2024-11-29T15:22:00,891 Created temporary directory: /tmp/pip-build-tracker-tknbflpb
2024-11-29T15:22:00,892 Initialized build tracking at /tmp/pip-build-tracker-tknbflpb
2024-11-29T15:22:00,893 Created build tracker: /tmp/pip-build-tracker-tknbflpb
2024-11-29T15:22:00,894 Entered build tracker: /tmp/pip-build-tracker-tknbflpb
2024-11-29T15:22:00,894 Created temporary directory: /tmp/pip-wheel-xjz47ryc
2024-11-29T15:22:00,898 Created temporary directory: /tmp/pip-ephem-wheel-cache-14r43fhv
2024-11-29T15:22:00,942 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-11-29T15:22:00,945 2 location(s) to search for versions of protenix:
2024-11-29T15:22:00,945 * https://pypi.org/simple/protenix/
2024-11-29T15:22:00,945 * https://www.piwheels.org/simple/protenix/
2024-11-29T15:22:00,946 Fetching project page and analyzing links: https://pypi.org/simple/protenix/
2024-11-29T15:22:00,947 Getting page https://pypi.org/simple/protenix/
2024-11-29T15:22:00,948 Found index url https://pypi.org/simple/
2024-11-29T15:22:01,168 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json
2024-11-29T15:22:01,170   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/)
2024-11-29T15:22:01,171   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/)
2024-11-29T15:22:01,172   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
2024-11-29T15:22:01,172   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)
2024-11-29T15:22:01,174   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
2024-11-29T15:22:01,174   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)
2024-11-29T15:22:01,175   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
2024-11-29T15:22:01,176 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/
2024-11-29T15:22:01,177 Getting page https://www.piwheels.org/simple/protenix/
2024-11-29T15:22:01,178 Found index url https://www.piwheels.org/simple/
2024-11-29T15:22:01,342 Fetched page https://www.piwheels.org/simple/protenix/ as text/html
2024-11-29T15:22:01,343   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)
2024-11-29T15:22:01,344   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/)
2024-11-29T15:22:01,345 Skipping link: not a file: https://www.piwheels.org/simple/protenix/
2024-11-29T15:22:01,345 Skipping link: not a file: https://pypi.org/simple/protenix/
2024-11-29T15:22:01,365 Given no hashes to check 1 links for project 'protenix': discarding no candidates
2024-11-29T15:22:01,366 Collecting protenix==0.1.1
2024-11-29T15:22:01,369   Created temporary directory: /tmp/pip-unpack-skposlnl
2024-11-29T15:22:01,590   Downloading protenix-0.1.1.tar.gz (298 kB)
2024-11-29T15:22:01,958   Added protenix==0.1.1 from https://files.pythonhosted.org/packages/2b/7b/20fe2818e890f5d25a892ba31a24b910d0cf34e9f86b990c042c3f91fd05/protenix-0.1.1.tar.gz to build tracker '/tmp/pip-build-tracker-tknbflpb'
2024-11-29T15:22:01,960   Running setup.py (path:/tmp/pip-wheel-xjz47ryc/protenix_715244f5e0e040d88c3ef32fcb6ab3e0/setup.py) egg_info for package protenix
2024-11-29T15:22:01,961   Created temporary directory: /tmp/pip-pip-egg-info-n47r29vs
2024-11-29T15:22:01,961   Preparing metadata (setup.py): started
2024-11-29T15:22:01,962   Running command python setup.py egg_info
2024-11-29T15:22:03,055   running egg_info
2024-11-29T15:22:03,082   creating /tmp/pip-pip-egg-info-n47r29vs/protenix.egg-info
2024-11-29T15:22:03,083   writing /tmp/pip-pip-egg-info-n47r29vs/protenix.egg-info/PKG-INFO
2024-11-29T15:22:03,087   writing dependency_links to /tmp/pip-pip-egg-info-n47r29vs/protenix.egg-info/dependency_links.txt
2024-11-29T15:22:03,088   writing entry points to /tmp/pip-pip-egg-info-n47r29vs/protenix.egg-info/entry_points.txt
2024-11-29T15:22:03,090   writing requirements to /tmp/pip-pip-egg-info-n47r29vs/protenix.egg-info/requires.txt
2024-11-29T15:22:03,091   writing top-level names to /tmp/pip-pip-egg-info-n47r29vs/protenix.egg-info/top_level.txt
2024-11-29T15:22:03,093   writing manifest file '/tmp/pip-pip-egg-info-n47r29vs/protenix.egg-info/SOURCES.txt'
