33:38,453 Alternatively, you can also rely on setuptools' discovery methods 2024-12-13T11:33:38,453 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-12-13T11:33:38,454 instead of `find_packages(...)`/`find:`). 2024-12-13T11:33:38,455 You can read more about "package discovery" on setuptools documentation page: 2024-12-13T11:33:38,456 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-12-13T11:33:38,457 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2024-12-13T11:33:38,458 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2024-12-13T11:33:38,458 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-12-13T11:33:38,459 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-12-13T11:33:38,459 combination with a more fine grained `package-data` configuration. 2024-12-13T11:33:38,461 You can read more about "package data files" on setuptools documentation page: 2024-12-13T11:33:38,462 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-12-13T11:33:38,463 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-12-13T11:33:38,464 even if it does not contain any `.py` files. 2024-12-13T11:33:38,464 On the other hand, currently there is no concept of package data 2024-12-13T11:33:38,465 directory, all directories are treated like packages. 2024-12-13T11:33:38,465 ******************************************************************************** 2024-12-13T11:33:38,466 !! 2024-12-13T11:33:38,467 check.warn(importable) 2024-12-13T11:33:38,468 creating build/lib/protenix/model/layer_norm/kernel 2024-12-13T11:33:38,468 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2024-12-13T11:33:38,469 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2024-12-13T11:33:38,469 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2024-12-13T11:33:38,472 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2024-12-13T11:33:38,514 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-12-13T11:33:38,515 !! 2024-12-13T11:33:38,516 ******************************************************************************** 2024-12-13T11:33:38,516 Please avoid running ``setup.py`` directly. 2024-12-13T11:33:38,517 Instead, use pypa/build, pypa/installer or other 2024-12-13T11:33:38,517 standards-based tools. 2024-12-13T11:33:38,518 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-12-13T11:33:38,519 ******************************************************************************** 2024-12-13T11:33:38,519 !! 2024-12-13T11:33:38,520 self.initialize_options() 2024-12-13T11:33:38,543 installing to build/bdist.linux-armv7l/wheel 2024-12-13T11:33:38,543 running install 2024-12-13T11:33:38,568 running install_lib 2024-12-13T11:33:38,595 creating build/bdist.linux-armv7l/wheel 2024-12-13T11:33:38,597 creating build/bdist.linux-armv7l/wheel/runner 2024-12-13T11:33:38,598 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-13T11:33:38,599 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-13T11:33:38,602 copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-13T11:33:38,605 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-13T11:33:38,607 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-13T11:33:38,609 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-13T11:33:38,612 creating build/bdist.linux-armv7l/wheel/protenix 2024-12-13T11:33:38,614 creating build/bdist.linux-armv7l/wheel/protenix/config 2024-12-13T11:33:38,615 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-13T11:33:38,617 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-13T11:33:38,619 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-13T11:33:38,622 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2024-12-13T11:33:38,623 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-13T11:33:38,626 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-13T11:33:38,627 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-13T11:33:38,630 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-13T11:33:38,632 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-13T11:33:38,634 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-13T11:33:38,637 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2024-12-13T11:33:38,638 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2024-12-13T11:33:38,641 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2024-12-13T11:33:38,642 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-13T11:33:38,644 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-13T11:33:38,647 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2024-12-13T11:33:38,649 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-13T11:33:38,650 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-13T11:33:38,653 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-13T11:33:38,655 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-13T11:33:38,656 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-13T11:33:38,659 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-13T11:33:38,661 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-13T11:33:38,663 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-13T11:33:38,665 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-13T11:33:38,669 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2024-12-13T11:33:38,670 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-13T11:33:38,672 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-13T11:33:38,674 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-13T11:33:38,676 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-13T11:33:38,679 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-13T11:33:38,680 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-13T11:33:38,683 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2024-12-13T11:33:38,684 