2024-12-11T18:36:08,329 Created temporary directory: /tmp/pip-build-tracker-k7pwwe5j 2024-12-11T18:36:08,331 Initialized build tracking at /tmp/pip-build-tracker-k7pwwe5j 2024-12-11T18:36:08,331 Created build tracker: /tmp/pip-build-tracker-k7pwwe5j 2024-12-11T18:36:08,332 Entered build tracker: /tmp/pip-build-tracker-k7pwwe5j 2024-12-11T18:36:08,333 Created temporary directory: /tmp/pip-wheel-7s0ffp8u 2024-12-11T18:36:08,337 Created temporary directory: /tmp/pip-ephem-wheel-cache-fur2q86x 2024-12-11T18:36:08,381 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-12-11T18:36:08,384 2 location(s) to search for versions of protenix: 2024-12-11T18:36:08,384 * https://pypi.org/simple/protenix/ 2024-12-11T18:36:08,384 * https://www.piwheels.org/simple/protenix/ 2024-12-11T18:36:08,385 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2024-12-11T18:36:08,385 Getting page https://pypi.org/simple/protenix/ 2024-12-11T18:36:08,387 Found index url https://pypi.org/simple/ 2024-12-11T18:36:08,533 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2024-12-11T18:36:08,536 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/) 2024-12-11T18:36:08,537 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/) 2024-12-11T18:36:08,537 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 2024-12-11T18:36:08,538 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) 2024-12-11T18:36:08,539 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 2024-12-11T18:36:08,540 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) 2024-12-11T18:36:08,541 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 2024-12-11T18:36:08,542 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) 2024-12-11T18:36:08,543 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 2024-12-11T18:36:08,544 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) 2024-12-11T18:36:08,544 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 2024-12-11T18:36:08,545 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2024-12-11T18:36:08,546 Getting page https://www.piwheels.org/simple/protenix/ 2024-12-11T18:36:08,547 Found index url https://www.piwheels.org/simple/ 2024-12-11T18:36:08,711 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2024-12-11T18:36:08,713 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) 2024-12-11T18:36:08,714 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) 2024-12-11T18:36:08,714 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) 2024-12-11T18:36:08,715 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/) 2024-12-11T18:36:08,715 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2024-12-11T18:36:08,715 Skipping link: not a file: https://pypi.org/simple/protenix/ 2024-12-11T18:36:08,735 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2024-12-11T18:36:08,737 Collecting protenix==0.1.3 2024-12-11T18:36:08,739 Created temporary directory: /tmp/pip-unpack-li1xktuq 2024-12-11T18:36:08,959 Downloading protenix-0.1.3.tar.gz (308 kB) 2024-12-11T18:36:09,318 Added protenix==0.1.3 from https://files.pythonhosted.org/packages/2c/1c/0788760bb4cd6bae9edc74ef1341e9cc74ad6190b8b5dbd972a361184b97/protenix-0.1.3.tar.gz to build tracker '/tmp/pip-build-tracker-k7pwwe5j' 2024-12-11T18:36:09,320 Running setup.py (path:/tmp/pip-wheel-7s0ffp8u/protenix_6d92cb65784949cfa31f019f5595cadc/setup.py) egg_info for package protenix 2024-12-11T18:36:09,321 Created temporary directory: /tmp/pip-pip-egg-info-5vzd_pdb 2024-12-11T18:36:09,322 Preparing metadata (setup.py): started 2024-12-11T18:36:09,323 Running command python setup.py egg_info 2024-12-11T18:36:10,438 running egg_info 2024-12-11T18:36:10,466 creating /tmp/pip-pip-egg-info-5vzd_pdb/protenix.egg-info 2024-12-11T18:36:10,467 writing /tmp/pip-pip-egg-info-5vzd_pdb/protenix.egg-info/PKG-INFO 2024-12-11T18:36:10,471 writing dependency_links to /tmp/pip-pip-egg-info-5vzd_pdb/protenix.egg-info/dependency_links.txt 2024-12-11T18:36:10,472 writing entry points to /tmp/pip-pip-egg-info-5vzd_pdb/protenix.egg-info/entry_points.txt 2024-12-11T18:36:10,474 writing requirements to /tmp/pip-pip-egg-info-5vzd_pdb/protenix.egg-info/requires.txt 2024-12-11T18:36:10,476 writing top-level names to /tmp/pip-pip-egg-info-5vzd_pdb/protenix.egg-info/top_level.txt 2024-12-11T18:36:10,477 writing manifest file '/tmp/pip-pip-egg-info-5vzd_pdb/protenix.egg-info/SOURCES.txt' 2024-12-11T18:36:10,586 reading manifest file '/tmp/pip-pip-egg-info-5vzd_pdb/protenix.egg-info/SOURCES.txt' 2024-12-11T18:36:10,587 adding license file 'LICENSE' 2024-12-11T18:36:10,593 writing manifest file '/tmp/pip-pip-egg-info-5vzd_pdb/protenix.egg-info/SOURCES.txt' 2024-12-11T18:36:10,702 Preparing metadata (setup.py): finished with status 'done' 2024-12-11T18:36:10,709 Source in /tmp/pip-wheel-7s0ffp8u/protenix_6d92cb65784949cfa31f019f5595cadc has version 0.1.3, which satisfies requirement protenix==0.1.3 from https://files.pythonhosted.org/packages/2c/1c/0788760bb4cd6bae9edc74ef1341e9cc74ad6190b8b5dbd972a361184b97/protenix-0.1.3.tar.gz 