2024-11-29T15:22:03,202   reading manifest file '/tmp/pip-pip-egg-info-n47r29vs/protenix.egg-info/SOURCES.txt'
2024-11-29T15:22:03,203   adding license file 'LICENSE'
2024-11-29T15:22:03,209   writing manifest file '/tmp/pip-pip-egg-info-n47r29vs/protenix.egg-info/SOURCES.txt'
2024-11-29T15:22:03,322   Preparing metadata (setup.py): finished with status 'done'
2024-11-29T15:22:03,326   Source in /tmp/pip-wheel-xjz47ryc/protenix_715244f5e0e040d88c3ef32fcb6ab3e0 has version 0.1.1, which satisfies requirement protenix==0.1.1 from https://files.pythonhosted.org/packages/2b/7b/20fe2818e890f5d25a892ba31a24b910d0cf34e9f86b990c042c3f91fd05/protenix-0.1.1.tar.gz
2024-11-29T15:22:03,327   Removed protenix==0.1.1 from https://files.pythonhosted.org/packages/2b/7b/20fe2818e890f5d25a892ba31a24b910d0cf34e9f86b990c042c3f91fd05/protenix-0.1.1.tar.gz from build tracker '/tmp/pip-build-tracker-tknbflpb'
2024-11-29T15:22:03,337 Created temporary directory: /tmp/pip-unpack-e4rabt69
2024-11-29T15:22:03,338 Created temporary directory: /tmp/pip-unpack-m19zarb2
2024-11-29T15:22:03,339 Building wheels for collected packages: protenix
2024-11-29T15:22:03,343   Created temporary directory: /tmp/pip-wheel-uueractf
2024-11-29T15:22:03,344   Building wheel for protenix (setup.py): started
2024-11-29T15:22:03,345   Destination directory: /tmp/pip-wheel-uueractf
2024-11-29T15:22:03,345   Running command python setup.py bdist_wheel
2024-11-29T15:22:04,396   running bdist_wheel
2024-11-29T15:22:04,552   running build
2024-11-29T15:22:04,554   running build_py
2024-11-29T15:22:04,591   creating build/lib/runner
2024-11-29T15:22:04,593   copying runner/inference.py -> build/lib/runner
2024-11-29T15:22:04,596   copying runner/ema.py -> build/lib/runner
2024-11-29T15:22:04,598   copying runner/train.py -> build/lib/runner
2024-11-29T15:22:04,600   copying runner/dumper.py -> build/lib/runner
2024-11-29T15:22:04,603   copying runner/__init__.py -> build/lib/runner
2024-11-29T15:22:04,605   creating build/lib/configs
2024-11-29T15:22:04,606   copying configs/configs_inference.py -> build/lib/configs
2024-11-29T15:22:04,608   copying configs/configs_base.py -> build/lib/configs
2024-11-29T15:22:04,611   copying configs/configs_data.py -> build/lib/configs
2024-11-29T15:22:04,614   copying configs/__init__.py -> build/lib/configs
2024-11-29T15:22:04,616   creating build/lib/protenix
2024-11-29T15:22:04,617   copying protenix/__init__.py -> build/lib/protenix
2024-11-29T15:22:04,619   creating build/lib/protenix/data
2024-11-29T15:22:04,620   copying protenix/data/utils.py -> build/lib/protenix/data
2024-11-29T15:22:04,623   copying protenix/data/dataset.py -> build/lib/protenix/data
2024-11-29T15:22:04,626   copying protenix/data/ccd.py -> build/lib/protenix/data
2024-11-29T15:22:04,629   copying protenix/data/msa_featurizer.py -> build/lib/protenix/data
2024-11-29T15:22:04,632   copying protenix/data/msa_utils.py -> build/lib/protenix/data
2024-11-29T15:22:04,635   copying protenix/data/substructure_perms.py -> build/lib/protenix/data
2024-11-29T15:22:04,638   copying protenix/data/json_parser.py -> build/lib/protenix/data
2024-11-29T15:22:04,640   copying protenix/data/tokenizer.py -> build/lib/protenix/data
2024-11-29T15:22:04,643   copying protenix/data/json_to_feature.py -> build/lib/protenix/data
2024-11-29T15:22:04,645   copying protenix/data/data_pipeline.py -> build/lib/protenix/data
2024-11-29T15:22:04,647   copying protenix/data/dataloader.py -> build/lib/protenix/data
2024-11-29T15:22:04,650   copying protenix/data/featurizer.py -> build/lib/protenix/data
2024-11-29T15:22:04,653   copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data
2024-11-29T15:22:04,655   copying protenix/data/__init__.py -> build/lib/protenix/data
2024-11-29T15:22:04,657   copying protenix/data/constants.py -> build/lib/protenix/data
2024-11-29T15:22:04,659   copying protenix/data/parser.py -> build/lib/protenix/data
2024-11-29T15:22:04,663   creating build/lib/protenix/web_service
