2024-12-18T13:03:02,587 Created temporary directory: /tmp/pip-build-tracker-9inwf5rc 2024-12-18T13:03:02,588 Initialized build tracking at /tmp/pip-build-tracker-9inwf5rc 2024-12-18T13:03:02,589 Created build tracker: /tmp/pip-build-tracker-9inwf5rc 2024-12-18T13:03:02,589 Entered build tracker: /tmp/pip-build-tracker-9inwf5rc 2024-12-18T13:03:02,590 Created temporary directory: /tmp/pip-wheel-6k_lvh2n 2024-12-18T13:03:02,594 Created temporary directory: /tmp/pip-ephem-wheel-cache-agucvb02 2024-12-18T13:03:02,638 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-12-18T13:03:02,641 2 location(s) to search for versions of protenix: 2024-12-18T13:03:02,641 * https://pypi.org/simple/protenix/ 2024-12-18T13:03:02,641 * https://www.piwheels.org/simple/protenix/ 2024-12-18T13:03:02,642 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2024-12-18T13:03:02,643 Getting page https://pypi.org/simple/protenix/ 2024-12-18T13:03:02,644 Found index url https://pypi.org/simple/ 2024-12-18T13:03:02,872 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2024-12-18T13:03:02,877 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/) 2024-12-18T13:03:02,877 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/) 2024-12-18T13:03:02,878 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 2024-12-18T13:03:02,879 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) 2024-12-18T13:03:02,879 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 2024-12-18T13:03:02,880 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) 2024-12-18T13:03:02,881 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 2024-12-18T13:03:02,882 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) 2024-12-18T13:03:02,883 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 2024-12-18T13:03:02,884 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) 2024-12-18T13:03:02,884 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 2024-12-18T13:03:02,885 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) 2024-12-18T13:03:02,886 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 2024-12-18T13:03:02,887 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) 2024-12-18T13:03:02,888 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 2024-12-18T13:03:02,888 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/bf/6b/1cb9d8eea4be4973f97bd1f138f6da0711fad309b76b5c977b316c6bc511/protenix-0.3.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2024-12-18T13:03:02,889 Found link https://files.pythonhosted.org/packages/9a/85/b1ec219c8b8a3ba735742164561a917f53e81f11d2a3a9544a206f9ac21b/protenix-0.3.1.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.1 2024-12-18T13:03:02,890 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/6d/11/4c2946b935b56d995c7418cfc783c16e9e647de72a34380c42e573d4b28d/protenix-0.3.2-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2024-12-18T13:03:02,891 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 2024-12-18T13:03:02,891 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2024-12-18T13:03:02,892 Getting page https://www.piwheels.org/simple/protenix/ 2024-12-18T13:03:02,893 Found index url https://www.piwheels.org/simple/ 2024-12-18T13:03:03,060 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2024-12-18T13:03:03,064 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.1-py3-none-any.whl#sha256=624b9eaf9450baa3748fbe7d038a393ab59d36d7b191a70d676d592c81f46d1f (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2024-12-18T13:03:03,064 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.0-py3-none-any.whl#sha256=c2af82dfdebc9606f320eb2d0ae308e644cd77922b443dcd59e7f778e756ac45 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2024-12-18T13:03:03,065 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) 2024-12-18T13:03:03,066 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) 2024-12-18T13:03:03,066 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) 2024-12-18T13:03:03,067 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) 2024-12-18T13:03:03,067 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) 2024-12-18T13:03:03,068 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/) 2024-12-18T13:03:03,069 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2024-12-18T13:03:03,069 Skipping link: not a file: https://pypi.org/simple/protenix/ 2024-12-18T13:03:03,089 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2024-12-18T13:03:03,091 Collecting protenix==0.3.2 2024-12-18T13:03:03,093 Created temporary directory: /tmp/pip-unpack-yjpp_6ba 2024-12-18T13:03:03,335 Downloading protenix-0.3.2.tar.gz (308 kB) 2024-12-18T13:03:03,738 Added protenix==0.3.2 from https://files.pythonhosted.org/packages/65/48/25fdef4629cd5ce68c65f733fc49388378cacd3658cd76b5e88893ca5227/protenix-0.3.2.tar.gz to build tracker '/tmp/pip-build-tracker-9inwf5rc' 2024-12-18T13:03:03,740 Running setup.py (path:/tmp/pip-wheel-6k_lvh2n/protenix_dc5ada721d66444684155da589eb98e0/setup.py) egg_info for package protenix 2024-12-18T13:03:03,741 Created temporary directory: /tmp/pip-pip-egg-info-de8g_6ef 2024-12-18T13:03:03,742 Preparing metadata (setup.py): started 2024-12-18T13:03:03,743 Running command python setup.py egg_info 2024-12-18T13:03:05,192 running egg_info 2024-12-18T13:03:05,220 creating /tmp/pip-pip-egg-info-de8g_6ef/protenix.egg-info 2024-12-18T13:03:05,221 writing /tmp/pip-pip-egg-info-de8g_6ef/protenix.egg-info/PKG-INFO 2024-12-18T13:03:05,225 writing dependency_links to /tmp/pip-pip-egg-info-de8g_6ef/protenix.egg-info/dependency_links.txt 2024-12-18T13:03:05,226 writing entry points to /tmp/pip-pip-egg-info-de8g_6ef/protenix.egg-info/entry_points.txt 2024-12-18T13:03:05,228 writing requirements to /tmp/pip-pip-egg-info-de8g_6ef/protenix.egg-info/requires.txt 2024-12-18T13:03:05,229 writing top-level names to /tmp/pip-pip-egg-info-de8g_6ef/protenix.egg-info/top_level.txt 2024-12-18T13:03:05,231 writing manifest file '/tmp/pip-pip-egg-info-de8g_6ef/protenix.egg-info/SOURCES.txt' 2024-12-18T13:03:05,560 reading manifest file '/tmp/pip-pip-egg-info-de8g_6ef/protenix.egg-info/SOURCES.txt' 2024-12-18T13:03:05,561 adding license file 'LICENSE' 2024-12-18T13:03:05,567 writing manifest file '/tmp/pip-pip-egg-info-de8g_6ef/protenix.egg-info/SOURCES.txt' 2024-12-18T13:03:05,677 Preparing metadata (setup.py): finished with status 'done' 2024-12-18T13:03:05,682 Source in /tmp/pip-wheel-6k_lvh2n/protenix_dc5ada721d66444684155da589eb98e0 has version 0.3.2, which satisfies requirement protenix==0.3.2 from https://files.pythonhosted.org/packages/65/48/25fdef4629cd5ce68c65f733fc49388378cacd3658cd76b5e88893ca5227/protenix-0.3.2.tar.gz 2024-12-18T13:03:05,683 Removed protenix==0.3.2 from https://files.pythonhosted.org/packages/65/48/25fdef4629cd5ce68c65f733fc49388378cacd3658cd76b5e88893ca5227/protenix-0.3.2.tar.gz from build tracker '/tmp/pip-build-tracker-9inwf5rc' 2024-12-18T13:03:05,691 Created temporary directory: /tmp/pip-unpack-_6i8syrj 2024-12-18T13:03:05,692 Created temporary directory: /tmp/pip-unpack-8aqooxor 2024-12-18T13:03:05,693 Building wheels for collected packages: protenix 2024-12-18T13:03:05,697 Created temporary directory: /tmp/pip-wheel-cvr3rw63 2024-12-18T13:03:05,698 Building wheel for protenix (setup.py): started 2024-12-18T13:03:05,699 Destination directory: /tmp/pip-wheel-cvr3rw63 2024-12-18T13:03:05,700 Running command python setup.py bdist_wheel 2024-12-18T13:03:06,813 running bdist_wheel 2024-12-18T13:03:06,946 running build 2024-12-18T13:03:06,947 running build_py 2024-12-18T13:03:06,978 creating build/lib/runner 2024-12-18T13:03:06,980 copying runner/train.py -> build/lib/runner 2024-12-18T13:03:06,984 copying runner/inference.py -> build/lib/runner 2024-12-18T13:03:06,986 copying runner/dumper.py -> build/lib/runner 2024-12-18T13:03:06,989 copying runner/batch_inference.py -> build/lib/runner 2024-12-18T13:03:06,991 copying runner/ema.py -> build/lib/runner 2024-12-18T13:03:06,993 copying runner/__init__.py -> build/lib/runner 2024-12-18T13:03:06,994 copying runner/msa_search.py -> build/lib/runner 2024-12-18T13:03:06,997 creating build/lib/protenix 2024-12-18T13:03:06,998 copying protenix/__init__.py -> build/lib/protenix 2024-12-18T13:03:07,000 creating build/lib/configs 2024-12-18T13:03:07,001 copying configs/configs_base.py -> build/lib/configs 2024-12-18T13:03:07,003 copying configs/configs_inference.py -> build/lib/configs 2024-12-18T13:03:07,005 copying configs/configs_data.py -> build/lib/configs 2024-12-18T13:03:07,008 copying configs/__init__.py -> build/lib/configs 2024-12-18T13:03:07,010 creating build/lib/protenix/config 2024-12-18T13:03:07,011 copying protenix/config/config.py -> build/lib/protenix/config 2024-12-18T13:03:07,013 copying protenix/config/extend_types.py -> build/lib/protenix/config 2024-12-18T13:03:07,015 copying protenix/config/__init__.py -> build/lib/protenix/config 2024-12-18T13:03:07,018 creating build/lib/protenix/model 2024-12-18T13:03:07,019 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2024-12-18T13:03:07,021 copying protenix/model/loss.py -> build/lib/protenix/model 2024-12-18T13:03:07,025 copying protenix/model/generator.py -> build/lib/protenix/model 2024-12-18T13:03:07,028 copying protenix/model/protenix.py -> build/lib/protenix/model 2024-12-18T13:03:07,031 copying protenix/model/utils.py -> build/lib/protenix/model 2024-12-18T13:03:07,033 copying protenix/model/__init__.py -> build/lib/protenix/model 2024-12-18T13:03:07,036 creating build/lib/protenix/web_service 2024-12-18T13:03:07,037 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2024-12-18T13:03:07,039 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2024-12-18T13:03:07,041 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2024-12-18T13:03:07,044 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2024-12-18T13:03:07,045 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2024-12-18T13:03:07,048 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2024-12-18T13:03:07,051 creating build/lib/protenix/utils 2024-12-18T13:03:07,052 copying protenix/utils/training.py -> build/lib/protenix/utils 2024-12-18T13:03:07,054 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2024-12-18T13:03:07,056 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2024-12-18T13:03:07,059 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2024-12-18T13:03:07,061 copying protenix/utils/seed.py -> build/lib/protenix/utils 2024-12-18T13:03:07,063 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2024-12-18T13:03:07,065 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2024-12-18T13:03:07,067 