2024-12-11T18:36:10,710 Removed protenix==0.1.3 from https://files.pythonhosted.org/packages/2c/1c/0788760bb4cd6bae9edc74ef1341e9cc74ad6190b8b5dbd972a361184b97/protenix-0.1.3.tar.gz from build tracker '/tmp/pip-build-tracker-k7pwwe5j' 2024-12-11T18:36:10,719 Created temporary directory: /tmp/pip-unpack-3jfa5q62 2024-12-11T18:36:10,720 Created temporary directory: /tmp/pip-unpack-izd45pc8 2024-12-11T18:36:10,721 Building wheels for collected packages: protenix 2024-12-11T18:36:10,725 Created temporary directory: /tmp/pip-wheel-2obdfng1 2024-12-11T18:36:10,726 Building wheel for protenix (setup.py): started 2024-12-11T18:36:10,727 Destination directory: /tmp/pip-wheel-2obdfng1 2024-12-11T18:36:10,727 Running command python setup.py bdist_wheel 2024-12-11T18:36:11,742 running bdist_wheel 2024-12-11T18:36:11,873 running build 2024-12-11T18:36:11,874 running build_py 2024-12-11T18:36:11,903 creating build/lib/runner 2024-12-11T18:36:11,905 copying runner/batch_inference.py -> build/lib/runner 2024-12-11T18:36:11,907 copying runner/inference.py -> build/lib/runner 2024-12-11T18:36:11,910 copying runner/ema.py -> build/lib/runner 2024-12-11T18:36:11,912 copying runner/train.py -> build/lib/runner 2024-12-11T18:36:11,915 copying runner/dumper.py -> build/lib/runner 2024-12-11T18:36:11,917 copying runner/__init__.py -> build/lib/runner 2024-12-11T18:36:11,919 creating build/lib/configs 2024-12-11T18:36:11,920 copying configs/configs_inference.py -> build/lib/configs 2024-12-11T18:36:11,922 copying configs/configs_base.py -> build/lib/configs 2024-12-11T18:36:11,925 copying configs/configs_data.py -> build/lib/configs 2024-12-11T18:36:11,927 copying configs/__init__.py -> build/lib/configs 2024-12-11T18:36:11,929 creating build/lib/protenix 2024-12-11T18:36:11,930 copying protenix/__init__.py -> build/lib/protenix 2024-12-11T18:36:11,933 creating build/lib/protenix/data 2024-12-11T18:36:11,934 copying protenix/data/utils.py -> build/lib/protenix/data 2024-12-11T18:36:11,936 copying protenix/data/dataset.py -> build/lib/protenix/data 2024-12-11T18:36:11,939 copying protenix/data/ccd.py -> build/lib/protenix/data 2024-12-11T18:36:11,942 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2024-12-11T18:36:11,945 copying protenix/data/json_maker.py -> build/lib/protenix/data 2024-12-11T18:36:11,947 copying protenix/data/filter.py -> build/lib/protenix/data 2024-12-11T18:36:11,949 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2024-12-11T18:36:11,952 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2024-12-11T18:36:11,954 copying protenix/data/json_parser.py -> build/lib/protenix/data 2024-12-11T18:36:11,957 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2024-12-11T18:36:11,959 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2024-12-11T18:36:11,962 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2024-12-11T18:36:11,964 copying protenix/data/dataloader.py -> build/lib/protenix/data 2024-12-11T18:36:11,967 copying protenix/data/featurizer.py -> build/lib/protenix/data 2024-12-11T18:36:11,970 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2024-12-11T18:36:11,972 copying protenix/data/__init__.py -> build/lib/protenix/data 2024-12-11T18:36:11,974 copying protenix/data/constants.py -> build/lib/protenix/data 2024-12-11T18:36:11,977 copying protenix/data/parser.py -> build/lib/protenix/data 2024-12-11T18:36:11,980 creating build/lib/protenix/web_service 2024-12-11T18:36:11,981 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2024-12-11T18:36:11,984 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2024-12-11T18:36:11,986 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2024-12-11T18:36:11,988 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2024-12-11T18:36:11,991 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2024-12-11T18:36:11,993 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2024-12-11T18:36:11,995 creating build/lib/protenix/model 2024-12-11T18:36:11,996 copying protenix/model/utils.py -> build/lib/protenix/model 2024-12-11T18:36:11,999 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2024-12-11T18:36:12,002 copying protenix/model/loss.py -> build/lib/protenix/model 2024-12-11T18:36:12,005 copying protenix/model/generator.py -> build/lib/protenix/model 2024-12-11T18:36:12,007 copying protenix/model/protenix.py -> build/lib/protenix/model 2024-12-11T18:36:12,010 copying protenix/model/__init__.py -> build/lib/protenix/model 2024-12-11T18:36:12,012 creating build/lib/protenix/config 2024-12-11T18:36:12,013 copying protenix/config/config.py -> build/lib/protenix/config 2024-12-11T18:36:12,015 copying protenix/config/extend_types.py -> build/lib/protenix/config 2024-12-11T18:36:12,017 copying protenix/config/__init__.py -> build/lib/protenix/config 2024-12-11T18:36:12,019 creating build/lib/protenix/utils 2024-12-11T18:36:12,021 copying protenix/utils/logger.py -> build/lib/protenix/utils 2024-12-11T18:36:12,023 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2024-12-11T18:36:12,025 