2024-12-23T04:24:40,945 Created temporary directory: /tmp/pip-build-tracker-1951jpw_ 2024-12-23T04:24:40,946 Initialized build tracking at /tmp/pip-build-tracker-1951jpw_ 2024-12-23T04:24:40,947 Created build tracker: /tmp/pip-build-tracker-1951jpw_ 2024-12-23T04:24:40,947 Entered build tracker: /tmp/pip-build-tracker-1951jpw_ 2024-12-23T04:24:40,948 Created temporary directory: /tmp/pip-wheel-tgk0h8gd 2024-12-23T04:24:40,952 Created temporary directory: /tmp/pip-ephem-wheel-cache-b2se2epu 2024-12-23T04:24:40,996 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-12-23T04:24:40,999 2 location(s) to search for versions of protenix: 2024-12-23T04:24:40,999 * https://pypi.org/simple/protenix/ 2024-12-23T04:24:40,999 * https://www.piwheels.org/simple/protenix/ 2024-12-23T04:24:41,000 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2024-12-23T04:24:41,001 Getting page https://pypi.org/simple/protenix/ 2024-12-23T04:24:41,002 Found index url https://pypi.org/simple/ 2024-12-23T04:24:41,222 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2024-12-23T04:24:41,227 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/) 2024-12-23T04:24:41,227 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/) 2024-12-23T04:24:41,228 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 2024-12-23T04:24:41,229 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) 2024-12-23T04:24:41,230 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 2024-12-23T04:24:41,230 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) 2024-12-23T04:24:41,231 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 2024-12-23T04:24:41,232 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) 2024-12-23T04:24:41,233 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 2024-12-23T04:24:41,234 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) 2024-12-23T04:24:41,234 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 2024-12-23T04:24:41,235 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) 2024-12-23T04:24:41,236 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 2024-12-23T04:24:41,237 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) 2024-12-23T04:24:41,237 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 2024-12-23T04:24:41,238 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) 2024-12-23T04:24:41,239 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 2024-12-23T04:24:41,239 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/6d/11/4c2946b935b56d995c7418cfc783c16e9e647de72a34380c42e573d4b28d/protenix-0.3.2-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2024-12-23T04:24:41,240 Found link https://files.pythonhosted.org/packages/65/48/25fdef4629cd5ce68c65f733fc49388378cacd3658cd76b5e88893ca5227/protenix-0.3.2.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.2 2024-12-23T04:24:41,241 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/c7/93/f19c14b2b49405f326fab9594ffd7252ef0e231cc348d61b5e406408c8cf/protenix-0.3.3-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2024-12-23T04:24:41,241 Found link https://files.pythonhosted.org/packages/83/67/8697c13e89ed881756f1d188346b4e241decea92545f611778baa9273a49/protenix-0.3.3.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.3 2024-12-23T04:24:41,242 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2024-12-23T04:24:41,243 Getting page https://www.piwheels.org/simple/protenix/ 2024-12-23T04:24:41,244 Found index url https://www.piwheels.org/simple/ 2024-12-23T04:24:41,409 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2024-12-23T04:24:41,413 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.2-py3-none-any.whl#sha256=0255f130567cda78b0dd7e9e1efee966d489a4302df91f47c2ce7d7c5f9b3400 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2024-12-23T04:24:41,413 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.1-py3-none-any.whl#sha256=624b9eaf9450baa3748fbe7d038a393ab59d36d7b191a70d676d592c81f46d1f (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2024-12-23T04:24:41,414 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) 2024-12-23T04:24:41,414 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) 2024-12-23T04:24:41,415 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) 2024-12-23T04:24:41,415 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) 2024-12-23T04:24:41,416 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) 2024-12-23T04:24:41,417 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) 2024-12-23T04:24:41,417 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/) 2024-12-23T04:24:41,417 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2024-12-23T04:24:41,418 Skipping link: not a file: https://pypi.org/simple/protenix/ 2024-12-23T04:24:41,438 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2024-12-23T04:24:41,440 Collecting protenix==0.3.3 2024-12-23T04:24:41,442 Created temporary directory: /tmp/pip-unpack-qwu8wztr 2024-12-23T04:24:41,822 Downloading protenix-0.3.3.tar.gz (309 kB) 2024-12-23T04:24:42,205 Added protenix==0.3.3 from https://files.pythonhosted.org/packages/83/67/8697c13e89ed881756f1d188346b4e241decea92545f611778baa9273a49/protenix-0.3.3.tar.gz to build tracker '/tmp/pip-build-tracker-1951jpw_' 2024-12-23T04:24:42,207 Running setup.py (path:/tmp/pip-wheel-tgk0h8gd/protenix_cf5270949f534e6d941089280d5fd7b4/setup.py) egg_info