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2024-12-18T13:03:07,070 copying protenix/utils/logger.py -> build/lib/protenix/utils 2024-12-18T13:03:07,072 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2024-12-18T13:03:07,074 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2024-12-18T13:03:07,076 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2024-12-18T13:03:07,079 creating build/lib/protenix/data 2024-12-18T13:03:07,080 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2024-12-18T13:03:07,082 copying protenix/data/json_maker.py -> build/lib/protenix/data 2024-12-18T13:03:07,084 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2024-12-18T13:03:07,087 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2024-12-18T13:03:07,089 copying protenix/data/json_parser.py -> build/lib/protenix/data 2024-12-18T13:03:07,091 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2024-12-18T13:03:07,094 copying protenix/data/dataloader.py -> build/lib/protenix/data 2024-12-18T13:03:07,096 copying protenix/data/constants.py -> build/lib/protenix/data 2024-12-18T13:03:07,099 copying protenix/data/featurizer.py -> build/lib/protenix/data 2024-12-18T13:03:07,101 copying protenix/data/parser.py -> build/lib/protenix/data 2024-12-18T13:03:07,105 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2024-12-18T13:03:07,108 copying protenix/data/ccd.py -> build/lib/protenix/data 2024-12-18T13:03:07,110 copying protenix/data/utils.py -> build/lib/protenix/data 2024-12-18T13:03:07,112 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2024-12-18T13:03:07,115 copying protenix/data/__init__.py -> build/lib/protenix/data 2024-12-18T13:03:07,117 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2024-12-18T13:03:07,121 copying protenix/data/filter.py -> build/lib/protenix/data 2024-12-18T13:03:07,123 copying protenix/data/dataset.py -> build/lib/protenix/data 2024-12-18T13:03:07,127 creating build/lib/protenix/openfold_local 2024-12-18T13:03:07,128 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2024-12-18T13:03:07,131 creating build/lib/protenix/metrics 2024-12-18T13:03:07,133 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2024-12-18T13:03:07,136 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2024-12-18T13:03:07,138 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2024-12-18T13:03:07,141 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2024-12-18T13:03:07,144 creating build/lib/protenix/model/layer_norm 2024-12-18T13:03:07,145 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2024-12-18T13:03:07,148 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2024-12-18T13:03:07,150 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2024-12-18T13:03:07,153 creating build/lib/protenix/model/modules 2024-12-18T13:03:07,155 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2024-12-18T13:03:07,157 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2024-12-18T13:03:07,160 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2024-12-18T13:03:07,164 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2024-12-18T13:03:07,166 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2024-12-18T13:03:07,169 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2024-12-18T13:03:07,172 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2024-12-18T13:03:07,175 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2024-12-18T13:03:07,177 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2024-12-18T13:03:07,179 creating build/lib/protenix/utils/permutation 2024-12-18T13:03:07,180 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2024-12-18T13:03:07,184 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2024-12-18T13:03:07,186 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2024-12-18T13:03:07,188 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2024-12-18T13:03:07,191 creating build/lib/protenix/utils/permutation/chain_permutation 2024-12-18T13:03:07,193 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-18T13:03:07,195 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-18T13:03:07,197 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-18T13:03:07,200 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-18T13:03:07,203 creating build/lib/protenix/openfold_local/np 2024-12-18T13:03:07,204 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2024-12-18T13:03:07,207 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2024-12-18T13:03:07,209 creating build/lib/protenix/openfold_local/model 2024-12-18T13:03:07,210 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2024-12-18T13:03:07,213 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2024-12-18T13:03:07,215 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2024-12-18T13:03:07,217 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2024-12-18T13:03:07,219 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2024-12-18T13:03:07,221 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2024-12-18T13:03:07,224 creating build/lib/protenix/openfold_local/utils 2024-12-18T13:03:07,226 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2024-12-18T13:03:07,228 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2024-12-18T13:03:07,230 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-18T13:03:07,233 