2024-12-12T14:16:46,098 Created temporary directory: /tmp/pip-build-tracker-cvilu2k6
2024-12-12T14:16:46,099 Initialized build tracking at /tmp/pip-build-tracker-cvilu2k6
2024-12-12T14:16:46,100 Created build tracker: /tmp/pip-build-tracker-cvilu2k6
2024-12-12T14:16:46,101 Entered build tracker: /tmp/pip-build-tracker-cvilu2k6
2024-12-12T14:16:46,101 Created temporary directory: /tmp/pip-wheel-uk0xctxj
2024-12-12T14:16:46,105 Created temporary directory: /tmp/pip-ephem-wheel-cache-kqljuju_
2024-12-12T14:16:46,149 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-12-12T14:16:46,152 2 location(s) to search for versions of protenix:
2024-12-12T14:16:46,152 * https://pypi.org/simple/protenix/
2024-12-12T14:16:46,152 * https://www.piwheels.org/simple/protenix/
2024-12-12T14:16:46,153 Fetching project page and analyzing links: https://pypi.org/simple/protenix/
2024-12-12T14:16:46,153 Getting page https://pypi.org/simple/protenix/
2024-12-12T14:16:46,155 Found index url https://pypi.org/simple/
2024-12-12T14:16:46,374 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json
2024-12-12T14:16:46,378   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/)
2024-12-12T14:16:46,378   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/)
2024-12-12T14:16:46,379   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
2024-12-12T14:16:46,380   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)
2024-12-12T14:16:46,380   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
2024-12-12T14:16:46,381   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)
2024-12-12T14:16:46,382   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
2024-12-12T14:16:46,383   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)
2024-12-12T14:16:46,384   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
2024-12-12T14:16:46,384   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)
2024-12-12T14:16:46,385   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
2024-12-12T14:16:46,386   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)
2024-12-12T14:16:46,387   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
2024-12-12T14:16:46,388 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/
2024-12-12T14:16:46,389 Getting page https://www.piwheels.org/simple/protenix/
2024-12-12T14:16:46,390 Found index url https://www.piwheels.org/simple/
2024-12-12T14:16:46,569 Fetched page https://www.piwheels.org/simple/protenix/ as text/html
2024-12-12T14:16:46,572   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)
2024-12-12T14:16:46,573   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)
2024-12-12T14:16:46,573   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)
2024-12-12T14:16:46,574   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)
2024-12-12T14:16:46,574   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/)
2024-12-12T14:16:46,575 Skipping link: not a file: https://www.piwheels.org/simple/protenix/
2024-12-12T14:16:46,575 Skipping link: not a file: https://pypi.org/simple/protenix/
2024-12-12T14:16:46,595 Given no hashes to check 1 links for project 'protenix': discarding no candidates
2024-12-12T14:16:46,597 Collecting protenix==0.2.0
2024-12-12T14:16:46,599   Created temporary directory: /tmp/pip-unpack-_d4b62ab
2024-12-12T14:16:46,819   Downloading protenix-0.2.0.tar.gz (308 kB)
2024-12-12T14:16:47,193   Added protenix==0.2.0 from https://files.pythonhosted.org/packages/0f/17/fdc141be77d735ddf3bfba80a660873fa13732b6c77847434b969aa66f51/protenix-0.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-cvilu2k6'
2024-12-12T14:16:47,194   Running setup.py (path:/tmp/pip-wheel-uk0xctxj/protenix_12298b9f87484855a1e16a03e0a8a586/setup.py) egg_info for package protenix
2024-12-12T14:16:47,195   Created temporary directory: /tmp/pip-pip-egg-info-8hfhi3y5
2024-12-12T14:16:47,196   Preparing metadata (setup.py): started
2024-12-12T14:16:47,197   Running command python setup.py egg_info
2024-12-12T14:16:48,330   running egg_info
2024-12-12T14:16:48,358   creating /tmp/pip-pip-egg-info-8hfhi3y5/protenix.egg-info
2024-12-12T14:16:48,360   writing /tmp/pip-pip-egg-info-8hfhi3y5/protenix.egg-info/PKG-INFO
2024-12-12T14:16:48,363   writing dependency_links to /tmp/pip-pip-egg-info-8hfhi3y5/protenix.egg-info/dependency_links.txt
2024-12-12T14:16:48,365   writing entry points to /tmp/pip-pip-egg-info-8hfhi3y5/protenix.egg-info/entry_points.txt
2024-12-12T14:16:48,367   writing requirements to /tmp/pip-pip-egg-info-8hfhi3y5/protenix.egg-info/requires.txt
2024-12-12T14:16:48,369   writing top-level names to /tmp/pip-pip-egg-info-8hfhi3y5/protenix.egg-info/top_level.txt
2024-12-12T14:16:48,371   writing manifest file '/tmp/pip-pip-egg-info-8hfhi3y5/protenix.egg-info/SOURCES.txt'
2024-12-12T14:16:48,481   reading manifest file '/tmp/pip-pip-egg-info-8hfhi3y5/protenix.egg-info/SOURCES.txt'
2024-12-12T14:16:48,483   adding license file 'LICENSE'
2024-12-12T14:16:48,489   writing manifest file '/tmp/pip-pip-egg-info-8hfhi3y5/protenix.egg-info/SOURCES.txt'
2024-12-12T14:16:48,599   Preparing metadata (setup.py): finished with status 'done'
2024-12-12T14:16:48,603   Source in /tmp/pip-wheel-uk0xctxj/protenix_12298b9f87484855a1e16a03e0a8a586 has version 0.2.0, which satisfies requirement protenix==0.2.0 from https://files.pythonhosted.org/packages/0f/17/fdc141be77d735ddf3bfba80a660873fa13732b6c77847434b969aa66f51/protenix-0.2.0.tar.gz