for package protenix 2024-12-23T04:24:42,208 Created temporary directory: /tmp/pip-pip-egg-info-ldjsr9pu 2024-12-23T04:24:42,209 Preparing metadata (setup.py): started 2024-12-23T04:24:42,210 Running command python setup.py egg_info 2024-12-23T04:24:43,303 running egg_info 2024-12-23T04:24:43,330 creating /tmp/pip-pip-egg-info-ldjsr9pu/protenix.egg-info 2024-12-23T04:24:43,332 writing /tmp/pip-pip-egg-info-ldjsr9pu/protenix.egg-info/PKG-INFO 2024-12-23T04:24:43,335 writing dependency_links to /tmp/pip-pip-egg-info-ldjsr9pu/protenix.egg-info/dependency_links.txt 2024-12-23T04:24:43,337 writing entry points to /tmp/pip-pip-egg-info-ldjsr9pu/protenix.egg-info/entry_points.txt 2024-12-23T04:24:43,339 writing requirements to /tmp/pip-pip-egg-info-ldjsr9pu/protenix.egg-info/requires.txt 2024-12-23T04:24:43,340 writing top-level names to /tmp/pip-pip-egg-info-ldjsr9pu/protenix.egg-info/top_level.txt 2024-12-23T04:24:43,342 writing manifest file '/tmp/pip-pip-egg-info-ldjsr9pu/protenix.egg-info/SOURCES.txt' 2024-12-23T04:24:43,451 reading manifest file '/tmp/pip-pip-egg-info-ldjsr9pu/protenix.egg-info/SOURCES.txt' 2024-12-23T04:24:43,453 adding license file 'LICENSE' 2024-12-23T04:24:43,459 writing manifest file '/tmp/pip-pip-egg-info-ldjsr9pu/protenix.egg-info/SOURCES.txt' 2024-12-23T04:24:43,568 Preparing metadata (setup.py): finished with status 'done' 2024-12-23T04:24:43,572 Source in /tmp/pip-wheel-tgk0h8gd/protenix_cf5270949f534e6d941089280d5fd7b4 has version 0.3.3, which satisfies requirement protenix==0.3.3 from https://files.pythonhosted.org/packages/83/67/8697c13e89ed881756f1d188346b4e241decea92545f611778baa9273a49/protenix-0.3.3.tar.gz 2024-12-23T04:24:43,573 Removed protenix==0.3.3 from https://files.pythonhosted.org/packages/83/67/8697c13e89ed881756f1d188346b4e241decea92545f611778baa9273a49/protenix-0.3.3.tar.gz from build tracker '/tmp/pip-build-tracker-1951jpw_' 2024-12-23T04:24:43,582 Created temporary directory: /tmp/pip-unpack-u6pbv41q 2024-12-23T04:24:43,583 Created temporary directory: /tmp/pip-unpack-q_kq94dl 2024-12-23T04:24:43,584 Building wheels for collected packages: protenix 2024-12-23T04:24:43,588 Created temporary directory: /tmp/pip-wheel-496l4o7n 2024-12-23T04:24:43,588 Building wheel for protenix (setup.py): started 2024-12-23T04:24:43,589 Destination directory: /tmp/pip-wheel-496l4o7n 2024-12-23T04:24:43,590 Running command python setup.py bdist_wheel 2024-12-23T04:24:44,654 running bdist_wheel 2024-12-23T04:24:44,786 running build 2024-12-23T04:24:44,787 running build_py 2024-12-23T04:24:44,817 creating build/lib/runner 2024-12-23T04:24:44,819 copying runner/__init__.py -> build/lib/runner 2024-12-23T04:24:44,821 copying runner/ema.py -> build/lib/runner 2024-12-23T04:24:44,823 copying runner/msa_search.py -> build/lib/runner 2024-12-23T04:24:44,825 copying runner/dumper.py -> build/lib/runner 2024-12-23T04:24:44,828 copying runner/inference.py -> build/lib/runner 2024-12-23T04:24:44,830 copying runner/batch_inference.py -> build/lib/runner 2024-12-23T04:24:44,833 copying runner/train.py -> build/lib/runner 2024-12-23T04:24:44,837 creating build/lib/configs 2024-12-23T04:24:44,838 copying configs/__init__.py -> build/lib/configs 2024-12-23T04:24:44,839 copying configs/configs_inference.py -> build/lib/configs 2024-12-23T04:24:44,841 copying configs/configs_base.py -> build/lib/configs 2024-12-23T04:24:44,844 copying configs/configs_data.py -> build/lib/configs 2024-12-23T04:24:44,846 creating build/lib/protenix 2024-12-23T04:24:44,847 copying protenix/__init__.py -> build/lib/protenix 2024-12-23T04:24:44,850 creating build/lib/protenix/utils 2024-12-23T04:24:44,851 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2024-12-23T04:24:44,853 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2024-12-23T04:24:44,856 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2024-12-23T04:24:44,858 copying protenix/utils/seed.py -> build/lib/protenix/utils 2024-12-23T04:24:44,859 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2024-12-23T04:24:44,863 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2024-12-23T04:24:44,865 copying protenix/utils/logger.py -> build/lib/protenix/utils 2024-12-23T04:24:44,867 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2024-12-23T04:24:44,869 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2024-12-23T04:24:44,871 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2024-12-23T04:24:44,874 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2024-12-23T04:24:44,877 copying protenix/utils/training.py -> build/lib/protenix/utils 2024-12-23T04:24:44,881 creating build/lib/protenix/model 2024-12-23T04:24:44,883 copying protenix/model/__init__.py -> build/lib/protenix/model 2024-12-23T04:24:44,886 copying protenix/model/utils.py -> build/lib/protenix/model 2024-12-23T04:24:44,888 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2024-12-23T04:24:44,891 copying protenix/model/loss.py -> build/lib/protenix/model 2024-12-23T04:24:44,894 copying protenix/model/generator.py -> build/lib/protenix/model 2024-12-23T04:24:44,897 copying protenix/model/protenix.py -> build/lib/protenix/model 2024-12-23T04:24:44,900 creating build/lib/protenix/metrics 2024-12-23T04:24:44,901 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2024-12-23T04:24:44,904 