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2024-12-18T13:03:07,236 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-18T13:03:07,238 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-18T13:03:07,240 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2024-12-18T13:03:07,242 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-18T13:03:07,244 creating build/lib/protenix/openfold_local/data 2024-12-18T13:03:07,246 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2024-12-18T13:03:07,248 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2024-12-18T13:03:07,251 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2024-12-18T13:03:07,254 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2024-12-18T13:03:07,255 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2024-12-18T13:03:07,258 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2024-12-18T13:03:07,260 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2024-12-18T13:03:07,262 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2024-12-18T13:03:07,264 creating build/lib/protenix/openfold_local/utils/kernel 2024-12-18T13:03:07,266 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2024-12-18T13:03:07,268 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2024-12-18T13:03:07,270 creating build/lib/protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,271 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,273 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,276 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,278 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,280 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,282 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,284 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,286 creating build/lib/protenix/openfold_local/data/tools 2024-12-18T13:03:07,287 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2024-12-18T13:03:07,289 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2024-12-18T13:03:07,291 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2024-12-18T13:03:07,293 running egg_info 2024-12-18T13:03:07,324 writing protenix.egg-info/PKG-INFO 2024-12-18T13:03:07,327 writing dependency_links to protenix.egg-info/dependency_links.txt 2024-12-18T13:03:07,329 writing entry points to protenix.egg-info/entry_points.txt 2024-12-18T13:03:07,330 writing requirements to protenix.egg-info/requires.txt 2024-12-18T13:03:07,332 writing top-level names to protenix.egg-info/top_level.txt 2024-12-18T13:03:07,380 reading manifest file 'protenix.egg-info/SOURCES.txt' 2024-12-18T13:03:07,389 adding license file 'LICENSE' 2024-12-18T13:03:07,397 writing manifest file 'protenix.egg-info/SOURCES.txt' 2024-12-18T13:03:07,400 /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. 2024-12-18T13:03:07,400 !! 2024-12-18T13:03:07,401 ******************************************************************************** 2024-12-18T13:03:07,402 ############################ 2024-12-18T13:03:07,402 # Package would be ignored # 2024-12-18T13:03:07,403 ############################ 2024-12-18T13:03:07,403 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2024-12-18T13:03:07,404 but it is absent from setuptools' `packages` configuration. 2024-12-18T13:03:07,405 This leads to an ambiguous overall configuration. If you want to distribute this 2024-12-18T13:03:07,405 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2024-12-18T13:03:07,406 to the `packages` configuration field. 2024-12-18T13:03:07,407 Alternatively, you can also rely on setuptools' discovery methods 2024-12-18T13:03:07,407 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-12-18T13:03:07,408 instead of `find_packages(...)`/`find:`). 2024-12-18T13:03:07,409 You can read more about "package discovery" on setuptools documentation page: 2024-12-18T13:03:07,410 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-12-18T13:03:07,411 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2024-12-18T13:03:07,412 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2024-12-18T13:03:07,412 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-12-18T13:03:07,413 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-12-18T13:03:07,414 combination with a more fine grained `package-data` configuration. 2024-12-18T13:03:07,415 You can read more about "package data files" on setuptools documentation page: 2024-12-18T13:03:07,415 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-12-18T13:03:07,417 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-12-18T13:03:07,417 even if it does not contain any `.py` files. 2024-12-18T13:03:07,418 On the other hand, currently there is no concept of package data 2024-12-18T13:03:07,418 directory, all directories are treated like packages. 2024-12-18T13:03:07,419 ******************************************************************************** 2024-12-18T13:03:07,419 !! 2024-12-18T13:03:07,420 check.warn(importable) 2024-12-18T13:03:07,421 creating build/lib/protenix/model/layer_norm/kernel 2024-12-18T13:03:07,421 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2024-12-18T13:03:07,423 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2024-12-18T13:03:07,425 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2024-12-18T13:03:07,427 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2024-12-18T13:03:07,469 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-12-18T13:03:07,469 !! 