2024-12-12T14:16:48,604   Removed protenix==0.2.0 from https://files.pythonhosted.org/packages/0f/17/fdc141be77d735ddf3bfba80a660873fa13732b6c77847434b969aa66f51/protenix-0.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-cvilu2k6'
2024-12-12T14:16:48,613 Created temporary directory: /tmp/pip-unpack-5e2ni199
2024-12-12T14:16:48,614 Created temporary directory: /tmp/pip-unpack-xyz2umxv
2024-12-12T14:16:48,614 Building wheels for collected packages: protenix
2024-12-12T14:16:48,618   Created temporary directory: /tmp/pip-wheel-btnh2dbb
2024-12-12T14:16:48,619   Building wheel for protenix (setup.py): started
2024-12-12T14:16:48,620   Destination directory: /tmp/pip-wheel-btnh2dbb
2024-12-12T14:16:48,621   Running command python setup.py bdist_wheel
2024-12-12T14:16:49,646   running bdist_wheel
2024-12-12T14:16:49,778   running build
2024-12-12T14:16:49,779   running build_py
2024-12-12T14:16:49,809   creating build/lib/runner
2024-12-12T14:16:49,811   copying runner/batch_inference.py -> build/lib/runner
2024-12-12T14:16:49,814   copying runner/inference.py -> build/lib/runner
2024-12-12T14:16:49,817   copying runner/ema.py -> build/lib/runner
2024-12-12T14:16:49,819   copying runner/train.py -> build/lib/runner
2024-12-12T14:16:49,822   copying runner/dumper.py -> build/lib/runner
2024-12-12T14:16:49,824   copying runner/__init__.py -> build/lib/runner
2024-12-12T14:16:49,826   creating build/lib/configs
2024-12-12T14:16:49,827   copying configs/configs_inference.py -> build/lib/configs
2024-12-12T14:16:49,830   copying configs/configs_base.py -> build/lib/configs
2024-12-12T14:16:49,832   copying configs/configs_data.py -> build/lib/configs
2024-12-12T14:16:49,834   copying configs/__init__.py -> build/lib/configs
2024-12-12T14:16:49,837   creating build/lib/protenix
2024-12-12T14:16:49,838   copying protenix/__init__.py -> build/lib/protenix
2024-12-12T14:16:49,840   creating build/lib/protenix/data
2024-12-12T14:16:49,841   copying protenix/data/utils.py -> build/lib/protenix/data
2024-12-12T14:16:49,844   copying protenix/data/dataset.py -> build/lib/protenix/data
2024-12-12T14:16:49,847   copying protenix/data/ccd.py -> build/lib/protenix/data
2024-12-12T14:16:49,851   copying protenix/data/msa_featurizer.py -> build/lib/protenix/data
2024-12-12T14:16:49,854   copying protenix/data/json_maker.py -> build/lib/protenix/data
2024-12-12T14:16:49,857   copying protenix/data/filter.py -> build/lib/protenix/data
2024-12-12T14:16:49,859   copying protenix/data/msa_utils.py -> build/lib/protenix/data
2024-12-12T14:16:49,862   copying protenix/data/substructure_perms.py -> build/lib/protenix/data
2024-12-12T14:16:49,865   copying protenix/data/json_parser.py -> build/lib/protenix/data
2024-12-12T14:16:49,867   copying protenix/data/tokenizer.py -> build/lib/protenix/data
2024-12-12T14:16:49,870   copying protenix/data/json_to_feature.py -> build/lib/protenix/data
2024-12-12T14:16:49,873   copying protenix/data/data_pipeline.py -> build/lib/protenix/data
2024-12-12T14:16:49,875   copying protenix/data/dataloader.py -> build/lib/protenix/data
2024-12-12T14:16:49,878   copying protenix/data/featurizer.py -> build/lib/protenix/data
2024-12-12T14:16:49,881   copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data
2024-12-12T14:16:49,884   copying protenix/data/__init__.py -> build/lib/protenix/data
2024-12-12T14:16:49,886   copying protenix/data/constants.py -> build/lib/protenix/data
2024-12-12T14:16:49,889   copying protenix/data/parser.py -> build/lib/protenix/data
2024-12-12T14:16:49,894   creating build/lib/protenix/web_service
2024-12-12T14:16:49,895   copying protenix/web_service/viewer.py -> build/lib/protenix/web_service
2024-12-12T14:16:49,898   copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service
2024-12-12T14:16:49,901   copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service
2024-12-12T14:16:49,903   copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service
2024-12-12T14:16:49,906   copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service
2024-12-12T14:16:49,908   copying protenix/web_service/__init__.py -> build/lib/protenix/web_service
2024-12-12T14:16:49,911   creating build/lib/protenix/model
2024-12-12T14:16:49,912   copying protenix/model/utils.py -> build/lib/protenix/model
2024-12-12T14:16:49,915   copying protenix/model/sample_confidence.py -> build/lib/protenix/model
2024-12-12T14:16:49,918   copying protenix/model/loss.py -> build/lib/protenix/model
2024-12-12T14:16:49,922   copying protenix/model/generator.py -> build/lib/protenix/model
2024-12-12T14:16:49,925   copying protenix/model/protenix.py -> build/lib/protenix/model
2024-12-12T14:16:49,928   copying protenix/model/__init__.py -> build/lib/protenix/model
2024-12-12T14:16:49,931   creating build/lib/protenix/config
2024-12-12T14:16:49,932   copying protenix/config/config.py -> build/lib/protenix/config
2024-12-12T14:16:49,935   copying protenix/config/extend_types.py -> build/lib/protenix/config
2024-12-12T14:16:49,936   copying protenix/config/__init__.py -> build/lib/protenix/config
2024-12-12T14:16:49,939   creating build/lib/protenix/utils
2024-12-12T14:16:49,940   copying protenix/utils/logger.py -> build/lib/protenix/utils
2024-12-12T14:16:49,942   copying protenix/utils/torch_utils.py -> build/lib/protenix/utils
2024-12-12T14:16:49,944   copying protenix/utils/metrics.py -> build/lib/protenix/utils
2024-12-12T14:16:49,946   copying protenix/utils/geometry.py -> build/lib/protenix/utils