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2024-12-11T18:36:12,026 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2024-12-11T18:36:12,028 copying protenix/utils/seed.py -> build/lib/protenix/utils 2024-12-11T18:36:12,030 copying protenix/utils/training.py -> build/lib/protenix/utils 2024-12-11T18:36:12,032 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2024-12-11T18:36:12,034 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2024-12-11T18:36:12,037 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2024-12-11T18:36:12,039 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2024-12-11T18:36:12,041 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2024-12-11T18:36:12,042 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2024-12-11T18:36:12,045 creating build/lib/protenix/openfold_local 2024-12-11T18:36:12,046 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2024-12-11T18:36:12,049 creating build/lib/protenix/metrics 2024-12-11T18:36:12,050 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2024-12-11T18:36:12,052 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2024-12-11T18:36:12,055 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2024-12-11T18:36:12,057 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2024-12-11T18:36:12,059 creating build/lib/protenix/model/modules 2024-12-11T18:36:12,060 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2024-12-11T18:36:12,062 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2024-12-11T18:36:12,065 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2024-12-11T18:36:12,068 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2024-12-11T18:36:12,069 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2024-12-11T18:36:12,073 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2024-12-11T18:36:12,075 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2024-12-11T18:36:12,078 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2024-12-11T18:36:12,081 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2024-12-11T18:36:12,083 creating build/lib/protenix/model/layer_norm 2024-12-11T18:36:12,084 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2024-12-11T18:36:12,086 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2024-12-11T18:36:12,088 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2024-12-11T18:36:12,090 creating build/lib/protenix/utils/permutation 2024-12-11T18:36:12,091 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2024-12-11T18:36:12,094 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2024-12-11T18:36:12,096 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2024-12-11T18:36:12,099 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2024-12-11T18:36:12,101 creating build/lib/protenix/utils/permutation/chain_permutation 2024-12-11T18:36:12,102 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-11T18:36:12,104 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-11T18:36:12,107 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-11T18:36:12,109 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-11T18:36:12,112 creating build/lib/protenix/openfold_local/np 2024-12-11T18:36:12,113 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2024-12-11T18:36:12,116 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2024-12-11T18:36:12,118 creating build/lib/protenix/openfold_local/data 2024-12-11T18:36:12,119 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:36:12,122 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:36:12,124 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:36:12,126 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:36:12,128 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:36:12,131 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:36:12,133 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:36:12,136 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:36:12,138 creating build/lib/protenix/openfold_local/model 2024-12-11T18:36:12,139 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2024-12-11T18:36:12,141 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2024-12-11T18:36:12,144 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2024-12-11T18:36:12,147 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2024-12-11T18:36:12,149 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2024-12-11T18:36:12,152 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2024-12-11T18:36:12,154 creating build/lib/protenix/openfold_local/utils 2024-12-11T18:36:12,156 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:36:12,159 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:36:12,161 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:36:12,163 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:36:12,166 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:36:12,169 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:36:12,172 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:36:12,174 