2024-12-18T13:03:07,470 ******************************************************************************** 2024-12-18T13:03:07,471 Please avoid running ``setup.py`` directly. 2024-12-18T13:03:07,471 Instead, use pypa/build, pypa/installer or other 2024-12-18T13:03:07,472 standards-based tools. 2024-12-18T13:03:07,473 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-12-18T13:03:07,474 ******************************************************************************** 2024-12-18T13:03:07,475 !! 2024-12-18T13:03:07,475 self.initialize_options() 2024-12-18T13:03:07,499 installing to build/bdist.linux-armv7l/wheel 2024-12-18T13:03:07,499 running install 2024-12-18T13:03:07,524 running install_lib 2024-12-18T13:03:07,552 creating build/bdist.linux-armv7l/wheel 2024-12-18T13:03:07,554 creating build/bdist.linux-armv7l/wheel/runner 2024-12-18T13:03:07,555 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-18T13:03:07,558 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-18T13:03:07,560 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-18T13:03:07,563 copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-18T13:03:07,565 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-18T13:03:07,567 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-18T13:03:07,569 copying build/lib/runner/msa_search.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-18T13:03:07,571 creating build/bdist.linux-armv7l/wheel/protenix 2024-12-18T13:03:07,573 creating build/bdist.linux-armv7l/wheel/protenix/config 2024-12-18T13:03:07,574 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-18T13:03:07,577 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-18T13:03:07,579 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-18T13:03:07,581 creating build/bdist.linux-armv7l/wheel/protenix/model 2024-12-18T13:03:07,584 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2024-12-18T13:03:07,586 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2024-12-18T13:03:07,588 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-18T13:03:07,590 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-18T13:03:07,592 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-18T13:03:07,595 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-18T13:03:07,597 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-18T13:03:07,599 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-18T13:03:07,601 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-18T13:03:07,603 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-18T13:03:07,606 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-18T13:03:07,609 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-18T13:03:07,612 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2024-12-18T13:03:07,613 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-18T13:03:07,615 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-18T13:03:07,618 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-18T13:03:07,621 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-18T13:03:07,622 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-18T13:03:07,625 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-18T13:03:07,628 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-18T13:03:07,631 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-18T13:03:07,633 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-18T13:03:07,635 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-18T13:03:07,637 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-18T13:03:07,640 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-18T13:03:07,642 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2024-12-18T13:03:07,643 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-18T13:03:07,645 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-18T13:03:07,648 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-18T13:03:07,650 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-18T13:03:07,652 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-18T13:03:07,655 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-18T13:03:07,658 creating build/bdist.linux-armv7l/wheel/protenix/utils 2024-12-18T13:03:07,659 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-18T13:03:07,661 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-18T13:03:07,663 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-18T13:03:07,666 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-18T13:03:07,668 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-18T13:03:07,670 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-18T13:03:07,672 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-18T13:03:07,675 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2024-12-18T13:03:07,677 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2024-12-18T13:03:07,678 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-18T13:03:07,680 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-18T13:03:07,682 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-18T13:03:07,685 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-18T13:03:07,688 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-18T13:03:07,690 