2024-12-17T09:54:22,566 Created temporary directory: /tmp/pip-build-tracker-zwemsl07 2024-12-17T09:54:22,567 Initialized build tracking at /tmp/pip-build-tracker-zwemsl07 2024-12-17T09:54:22,568 Created build tracker: /tmp/pip-build-tracker-zwemsl07 2024-12-17T09:54:22,568 Entered build tracker: /tmp/pip-build-tracker-zwemsl07 2024-12-17T09:54:22,569 Created temporary directory: /tmp/pip-wheel-9qsvp48s 2024-12-17T09:54:22,573 Created temporary directory: /tmp/pip-ephem-wheel-cache-rojwduc4 2024-12-17T09:54:22,617 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-12-17T09:54:22,620 2 location(s) to search for versions of protenix: 2024-12-17T09:54:22,620 * https://pypi.org/simple/protenix/ 2024-12-17T09:54:22,620 * https://www.piwheels.org/simple/protenix/ 2024-12-17T09:54:22,621 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2024-12-17T09:54:22,622 Getting page https://pypi.org/simple/protenix/ 2024-12-17T09:54:22,623 Found index url https://pypi.org/simple/ 2024-12-17T09:54:22,847 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2024-12-17T09:54:22,852 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/) 2024-12-17T09:54:22,852 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/) 2024-12-17T09:54:22,853 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 2024-12-17T09:54:22,854 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) 2024-12-17T09:54:22,854 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 2024-12-17T09:54:22,855 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) 2024-12-17T09:54:22,856 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 2024-12-17T09:54:22,857 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) 2024-12-17T09:54:22,858 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 2024-12-17T09:54:22,858 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) 2024-12-17T09:54:22,859 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 2024-12-17T09:54:22,860 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) 2024-12-17T09:54:22,861 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 2024-12-17T09:54:22,862 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) 2024-12-17T09:54:22,863 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 2024-12-17T09:54:22,863 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) 2024-12-17T09:54:22,864 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 2024-12-17T09:54:22,865 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2024-12-17T09:54:22,865 Getting page https://www.piwheels.org/simple/protenix/ 2024-12-17T09:54:22,866 Found index url https://www.piwheels.org/simple/ 2024-12-17T09:54:23,024 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2024-12-17T09:54:23,027 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) 2024-12-17T09:54:23,028 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) 2024-12-17T09:54:23,029 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) 2024-12-17T09:54:23,029 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) 2024-12-17T09:54:23,030 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) 2024-12-17T09:54:23,030 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) 2024-12-17T09:54:23,031 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/) 2024-12-17T09:54:23,031 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2024-12-17T09:54:23,032 Skipping link: not a file: https://pypi.org/simple/protenix/ 2024-12-17T09:54:23,052 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2024-12-17T09:54:23,054 Collecting protenix==0.3.1 2024-12-17T09:54:23,056 Created temporary directory: /tmp/pip-unpack-8zmkkuce 2024-12-17T09:54:23,275 Downloading protenix-0.3.1.tar.gz (308 kB) 2024-12-17T09:54:23,679 Added protenix==0.3.1 from https://files.pythonhosted.org/packages/9a/85/b1ec219c8b8a3ba735742164561a917f53e81f11d2a3a9544a206f9ac21b/protenix-0.3.1.tar.gz to build tracker '/tmp/pip-build-tracker-zwemsl07' 2024-12-17T09:54:23,681 Running setup.py (path:/tmp/pip-wheel-9qsvp48s/protenix_456fd5da2fc144c1b989ada5bd42b49a/setup.py) egg_info for package protenix 2024-12-17T09:54:23,682 Created temporary directory: /tmp/pip-pip-egg-info-y69_hl03 2024-12-17T09:54:23,682 Preparing metadata (setup.py): started 2024-12-17T09:54:23,683 Running command python setup.py egg_info 2024-12-17T09:54:24,741 running egg_info 2024-12-17T09:54:24,769 creating /tmp/pip-pip-egg-info-y69_hl03/protenix.egg-info 2024-12-17T09:54:24,771 writing /tmp/pip-pip-egg-info-y69_hl03/protenix.egg-info/PKG-INFO 2024-12-17T09:54:24,774 writing dependency_links to /tmp/pip-pip-egg-info-y69_hl03/protenix.egg-info/dependency_links.txt 2024-12-17T09:54:24,775 writing entry points to /tmp/pip-pip-egg-info-y69_hl03/protenix.egg-info/entry_points.txt 2024-12-17T09:54:24,777 writing requirements to /tmp/pip-pip-egg-info-y69_hl03/protenix.egg-info/requires.txt 2024-12-17T09:54:24,778 writing top-level names to /tmp/pip-pip-egg-info-y69_hl03/protenix.egg-info/top_level.txt 2024-12-17T09:54:24,780 writing manifest file '/tmp/pip-pip-egg-info-y69_hl03/protenix.egg-info/SOURCES.txt' 2024-12-17T09:54:24,890 reading manifest file '/tmp/pip-pip-egg-info-y69_hl03/protenix.egg-info/SOURCES.txt' 2024-12-17T09:54:24,892 