2024-12-12T14:16:49,948   copying protenix/utils/seed.py -> build/lib/protenix/utils
2024-12-12T14:16:49,950   copying protenix/utils/training.py -> build/lib/protenix/utils
2024-12-12T14:16:49,952   copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils
2024-12-12T14:16:49,954   copying protenix/utils/cropping.py -> build/lib/protenix/utils
2024-12-12T14:16:49,957   copying protenix/utils/file_io.py -> build/lib/protenix/utils
2024-12-12T14:16:49,959   copying protenix/utils/__init__.py -> build/lib/protenix/utils
2024-12-12T14:16:49,961   copying protenix/utils/distributed.py -> build/lib/protenix/utils
2024-12-12T14:16:49,963   copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils
2024-12-12T14:16:49,965   creating build/lib/protenix/openfold_local
2024-12-12T14:16:49,966   copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local
2024-12-12T14:16:49,969   creating build/lib/protenix/metrics
2024-12-12T14:16:49,970   copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics
2024-12-12T14:16:49,972   copying protenix/metrics/clash.py -> build/lib/protenix/metrics
2024-12-12T14:16:49,975   copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics
2024-12-12T14:16:49,977   copying protenix/metrics/__init__.py -> build/lib/protenix/metrics
2024-12-12T14:16:49,979   creating build/lib/protenix/model/modules
2024-12-12T14:16:49,980   copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules
2024-12-12T14:16:49,982   copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules
2024-12-12T14:16:49,985   copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules
2024-12-12T14:16:49,988   copying protenix/model/modules/head.py -> build/lib/protenix/model/modules
2024-12-12T14:16:49,990   copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules
2024-12-12T14:16:49,993   copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules
2024-12-12T14:16:49,995   copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules
2024-12-12T14:16:49,998   copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules
2024-12-12T14:16:50,000   copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules
2024-12-12T14:16:50,003   creating build/lib/protenix/model/layer_norm
2024-12-12T14:16:50,004   copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm
2024-12-12T14:16:50,006   copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm
2024-12-12T14:16:50,008   copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm
2024-12-12T14:16:50,010   creating build/lib/protenix/utils/permutation
2024-12-12T14:16:50,011   copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation
2024-12-12T14:16:50,014   copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation
2024-12-12T14:16:50,016   copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation
2024-12-12T14:16:50,019   copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation
2024-12-12T14:16:50,022   creating build/lib/protenix/utils/permutation/chain_permutation
2024-12-12T14:16:50,023   copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation
2024-12-12T14:16:50,025   copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation
2024-12-12T14:16:50,027   copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation
2024-12-12T14:16:50,030   copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation
2024-12-12T14:16:50,033   creating build/lib/protenix/openfold_local/np
2024-12-12T14:16:50,034   copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np
2024-12-12T14:16:50,038   copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np
2024-12-12T14:16:50,040   creating build/lib/protenix/openfold_local/data
2024-12-12T14:16:50,042   copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data
2024-12-12T14:16:50,045   copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data
2024-12-12T14:16:50,048   copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data
2024-12-12T14:16:50,050   copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data
2024-12-12T14:16:50,052   copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data
2024-12-12T14:16:50,055   copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data
2024-12-12T14:16:50,058   copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data
2024-12-12T14:16:50,061   copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data
2024-12-12T14:16:50,063   creating build/lib/protenix/openfold_local/model
2024-12-12T14:16:50,065   copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model
2024-12-12T14:16:50,067   copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model
2024-12-12T14:16:50,070   copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model
2024-12-12T14:16:50,073   copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model
2024-12-12T14:16:50,076   copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model
2024-12-12T14:16:50,078   copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model
2024-12-12T14:16:50,081   creating build/lib/protenix/openfold_local/utils
2024-12-12T14:16:50,082   copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils
2024-12-12T14:16:50,085   copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils
2024-12-12T14:16:50,087   copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils
2024-12-12T14:16:50,089   copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils
2024-12-12T14:16:50,092   copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils
2024-12-12T14:16:50,094   copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils
2024-12-12T14:16:50,096   copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils
2024-12-12T14:16:50,098   copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils
2024-12-12T14:16:50,100   creating build/lib/protenix/openfold_local/data/tools
2024-12-12T14:16:50,101   copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools
2024-12-12T14:16:50,103   copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools
2024-12-12T14:16:50,105   copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools
2024-12-12T14:16:50,107   creating build/lib/protenix/openfold_local/utils/kernel
2024-12-12T14:16:50,108   copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel
2024-12-12T14:16:50,110   copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel
2024-12-12T14:16:50,113   creating build/lib/protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,114   copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,116   copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,118   copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,120   copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,122   copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,124   copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,126   copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,128   running egg_info
2024-12-12T14:16:50,159   writing protenix.egg-info/PKG-INFO
2024-12-12T14:16:50,162   writing dependency_links to protenix.egg-info/dependency_links.txt
2024-12-12T14:16:50,164   writing entry points to protenix.egg-info/entry_points.txt
2024-12-12T14:16:50,165   writing requirements to protenix.egg-info/requires.txt
2024-12-12T14:16:50,167   writing top-level names to protenix.egg-info/top_level.txt
2024-12-12T14:16:50,215   reading manifest file 'protenix.egg-info/SOURCES.txt'
2024-12-12T14:16:50,223   adding license file 'LICENSE'
2024-12-12T14:16:50,231   writing manifest file 'protenix.egg-info/SOURCES.txt'
2024-12-12T14:16:50,234   /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.
2024-12-12T14:16:50,235   !!

2024-12-12T14:16:50,236           ********************************************************************************
2024-12-12T14:16:50,236           ############################
2024-12-12T14:16:50,237           # Package would be ignored #
2024-12-12T14:16:50,237           ############################
2024-12-12T14:16:50,238           Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1],
2024-12-12T14:16:50,238           but it is absent from setuptools' `packages` configuration.

2024-12-12T14:16:50,239           This leads to an ambiguous overall configuration. If you want to distribute this
2024-12-12T14:16:50,240           package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added
2024-12-12T14:16:50,240           to the `packages` configuration field.

2024-12-12T14:16:50,241           Alternatively, you can also rely on setuptools' discovery methods
2024-12-12T14:16:50,242           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-12-12T14:16:50,242           instead of `find_packages(...)`/`find:`).

2024-12-12T14:16:50,243           You can read more about "package discovery" on setuptools documentation page:

2024-12-12T14:16:50,244           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-12-12T14:16:50,245           If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are
2024-12-12T14:16:50,246           already explicitly excluding 'protenix.model.layer_norm.kernel' via
2024-12-12T14:16:50,246           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-12-12T14:16:50,247           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-12-12T14:16:50,247           combination with a more fine grained `package-data` configuration.

2024-12-12T14:16:50,248           You can read more about "package data files" on setuptools documentation page:

2024-12-12T14:16:50,249           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-12-12T14:16:50,251           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-12-12T14:16:50,252                 even if it does not contain any `.py` files.
2024-12-12T14:16:50,252                 On the other hand, currently there is no concept of package data
2024-12-12T14:16:50,253                 directory, all directories are treated like packages.
2024-12-12T14:16:50,253           ********************************************************************************

2024-12-12T14:16:50,254   !!
2024-12-12T14:16:50,255     check.warn(importable)
2024-12-12T14:16:50,255   creating build/lib/protenix/model/layer_norm/kernel
2024-12-12T14:16:50,256   copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel
2024-12-12T14:16:50,256   copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel
2024-12-12T14:16:50,257   copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel
2024-12-12T14:16:50,258   copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel
2024-12-12T14:16:50,315   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2024-12-12T14:16:50,316   !!

2024-12-12T14:16:50,318           ********************************************************************************
2024-12-12T14:16:50,318           Please avoid running ``setup.py`` directly.
2024-12-12T14:16:50,319           Instead, use pypa/build, pypa/installer or other
2024-12-12T14:16:50,320           standards-based tools.