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-18T13:03:07,692 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-18T13:03:07,694 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-18T13:03:07,697 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-18T13:03:07,699 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-18T13:03:07,701 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-18T13:03:07,703 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-18T13:03:07,705 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-18T13:03:07,707 creating build/bdist.linux-armv7l/wheel/protenix/data 2024-12-18T13:03:07,708 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,711 copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,714 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,716 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,719 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,721 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,724 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,726 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,729 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,733 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,736 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,739 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,741 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,744 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,747 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,748 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,751 copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,753 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-18T13:03:07,756 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2024-12-18T13:03:07,758 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2024-12-18T13:03:07,759 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-12-18T13:03:07,762 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-12-18T13:03:07,764 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2024-12-18T13:03:07,766 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-18T13:03:07,768 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-18T13:03:07,770 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-18T13:03:07,772 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-18T13:03:07,775 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-18T13:03:07,776 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-18T13:03:07,779 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2024-12-18T13:03:07,781 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-18T13:03:07,783 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-18T13:03:07,785 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-18T13:03:07,789 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2024-12-18T13:03:07,790 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-12-18T13:03:07,792 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-12-18T13:03:07,794 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-18T13:03:07,796 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-18T13:03:07,799 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-18T13:03:07,801 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-18T13:03:07,802 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-18T13:03:07,805 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,806 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,808 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,810 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,812 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,815 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,816 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,818 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-18T13:03:07,821 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2024-12-18T13:03:07,822 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-18T13:03:07,825 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-18T13:03:07,828 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2024-12-18T13:03:07,830 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-18T13:03:07,832 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-18T13:03:07,833 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-18T13:03:07,836 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-18T13:03:07,839 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-18T13:03:07,841 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-18T13:03:07,844 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-18T13:03:07,846 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-18T13:03:07,849 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-18T13:03:07,851 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2024-12-18T13:03:07,854 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2024-12-18T13:03:07,855 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-18T13:03:07,859 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-18T13:03:07,861 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-18T13:03:07,864 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-18T13:03:07,866 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2024-12-18T13:03:07,868 