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:36:12,176 creating build/lib/protenix/openfold_local/data/tools 2024-12-11T18:36:12,178 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2024-12-11T18:36:12,180 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2024-12-11T18:36:12,182 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2024-12-11T18:36:12,185 creating build/lib/protenix/openfold_local/utils/kernel 2024-12-11T18:36:12,186 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2024-12-11T18:36:12,188 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2024-12-11T18:36:12,190 creating build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,192 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,194 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,196 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,198 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,201 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,203 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,205 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,207 running egg_info 2024-12-11T18:36:12,238 writing protenix.egg-info/PKG-INFO 2024-12-11T18:36:12,242 writing dependency_links to protenix.egg-info/dependency_links.txt 2024-12-11T18:36:12,243 writing entry points to protenix.egg-info/entry_points.txt 2024-12-11T18:36:12,245 writing requirements to protenix.egg-info/requires.txt 2024-12-11T18:36:12,247 writing top-level names to protenix.egg-info/top_level.txt 2024-12-11T18:36:12,295 reading manifest file 'protenix.egg-info/SOURCES.txt' 2024-12-11T18:36:12,303 adding license file 'LICENSE' 2024-12-11T18:36:12,311 writing manifest file 'protenix.egg-info/SOURCES.txt' 2024-12-11T18:36:12,315 /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. 2024-12-11T18:36:12,315 !! 2024-12-11T18:36:12,316 ******************************************************************************** 2024-12-11T18:36:12,317 ############################ 2024-12-11T18:36:12,317 # Package would be ignored # 2024-12-11T18:36:12,318 ############################ 2024-12-11T18:36:12,318 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2024-12-11T18:36:12,319 but it is absent from setuptools' `packages` configuration. 2024-12-11T18:36:12,320 This leads to an ambiguous overall configuration. If you want to distribute this 2024-12-11T18:36:12,321 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2024-12-11T18:36:12,321 to the `packages` configuration field. 2024-12-11T18:36:12,322 Alternatively, you can also rely on setuptools' discovery methods 2024-12-11T18:36:12,323 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-12-11T18:36:12,324 instead of `find_packages(...)`/`find:`). 2024-12-11T18:36:12,325 You can read more about "package discovery" on setuptools documentation page: 2024-12-11T18:36:12,326 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-12-11T18:36:12,326 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2024-12-11T18:36:12,327 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2024-12-11T18:36:12,327 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-12-11T18:36:12,327 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-12-11T18:36:12,328 combination with a more fine grained `package-data` configuration. 2024-12-11T18:36:12,329 You can read more about "package data files" on setuptools documentation page: 2024-12-11T18:36:12,330 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-12-11T18:36:12,331 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-12-11T18:36:12,332 even if it does not contain any `.py` files. 2024-12-11T18:36:12,332 On the other hand, currently there is no concept of package data 2024-12-11T18:36:12,333 directory, all directories are treated like packages. 2024-12-11T18:36:12,333 ******************************************************************************** 2024-12-11T18:36:12,334 !! 2024-12-11T18:36:12,334 check.warn(importable) 2024-12-11T18:36:12,340 creating build/lib/protenix/model/layer_norm/kernel 2024-12-11T18:36:12,342 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2024-12-11T18:36:12,345 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2024-12-11T18:36:12,348 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2024-12-11T18:36:12,350 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2024-12-11T18:36:12,390 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-12-11T18:36:12,390 !! 2024-12-11T18:36:12,391 ******************************************************************************** 2024-12-11T18:36:12,392 Please avoid running ``setup.py`` directly. 2024-12-11T18:36:12,393 Instead, use pypa/build, pypa/installer or other 2024-12-11T18:36:12,393 standards-based tools. 2024-12-11T18:36:12,394 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-12-11T18:36:12,395 ******************************************************************************** 2024-12-11T18:36:12,396 !! 