adding license file 'LICENSE' 2024-12-17T09:54:24,898 writing manifest file '/tmp/pip-pip-egg-info-y69_hl03/protenix.egg-info/SOURCES.txt' 2024-12-17T09:54:25,007 Preparing metadata (setup.py): finished with status 'done' 2024-12-17T09:54:25,011 Source in /tmp/pip-wheel-9qsvp48s/protenix_456fd5da2fc144c1b989ada5bd42b49a has version 0.3.1, which satisfies requirement protenix==0.3.1 from https://files.pythonhosted.org/packages/9a/85/b1ec219c8b8a3ba735742164561a917f53e81f11d2a3a9544a206f9ac21b/protenix-0.3.1.tar.gz 2024-12-17T09:54:25,012 Removed protenix==0.3.1 from https://files.pythonhosted.org/packages/9a/85/b1ec219c8b8a3ba735742164561a917f53e81f11d2a3a9544a206f9ac21b/protenix-0.3.1.tar.gz from build tracker '/tmp/pip-build-tracker-zwemsl07' 2024-12-17T09:54:25,021 Created temporary directory: /tmp/pip-unpack-fed6p6rw 2024-12-17T09:54:25,022 Created temporary directory: /tmp/pip-unpack-m0a69p1a 2024-12-17T09:54:25,022 Building wheels for collected packages: protenix 2024-12-17T09:54:25,027 Created temporary directory: /tmp/pip-wheel-n8tz9v4l 2024-12-17T09:54:25,027 Building wheel for protenix (setup.py): started 2024-12-17T09:54:25,029 Destination directory: /tmp/pip-wheel-n8tz9v4l 2024-12-17T09:54:25,029 Running command python setup.py bdist_wheel 2024-12-17T09:54:26,300 running bdist_wheel 2024-12-17T09:54:26,436 running build 2024-12-17T09:54:26,437 running build_py 2024-12-17T09:54:26,468 creating build/lib/runner 2024-12-17T09:54:26,470 copying runner/batch_inference.py -> build/lib/runner 2024-12-17T09:54:26,473 copying runner/inference.py -> build/lib/runner 2024-12-17T09:54:26,476 copying runner/ema.py -> build/lib/runner 2024-12-17T09:54:26,478 copying runner/msa_search.py -> build/lib/runner 2024-12-17T09:54:26,480 copying runner/train.py -> build/lib/runner 2024-12-17T09:54:26,483 copying runner/dumper.py -> build/lib/runner 2024-12-17T09:54:26,485 copying runner/__init__.py -> build/lib/runner 2024-12-17T09:54:26,487 creating build/lib/configs 2024-12-17T09:54:26,488 copying configs/configs_inference.py -> build/lib/configs 2024-12-17T09:54:26,491 copying configs/configs_base.py -> build/lib/configs 2024-12-17T09:54:26,493 copying configs/configs_data.py -> build/lib/configs 2024-12-17T09:54:26,496 copying configs/__init__.py -> build/lib/configs 2024-12-17T09:54:26,498 creating build/lib/protenix 2024-12-17T09:54:26,499 copying protenix/__init__.py -> build/lib/protenix 2024-12-17T09:54:26,502 creating build/lib/protenix/data 2024-12-17T09:54:26,503 copying protenix/data/utils.py -> build/lib/protenix/data 2024-12-17T09:54:26,506 copying protenix/data/dataset.py -> build/lib/protenix/data 2024-12-17T09:54:26,509 copying protenix/data/ccd.py -> build/lib/protenix/data 2024-12-17T09:54:26,511 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2024-12-17T09:54:26,515 copying protenix/data/json_maker.py -> build/lib/protenix/data 2024-12-17T09:54:26,517 copying protenix/data/filter.py -> build/lib/protenix/data 2024-12-17T09:54:26,519 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2024-12-17T09:54:26,522 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2024-12-17T09:54:26,524 copying protenix/data/json_parser.py -> build/lib/protenix/data 2024-12-17T09:54:26,527 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2024-12-17T09:54:26,529 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2024-12-17T09:54:26,532 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2024-12-17T09:54:26,534 copying protenix/data/dataloader.py -> build/lib/protenix/data 2024-12-17T09:54:26,536 copying protenix/data/featurizer.py -> build/lib/protenix/data 2024-12-17T09:54:26,539 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2024-12-17T09:54:26,542 copying protenix/data/__init__.py -> build/lib/protenix/data 2024-12-17T09:54:26,543 copying protenix/data/constants.py -> build/lib/protenix/data 2024-12-17T09:54:26,546 copying protenix/data/parser.py -> build/lib/protenix/data 2024-12-17T09:54:26,551 creating build/lib/protenix/web_service 2024-12-17T09:54:26,552 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2024-12-17T09:54:26,555 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2024-12-17T09:54:26,557 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2024-12-17T09:54:26,559 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2024-12-17T09:54:26,562 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2024-12-17T09:54:26,564 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2024-12-17T09:54:26,566 creating build/lib/protenix/model 2024-12-17T09:54:26,567 copying protenix/model/utils.py -> build/lib/protenix/model 2024-12-17T09:54:26,570 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2024-12-17T09:54:26,572 copying protenix/model/loss.py -> build/lib/protenix/model 2024-12-17T09:54:26,576 copying protenix/model/generator.py -> build/lib/protenix/model 2024-12-17T09:54:26,579 copying protenix/model/protenix.py -> build/lib/protenix/model 2024-12-17T09:54:26,582 copying protenix/model/__init__.py -> build/lib/protenix/model 2024-12-17T09:54:26,584 creating build/lib/protenix/config 2024-12-17T09:54:26,585 copying protenix/config/config.py -> build/lib/protenix/config 