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2024-12-23T04:24:44,905 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2024-12-23T04:24:44,908 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2024-12-23T04:24:44,910 creating build/lib/protenix/openfold_local 2024-12-23T04:24:44,912 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2024-12-23T04:24:44,915 creating build/lib/protenix/data 2024-12-23T04:24:44,916 copying protenix/data/__init__.py -> build/lib/protenix/data 2024-12-23T04:24:44,917 copying protenix/data/json_parser.py -> build/lib/protenix/data 2024-12-23T04:24:44,920 copying protenix/data/parser.py -> build/lib/protenix/data 2024-12-23T04:24:44,923 copying protenix/data/filter.py -> build/lib/protenix/data 2024-12-23T04:24:44,925 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2024-12-23T04:24:44,927 copying protenix/data/utils.py -> build/lib/protenix/data 2024-12-23T04:24:44,930 copying protenix/data/constants.py -> build/lib/protenix/data 2024-12-23T04:24:44,932 copying protenix/data/featurizer.py -> build/lib/protenix/data 2024-12-23T04:24:44,935 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2024-12-23T04:24:44,938 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2024-12-23T04:24:44,940 copying protenix/data/dataset.py -> build/lib/protenix/data 2024-12-23T04:24:44,943 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2024-12-23T04:24:44,947 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2024-12-23T04:24:44,949 copying protenix/data/ccd.py -> build/lib/protenix/data 2024-12-23T04:24:44,952 copying protenix/data/dataloader.py -> build/lib/protenix/data 2024-12-23T04:24:44,954 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2024-12-23T04:24:44,956 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2024-12-23T04:24:44,958 copying protenix/data/json_maker.py -> build/lib/protenix/data 2024-12-23T04:24:44,961 creating build/lib/protenix/config 2024-12-23T04:24:44,962 copying protenix/config/__init__.py -> build/lib/protenix/config 2024-12-23T04:24:44,965 copying protenix/config/config.py -> build/lib/protenix/config 2024-12-23T04:24:44,967 copying protenix/config/extend_types.py -> build/lib/protenix/config 2024-12-23T04:24:44,969 creating build/lib/protenix/web_service 2024-12-23T04:24:44,970 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2024-12-23T04:24:44,972 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2024-12-23T04:24:44,974 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2024-12-23T04:24:44,976 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2024-12-23T04:24:44,979 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2024-12-23T04:24:44,981 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2024-12-23T04:24:44,984 creating build/lib/protenix/utils/permutation 2024-12-23T04:24:44,985 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2024-12-23T04:24:44,987 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2024-12-23T04:24:44,990 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2024-12-23T04:24:44,993 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2024-12-23T04:24:44,995 creating build/lib/protenix/utils/permutation/chain_permutation 2024-12-23T04:24:44,997 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-23T04:24:44,999 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-23T04:24:45,002 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-23T04:24:45,004 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-23T04:24:45,007 creating build/lib/protenix/model/layer_norm 2024-12-23T04:24:45,008 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2024-12-23T04:24:45,010 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2024-12-23T04:24:45,012 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2024-12-23T04:24:45,015 creating build/lib/protenix/model/modules 2024-12-23T04:24:45,016 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2024-12-23T04:24:45,019 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2024-12-23T04:24:45,021 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2024-12-23T04:24:45,024 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2024-12-23T04:24:45,027 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2024-12-23T04:24:45,030 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2024-12-23T04:24:45,032 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2024-12-23T04:24:45,034 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2024-12-23T04:24:45,036 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2024-12-23T04:24:45,039 creating build/lib/protenix/openfold_local/utils 2024-12-23T04:24:45,040 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2024-12-23T04:24:45,042 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-23T04:24:45,044 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-23T04:24:45,046 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2024-12-23T04:24:45,049 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2024-12-23T04:24:45,051 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-23T04:24:45,054 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2024-12-23T04:24:45,056 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-23T04:24:45,058 creating build/lib/protenix/openfold_local/np 2024-12-23T04:24:45,060 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2024-12-23T04:24:45,062 