2024-12-11T18:36:12,397 self.initialize_options() 2024-12-11T18:36:12,417 installing to build/bdist.linux-armv7l/wheel 2024-12-11T18:36:12,417 running install 2024-12-11T18:36:12,442 running install_lib 2024-12-11T18:36:12,469 creating build/bdist.linux-armv7l/wheel 2024-12-11T18:36:12,471 creating build/bdist.linux-armv7l/wheel/runner 2024-12-11T18:36:12,473 copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-11T18:36:12,475 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-11T18:36:12,478 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-11T18:36:12,480 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-11T18:36:12,483 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-11T18:36:12,485 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-11T18:36:12,487 creating build/bdist.linux-armv7l/wheel/configs 2024-12-11T18:36:12,489 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-11T18:36:12,491 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-11T18:36:12,493 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-11T18:36:12,495 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-11T18:36:12,497 creating build/bdist.linux-armv7l/wheel/protenix 2024-12-11T18:36:12,499 creating build/bdist.linux-armv7l/wheel/protenix/data 2024-12-11T18:36:12,500 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,503 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,506 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,508 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,511 copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,513 copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,515 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,518 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,520 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,523 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,525 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,527 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,530 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,532 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,535 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,537 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,538 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,541 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:36:12,546 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2024-12-11T18:36:12,547 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-11T18:36:12,550 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-11T18:36:12,551 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-11T18:36:12,554 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-11T18:36:12,556 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-11T18:36:12,558 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-11T18:36:12,560 creating build/bdist.linux-armv7l/wheel/protenix/model 2024-12-11T18:36:12,562 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-11T18:36:12,564 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-11T18:36:12,567 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-11T18:36:12,571 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2024-12-11T18:36:12,572 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:36:12,574 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:36:12,577 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:36:12,579 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:36:12,581 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:36:12,584 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:36:12,587 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:36:12,590 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:36:12,592 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:36:12,594 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2024-12-11T18:36:12,595 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-11T18:36:12,597 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-11T18:36:12,600 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2024-12-11T18:36:12,601 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-11T18:36:12,604 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-11T18:36:12,606 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-11T18:36:12,608 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-11T18:36:12,610 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-11T18:36:12,613 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-11T18:36:12,615 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-11T18:36:12,618 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-11T18:36:12,620 creating build/bdist.linux-armv7l/wheel/protenix/config 2024-12-11T18:36:12,621 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-11T18:36:12,623 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-11T18:36:12,625 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-11T18:36:12,627 creating build/bdist.linux-armv7l/wheel/protenix/utils 2024-12-11T18:36:12,629 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:36:12,631 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:36:12,633 