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-12-13T11:33:38,686 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-12-13T11:33:38,688 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,690 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,692 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,693 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,696 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,698 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,700 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,702 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-13T11:33:38,704 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-13T11:33:38,706 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-13T11:33:38,710 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2024-12-13T11:33:38,711 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-12-13T11:33:38,712 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-12-13T11:33:38,715 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2024-12-13T11:33:38,717 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-13T11:33:38,719 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-13T11:33:38,721 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-13T11:33:38,723 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-13T11:33:38,724 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-13T11:33:38,727 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-13T11:33:38,730 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2024-12-13T11:33:38,732 creating build/bdist.linux-armv7l/wheel/protenix/data 2024-12-13T11:33:38,733 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,736 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,738 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,741 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,743 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,746 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,749 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,751 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,754 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,757 copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,759 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,761 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,764 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,767 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,770 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,772 copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,774 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,777 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-13T11:33:38,780 creating build/bdist.linux-armv7l/wheel/protenix/utils 2024-12-13T11:33:38,781 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-13T11:33:38,783 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-13T11:33:38,786 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-13T11:33:38,787 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-13T11:33:38,790 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-13T11:33:38,792 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2024-12-13T11:33:38,793 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-13T11:33:38,795 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2024-12-13T11:33:38,797 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-13T11:33:38,799 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-13T11:33:38,802 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-13T11:33:38,804 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-13T11:33:38,806 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-13T11:33:38,809 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-13T11:33:38,812 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-13T11:33:38,814 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-13T11:33:38,816 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-13T11:33:38,818 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-13T11:33:38,819 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-13T11:33:38,822 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-13T11:33:38,824 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-13T11:33:38,826 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-13T11:33:38,829 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2024-12-13T11:33:38,830 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-13T11:33:38,832 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-13T11:33:38,835 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-13T11:33:38,837 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-13T11:33:38,840 creating build/bdist.linux-armv7l/wheel/protenix/model 2024-12-13T11:33:38,841 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-13T11:33:38,845 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2024-12-13T11:33:38,846 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-13T11:33:38,848 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-13T11:33:38,851 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-13T11:33:38,854 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-13T11:33:38,855 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-13T11:33:38,858 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-13T11:33:38,861 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-13T11:33:38,862 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-13T11:33:38,864 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-13T11:33:38,867 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2024-12-13T11:33:38,869 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-13T11:33:38,871 