creating build/bdist.linux-armv7l/wheel/configs 2024-12-18T13:03:07,869 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-18T13:03:07,872 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-18T13:03:07,874 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-18T13:03:07,876 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-18T13:03:07,877 running install_data 2024-12-18T13:03:07,907 creating build/bdist.linux-armv7l/wheel/protenix-0.3.2.data/data 2024-12-18T13:03:07,908 warning: install_data: setup script did not provide a directory for 'requirements.txt' -- installing right in 'build/bdist.linux-armv7l/wheel/protenix-0.3.2.data/data' 2024-12-18T13:03:07,909 copying requirements.txt -> build/bdist.linux-armv7l/wheel/protenix-0.3.2.data/data 2024-12-18T13:03:07,910 running install_egg_info 2024-12-18T13:03:07,946 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.3.2-py3.11.egg-info 2024-12-18T13:03:07,957 running install_scripts 2024-12-18T13:03:07,976 creating build/bdist.linux-armv7l/wheel/protenix-0.3.2.dist-info/WHEEL 2024-12-18T13:03:07,979 creating '/tmp/pip-wheel-cvr3rw63/protenix-0.3.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-12-18T13:03:07,981 adding 'configs/__init__.py' 2024-12-18T13:03:07,983 adding 'configs/configs_base.py' 2024-12-18T13:03:07,985 adding 'configs/configs_data.py' 2024-12-18T13:03:07,987 adding 'configs/configs_inference.py' 2024-12-18T13:03:07,988 adding 'protenix/__init__.py' 2024-12-18T13:03:07,990 adding 'protenix/config/__init__.py' 2024-12-18T13:03:07,992 adding 'protenix/config/config.py' 2024-12-18T13:03:07,994 adding 'protenix/config/extend_types.py' 2024-12-18T13:03:07,995 adding 'protenix/data/__init__.py' 2024-12-18T13:03:07,998 adding 'protenix/data/ccd.py' 2024-12-18T13:03:08,002 adding 'protenix/data/constants.py' 2024-12-18T13:03:08,004 adding 'protenix/data/data_pipeline.py' 2024-12-18T13:03:08,006 adding 'protenix/data/dataloader.py' 2024-12-18T13:03:08,011 adding 'protenix/data/dataset.py' 2024-12-18T13:03:08,015 adding 'protenix/data/featurizer.py' 2024-12-18T13:03:08,016 adding 'protenix/data/filter.py' 2024-12-18T13:03:08,018 adding 'protenix/data/infer_data_pipeline.py' 2024-12-18T13:03:08,020 adding 'protenix/data/json_maker.py' 2024-12-18T13:03:08,023 adding 'protenix/data/json_parser.py' 2024-12-18T13:03:08,025 adding 'protenix/data/json_to_feature.py' 2024-12-18T13:03:08,030 adding 'protenix/data/msa_featurizer.py' 2024-12-18T13:03:08,035 adding 'protenix/data/msa_utils.py' 2024-12-18T13:03:08,041 adding 'protenix/data/parser.py' 2024-12-18T13:03:08,043 adding 'protenix/data/substructure_perms.py' 2024-12-18T13:03:08,044 adding 'protenix/data/tokenizer.py' 2024-12-18T13:03:08,047 adding 'protenix/data/utils.py' 2024-12-18T13:03:08,049 adding 'protenix/metrics/__init__.py' 2024-12-18T13:03:08,051 adding 'protenix/metrics/clash.py' 2024-12-18T13:03:08,053 adding 'protenix/metrics/lddt_metrics.py' 2024-12-18T13:03:08,055 adding 'protenix/metrics/rmsd.py' 2024-12-18T13:03:08,056 adding 'protenix/model/__init__.py' 2024-12-18T13:03:08,058 adding 'protenix/model/generator.py' 2024-12-18T13:03:08,065 adding 'protenix/model/loss.py' 2024-12-18T13:03:08,068 adding 'protenix/model/protenix.py' 2024-12-18T13:03:08,071 adding 'protenix/model/sample_confidence.py' 2024-12-18T13:03:08,073 adding 'protenix/model/utils.py' 2024-12-18T13:03:08,075 adding 'protenix/model/layer_norm/__init__.py' 2024-12-18T13:03:08,076 adding 'protenix/model/layer_norm/layer_norm.py' 2024-12-18T13:03:08,077 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2024-12-18T13:03:08,079 adding 'protenix/model/layer_norm/kernel/compat.h' 2024-12-18T13:03:08,081 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2024-12-18T13:03:08,083 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2024-12-18T13:03:08,085 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2024-12-18T13:03:08,087 adding 'protenix/model/modules/__init__.py' 2024-12-18T13:03:08,089 adding 'protenix/model/modules/confidence.py' 2024-12-18T13:03:08,091 adding 'protenix/model/modules/diffusion.py' 2024-12-18T13:03:08,093 adding 'protenix/model/modules/embedders.py' 2024-12-18T13:03:08,094 adding 'protenix/model/modules/frames.py' 2024-12-18T13:03:08,096 adding 'protenix/model/modules/head.py' 2024-12-18T13:03:08,099 adding 'protenix/model/modules/pairformer.py' 2024-12-18T13:03:08,102 adding 'protenix/model/modules/primitives.py' 2024-12-18T13:03:08,106 adding 'protenix/model/modules/transformer.py' 2024-12-18T13:03:08,108 adding 'protenix/openfold_local/__init__.py' 2024-12-18T13:03:08,110 adding 'protenix/openfold_local/data/__init__.py' 2024-12-18T13:03:08,112 adding 'protenix/openfold_local/data/data_transforms.py' 2024-12-18T13:03:08,113 adding 'protenix/openfold_local/data/errors.py' 2024-12-18T13:03:08,116 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2024-12-18T13:03:08,117 adding 'protenix/openfold_local/data/msa_identifiers.py' 2024-12-18T13:03:08,120 adding 'protenix/openfold_local/data/msa_pairing.py' 2024-12-18T13:03:08,123 adding 'protenix/openfold_local/data/parsers.py' 2024-12-18T13:03:08,126 adding 'protenix/openfold_local/data/templates.py' 2024-12-18T13:03:08,128 adding 'protenix/openfold_local/data/tools/__init__.py' 2024-12-18T13:03:08,129 