2024-12-17T09:54:26,588 copying protenix/config/extend_types.py -> build/lib/protenix/config 2024-12-17T09:54:26,590 copying protenix/config/__init__.py -> build/lib/protenix/config 2024-12-17T09:54:26,593 creating build/lib/protenix/utils 2024-12-17T09:54:26,594 copying protenix/utils/logger.py -> build/lib/protenix/utils 2024-12-17T09:54:26,596 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2024-12-17T09:54:26,598 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2024-12-17T09:54:26,600 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2024-12-17T09:54:26,602 copying protenix/utils/seed.py -> build/lib/protenix/utils 2024-12-17T09:54:26,604 copying protenix/utils/training.py -> build/lib/protenix/utils 2024-12-17T09:54:26,606 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2024-12-17T09:54:26,608 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2024-12-17T09:54:26,611 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2024-12-17T09:54:26,613 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2024-12-17T09:54:26,615 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2024-12-17T09:54:26,617 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2024-12-17T09:54:26,619 creating build/lib/protenix/openfold_local 2024-12-17T09:54:26,620 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2024-12-17T09:54:26,623 creating build/lib/protenix/metrics 2024-12-17T09:54:26,624 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2024-12-17T09:54:26,627 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2024-12-17T09:54:26,629 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2024-12-17T09:54:26,632 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2024-12-17T09:54:26,634 creating build/lib/protenix/model/modules 2024-12-17T09:54:26,635 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2024-12-17T09:54:26,637 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2024-12-17T09:54:26,640 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2024-12-17T09:54:26,643 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2024-12-17T09:54:26,645 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2024-12-17T09:54:26,648 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2024-12-17T09:54:26,650 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2024-12-17T09:54:26,653 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2024-12-17T09:54:26,656 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2024-12-17T09:54:26,658 creating build/lib/protenix/model/layer_norm 2024-12-17T09:54:26,659 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2024-12-17T09:54:26,662 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2024-12-17T09:54:26,664 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2024-12-17T09:54:26,667 creating build/lib/protenix/utils/permutation 2024-12-17T09:54:26,668 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2024-12-17T09:54:26,670 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2024-12-17T09:54:26,673 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2024-12-17T09:54:26,676 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2024-12-17T09:54:26,678 creating build/lib/protenix/utils/permutation/chain_permutation 2024-12-17T09:54:26,680 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-17T09:54:26,682 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-17T09:54:26,684 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-17T09:54:26,687 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-17T09:54:26,690 creating build/lib/protenix/openfold_local/np 2024-12-17T09:54:26,692 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2024-12-17T09:54:26,695 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2024-12-17T09:54:26,697 creating build/lib/protenix/openfold_local/data 2024-12-17T09:54:26,698 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2024-12-17T09:54:26,701 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2024-12-17T09:54:26,704 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2024-12-17T09:54:26,706 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2024-12-17T09:54:26,708 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2024-12-17T09:54:26,710 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2024-12-17T09:54:26,713 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2024-12-17T09:54:26,716 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2024-12-17T09:54:26,718 creating build/lib/protenix/openfold_local/model 2024-12-17T09:54:26,720 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2024-12-17T09:54:26,722 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2024-12-17T09:54:26,725 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2024-12-17T09:54:26,727 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2024-12-17T09:54:26,730 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2024-12-17T09:54:26,732 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2024-12-17T09:54:26,734 creating build/lib/protenix/openfold_local/utils 2024-12-17T09:54:26,736 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-17T09:54:26,738 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2024-12-17T09:54:26,741 