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2024-12-23T04:24:45,065 creating build/lib/protenix/openfold_local/model 2024-12-23T04:24:45,066 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2024-12-23T04:24:45,068 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2024-12-23T04:24:45,070 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2024-12-23T04:24:45,073 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2024-12-23T04:24:45,075 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2024-12-23T04:24:45,077 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2024-12-23T04:24:45,081 creating build/lib/protenix/openfold_local/data 2024-12-23T04:24:45,082 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2024-12-23T04:24:45,084 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2024-12-23T04:24:45,086 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2024-12-23T04:24:45,088 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2024-12-23T04:24:45,090 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2024-12-23T04:24:45,093 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2024-12-23T04:24:45,094 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2024-12-23T04:24:45,097 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2024-12-23T04:24:45,100 creating build/lib/protenix/openfold_local/utils/kernel 2024-12-23T04:24:45,101 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2024-12-23T04:24:45,103 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2024-12-23T04:24:45,106 creating build/lib/protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,107 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,109 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,111 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,113 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,115 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,117 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,119 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,121 creating build/lib/protenix/openfold_local/data/tools 2024-12-23T04:24:45,123 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2024-12-23T04:24:45,124 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2024-12-23T04:24:45,127 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2024-12-23T04:24:45,128 running egg_info 2024-12-23T04:24:45,158 writing protenix.egg-info/PKG-INFO 2024-12-23T04:24:45,162 writing dependency_links to protenix.egg-info/dependency_links.txt 2024-12-23T04:24:45,163 writing entry points to protenix.egg-info/entry_points.txt 2024-12-23T04:24:45,165 writing requirements to protenix.egg-info/requires.txt 2024-12-23T04:24:45,166 writing top-level names to protenix.egg-info/top_level.txt 2024-12-23T04:24:45,216 reading manifest file 'protenix.egg-info/SOURCES.txt' 2024-12-23T04:24:45,224 adding license file 'LICENSE' 2024-12-23T04:24:45,231 writing manifest file 'protenix.egg-info/SOURCES.txt' 2024-12-23T04:24:45,234 /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. 2024-12-23T04:24:45,235 !! 2024-12-23T04:24:45,236 ******************************************************************************** 2024-12-23T04:24:45,237 ############################ 2024-12-23T04:24:45,237 # Package would be ignored # 2024-12-23T04:24:45,238 ############################ 2024-12-23T04:24:45,238 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2024-12-23T04:24:45,239 but it is absent from setuptools' `packages` configuration. 2024-12-23T04:24:45,240 This leads to an ambiguous overall configuration. If you want to distribute this 2024-12-23T04:24:45,240 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2024-12-23T04:24:45,241 to the `packages` configuration field. 2024-12-23T04:24:45,242 Alternatively, you can also rely on setuptools' discovery methods 2024-12-23T04:24:45,243 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-12-23T04:24:45,243 instead of `find_packages(...)`/`find:`). 2024-12-23T04:24:45,244 You can read more about "package discovery" on setuptools documentation page: 2024-12-23T04:24:45,245 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-12-23T04:24:45,246 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2024-12-23T04:24:45,246 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2024-12-23T04:24:45,247 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-12-23T04:24:45,247 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-12-23T04:24:45,248 combination with a more fine grained `package-data` configuration. 2024-12-23T04:24:45,249 You can read more about "package data files" on setuptools documentation page: 2024-12-23T04:24:45,249 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-12-23T04:24:45,251 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-12-23T04:24:45,251 even if it does not contain any `.py` files. 2024-12-23T04:24:45,252 On the other hand, currently there is no concept of package data 2024-12-23T04:24:45,252 directory, all directories are treated like packages. 2024-12-23T04:24:45,253 ******************************************************************************** 2024-12-23T04:24:45,254 !! 