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:36:12,635 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:36:12,637 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:36:12,639 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:36:12,641 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:36:12,643 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:36:12,646 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:36:12,647 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:36:12,649 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:36:12,651 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:36:12,653 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2024-12-11T18:36:12,655 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-11T18:36:12,658 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2024-12-11T18:36:12,659 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-11T18:36:12,661 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-11T18:36:12,663 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-11T18:36:12,666 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-11T18:36:12,668 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-11T18:36:12,670 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-11T18:36:12,673 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-11T18:36:12,675 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2024-12-11T18:36:12,677 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2024-12-11T18:36:12,678 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-12-11T18:36:12,681 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-12-11T18:36:12,683 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2024-12-11T18:36:12,684 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:36:12,687 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:36:12,689 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:36:12,691 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:36:12,693 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:36:12,696 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2024-12-11T18:36:12,697 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-11T18:36:12,699 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-11T18:36:12,702 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-11T18:36:12,703 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:36:12,705 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:36:12,708 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:36:12,710 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2024-12-11T18:36:12,711 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-11T18:36:12,713 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-11T18:36:12,715 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-11T18:36:12,718 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-11T18:36:12,720 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-11T18:36:12,722 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-11T18:36:12,725 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2024-12-11T18:36:12,726 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:36:12,728 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:36:12,730 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:36:12,732 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:36:12,736 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:36:12,738 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:36:12,741 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2024-12-11T18:36:12,742 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-12-11T18:36:12,744 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-12-11T18:36:12,746 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:36:12,747 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:36:12,750 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,751 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,753 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,755 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,757 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,759 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,761 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,763 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:36:12,765 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2024-12-11T18:36:12,767 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2024-12-11T18:36:12,769 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2024-12-11T18:36:12,770 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-11T18:36:12,772 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-11T18:36:12,774 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-11T18:36:12,777 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-11T18:36:12,778 running install_data 2024-12-11T18:36:12,810 creating build/bdist.linux-armv7l/wheel/protenix-0.1.3.data/data 2024-12-11T18:36:12,812 warning: install_data: setup script did not provide a directory for 'requirements.txt' -- installing right in 'build/bdist.linux-armv7l/wheel/protenix-0.1.3.data/data' 2024-12-11T18:36:12,813 copying requirements.txt -> build/bdist.linux-armv7l/wheel/protenix-0.1.3.data/data 2024-12-11T18:36:12,814 running install_egg_info 2024-12-11T18:36:12,849 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.1.3-py3.11.egg-info 2024-12-11T18:36:12,860 running install_scripts 2024-12-11T18:36:12,880 creating build/bdist.linux-armv7l/wheel/protenix-0.1.3.dist-info/WHEEL 2024-12-11T18:36:12,883 creating '/tmp/pip-wheel-2obdfng1/protenix-0.1.