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-17T09:54:26,743 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-17T09:54:26,746 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2024-12-17T09:54:26,748 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2024-12-17T09:54:26,751 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-17T09:54:26,753 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2024-12-17T09:54:26,755 creating build/lib/protenix/openfold_local/data/tools 2024-12-17T09:54:26,757 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2024-12-17T09:54:26,759 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2024-12-17T09:54:26,761 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2024-12-17T09:54:26,764 creating build/lib/protenix/openfold_local/utils/kernel 2024-12-17T09:54:26,765 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2024-12-17T09:54:26,767 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2024-12-17T09:54:26,770 creating build/lib/protenix/openfold_local/utils/geometry 2024-12-17T09:54:26,771 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-17T09:54:26,773 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-17T09:54:26,776 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-17T09:54:26,778 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-17T09:54:26,779 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-17T09:54:26,782 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-17T09:54:26,784 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-17T09:54:26,786 running egg_info 2024-12-17T09:54:26,817 writing protenix.egg-info/PKG-INFO 2024-12-17T09:54:26,821 writing dependency_links to protenix.egg-info/dependency_links.txt 2024-12-17T09:54:26,822 writing entry points to protenix.egg-info/entry_points.txt 2024-12-17T09:54:26,824 writing requirements to protenix.egg-info/requires.txt 2024-12-17T09:54:26,825 writing top-level names to protenix.egg-info/top_level.txt 2024-12-17T09:54:26,878 reading manifest file 'protenix.egg-info/SOURCES.txt' 2024-12-17T09:54:26,887 adding license file 'LICENSE' 2024-12-17T09:54:26,895 writing manifest file 'protenix.egg-info/SOURCES.txt' 2024-12-17T09:54:26,898 /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. 2024-12-17T09:54:26,898 !! 2024-12-17T09:54:26,899 ******************************************************************************** 2024-12-17T09:54:26,900 ############################ 2024-12-17T09:54:26,900 # Package would be ignored # 2024-12-17T09:54:26,901 ############################ 2024-12-17T09:54:26,901 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2024-12-17T09:54:26,902 but it is absent from setuptools' `packages` configuration. 2024-12-17T09:54:26,903 This leads to an ambiguous overall configuration. If you want to distribute this 2024-12-17T09:54:26,903 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2024-12-17T09:54:26,904 to the `packages` configuration field. 2024-12-17T09:54:26,905 Alternatively, you can also rely on setuptools' discovery methods 2024-12-17T09:54:26,906 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-12-17T09:54:26,906 instead of `find_packages(...)`/`find:`). 2024-12-17T09:54:26,908 You can read more about "package discovery" on setuptools documentation page: 2024-12-17T09:54:26,909 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-12-17T09:54:26,910 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2024-12-17T09:54:26,911 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2024-12-17T09:54:26,912 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-12-17T09:54:26,913 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-12-17T09:54:26,913 combination with a more fine grained `package-data` configuration. 2024-12-17T09:54:26,914 You can read more about "package data files" on setuptools documentation page: 2024-12-17T09:54:26,915 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-12-17T09:54:26,917 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-12-17T09:54:26,918 even if it does not contain any `.py` files. 2024-12-17T09:54:26,918 On the other hand, currently there is no concept of package data 2024-12-17T09:54:26,919 directory, all directories are treated like packages. 2024-12-17T09:54:26,920 ******************************************************************************** 2024-12-17T09:54:26,921 !! 2024-12-17T09:54:26,922 check.warn(importable) 2024-12-17T09:54:26,922 creating build/lib/protenix/model/layer_norm/kernel 2024-12-17T09:54:26,923 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2024-12-17T09:54:26,923 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2024-12-17T09:54:26,926 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2024-12-17T09:54:26,929 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2024-12-17T09:54:26,973 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-12-17T09:54:26,973 !! 2024-12-17T09:54:26,974 ******************************************************************************** 2024-12-17T09:54:26,975 Please avoid running ``setup.py`` directly. 2024-12-17T09:54:26,975 Instead, use pypa/build, pypa/installer or other 2024-12-17T09:54:26,976 standards-based tools. 