2024-12-12T14:16:50,321           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2024-12-12T14:16:50,322           ********************************************************************************

2024-12-12T14:16:50,324   !!
2024-12-12T14:16:50,325     self.initialize_options()
2024-12-12T14:16:50,354   installing to build/bdist.linux-armv7l/wheel
2024-12-12T14:16:50,355   running install
2024-12-12T14:16:50,382   running install_lib
2024-12-12T14:16:50,409   creating build/bdist.linux-armv7l/wheel
2024-12-12T14:16:50,411   creating build/bdist.linux-armv7l/wheel/runner
2024-12-12T14:16:50,412   copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner
2024-12-12T14:16:50,415   copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner
2024-12-12T14:16:50,417   copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner
2024-12-12T14:16:50,419   copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner
2024-12-12T14:16:50,421   copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner
2024-12-12T14:16:50,423   copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner
2024-12-12T14:16:50,425   creating build/bdist.linux-armv7l/wheel/configs
2024-12-12T14:16:50,426   copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs
2024-12-12T14:16:50,428   copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs
2024-12-12T14:16:50,430   copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs
2024-12-12T14:16:50,432   copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs
2024-12-12T14:16:50,434   creating build/bdist.linux-armv7l/wheel/protenix
2024-12-12T14:16:50,436   creating build/bdist.linux-armv7l/wheel/protenix/data
2024-12-12T14:16:50,438   copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,440   copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,443   copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,445   copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,448   copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,451   copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,453   copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,456   copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,458   copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,461   copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,463   copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,465   copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,468   copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,470   copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,473   copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,476   copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,477   copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,480   copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-12-12T14:16:50,484   creating build/bdist.linux-armv7l/wheel/protenix/web_service
2024-12-12T14:16:50,485   copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service
2024-12-12T14:16:50,488   copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service
2024-12-12T14:16:50,490   copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service
2024-12-12T14:16:50,492   copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service
2024-12-12T14:16:50,494   copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service
2024-12-12T14:16:50,497   copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service
2024-12-12T14:16:50,499   creating build/bdist.linux-armv7l/wheel/protenix/model
2024-12-12T14:16:50,500   copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model
2024-12-12T14:16:50,502   copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model
2024-12-12T14:16:50,505   copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model
2024-12-12T14:16:50,509   creating build/bdist.linux-armv7l/wheel/protenix/model/modules
2024-12-12T14:16:50,510   copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-12-12T14:16:50,512   copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-12-12T14:16:50,515   copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-12-12T14:16:50,517   copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-12-12T14:16:50,519   copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-12-12T14:16:50,521   copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-12-12T14:16:50,524   copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-12-12T14:16:50,526   copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-12-12T14:16:50,529   copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-12-12T14:16:50,531   creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm
2024-12-12T14:16:50,532   copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm
2024-12-12T14:16:50,534   copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm
2024-12-12T14:16:50,537   creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel
2024-12-12T14:16:50,538   copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel
2024-12-12T14:16:50,541   copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel
2024-12-12T14:16:50,544   copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel
2024-12-12T14:16:50,545   copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel
2024-12-12T14:16:50,547   copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm
2024-12-12T14:16:50,549   copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model
2024-12-12T14:16:50,552   copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model
2024-12-12T14:16:50,554   copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model