2024-12-23T04:24:45,254 check.warn(importable) 2024-12-23T04:24:45,255 creating build/lib/protenix/model/layer_norm/kernel 2024-12-23T04:24:45,255 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2024-12-23T04:24:45,256 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2024-12-23T04:24:45,258 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2024-12-23T04:24:45,261 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2024-12-23T04:24:45,301 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-12-23T04:24:45,301 !! 2024-12-23T04:24:45,302 ******************************************************************************** 2024-12-23T04:24:45,303 Please avoid running ``setup.py`` directly. 2024-12-23T04:24:45,304 Instead, use pypa/build, pypa/installer or other 2024-12-23T04:24:45,304 standards-based tools. 2024-12-23T04:24:45,305 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-12-23T04:24:45,306 ******************************************************************************** 2024-12-23T04:24:45,307 !! 2024-12-23T04:24:45,307 self.initialize_options() 2024-12-23T04:24:45,330 installing to build/bdist.linux-armv7l/wheel 2024-12-23T04:24:45,330 running install 2024-12-23T04:24:45,355 running install_lib 2024-12-23T04:24:45,382 creating build/bdist.linux-armv7l/wheel 2024-12-23T04:24:45,385 creating build/bdist.linux-armv7l/wheel/runner 2024-12-23T04:24:45,386 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-23T04:24:45,388 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-23T04:24:45,390 copying build/lib/runner/msa_search.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-23T04:24:45,392 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-23T04:24:45,394 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-23T04:24:45,396 copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-23T04:24:45,399 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-23T04:24:45,402 creating build/bdist.linux-armv7l/wheel/configs 2024-12-23T04:24:45,403 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-23T04:24:45,405 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-23T04:24:45,407 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-23T04:24:45,409 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-23T04:24:45,412 creating build/bdist.linux-armv7l/wheel/protenix 2024-12-23T04:24:45,413 creating build/bdist.linux-armv7l/wheel/protenix/utils 2024-12-23T04:24:45,415 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-23T04:24:45,416 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-23T04:24:45,418 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-23T04:24:45,420 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-23T04:24:45,422 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-23T04:24:45,423 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-23T04:24:45,425 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-23T04:24:45,428 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2024-12-23T04:24:45,430 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2024-12-23T04:24:45,431 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-23T04:24:45,433 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-23T04:24:45,436 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-23T04:24:45,438 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-23T04:24:45,441 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-23T04:24:45,442 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-23T04:24:45,445 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-23T04:24:45,447 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-23T04:24:45,449 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-23T04:24:45,451 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-23T04:24:45,453 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-23T04:24:45,456 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-23T04:24:45,459 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-23T04:24:45,461 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2024-12-23T04:24:45,463 creating build/bdist.linux-armv7l/wheel/protenix/model 2024-12-23T04:24:45,464 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-23T04:24:45,466 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-23T04:24:45,469 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-23T04:24:45,471 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-23T04:24:45,474 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-23T04:24:45,477 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-23T04:24:45,480 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2024-12-23T04:24:45,481 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-23T04:24:45,484 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2024-12-23T04:24:45,485 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-23T04:24:45,487 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-23T04:24:45,489 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-23T04:24:45,492 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-23T04:24:45,494 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-23T04:24:45,496 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-23T04:24:45,498 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2024-12-23T04:24:45,500 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-23T04:24:45,503 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-23T04:24:45,504 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-23T04:24:45,507 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-23T04:24:45,510 