2024-12-17T09:54:26,977 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-12-17T09:54:26,977 ******************************************************************************** 2024-12-17T09:54:26,978 !! 2024-12-17T09:54:26,979 self.initialize_options() 2024-12-17T09:54:27,001 installing to build/bdist.linux-armv7l/wheel 2024-12-17T09:54:27,002 running install 2024-12-17T09:54:27,026 running install_lib 2024-12-17T09:54:27,053 creating build/bdist.linux-armv7l/wheel 2024-12-17T09:54:27,056 creating build/bdist.linux-armv7l/wheel/runner 2024-12-17T09:54:27,057 copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-17T09:54:27,060 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-17T09:54:27,063 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-17T09:54:27,065 copying build/lib/runner/msa_search.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-17T09:54:27,067 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-17T09:54:27,070 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-17T09:54:27,072 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-17T09:54:27,074 creating build/bdist.linux-armv7l/wheel/configs 2024-12-17T09:54:27,076 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-17T09:54:27,078 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-17T09:54:27,080 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-17T09:54:27,083 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-17T09:54:27,085 creating build/bdist.linux-armv7l/wheel/protenix 2024-12-17T09:54:27,087 creating build/bdist.linux-armv7l/wheel/protenix/data 2024-12-17T09:54:27,089 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,092 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,095 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,098 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,101 copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,103 copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,105 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,109 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,111 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,114 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,116 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,119 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,121 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,124 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,127 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,129 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,131 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,134 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-17T09:54:27,138 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2024-12-17T09:54:27,140 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-17T09:54:27,143 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-17T09:54:27,145 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-17T09:54:27,148 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-17T09:54:27,150 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-17T09:54:27,153 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-17T09:54:27,155 creating build/bdist.linux-armv7l/wheel/protenix/model 2024-12-17T09:54:27,156 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-17T09:54:27,159 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-17T09:54:27,162 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-17T09:54:27,167 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2024-12-17T09:54:27,168 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-17T09:54:27,171 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-17T09:54:27,174 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-17T09:54:27,177 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-17T09:54:27,179 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-17T09:54:27,182 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-17T09:54:27,184 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-17T09:54:27,188 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-17T09:54:27,191 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-17T09:54:27,193 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2024-12-17T09:54:27,194 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-17T09:54:27,197 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-17T09:54:27,199 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2024-12-17T09:54:27,200 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-17T09:54:27,204 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-17T09:54:27,206 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-17T09:54:27,208 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-17T09:54:27,210 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-17T09:54:27,212 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-17T09:54:27,215 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-17T09:54:27,218 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-17T09:54:27,220 creating build/bdist.linux-armv7l/wheel/protenix/config 2024-12-17T09:54:27,221 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-17T09:54:27,224 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-17T09:54:27,226 