2024-12-12T14:16:50,557   creating build/bdist.linux-armv7l/wheel/protenix/config
2024-12-12T14:16:50,558   copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config
2024-12-12T14:16:50,560   copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config
2024-12-12T14:16:50,562   copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config
2024-12-12T14:16:50,564   creating build/bdist.linux-armv7l/wheel/protenix/utils
2024-12-12T14:16:50,565   copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-12-12T14:16:50,567   copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-12-12T14:16:50,569   copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-12-12T14:16:50,571   copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-12-12T14:16:50,573   copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-12-12T14:16:50,574   copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-12-12T14:16:50,576   copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-12-12T14:16:50,578   copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-12-12T14:16:50,581   copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-12-12T14:16:50,583   copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-12-12T14:16:50,584   copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-12-12T14:16:50,586   copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-12-12T14:16:50,589   creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation
2024-12-12T14:16:50,590   copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation
2024-12-12T14:16:50,593   creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation
2024-12-12T14:16:50,594   copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation
2024-12-12T14:16:50,596   copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation
2024-12-12T14:16:50,598   copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation
2024-12-12T14:16:50,602   copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation
2024-12-12T14:16:50,604   copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation
2024-12-12T14:16:50,606   copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation
2024-12-12T14:16:50,609   copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation
2024-12-12T14:16:50,611   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local
2024-12-12T14:16:50,613   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np
2024-12-12T14:16:50,614   copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np
2024-12-12T14:16:50,617   copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np
2024-12-12T14:16:50,620   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data
2024-12-12T14:16:50,621   copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-12-12T14:16:50,623   copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-12-12T14:16:50,625   copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-12-12T14:16:50,627   copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-12-12T14:16:50,629   copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-12-12T14:16:50,632   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools
2024-12-12T14:16:50,633   copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools
2024-12-12T14:16:50,634   copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools
2024-12-12T14:16:50,637   copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools
2024-12-12T14:16:50,638   copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-12-12T14:16:50,641   copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-12-12T14:16:50,643   copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-12-12T14:16:50,645   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model
2024-12-12T14:16:50,646   copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model
2024-12-12T14:16:50,648   copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model
2024-12-12T14:16:50,651   copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model
2024-12-12T14:16:50,654   copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model
2024-12-12T14:16:50,656   copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model
2024-12-12T14:16:50,659   copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model
2024-12-12T14:16:50,661   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils
2024-12-12T14:16:50,662   copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-12-12T14:16:50,664   copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-12-12T14:16:50,666   copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-12-12T14:16:50,668   copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-12-12T14:16:50,671   copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-12-12T14:16:50,673   copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-12-12T14:16:50,676   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel
2024-12-12T14:16:50,678   copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel
2024-12-12T14:16:50,680   copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel
2024-12-12T14:16:50,681   copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-12-12T14:16:50,683   copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-12-12T14:16:50,685   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,686   copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,688   copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,690   copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,692   copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,694   copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,696   copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,698   copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-12-12T14:16:50,700   copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local