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-12-11T18:36:12,885 adding 'configs/__init__.py' 2024-12-11T18:36:12,887 adding 'configs/configs_base.py' 2024-12-11T18:36:12,889 adding 'configs/configs_data.py' 2024-12-11T18:36:12,890 adding 'configs/configs_inference.py' 2024-12-11T18:36:12,892 adding 'protenix/__init__.py' 2024-12-11T18:36:12,894 adding 'protenix/config/__init__.py' 2024-12-11T18:36:12,896 adding 'protenix/config/config.py' 2024-12-11T18:36:12,897 adding 'protenix/config/extend_types.py' 2024-12-11T18:36:12,899 adding 'protenix/data/__init__.py' 2024-12-11T18:36:12,902 adding 'protenix/data/ccd.py' 2024-12-11T18:36:12,906 adding 'protenix/data/constants.py' 2024-12-11T18:36:12,908 adding 'protenix/data/data_pipeline.py' 2024-12-11T18:36:12,910 adding 'protenix/data/dataloader.py' 2024-12-11T18:36:12,916 adding 'protenix/data/dataset.py' 2024-12-11T18:36:12,920 adding 'protenix/data/featurizer.py' 2024-12-11T18:36:12,922 adding 'protenix/data/filter.py' 2024-12-11T18:36:12,923 adding 'protenix/data/infer_data_pipeline.py' 2024-12-11T18:36:12,926 adding 'protenix/data/json_maker.py' 2024-12-11T18:36:12,929 adding 'protenix/data/json_parser.py' 2024-12-11T18:36:12,931 adding 'protenix/data/json_to_feature.py' 2024-12-11T18:36:12,935 adding 'protenix/data/msa_featurizer.py' 2024-12-11T18:36:12,941 adding 'protenix/data/msa_utils.py' 2024-12-11T18:36:12,947 adding 'protenix/data/parser.py' 2024-12-11T18:36:12,949 adding 'protenix/data/substructure_perms.py' 2024-12-11T18:36:12,950 adding 'protenix/data/tokenizer.py' 2024-12-11T18:36:12,953 adding 'protenix/data/utils.py' 2024-12-11T18:36:12,955 adding 'protenix/metrics/__init__.py' 2024-12-11T18:36:12,956 adding 'protenix/metrics/clash.py' 2024-12-11T18:36:12,958 adding 'protenix/metrics/lddt_metrics.py' 2024-12-11T18:36:12,960 adding 'protenix/metrics/rmsd.py' 2024-12-11T18:36:12,961 adding 'protenix/model/__init__.py' 2024-12-11T18:36:12,963 adding 'protenix/model/generator.py' 2024-12-11T18:36:12,969 adding 'protenix/model/loss.py' 2024-12-11T18:36:12,972 adding 'protenix/model/protenix.py' 2024-12-11T18:36:12,975 adding 'protenix/model/sample_confidence.py' 2024-12-11T18:36:12,978 adding 'protenix/model/utils.py' 2024-12-11T18:36:12,980 adding 'protenix/model/layer_norm/__init__.py' 2024-12-11T18:36:12,981 adding 'protenix/model/layer_norm/layer_norm.py' 2024-12-11T18:36:12,982 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2024-12-11T18:36:12,984 adding 'protenix/model/layer_norm/kernel/compat.h' 2024-12-11T18:36:12,985 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2024-12-11T18:36:12,988 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2024-12-11T18:36:12,990 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2024-12-11T18:36:12,991 adding 'protenix/model/modules/__init__.py' 2024-12-11T18:36:12,993 adding 'protenix/model/modules/confidence.py' 2024-12-11T18:36:12,996 adding 'protenix/model/modules/diffusion.py' 2024-12-11T18:36:12,998 adding 'protenix/model/modules/embedders.py' 2024-12-11T18:36:12,999 adding 'protenix/model/modules/frames.py' 2024-12-11T18:36:13,000 adding 'protenix/model/modules/head.py' 2024-12-11T18:36:13,003 adding 'protenix/model/modules/pairformer.py' 2024-12-11T18:36:13,007 adding 'protenix/model/modules/primitives.py' 2024-12-11T18:36:13,010 adding 'protenix/model/modules/transformer.py' 2024-12-11T18:36:13,012 adding 'protenix/openfold_local/__init__.py' 2024-12-11T18:36:13,014 adding 'protenix/openfold_local/data/__init__.py' 2024-12-11T18:36:13,015 adding 'protenix/openfold_local/data/data_transforms.py' 2024-12-11T18:36:13,017 adding 'protenix/openfold_local/data/errors.py' 2024-12-11T18:36:13,019 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2024-12-11T18:36:13,021 adding 'protenix/openfold_local/data/msa_identifiers.py' 2024-12-11T18:36:13,023 adding 'protenix/openfold_local/data/msa_pairing.py' 2024-12-11T18:36:13,026 adding 'protenix/openfold_local/data/parsers.py' 2024-12-11T18:36:13,029 adding 'protenix/openfold_local/data/templates.py' 2024-12-11T18:36:13,031 adding 'protenix/openfold_local/data/tools/__init__.py' 2024-12-11T18:36:13,033 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2024-12-11T18:36:13,034 adding 'protenix/openfold_local/data/tools/utils.py' 2024-12-11T18:36:13,036 adding 'protenix/openfold_local/model/__init__.py' 2024-12-11T18:36:13,037 adding 