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-17T09:54:27,228 creating build/bdist.linux-armv7l/wheel/protenix/utils 2024-12-17T09:54:27,230 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-17T09:54:27,232 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-17T09:54:27,234 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-17T09:54:27,236 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-17T09:54:27,238 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-17T09:54:27,241 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-17T09:54:27,243 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-17T09:54:27,245 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-17T09:54:27,249 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-17T09:54:27,251 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-17T09:54:27,252 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-17T09:54:27,254 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-17T09:54:27,257 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2024-12-17T09:54:27,259 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-17T09:54:27,262 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2024-12-17T09:54:27,264 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-17T09:54:27,267 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-17T09:54:27,270 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-17T09:54:27,274 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-17T09:54:27,277 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-17T09:54:27,280 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-17T09:54:27,284 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-17T09:54:27,286 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2024-12-17T09:54:27,288 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2024-12-17T09:54:27,289 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-12-17T09:54:27,292 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-12-17T09:54:27,294 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2024-12-17T09:54:27,296 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-17T09:54:27,298 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-17T09:54:27,301 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-17T09:54:27,304 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-17T09:54:27,306 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-17T09:54:27,309 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2024-12-17T09:54:27,311 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-17T09:54:27,313 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-17T09:54:27,316 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-17T09:54:27,318 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-17T09:54:27,321 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-17T09:54:27,324 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-17T09:54:27,327 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2024-12-17T09:54:27,329 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-17T09:54:27,331 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-17T09:54:27,335 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-17T09:54:27,338 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-17T09:54:27,341 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-17T09:54:27,344 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-17T09:54:27,346 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2024-12-17T09:54:27,348 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-17T09:54:27,351 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-17T09:54:27,353 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-17T09:54:27,355 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-17T09:54:27,359 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-17T09:54:27,361 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-17T09:54:27,366 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2024-12-17T09:54:27,368 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-12-17T09:54:27,374 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-12-17T09:54:27,378 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-17T09:54:27,383 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-17T09:54:27,389 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2024-12-17T09:54:27,390 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-17T09:54:27,393 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-17T09:54:27,395 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-17T09:54:27,398 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-17T09:54:27,401 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-17T09:54:27,406 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-17T09:54:27,410 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-17T09:54:27,416 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2024-12-17T09:54:27,422 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2024-12-17T09:54:27,430 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2024-12-17T09:54:27,433 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-17T09:54:27,442 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-17T09:54:27,453 