2024-12-12T14:16:50,702   copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix
2024-12-12T14:16:50,704   creating build/bdist.linux-armv7l/wheel/protenix/metrics
2024-12-12T14:16:50,705   copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics
2024-12-12T14:16:50,708   copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics
2024-12-12T14:16:50,710   copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics
2024-12-12T14:16:50,712   copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics
2024-12-12T14:16:50,713   running install_data
2024-12-12T14:16:50,741   creating build/bdist.linux-armv7l/wheel/protenix-0.2.0.data/data
2024-12-12T14:16:50,743   warning: install_data: setup script did not provide a directory for 'requirements.txt' -- installing right in 'build/bdist.linux-armv7l/wheel/protenix-0.2.0.data/data'

2024-12-12T14:16:50,744   copying requirements.txt -> build/bdist.linux-armv7l/wheel/protenix-0.2.0.data/data
2024-12-12T14:16:50,745   running install_egg_info
2024-12-12T14:16:50,778   Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.2.0-py3.11.egg-info
2024-12-12T14:16:50,790   running install_scripts
2024-12-12T14:16:50,810   creating build/bdist.linux-armv7l/wheel/protenix-0.2.0.dist-info/WHEEL
2024-12-12T14:16:50,813   creating '/tmp/pip-wheel-btnh2dbb/protenix-0.2.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-12-12T14:16:50,815   adding 'configs/__init__.py'
2024-12-12T14:16:50,817   adding 'configs/configs_base.py'
2024-12-12T14:16:50,819   adding 'configs/configs_data.py'
2024-12-12T14:16:50,820   adding 'configs/configs_inference.py'
2024-12-12T14:16:50,822   adding 'protenix/__init__.py'
2024-12-12T14:16:50,824   adding 'protenix/config/__init__.py'
2024-12-12T14:16:50,826   adding 'protenix/config/config.py'
2024-12-12T14:16:50,828   adding 'protenix/config/extend_types.py'
2024-12-12T14:16:50,830   adding 'protenix/data/__init__.py'
2024-12-12T14:16:50,832   adding 'protenix/data/ccd.py'
2024-12-12T14:16:50,836   adding 'protenix/data/constants.py'
2024-12-12T14:16:50,838   adding 'protenix/data/data_pipeline.py'
2024-12-12T14:16:50,840   adding 'protenix/data/dataloader.py'
2024-12-12T14:16:50,845   adding 'protenix/data/dataset.py'
2024-12-12T14:16:50,849   adding 'protenix/data/featurizer.py'
2024-12-12T14:16:50,851   adding 'protenix/data/filter.py'
2024-12-12T14:16:50,852   adding 'protenix/data/infer_data_pipeline.py'
2024-12-12T14:16:50,854   adding 'protenix/data/json_maker.py'
2024-12-12T14:16:50,857   adding 'protenix/data/json_parser.py'
2024-12-12T14:16:50,859   adding 'protenix/data/json_to_feature.py'
2024-12-12T14:16:50,864   adding 'protenix/data/msa_featurizer.py'
2024-12-12T14:16:50,869   adding 'protenix/data/msa_utils.py'
2024-12-12T14:16:50,875   adding 'protenix/data/parser.py'
2024-12-12T14:16:50,877   adding 'protenix/data/substructure_perms.py'
2024-12-12T14:16:50,879   adding 'protenix/data/tokenizer.py'
2024-12-12T14:16:50,882   adding 'protenix/data/utils.py'
2024-12-12T14:16:50,883   adding 'protenix/metrics/__init__.py'
2024-12-12T14:16:50,885   adding 'protenix/metrics/clash.py'
2024-12-12T14:16:50,887   adding 'protenix/metrics/lddt_metrics.py'
2024-12-12T14:16:50,889   adding 'protenix/metrics/rmsd.py'
2024-12-12T14:16:50,890   adding 'protenix/model/__init__.py'
2024-12-12T14:16:50,892   adding 'protenix/model/generator.py'
2024-12-12T14:16:50,898   adding 'protenix/model/loss.py'
2024-12-12T14:16:50,901   adding 'protenix/model/protenix.py'
2024-12-12T14:16:50,905   adding 'protenix/model/sample_confidence.py'
2024-12-12T14:16:50,907   adding 'protenix/model/utils.py'
2024-12-12T14:16:50,908   adding 'protenix/model/layer_norm/__init__.py'
2024-12-12T14:16:50,910   adding 'protenix/model/layer_norm/layer_norm.py'
2024-12-12T14:16:50,911   adding 'protenix/model/layer_norm/torch_ext_compile.py'
2024-12-12T14:16:50,913   adding 'protenix/model/layer_norm/kernel/compat.h'
2024-12-12T14:16:50,914   adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp'
2024-12-12T14:16:50,917   adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu'
2024-12-12T14:16:50,918   adding 'protenix/model/layer_norm/kernel/type_shim.h'
2024-12-12T14:16:50,920   adding 'protenix/model/modules/__init__.py'
2024-12-12T14:16:50,922   adding 'protenix/model/modules/confidence.py'
2024-12-12T14:16:50,925   adding 'protenix/model/modules/diffusion.py'
2024-12-12T14:16:50,927   adding 'protenix/model/modules/embedders.py'
2024-12-12T14:16:50,928   adding 'protenix/model/modules/frames.py'
2024-12-12T14:16:50,929   adding 'protenix/model/modules/head.py'
2024-12-12T14:16:50,932   adding 'protenix/model/modules/pairformer.py'
2024-12-12T14:16:50,936   adding 'protenix/model/modules/primitives.py'
2024-12-12T14:16:50,939   adding 'protenix/model/modules/transformer.py'
2024-12-12T14:16:50,941   adding 'protenix/openfold_local/__init__.py'
2024-12-12T14:16:50,943   adding 'protenix/openfold_local/data/__init__.py'
2024-12-12T14:16:50,945   adding 'protenix/openfold_local/data/data_transforms.py'
2024-12-12T14:16:50,946   adding 'protenix/openfold_local/data/errors.py'
2024-12-12T14:16:50,949   adding 'protenix/openfold_local/data/mmcif_parsing.py'
2024-12-12T14:16:50,950   adding 'protenix/openfold_local/data/msa_identifiers.py'
2024-12-12T14:16:50,953   adding 'protenix/openfold_local/data/msa_pairing.py'
2024-12-12T14:16:50,956   adding 'protenix/openfold_local/data/parsers.py'
2024-12-12T14:16:50,960   adding 'protenix/openfold_local/data/templates.py'