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-13T11:33:38,873 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2024-12-13T11:33:38,874 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-13T11:33:38,876 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-13T11:33:38,879 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-13T11:33:38,881 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-13T11:33:38,883 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-13T11:33:38,886 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-13T11:33:38,887 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-13T11:33:38,890 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-13T11:33:38,894 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-13T11:33:38,896 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-13T11:33:38,899 creating build/bdist.linux-armv7l/wheel/configs 2024-12-13T11:33:38,900 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-13T11:33:38,902 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-13T11:33:38,904 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-13T11:33:38,906 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-13T11:33:38,908 running install_data 2024-12-13T11:33:38,938 creating build/bdist.linux-armv7l/wheel/protenix-0.3.0.data/data 2024-12-13T11:33:38,940 warning: install_data: setup script did not provide a directory for 'requirements.txt' -- installing right in 'build/bdist.linux-armv7l/wheel/protenix-0.3.0.data/data' 2024-12-13T11:33:38,941 copying requirements.txt -> build/bdist.linux-armv7l/wheel/protenix-0.3.0.data/data 2024-12-13T11:33:38,942 running install_egg_info 2024-12-13T11:33:38,976 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.3.0-py3.11.egg-info 2024-12-13T11:33:38,988 running install_scripts 2024-12-13T11:33:39,009 creating build/bdist.linux-armv7l/wheel/protenix-0.3.0.dist-info/WHEEL 2024-12-13T11:33:39,012 creating '/tmp/pip-wheel-vofe9lt3/protenix-0.3.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-12-13T11:33:39,014 adding 'configs/__init__.py' 2024-12-13T11:33:39,016 adding 'configs/configs_base.py' 2024-12-13T11:33:39,018 adding 'configs/configs_data.py' 2024-12-13T11:33:39,019 adding 'configs/configs_inference.py' 2024-12-13T11:33:39,021 adding 'protenix/__init__.py' 2024-12-13T11:33:39,023 adding 'protenix/config/__init__.py' 2024-12-13T11:33:39,025 adding 'protenix/config/config.py' 2024-12-13T11:33:39,026 adding 'protenix/config/extend_types.py' 2024-12-13T11:33:39,028 adding 'protenix/data/__init__.py' 2024-12-13T11:33:39,031 adding 'protenix/data/ccd.py' 2024-12-13T11:33:39,035 adding 'protenix/data/constants.py' 2024-12-13T11:33:39,037 adding 'protenix/data/data_pipeline.py' 2024-12-13T11:33:39,039 adding 'protenix/data/dataloader.py' 2024-12-13T11:33:39,044 adding 'protenix/data/dataset.py' 2024-12-13T11:33:39,048 adding 'protenix/data/featurizer.py' 2024-12-13T11:33:39,050 adding 'protenix/data/filter.py' 2024-12-13T11:33:39,052 adding 'protenix/data/infer_data_pipeline.py' 2024-12-13T11:33:39,054 adding 'protenix/data/json_maker.py' 2024-12-13T11:33:39,056 adding 'protenix/data/json_parser.py' 2024-12-13T11:33:39,058 adding 'protenix/data/json_to_feature.py' 2024-12-13T11:33:39,063 adding 'protenix/data/msa_featurizer.py' 2024-12-13T11:33:39,069 adding 'protenix/data/msa_utils.py' 2024-12-13T11:33:39,074 adding 'protenix/data/parser.py' 2024-12-13T11:33:39,077 adding 'protenix/data/substructure_perms.py' 2024-12-13T11:33:39,078 adding 'protenix/data/tokenizer.py' 2024-12-13T11:33:39,081 adding 'protenix/data/utils.py' 2024-12-13T11:33:39,083 adding 'protenix/metrics/__init__.py' 2024-12-13T11:33:39,085 adding 'protenix/metrics/clash.py' 2024-12-13T11:33:39,087 adding 'protenix/metrics/lddt_metrics.py' 2024-12-13T11:33:39,088 adding 'protenix/metrics/rmsd.py' 2024-12-13T11:33:39,090 adding 'protenix/model/__init__.py' 2024-12-13T11:33:39,092 adding 'protenix/model/generator.py' 2024-12-13T11:33:39,098 adding 'protenix/model/loss.py' 2024-12-13T11:33:39,102 adding 'protenix/model/protenix.py' 2024-12-13T11:33:39,105 adding 'protenix/model/sample_confidence.py' 2024-12-13T11:33:39,107 adding 'protenix/model/utils.py' 2024-12-13T11:33:39,109 adding 'protenix/model/layer_norm/__init__.py' 2024-12-13T11:33:39,111 adding 'protenix/model/layer_norm/layer_norm.py' 2024-12-13T11:33:39,112 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2024-12-13T11:33:39,114 adding 'protenix/model/layer_norm/kernel/compat.h' 2024-12-13T11:33:39,115 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2024-12-13T11:33:39,118 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2024-12-13T11:33:39,119 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2024-12-13T11:33:39,121 adding 'protenix/model/modules/__init__.py' 2024-12-13T11:33:39,123 adding 'protenix/model/modules/confidence.py' 2024-12-13T11:33:39,126 adding 'protenix/model/modules/diffusion.py' 2024-12-13T11:33:39,127 adding 'protenix/model/modules/embedders.py' 2024-12-13T11:33:39,129 adding 'protenix/model/modules/frames.py' 2024-12-13T11:33:39,130 adding 'protenix/model/modules/head.py' 2024-12-13T11:33:39,133 adding 'protenix/model/modules/pairformer.py' 2024-12-13T11:33:39,137 adding 'protenix/model/modules/primitives.py' 2024-12-13T11:33:39,140 adding 'protenix/model/modules/transformer.py' 2024-12-13T11:33:39,142 adding 'protenix/openfold_local/__init__.py' 2024-12-13T11:33:39,144 adding 'protenix/openfold_local/data/__init__.py' 2024-12-13T11:33:39,146 adding 'protenix/openfold_local/data/data_transforms.py' 2024-12-13T11:33:39,147 adding 'protenix/openfold_local/data/errors.py' 2024-12-13T11:33:39,149 