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-17T09:54:27,464 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-17T09:54:27,471 running install_data 2024-12-17T09:54:27,536 creating build/bdist.linux-armv7l/wheel/protenix-0.3.1.data/data 2024-12-17T09:54:27,541 warning: install_data: setup script did not provide a directory for 'requirements.txt' -- installing right in 'build/bdist.linux-armv7l/wheel/protenix-0.3.1.data/data' 2024-12-17T09:54:27,545 copying requirements.txt -> build/bdist.linux-armv7l/wheel/protenix-0.3.1.data/data 2024-12-17T09:54:27,553 running install_egg_info 2024-12-17T09:54:27,601 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.3.1-py3.11.egg-info 2024-12-17T09:54:27,613 running install_scripts 2024-12-17T09:54:27,633 creating build/bdist.linux-armv7l/wheel/protenix-0.3.1.dist-info/WHEEL 2024-12-17T09:54:27,636 creating '/tmp/pip-wheel-n8tz9v4l/protenix-0.3.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-12-17T09:54:27,638 adding 'configs/__init__.py' 2024-12-17T09:54:27,640 adding 'configs/configs_base.py' 2024-12-17T09:54:27,642 adding 'configs/configs_data.py' 2024-12-17T09:54:27,643 adding 'configs/configs_inference.py' 2024-12-17T09:54:27,645 adding 'protenix/__init__.py' 2024-12-17T09:54:27,646 adding 'protenix/config/__init__.py' 2024-12-17T09:54:27,648 adding 'protenix/config/config.py' 2024-12-17T09:54:27,649 adding 'protenix/config/extend_types.py' 2024-12-17T09:54:27,651 adding 'protenix/data/__init__.py' 2024-12-17T09:54:27,654 adding 'protenix/data/ccd.py' 2024-12-17T09:54:27,658 adding 'protenix/data/constants.py' 2024-12-17T09:54:27,660 adding 'protenix/data/data_pipeline.py' 2024-12-17T09:54:27,662 adding 'protenix/data/dataloader.py' 2024-12-17T09:54:27,667 adding 'protenix/data/dataset.py' 2024-12-17T09:54:27,671 adding 'protenix/data/featurizer.py' 2024-12-17T09:54:27,672 adding 'protenix/data/filter.py' 2024-12-17T09:54:27,674 adding 'protenix/data/infer_data_pipeline.py' 2024-12-17T09:54:27,676 adding 'protenix/data/json_maker.py' 2024-12-17T09:54:27,679 adding 'protenix/data/json_parser.py' 2024-12-17T09:54:27,681 adding 'protenix/data/json_to_feature.py' 2024-12-17T09:54:27,685 adding 'protenix/data/msa_featurizer.py' 2024-12-17T09:54:27,691 adding 'protenix/data/msa_utils.py' 2024-12-17T09:54:27,697 adding 'protenix/data/parser.py' 2024-12-17T09:54:27,699 adding 'protenix/data/substructure_perms.py' 2024-12-17T09:54:27,701 adding 'protenix/data/tokenizer.py' 2024-12-17T09:54:27,704 adding 'protenix/data/utils.py' 2024-12-17T09:54:27,706 adding 'protenix/metrics/__init__.py' 2024-12-17T09:54:27,707 adding 'protenix/metrics/clash.py' 2024-12-17T09:54:27,709 adding 'protenix/metrics/lddt_metrics.py' 2024-12-17T09:54:27,711 adding 'protenix/metrics/rmsd.py' 2024-12-17T09:54:27,713 adding 'protenix/model/__init__.py' 2024-12-17T09:54:27,715 adding 'protenix/model/generator.py' 2024-12-17T09:54:27,721 adding 'protenix/model/loss.py' 2024-12-17T09:54:27,725 adding 'protenix/model/protenix.py' 2024-12-17T09:54:27,728 adding 'protenix/model/sample_confidence.py' 2024-12-17T09:54:27,730 adding 'protenix/model/utils.py' 2024-12-17T09:54:27,732 adding 'protenix/model/layer_norm/__init__.py' 2024-12-17T09:54:27,733 adding 'protenix/model/layer_norm/layer_norm.py' 2024-12-17T09:54:27,735 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2024-12-17T09:54:27,737 adding 'protenix/model/layer_norm/kernel/compat.h' 2024-12-17T09:54:27,738 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2024-12-17T09:54:27,740 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2024-12-17T09:54:27,742 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2024-12-17T09:54:27,744 adding 'protenix/model/modules/__init__.py' 2024-12-17T09:54:27,746 adding 'protenix/model/modules/confidence.py' 2024-12-17T09:54:27,748 adding 'protenix/model/modules/diffusion.py' 2024-12-17T09:54:27,750 adding 'protenix/model/modules/embedders.py' 2024-12-17T09:54:27,752 adding 'protenix/model/modules/frames.py' 2024-12-17T09:54:27,753 adding 'protenix/model/modules/head.py' 2024-12-17T09:54:27,756 adding 'protenix/model/modules/pairformer.py' 2024-12-17T09:54:27,760 adding 'protenix/model/modules/primitives.py' 2024-12-17T09:54:27,763 adding 'protenix/model/modules/transformer.py' 2024-12-17T09:54:27,765 adding 'protenix/openfold_local/__init__.py' 2024-12-17T09:54:27,766 adding 'protenix/openfold_local/data/__init__.py' 2024-12-17T09:54:27,768 adding 'protenix/openfold_local/data/data_transforms.py' 2024-12-17T09:54:27,770 adding 'protenix/openfold_local/data/errors.py' 2024-12-17T09:54:27,772 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2024-12-17T09:54:27,773 adding 'protenix/openfold_local/data/msa_identifiers.py' 2024-12-17T09:54:27,776 adding 'protenix/openfold_local/data/msa_pairing.py' 2024-12-17T09:54:27,779 adding 'protenix/openfold_local/data/parsers.py' 2024-12-17T09:54:27,782 adding 'protenix/openfold_local/data/templates.py' 2024-12-17T09:54:27,784 adding 'protenix/openfold_local/data/tools/__init__.py' 2024-12-17T09:54:27,786 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2024-12-17T09:54:27,788 adding 'protenix/openfold_local/data/tools/utils.py' 