2024-12-12T14:16:50,961   adding 'protenix/openfold_local/data/tools/__init__.py'
2024-12-12T14:16:50,963   adding 'protenix/openfold_local/data/tools/jackhmmer.py'
2024-12-12T14:16:50,965   adding 'protenix/openfold_local/data/tools/utils.py'
2024-12-12T14:16:50,966   adding 'protenix/openfold_local/model/__init__.py'
2024-12-12T14:16:50,968   adding 'protenix/openfold_local/model/dropout.py'
2024-12-12T14:16:50,969   adding 'protenix/openfold_local/model/outer_product_mean.py'
2024-12-12T14:16:50,972   adding 'protenix/openfold_local/model/primitives.py'
2024-12-12T14:16:50,974   adding 'protenix/openfold_local/model/triangular_attention.py'
2024-12-12T14:16:50,976   adding 'protenix/openfold_local/model/triangular_multiplicative_update.py'
2024-12-12T14:16:50,978   adding 'protenix/openfold_local/np/__init__.py'
2024-12-12T14:16:50,983   adding 'protenix/openfold_local/np/residue_constants.py'
2024-12-12T14:16:50,985   adding 'protenix/openfold_local/utils/__init__.py'
2024-12-12T14:16:50,988   adding 'protenix/openfold_local/utils/all_atom_multimer.py'
2024-12-12T14:16:50,989   adding 'protenix/openfold_local/utils/checkpointing.py'
2024-12-12T14:16:50,991   adding 'protenix/openfold_local/utils/chunk_utils.py'
2024-12-12T14:16:50,993   adding 'protenix/openfold_local/utils/feats.py'
2024-12-12T14:16:50,994   adding 'protenix/openfold_local/utils/precision_utils.py'
2024-12-12T14:16:50,998   adding 'protenix/openfold_local/utils/rigid_utils.py'
2024-12-12T14:16:51,000   adding 'protenix/openfold_local/utils/tensor_utils.py'
2024-12-12T14:16:51,002   adding 'protenix/openfold_local/utils/geometry/__init__.py'
2024-12-12T14:16:51,003   adding 'protenix/openfold_local/utils/geometry/quat_rigid.py'
2024-12-12T14:16:51,005   adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py'
2024-12-12T14:16:51,007   adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py'
2024-12-12T14:16:51,008   adding 'protenix/openfold_local/utils/geometry/test_utils.py'
2024-12-12T14:16:51,009   adding 'protenix/openfold_local/utils/geometry/utils.py'
2024-12-12T14:16:51,011   adding 'protenix/openfold_local/utils/geometry/vector.py'
2024-12-12T14:16:51,013   adding 'protenix/openfold_local/utils/kernel/__init__.py'
2024-12-12T14:16:51,014   adding 'protenix/openfold_local/utils/kernel/attention_core.py'
2024-12-12T14:16:51,016   adding 'protenix/utils/__init__.py'
2024-12-12T14:16:51,019   adding 'protenix/utils/cropping.py'
2024-12-12T14:16:51,021   adding 'protenix/utils/distributed.py'
2024-12-12T14:16:51,022   adding 'protenix/utils/file_io.py'
2024-12-12T14:16:51,023   adding 'protenix/utils/geometry.py'
2024-12-12T14:16:51,025   adding 'protenix/utils/logger.py'
2024-12-12T14:16:51,026   adding 'protenix/utils/lr_scheduler.py'
2024-12-12T14:16:51,028   adding 'protenix/utils/metrics.py'
2024-12-12T14:16:51,029   adding 'protenix/utils/scatter_utils.py'
2024-12-12T14:16:51,031   adding 'protenix/utils/seed.py'
2024-12-12T14:16:51,032   adding 'protenix/utils/torch_utils.py'
2024-12-12T14:16:51,034   adding 'protenix/utils/training.py'
2024-12-12T14:16:51,036   adding 'protenix/utils/permutation/__init__.py'
2024-12-12T14:16:51,040   adding 'protenix/utils/permutation/atom_permutation.py'
2024-12-12T14:16:51,042   adding 'protenix/utils/permutation/permutation.py'
2024-12-12T14:16:51,044   adding 'protenix/utils/permutation/utils.py'
2024-12-12T14:16:51,046   adding 'protenix/utils/permutation/chain_permutation/__init__.py'
2024-12-12T14:16:51,050   adding 'protenix/utils/permutation/chain_permutation/heuristic.py'
2024-12-12T14:16:51,052   adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py'
2024-12-12T14:16:51,054   adding 'protenix/utils/permutation/chain_permutation/utils.py'
2024-12-12T14:16:51,055   adding 'protenix/web_service/__init__.py'
2024-12-12T14:16:51,057   adding 'protenix/web_service/colab_request_parser.py'
2024-12-12T14:16:51,059   adding 'protenix/web_service/colab_request_utils.py'
2024-12-12T14:16:51,061   adding 'protenix/web_service/dependency_url.py'
2024-12-12T14:16:51,063   adding 'protenix/web_service/prediction_visualization.py'
2024-12-12T14:16:51,065   adding 'protenix/web_service/viewer.py'
2024-12-12T14:16:51,067   adding 'protenix-0.2.0.data/data/requirements.txt'
2024-12-12T14:16:51,070   adding 'runner/__init__.py'
2024-12-12T14:16:51,072   adding 'runner/batch_inference.py'
2024-12-12T14:16:51,074   adding 'runner/dumper.py'
2024-12-12T14:16:51,075   adding 'runner/ema.py'
2024-12-12T14:16:51,078   adding 'runner/inference.py'
2024-12-12T14:16:51,081   adding 'runner/train.py'
2024-12-12T14:16:51,084   adding 'protenix-0.2.0.dist-info/LICENSE'
2024-12-12T14:16:51,085   adding 'protenix-0.2.0.dist-info/METADATA'
2024-12-12T14:16:51,086   adding 'protenix-0.2.0.dist-info/WHEEL'
2024-12-12T14:16:51,087   adding 'protenix-0.2.0.dist-info/entry_points.txt'
2024-12-12T14:16:51,088   adding 'protenix-0.2.0.dist-info/top_level.txt'
2024-12-12T14:16:51,090   adding 'protenix-0.2.0.dist-info/RECORD'
2024-12-12T14:16:51,096   removing build/bdist.linux-armv7l/wheel
2024-12-12T14:16:51,242   Building wheel for protenix (setup.py): finished with status 'done'
2024-12-12T14:16:51,248   Created wheel for protenix: filename=protenix-0.2.0-py3-none-any.whl size=382580 sha256=0de87030b4ba1d9e3c2b67265493001f00eca096d862816f65f818b739c96c6f
2024-12-12T14:16:51,250   Stored in directory: /tmp/pip-ephem-wheel-cache-kqljuju_/wheels/00/9e/bb/eeb2924c4bc41a6d1c752937a6209c9b68e2eee560f666421d
2024-12-12T14:16:51,263 Successfully built protenix
2024-12-12T14:16:51,281 Removed build tracker: '/tmp/pip-build-tracker-cvilu2k6'