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2024-12-18T13:03:08,131 adding 'protenix/openfold_local/data/tools/utils.py' 2024-12-18T13:03:08,132 adding 'protenix/openfold_local/model/__init__.py' 2024-12-18T13:03:08,134 adding 'protenix/openfold_local/model/dropout.py' 2024-12-18T13:03:08,135 adding 'protenix/openfold_local/model/outer_product_mean.py' 2024-12-18T13:03:08,138 adding 'protenix/openfold_local/model/primitives.py' 2024-12-18T13:03:08,140 adding 'protenix/openfold_local/model/triangular_attention.py' 2024-12-18T13:03:08,143 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2024-12-18T13:03:08,144 adding 'protenix/openfold_local/np/__init__.py' 2024-12-18T13:03:08,149 adding 'protenix/openfold_local/np/residue_constants.py' 2024-12-18T13:03:08,151 adding 'protenix/openfold_local/utils/__init__.py' 2024-12-18T13:03:08,153 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2024-12-18T13:03:08,155 adding 'protenix/openfold_local/utils/checkpointing.py' 2024-12-18T13:03:08,157 adding 'protenix/openfold_local/utils/chunk_utils.py' 2024-12-18T13:03:08,159 adding 'protenix/openfold_local/utils/feats.py' 2024-12-18T13:03:08,161 adding 'protenix/openfold_local/utils/precision_utils.py' 2024-12-18T13:03:08,165 adding 'protenix/openfold_local/utils/rigid_utils.py' 2024-12-18T13:03:08,167 adding 'protenix/openfold_local/utils/tensor_utils.py' 2024-12-18T13:03:08,169 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2024-12-18T13:03:08,170 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2024-12-18T13:03:08,172 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2024-12-18T13:03:08,174 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2024-12-18T13:03:08,175 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2024-12-18T13:03:08,177 adding 'protenix/openfold_local/utils/geometry/utils.py' 2024-12-18T13:03:08,179 adding 'protenix/openfold_local/utils/geometry/vector.py' 2024-12-18T13:03:08,180 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2024-12-18T13:03:08,181 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2024-12-18T13:03:08,183 adding 'protenix/utils/__init__.py' 2024-12-18T13:03:08,186 adding 'protenix/utils/cropping.py' 2024-12-18T13:03:08,188 adding 'protenix/utils/distributed.py' 2024-12-18T13:03:08,189 adding 'protenix/utils/file_io.py' 2024-12-18T13:03:08,190 adding 'protenix/utils/geometry.py' 2024-12-18T13:03:08,192 adding 'protenix/utils/logger.py' 2024-12-18T13:03:08,193 adding 'protenix/utils/lr_scheduler.py' 2024-12-18T13:03:08,195 adding 'protenix/utils/metrics.py' 2024-12-18T13:03:08,196 adding 'protenix/utils/scatter_utils.py' 2024-12-18T13:03:08,197 adding 'protenix/utils/seed.py' 2024-12-18T13:03:08,199 adding 'protenix/utils/torch_utils.py' 2024-12-18T13:03:08,201 adding 'protenix/utils/training.py' 2024-12-18T13:03:08,203 adding 'protenix/utils/permutation/__init__.py' 2024-12-18T13:03:08,208 adding 'protenix/utils/permutation/atom_permutation.py' 2024-12-18T13:03:08,212 adding 'protenix/utils/permutation/permutation.py' 2024-12-18T13:03:08,215 adding 'protenix/utils/permutation/utils.py' 2024-12-18T13:03:08,217 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2024-12-18T13:03:08,223 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2024-12-18T13:03:08,226 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2024-12-18T13:03:08,228 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2024-12-18T13:03:08,230 adding 'protenix/web_service/__init__.py' 2024-12-18T13:03:08,232 adding 'protenix/web_service/colab_request_parser.py' 2024-12-18T13:03:08,235 adding 'protenix/web_service/colab_request_utils.py' 2024-12-18T13:03:08,237 adding 'protenix/web_service/dependency_url.py' 2024-12-18T13:03:08,239 adding 'protenix/web_service/prediction_visualization.py' 2024-12-18T13:03:08,242 adding 'protenix/web_service/viewer.py' 2024-12-18T13:03:08,245 adding 'protenix-0.3.2.data/data/requirements.txt' 2024-12-18T13:03:08,248 adding 'runner/__init__.py' 2024-12-18T13:03:08,251 adding 'runner/batch_inference.py' 2024-12-18T13:03:08,254 adding 'runner/dumper.py' 2024-12-18T13:03:08,255 adding 'runner/ema.py' 2024-12-18T13:03:08,258 adding 'runner/inference.py' 2024-12-18T13:03:08,259 adding 'runner/msa_search.py' 2024-12-18T13:03:08,263 adding 'runner/train.py' 2024-12-18T13:03:08,266 adding 'protenix-0.3.2.dist-info/LICENSE' 2024-12-18T13:03:08,268 adding 'protenix-0.3.2.dist-info/METADATA' 2024-12-18T13:03:08,269 adding 'protenix-0.3.2.dist-info/WHEEL' 2024-12-18T13:03:08,270 adding 'protenix-0.3.2.dist-info/entry_points.txt' 2024-12-18T13:03:08,271 adding 'protenix-0.3.2.dist-info/top_level.txt' 2024-12-18T13:03:08,275 adding 'protenix-0.3.2.dist-info/RECORD' 2024-12-18T13:03:08,284 removing build/bdist.linux-armv7l/wheel 2024-12-18T13:03:08,435 Building wheel for protenix (setup.py): finished with status 'done' 2024-12-18T13:03:08,442 Created wheel for protenix: filename=protenix-0.3.2-py3-none-any.whl size=382688 sha256=0255f130567cda78b0dd7e9e1efee966d489a4302df91f47c2ce7d7c5f9b3400 2024-12-18T13:03:08,443 Stored in directory: /tmp/pip-ephem-wheel-cache-agucvb02/wheels/d7/21/71/ef140937b06a52ed62d647e51ddd78be95025e936874d11a0e 2024-12-18T13:03:08,457 Successfully built protenix 2024-12-18T13:03:08,474 Removed build tracker: '/tmp/pip-build-tracker-9inwf5rc'