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-23T04:24:45,512 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-23T04:24:45,514 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-23T04:24:45,517 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-23T04:24:45,518 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-23T04:24:45,522 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2024-12-23T04:24:45,523 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-23T04:24:45,525 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-23T04:24:45,527 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-23T04:24:45,529 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-23T04:24:45,532 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2024-12-23T04:24:45,534 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2024-12-23T04:24:45,535 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-23T04:24:45,537 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-23T04:24:45,538 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-23T04:24:45,541 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2024-12-23T04:24:45,543 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-12-23T04:24:45,544 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-12-23T04:24:45,546 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-23T04:24:45,549 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,550 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,552 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,554 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,556 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,558 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,561 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,562 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-23T04:24:45,564 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-23T04:24:45,566 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-23T04:24:45,570 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-23T04:24:45,571 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-23T04:24:45,573 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2024-12-23T04:24:45,575 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2024-12-23T04:24:45,577 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-12-23T04:24:45,578 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-12-23T04:24:45,582 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2024-12-23T04:24:45,583 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-23T04:24:45,585 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-23T04:24:45,587 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-23T04:24:45,589 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-23T04:24:45,592 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-23T04:24:45,593 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-23T04:24:45,597 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2024-12-23T04:24:45,598 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-23T04:24:45,600 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-23T04:24:45,602 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-23T04:24:45,604 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2024-12-23T04:24:45,605 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-23T04:24:45,607 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-23T04:24:45,609 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-23T04:24:45,611 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-23T04:24:45,613 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-23T04:24:45,616 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-23T04:24:45,618 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-23T04:24:45,621 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-23T04:24:45,624 creating build/bdist.linux-armv7l/wheel/protenix/data 2024-12-23T04:24:45,625 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,627 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,630 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,633 copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,634 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,637 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,640 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,642 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,645 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,648 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,650 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,654 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,657 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,659 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,661 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,664 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,667 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,669 copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-23T04:24:45,672 creating build/bdist.linux-armv7l/wheel/protenix/config 2024-12-23T04:24:45,673 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-23T04:24:45,675 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-23T04:24:45,677 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-23T04:24:45,679 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2024-12-23T04:24:45,681 