'protenix/openfold_local/model/dropout.py' 2024-12-11T18:36:13,039 adding 'protenix/openfold_local/model/outer_product_mean.py' 2024-12-11T18:36:13,042 adding 'protenix/openfold_local/model/primitives.py' 2024-12-11T18:36:13,043 adding 'protenix/openfold_local/model/triangular_attention.py' 2024-12-11T18:36:13,046 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2024-12-11T18:36:13,047 adding 'protenix/openfold_local/np/__init__.py' 2024-12-11T18:36:13,052 adding 'protenix/openfold_local/np/residue_constants.py' 2024-12-11T18:36:13,054 adding 'protenix/openfold_local/utils/__init__.py' 2024-12-11T18:36:13,057 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2024-12-11T18:36:13,058 adding 'protenix/openfold_local/utils/checkpointing.py' 2024-12-11T18:36:13,061 adding 'protenix/openfold_local/utils/chunk_utils.py' 2024-12-11T18:36:13,062 adding 'protenix/openfold_local/utils/feats.py' 2024-12-11T18:36:13,064 adding 'protenix/openfold_local/utils/precision_utils.py' 2024-12-11T18:36:13,068 adding 'protenix/openfold_local/utils/rigid_utils.py' 2024-12-11T18:36:13,070 adding 'protenix/openfold_local/utils/tensor_utils.py' 2024-12-11T18:36:13,071 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2024-12-11T18:36:13,073 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2024-12-11T18:36:13,074 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2024-12-11T18:36:13,075 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2024-12-11T18:36:13,077 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2024-12-11T18:36:13,078 adding 'protenix/openfold_local/utils/geometry/utils.py' 2024-12-11T18:36:13,079 adding 'protenix/openfold_local/utils/geometry/vector.py' 2024-12-11T18:36:13,081 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2024-12-11T18:36:13,082 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2024-12-11T18:36:13,084 adding 'protenix/utils/__init__.py' 2024-12-11T18:36:13,087 adding 'protenix/utils/cropping.py' 2024-12-11T18:36:13,088 adding 'protenix/utils/distributed.py' 2024-12-11T18:36:13,090 adding 'protenix/utils/file_io.py' 2024-12-11T18:36:13,091 adding 'protenix/utils/geometry.py' 2024-12-11T18:36:13,093 adding 'protenix/utils/logger.py' 2024-12-11T18:36:13,094 adding 'protenix/utils/lr_scheduler.py' 2024-12-11T18:36:13,095 adding 'protenix/utils/metrics.py' 2024-12-11T18:36:13,097 adding 'protenix/utils/scatter_utils.py' 2024-12-11T18:36:13,098 adding 'protenix/utils/seed.py' 2024-12-11T18:36:13,100 adding 'protenix/utils/torch_utils.py' 2024-12-11T18:36:13,101 adding 'protenix/utils/training.py' 2024-12-11T18:36:13,104 adding 'protenix/utils/permutation/__init__.py' 2024-12-11T18:36:13,109 adding 'protenix/utils/permutation/atom_permutation.py' 2024-12-11T18:36:13,112 adding 'protenix/utils/permutation/permutation.py' 2024-12-11T18:36:13,114 adding 'protenix/utils/permutation/utils.py' 2024-12-11T18:36:13,117 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2024-12-11T18:36:13,123 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2024-12-11T18:36:13,125 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2024-12-11T18:36:13,127 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2024-12-11T18:36:13,129 adding 'protenix/web_service/__init__.py' 2024-12-11T18:36:13,132 adding 'protenix/web_service/colab_request_parser.py' 2024-12-11T18:36:13,134 adding 'protenix/web_service/colab_request_utils.py' 2024-12-11T18:36:13,136 adding 'protenix/web_service/dependency_url.py' 2024-12-11T18:36:13,138 adding 'protenix/web_service/prediction_visualization.py' 2024-12-11T18:36:13,141 adding 'protenix/web_service/viewer.py' 2024-12-11T18:36:13,144 adding 'protenix-0.1.3.data/data/requirements.txt' 2024-12-11T18:36:13,147 adding 'runner/__init__.py' 2024-12-11T18:36:13,150 adding 'runner/batch_inference.py' 2024-12-11T18:36:13,152 adding 'runner/dumper.py' 2024-12-11T18:36:13,154 adding 'runner/ema.py' 2024-12-11T18:36:13,156 adding 'runner/inference.py' 2024-12-11T18:36:13,160 adding 'runner/train.py' 2024-12-11T18:36:13,164 adding 'protenix-0.1.3.dist-info/LICENSE' 2024-12-11T18:36:13,166 adding 'protenix-0.1.3.dist-info/METADATA' 2024-12-11T18:36:13,167 adding 'protenix-0.1.3.dist-info/WHEEL' 2024-12-11T18:36:13,168 adding 'protenix-0.1.3.dist-info/entry_points.txt' 2024-12-11T18:36:13,169 adding 'protenix-0.1.3.dist-info/top_level.txt' 2024-12-11T18:36:13,173 adding 'protenix-0.1.3.dist-info/RECORD' 2024-12-11T18:36:13,182 removing build/bdist.linux-armv7l/wheel 2024-12-11T18:36:13,330 Building wheel for protenix (setup.py): finished with status 'done' 2024-12-11T18:36:13,336 Created wheel for protenix: filename=protenix-0.1.3-py3-none-any.whl size=382258 sha256=be21c60c572799c5562933a71a3087ae1441533805771913e77578fc6280e314 2024-12-11T18:36:13,338 Stored in directory: /tmp/pip-ephem-wheel-cache-fur2q86x/wheels/40/67/5f/dd3a9e3824e0ecee8d1609347246fe48f894294184e7d831d9 2024-12-11T18:36:13,352 Successfully built protenix 2024-12-11T18:36:13,369 Removed build tracker: '/tmp/pip-build-tracker-k7pwwe5j'