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2024-12-13T11:33:39,151 adding 'protenix/openfold_local/data/msa_identifiers.py' 2024-12-13T11:33:39,153 adding 'protenix/openfold_local/data/msa_pairing.py' 2024-12-13T11:33:39,157 adding 'protenix/openfold_local/data/parsers.py' 2024-12-13T11:33:39,160 adding 'protenix/openfold_local/data/templates.py' 2024-12-13T11:33:39,162 adding 'protenix/openfold_local/data/tools/__init__.py' 2024-12-13T11:33:39,163 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2024-12-13T11:33:39,165 adding 'protenix/openfold_local/data/tools/utils.py' 2024-12-13T11:33:39,166 adding 'protenix/openfold_local/model/__init__.py' 2024-12-13T11:33:39,167 adding 'protenix/openfold_local/model/dropout.py' 2024-12-13T11:33:39,169 adding 'protenix/openfold_local/model/outer_product_mean.py' 2024-12-13T11:33:39,172 adding 'protenix/openfold_local/model/primitives.py' 2024-12-13T11:33:39,174 adding 'protenix/openfold_local/model/triangular_attention.py' 2024-12-13T11:33:39,176 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2024-12-13T11:33:39,178 adding 'protenix/openfold_local/np/__init__.py' 2024-12-13T11:33:39,183 adding 'protenix/openfold_local/np/residue_constants.py' 2024-12-13T11:33:39,185 adding 'protenix/openfold_local/utils/__init__.py' 2024-12-13T11:33:39,187 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2024-12-13T11:33:39,188 adding 'protenix/openfold_local/utils/checkpointing.py' 2024-12-13T11:33:39,191 adding 'protenix/openfold_local/utils/chunk_utils.py' 2024-12-13T11:33:39,192 adding 'protenix/openfold_local/utils/feats.py' 2024-12-13T11:33:39,193 adding 'protenix/openfold_local/utils/precision_utils.py' 2024-12-13T11:33:39,198 adding 'protenix/openfold_local/utils/rigid_utils.py' 2024-12-13T11:33:39,199 adding 'protenix/openfold_local/utils/tensor_utils.py' 2024-12-13T11:33:39,202 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2024-12-13T11:33:39,203 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2024-12-13T11:33:39,204 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2024-12-13T11:33:39,206 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2024-12-13T11:33:39,207 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2024-12-13T11:33:39,208 adding 'protenix/openfold_local/utils/geometry/utils.py' 2024-12-13T11:33:39,210 adding 'protenix/openfold_local/utils/geometry/vector.py' 2024-12-13T11:33:39,212 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2024-12-13T11:33:39,213 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2024-12-13T11:33:39,215 adding 'protenix/utils/__init__.py' 2024-12-13T11:33:39,219 adding 'protenix/utils/cropping.py' 2024-12-13T11:33:39,220 adding 'protenix/utils/distributed.py' 2024-12-13T11:33:39,221 adding 'protenix/utils/file_io.py' 2024-12-13T11:33:39,223 adding 'protenix/utils/geometry.py' 2024-12-13T11:33:39,224 adding 'protenix/utils/logger.py' 2024-12-13T11:33:39,226 adding 'protenix/utils/lr_scheduler.py' 2024-12-13T11:33:39,227 adding 'protenix/utils/metrics.py' 2024-12-13T11:33:39,228 adding 'protenix/utils/scatter_utils.py' 2024-12-13T11:33:39,230 adding 'protenix/utils/seed.py' 2024-12-13T11:33:39,231 adding 'protenix/utils/torch_utils.py' 2024-12-13T11:33:39,233 adding 'protenix/utils/training.py' 2024-12-13T11:33:39,235 adding 'protenix/utils/permutation/__init__.py' 2024-12-13T11:33:39,238 adding 'protenix/utils/permutation/atom_permutation.py' 2024-12-13T11:33:39,241 adding 'protenix/utils/permutation/permutation.py' 2024-12-13T11:33:39,242 adding 'protenix/utils/permutation/utils.py' 2024-12-13T11:33:39,245 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2024-12-13T11:33:39,249 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2024-12-13T11:33:39,251 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2024-12-13T11:33:39,252 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2024-12-13T11:33:39,254 adding 'protenix/web_service/__init__.py' 2024-12-13T11:33:39,256 adding 'protenix/web_service/colab_request_parser.py' 2024-12-13T11:33:39,258 adding 'protenix/web_service/colab_request_utils.py' 2024-12-13T11:33:39,259 adding 'protenix/web_service/dependency_url.py' 2024-12-13T11:33:39,261 adding 'protenix/web_service/prediction_visualization.py' 2024-12-13T11:33:39,264 adding 'protenix/web_service/viewer.py' 2024-12-13T11:33:39,266 adding 'protenix-0.3.0.data/data/requirements.txt' 2024-12-13T11:33:39,269 adding 'runner/__init__.py' 2024-12-13T11:33:39,271 adding 'runner/batch_inference.py' 2024-12-13T11:33:39,274 adding 'runner/dumper.py' 2024-12-13T11:33:39,275 adding 'runner/ema.py' 2024-12-13T11:33:39,277 adding 'runner/inference.py' 2024-12-13T11:33:39,280 adding 'runner/train.py' 2024-12-13T11:33:39,282 adding 'protenix-0.3.0.dist-info/LICENSE' 2024-12-13T11:33:39,283 adding 'protenix-0.3.0.dist-info/METADATA' 2024-12-13T11:33:39,284 adding 'protenix-0.3.0.dist-info/WHEEL' 2024-12-13T11:33:39,285 adding 'protenix-0.3.0.dist-info/entry_points.txt' 2024-12-13T11:33:39,286 adding 'protenix-0.3.0.dist-info/top_level.txt' 2024-12-13T11:33:39,289 adding 'protenix-0.3.0.dist-info/RECORD' 2024-12-13T11:33:39,296 removing build/bdist.linux-armv7l/wheel 2024-12-13T11:33:39,444 Building wheel for protenix (setup.py): finished with status 'done' 2024-12-13T11:33:39,450 Created wheel for protenix: filename=protenix-0.3.0-py3-none-any.whl size=381124 sha256=c2af82dfdebc9606f320eb2d0ae308e644cd77922b443dcd59e7f778e756ac45 2024-12-13T11:33:39,451 Stored in directory: /tmp/pip-ephem-wheel-cache-be5hgfw3/wheels/f8/98/fa/b4c2009de6663bcdf779c583c128093705f24c91ef1aae98d6 2024-12-13T11:33:39,465 Successfully built protenix 2024-12-13T11:33:39,481 Removed build tracker: '/tmp/pip-build-tracker-rg9_zd9c'