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-23T04:24:45,683 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-23T04:24:45,684 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-23T04:24:45,687 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-23T04:24:45,689 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-23T04:24:45,692 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-23T04:24:45,694 running install_data 2024-12-23T04:24:45,722 creating build/bdist.linux-armv7l/wheel/protenix-0.3.3.data/data 2024-12-23T04:24:45,723 warning: install_data: setup script did not provide a directory for 'requirements.txt' -- installing right in 'build/bdist.linux-armv7l/wheel/protenix-0.3.3.data/data' 2024-12-23T04:24:45,724 copying requirements.txt -> build/bdist.linux-armv7l/wheel/protenix-0.3.3.data/data 2024-12-23T04:24:45,725 running install_egg_info 2024-12-23T04:24:45,758 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.3.3-py3.11.egg-info 2024-12-23T04:24:45,769 running install_scripts 2024-12-23T04:24:45,789 creating build/bdist.linux-armv7l/wheel/protenix-0.3.3.dist-info/WHEEL 2024-12-23T04:24:45,791 creating '/tmp/pip-wheel-496l4o7n/protenix-0.3.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-12-23T04:24:45,793 adding 'configs/__init__.py' 2024-12-23T04:24:45,795 adding 'configs/configs_base.py' 2024-12-23T04:24:45,797 adding 'configs/configs_data.py' 2024-12-23T04:24:45,799 adding 'configs/configs_inference.py' 2024-12-23T04:24:45,801 adding 'protenix/__init__.py' 2024-12-23T04:24:45,802 adding 'protenix/config/__init__.py' 2024-12-23T04:24:45,804 adding 'protenix/config/config.py' 2024-12-23T04:24:45,806 adding 'protenix/config/extend_types.py' 2024-12-23T04:24:45,808 adding 'protenix/data/__init__.py' 2024-12-23T04:24:45,811 adding 'protenix/data/ccd.py' 2024-12-23T04:24:45,815 adding 'protenix/data/constants.py' 2024-12-23T04:24:45,817 adding 'protenix/data/data_pipeline.py' 2024-12-23T04:24:45,819 adding 'protenix/data/dataloader.py' 2024-12-23T04:24:45,824 adding 'protenix/data/dataset.py' 2024-12-23T04:24:45,828 adding 'protenix/data/featurizer.py' 2024-12-23T04:24:45,829 adding 'protenix/data/filter.py' 2024-12-23T04:24:45,832 adding 'protenix/data/infer_data_pipeline.py' 2024-12-23T04:24:45,834 adding 'protenix/data/json_maker.py' 2024-12-23T04:24:45,837 adding 'protenix/data/json_parser.py' 2024-12-23T04:24:45,839 adding 'protenix/data/json_to_feature.py' 2024-12-23T04:24:45,843 adding 'protenix/data/msa_featurizer.py' 2024-12-23T04:24:45,849 adding 'protenix/data/msa_utils.py' 2024-12-23T04:24:45,854 adding 'protenix/data/parser.py' 2024-12-23T04:24:45,856 adding 'protenix/data/substructure_perms.py' 2024-12-23T04:24:45,858 adding 'protenix/data/tokenizer.py' 2024-12-23T04:24:45,861 adding 'protenix/data/utils.py' 2024-12-23T04:24:45,863 adding 'protenix/metrics/__init__.py' 2024-12-23T04:24:45,864 adding 'protenix/metrics/clash.py' 2024-12-23T04:24:45,866 adding 'protenix/metrics/lddt_metrics.py' 2024-12-23T04:24:45,868 adding 'protenix/metrics/rmsd.py' 2024-12-23T04:24:45,869 adding 'protenix/model/__init__.py' 2024-12-23T04:24:45,871 adding 'protenix/model/generator.py' 2024-12-23T04:24:45,877 adding 'protenix/model/loss.py' 2024-12-23T04:24:45,880 adding 'protenix/model/protenix.py' 2024-12-23T04:24:45,883 adding 'protenix/model/sample_confidence.py' 2024-12-23T04:24:45,886 adding 'protenix/model/utils.py' 2024-12-23T04:24:45,888 adding 'protenix/model/layer_norm/__init__.py' 2024-12-23T04:24:45,889 adding 'protenix/model/layer_norm/layer_norm.py' 2024-12-23T04:24:45,891 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2024-12-23T04:24:45,892 adding 'protenix/model/layer_norm/kernel/compat.h' 2024-12-23T04:24:45,894 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2024-12-23T04:24:45,896 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2024-12-23T04:24:45,898 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2024-12-23T04:24:45,900 adding 'protenix/model/modules/__init__.py' 2024-12-23T04:24:45,902 adding 'protenix/model/modules/confidence.py' 2024-12-23T04:24:45,904 adding 'protenix/model/modules/diffusion.py' 2024-12-23T04:24:45,906 adding 'protenix/model/modules/embedders.py' 2024-12-23T04:24:45,907 adding 'protenix/model/modules/frames.py' 2024-12-23T04:24:45,909 adding 'protenix/model/modules/head.py' 2024-12-23T04:24:45,911 adding 'protenix/model/modules/pairformer.py' 2024-12-23T04:24:45,915 adding 'protenix/model/modules/primitives.py' 2024-12-23T04:24:45,919 adding 'protenix/model/modules/transformer.py' 2024-12-23T04:24:45,921 adding 'protenix/openfold_local/__init__.py' 2024-12-23T04:24:45,922 adding 'protenix/openfold_local/data/__init__.py' 2024-12-23T04:24:45,924 adding 'protenix/openfold_local/data/data_transforms.py' 2024-12-23T04:24:45,925 adding 'protenix/openfold_local/data/errors.py' 2024-12-23T04:24:45,928 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2024-12-23T04:24:45,929 adding 'protenix/openfold_local/data/msa_identifiers.py' 2024-12-23T04:24:45,932 adding 'protenix/openfold_local/data/msa_pairing.py' 2024-12-23T04:24:45,935 adding 'protenix/openfold_local/data/parsers.py' 2024-12-23T04:24:45,938 adding 'protenix/openfold_local/data/templates.py' 2024-12-23T04:24:45,940 adding 'protenix/openfold_local/data/tools/__init__.py' 