2024-12-17T09:54:27,790 adding 'protenix/openfold_local/model/__init__.py' 2024-12-17T09:54:27,792 adding 'protenix/openfold_local/model/dropout.py' 2024-12-17T09:54:27,793 adding 'protenix/openfold_local/model/outer_product_mean.py' 2024-12-17T09:54:27,796 adding 'protenix/openfold_local/model/primitives.py' 2024-12-17T09:54:27,798 adding 'protenix/openfold_local/model/triangular_attention.py' 2024-12-17T09:54:27,802 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2024-12-17T09:54:27,804 adding 'protenix/openfold_local/np/__init__.py' 2024-12-17T09:54:27,809 adding 'protenix/openfold_local/np/residue_constants.py' 2024-12-17T09:54:27,813 adding 'protenix/openfold_local/utils/__init__.py' 2024-12-17T09:54:27,817 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2024-12-17T09:54:27,819 adding 'protenix/openfold_local/utils/checkpointing.py' 2024-12-17T09:54:27,823 adding 'protenix/openfold_local/utils/chunk_utils.py' 2024-12-17T09:54:27,826 adding 'protenix/openfold_local/utils/feats.py' 2024-12-17T09:54:27,829 adding 'protenix/openfold_local/utils/precision_utils.py' 2024-12-17T09:54:27,836 adding 'protenix/openfold_local/utils/rigid_utils.py' 2024-12-17T09:54:27,839 adding 'protenix/openfold_local/utils/tensor_utils.py' 2024-12-17T09:54:27,842 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2024-12-17T09:54:27,845 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2024-12-17T09:54:27,847 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2024-12-17T09:54:27,849 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2024-12-17T09:54:27,851 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2024-12-17T09:54:27,853 adding 'protenix/openfold_local/utils/geometry/utils.py' 2024-12-17T09:54:27,855 adding 'protenix/openfold_local/utils/geometry/vector.py' 2024-12-17T09:54:27,857 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2024-12-17T09:54:27,859 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2024-12-17T09:54:27,862 adding 'protenix/utils/__init__.py' 2024-12-17T09:54:27,867 adding 'protenix/utils/cropping.py' 2024-12-17T09:54:27,869 adding 'protenix/utils/distributed.py' 2024-12-17T09:54:27,872 adding 'protenix/utils/file_io.py' 2024-12-17T09:54:27,874 adding 'protenix/utils/geometry.py' 2024-12-17T09:54:27,877 adding 'protenix/utils/logger.py' 2024-12-17T09:54:27,879 adding 'protenix/utils/lr_scheduler.py' 2024-12-17T09:54:27,882 adding 'protenix/utils/metrics.py' 2024-12-17T09:54:27,885 adding 'protenix/utils/scatter_utils.py' 2024-12-17T09:54:27,887 adding 'protenix/utils/seed.py' 2024-12-17T09:54:27,889 adding 'protenix/utils/torch_utils.py' 2024-12-17T09:54:27,892 adding 'protenix/utils/training.py' 2024-12-17T09:54:27,894 adding 'protenix/utils/permutation/__init__.py' 2024-12-17T09:54:27,900 adding 'protenix/utils/permutation/atom_permutation.py' 2024-12-17T09:54:27,904 adding 'protenix/utils/permutation/permutation.py' 2024-12-17T09:54:27,907 adding 'protenix/utils/permutation/utils.py' 2024-12-17T09:54:27,910 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2024-12-17T09:54:27,915 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2024-12-17T09:54:27,917 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2024-12-17T09:54:27,918 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2024-12-17T09:54:27,921 adding 'protenix/web_service/__init__.py' 2024-12-17T09:54:27,923 adding 'protenix/web_service/colab_request_parser.py' 2024-12-17T09:54:27,924 adding 'protenix/web_service/colab_request_utils.py' 2024-12-17T09:54:27,926 adding 'protenix/web_service/dependency_url.py' 2024-12-17T09:54:27,928 adding 'protenix/web_service/prediction_visualization.py' 2024-12-17T09:54:27,930 adding 'protenix/web_service/viewer.py' 2024-12-17T09:54:27,932 adding 'protenix-0.3.1.data/data/requirements.txt' 2024-12-17T09:54:27,935 adding 'runner/__init__.py' 2024-12-17T09:54:27,937 adding 'runner/batch_inference.py' 2024-12-17T09:54:27,939 adding 'runner/dumper.py' 2024-12-17T09:54:27,940 adding 'runner/ema.py' 2024-12-17T09:54:27,942 adding 'runner/inference.py' 2024-12-17T09:54:27,944 adding 'runner/msa_search.py' 2024-12-17T09:54:27,947 adding 'runner/train.py' 2024-12-17T09:54:27,949 adding 'protenix-0.3.1.dist-info/LICENSE' 2024-12-17T09:54:27,950 adding 'protenix-0.3.1.dist-info/METADATA' 2024-12-17T09:54:27,951 adding 'protenix-0.3.1.dist-info/WHEEL' 2024-12-17T09:54:27,952 adding 'protenix-0.3.1.dist-info/entry_points.txt' 2024-12-17T09:54:27,953 adding 'protenix-0.3.1.dist-info/top_level.txt' 2024-12-17T09:54:27,955 adding 'protenix-0.3.1.dist-info/RECORD' 2024-12-17T09:54:27,963 removing build/bdist.linux-armv7l/wheel 2024-12-17T09:54:28,110 Building wheel for protenix (setup.py): finished with status 'done' 2024-12-17T09:54:28,117 Created wheel for protenix: filename=protenix-0.3.1-py3-none-any.whl size=382724 sha256=624b9eaf9450baa3748fbe7d038a393ab59d36d7b191a70d676d592c81f46d1f 2024-12-17T09:54:28,118 Stored in directory: /tmp/pip-ephem-wheel-cache-rojwduc4/wheels/80/34/11/063d45a7a74abed199d1db0c2fb9ee33669ac83322574dd6a6 2024-12-17T09:54:28,132 Successfully built protenix 2024-12-17T09:54:28,146 Removed build tracker: '/tmp/pip-build-tracker-zwemsl07'