2024-12-23T04:24:45,942 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2024-12-23T04:24:45,943 adding 'protenix/openfold_local/data/tools/utils.py' 2024-12-23T04:24:45,945 adding 'protenix/openfold_local/model/__init__.py' 2024-12-23T04:24:45,946 adding 'protenix/openfold_local/model/dropout.py' 2024-12-23T04:24:45,948 adding 'protenix/openfold_local/model/outer_product_mean.py' 2024-12-23T04:24:45,951 adding 'protenix/openfold_local/model/primitives.py' 2024-12-23T04:24:45,952 adding 'protenix/openfold_local/model/triangular_attention.py' 2024-12-23T04:24:45,955 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2024-12-23T04:24:45,956 adding 'protenix/openfold_local/np/__init__.py' 2024-12-23T04:24:45,961 adding 'protenix/openfold_local/np/residue_constants.py' 2024-12-23T04:24:45,963 adding 'protenix/openfold_local/utils/__init__.py' 2024-12-23T04:24:45,966 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2024-12-23T04:24:45,967 adding 'protenix/openfold_local/utils/checkpointing.py' 2024-12-23T04:24:45,970 adding 'protenix/openfold_local/utils/chunk_utils.py' 2024-12-23T04:24:45,971 adding 'protenix/openfold_local/utils/feats.py' 2024-12-23T04:24:45,973 adding 'protenix/openfold_local/utils/precision_utils.py' 2024-12-23T04:24:45,977 adding 'protenix/openfold_local/utils/rigid_utils.py' 2024-12-23T04:24:45,979 adding 'protenix/openfold_local/utils/tensor_utils.py' 2024-12-23T04:24:45,980 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2024-12-23T04:24:45,981 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2024-12-23T04:24:45,983 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2024-12-23T04:24:45,984 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2024-12-23T04:24:45,986 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2024-12-23T04:24:45,987 adding 'protenix/openfold_local/utils/geometry/utils.py' 2024-12-23T04:24:45,988 adding 'protenix/openfold_local/utils/geometry/vector.py' 2024-12-23T04:24:45,990 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2024-12-23T04:24:45,991 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2024-12-23T04:24:45,993 adding 'protenix/utils/__init__.py' 2024-12-23T04:24:45,996 adding 'protenix/utils/cropping.py' 2024-12-23T04:24:45,998 adding 'protenix/utils/distributed.py' 2024-12-23T04:24:45,999 adding 'protenix/utils/file_io.py' 2024-12-23T04:24:46,000 adding 'protenix/utils/geometry.py' 2024-12-23T04:24:46,002 adding 'protenix/utils/logger.py' 2024-12-23T04:24:46,003 adding 'protenix/utils/lr_scheduler.py' 2024-12-23T04:24:46,004 adding 'protenix/utils/metrics.py' 2024-12-23T04:24:46,006 adding 'protenix/utils/scatter_utils.py' 2024-12-23T04:24:46,007 adding 'protenix/utils/seed.py' 2024-12-23T04:24:46,009 adding 'protenix/utils/torch_utils.py' 2024-12-23T04:24:46,010 adding 'protenix/utils/training.py' 2024-12-23T04:24:46,012 adding 'protenix/utils/permutation/__init__.py' 2024-12-23T04:24:46,016 adding 'protenix/utils/permutation/atom_permutation.py' 2024-12-23T04:24:46,018 adding 'protenix/utils/permutation/permutation.py' 2024-12-23T04:24:46,020 adding 'protenix/utils/permutation/utils.py' 2024-12-23T04:24:46,022 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2024-12-23T04:24:46,026 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2024-12-23T04:24:46,028 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2024-12-23T04:24:46,030 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2024-12-23T04:24:46,032 adding 'protenix/web_service/__init__.py' 2024-12-23T04:24:46,034 adding 'protenix/web_service/colab_request_parser.py' 2024-12-23T04:24:46,035 adding 'protenix/web_service/colab_request_utils.py' 2024-12-23T04:24:46,037 adding 'protenix/web_service/dependency_url.py' 2024-12-23T04:24:46,039 adding 'protenix/web_service/prediction_visualization.py' 2024-12-23T04:24:46,041 adding 'protenix/web_service/viewer.py' 2024-12-23T04:24:46,043 adding 'protenix-0.3.3.data/data/requirements.txt' 2024-12-23T04:24:46,046 adding 'runner/__init__.py' 2024-12-23T04:24:46,048 adding 'runner/batch_inference.py' 2024-12-23T04:24:46,050 adding 'runner/dumper.py' 2024-12-23T04:24:46,051 adding 'runner/ema.py' 2024-12-23T04:24:46,053 adding 'runner/inference.py' 2024-12-23T04:24:46,055 adding 'runner/msa_search.py' 2024-12-23T04:24:46,058 adding 'runner/train.py' 2024-12-23T04:24:46,060 adding 'protenix-0.3.3.dist-info/LICENSE' 2024-12-23T04:24:46,061 adding 'protenix-0.3.3.dist-info/METADATA' 2024-12-23T04:24:46,062 adding 'protenix-0.3.3.dist-info/WHEEL' 2024-12-23T04:24:46,063 adding 'protenix-0.3.3.dist-info/entry_points.txt' 2024-12-23T04:24:46,064 adding 'protenix-0.3.3.dist-info/top_level.txt' 2024-12-23T04:24:46,066 adding 'protenix-0.3.3.dist-info/RECORD' 2024-12-23T04:24:46,073 removing build/bdist.linux-armv7l/wheel 2024-12-23T04:24:46,230 Building wheel for protenix (setup.py): finished with status 'done' 2024-12-23T04:24:46,237 Created wheel for protenix: filename=protenix-0.3.3-py3-none-any.whl size=383742 sha256=bce00ef75c8d8f408dca3bd0105c8bc555da5e34c8998748544be1bb5f763c02 2024-12-23T04:24:46,238 Stored in directory: /tmp/pip-ephem-wheel-cache-b2se2epu/wheels/8e/29/ed/f77b741b4e7db5a6cf8a6733c2ac2f587a3a0f3bda5181145a 2024-12-23T04:24:46,252 Successfully built protenix 2024-12-23T04:24:46,264 Removed build tracker: '/tmp/pip-build-tracker-1951jpw_'