2024-11-29T15:22:04,664   copying protenix/web_service/viewer.py -> build/lib/protenix/web_service
2024-11-29T15:22:04,667   copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service
2024-11-29T15:22:04,669   copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service
2024-11-29T15:22:04,671   copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service
2024-11-29T15:22:04,674   copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service
2024-11-29T15:22:04,676   copying protenix/web_service/__init__.py -> build/lib/protenix/web_service
2024-11-29T15:22:04,678   creating build/lib/protenix/model
2024-11-29T15:22:04,679   copying protenix/model/utils.py -> build/lib/protenix/model
2024-11-29T15:22:04,682   copying protenix/model/sample_confidence.py -> build/lib/protenix/model
2024-11-29T15:22:04,684   copying protenix/model/loss.py -> build/lib/protenix/model
2024-11-29T15:22:04,688   copying protenix/model/generator.py -> build/lib/protenix/model
2024-11-29T15:22:04,691   copying protenix/model/protenix.py -> build/lib/protenix/model
2024-11-29T15:22:04,694   copying protenix/model/__init__.py -> build/lib/protenix/model
2024-11-29T15:22:04,696   creating build/lib/protenix/config
2024-11-29T15:22:04,697   copying protenix/config/config.py -> build/lib/protenix/config
2024-11-29T15:22:04,700   copying protenix/config/extend_types.py -> build/lib/protenix/config
2024-11-29T15:22:04,702   copying protenix/config/__init__.py -> build/lib/protenix/config
2024-11-29T15:22:04,704   creating build/lib/protenix/utils
2024-11-29T15:22:04,705   copying protenix/utils/logger.py -> build/lib/protenix/utils
2024-11-29T15:22:04,708   copying protenix/utils/torch_utils.py -> build/lib/protenix/utils
2024-11-29T15:22:04,710   copying protenix/utils/metrics.py -> build/lib/protenix/utils
2024-11-29T15:22:04,712   copying protenix/utils/geometry.py -> build/lib/protenix/utils
2024-11-29T15:22:04,714   copying protenix/utils/seed.py -> build/lib/protenix/utils
2024-11-29T15:22:04,716   copying protenix/utils/training.py -> build/lib/protenix/utils
2024-11-29T15:22:04,718   copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils
2024-11-29T15:22:04,720   copying protenix/utils/cropping.py -> build/lib/protenix/utils
2024-11-29T15:22:04,723   copying protenix/utils/file_io.py -> build/lib/protenix/utils
2024-11-29T15:22:04,726   copying protenix/utils/__init__.py -> build/lib/protenix/utils
2024-11-29T15:22:04,728   copying protenix/utils/distributed.py -> build/lib/protenix/utils
2024-11-29T15:22:04,730   copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils
2024-11-29T15:22:04,733   creating build/lib/protenix/openfold_local
2024-11-29T15:22:04,734   copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local
2024-11-29T15:22:04,737   creating build/lib/protenix/metrics
2024-11-29T15:22:04,738   copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics
2024-11-29T15:22:04,741   copying protenix/metrics/clash.py -> build/lib/protenix/metrics
2024-11-29T15:22:04,744   copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics
2024-11-29T15:22:04,747   copying protenix/metrics/__init__.py -> build/lib/protenix/metrics
2024-11-29T15:22:04,749   creating build/lib/protenix/model/modules
2024-11-29T15:22:04,750   copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules
2024-11-29T15:22:04,753   copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules
2024-11-29T15:22:04,756   copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules
2024-11-29T15:22:04,759   copying protenix/model/modules/head.py -> build/lib/protenix/model/modules
2024-11-29T15:22:04,761   copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules
2024-11-29T15:22:04,764   copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules
2024-11-29T15:22:04,767   copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules
2024-11-29T15:22:04,770   copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules
2024-11-29T15:22:04,774   copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules
2024-11-29T15:22:04,776   creating build/lib/protenix/model/layer_norm
2024-11-29T15:22:04,777   copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm
2024-11-29T15:22:04,780   copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm
2024-11-29T15:22:04,783   copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm
2024-11-29T15:22:04,785   creating build/lib/protenix/utils/permutation
2024-11-29T15:22:04,787   copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation
2024-11-29T15:22:04,790   copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation
2024-11-29T15:22:04,792   copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation
2024-11-29T15:22:04,796   copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation
2024-11-29T15:22:04,798   creating build/lib/protenix/utils/permutation/chain_permutation
2024-11-29T15:22:04,800   copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation
2024-11-29T15:22:04,802   copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation
2024-11-29T15:22:04,805   copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation
2024-11-29T15:22:04,808   copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation
2024-11-29T15:22:04,812   creating build/lib/protenix/openfold_local/np
2024-11-29T15:22:04,813   copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np
2024-11-29T15:22:04,817   copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np
2024-11-29T15:22:04,820   creating build/lib/protenix/openfold_local/data
2024-11-29T15:22:04,821   copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data
2024-11-29T15:22:04,824   copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data
2024-11-29T15:22:04,827   copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data
2024-11-29T15:22:04,829   copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data
2024-11-29T15:22:04,832   copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data
2024-11-29T15:22:04,834   copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data
2024-11-29T15:22:04,837   copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data
2024-11-29T15:22:04,840   copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data
2024-11-29T15:22:04,843   creating build/lib/protenix/openfold_local/model
2024-11-29T15:22:04,844   copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model
2024-11-29T15:22:04,846   copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model
2024-11-29T15:22:04,849   copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model
2024-11-29T15:22:04,852   copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model
2024-11-29T15:22:04,855   copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model
2024-11-29T15:22:04,858   copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model
2024-11-29T15:22:04,860   creating build/lib/protenix/openfold_local/utils
2024-11-29T15:22:04,862   copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils
2024-11-29T15:22:04,864   copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils
2024-11-29T15:22:04,867   copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils
2024-11-29T15:22:04,869   copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils
2024-11-29T15:22:04,872   copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils
2024-11-29T15:22:04,874   copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils
2024-11-29T15:22:04,877   copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils
2024-11-29T15:22:04,879   copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils
2024-11-29T15:22:04,882   creating build/lib/protenix/openfold_local/data/tools
2024-11-29T15:22:04,883   copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools
2024-11-29T15:22:04,886   copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools
2024-11-29T15:22:04,888   copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools
2024-11-29T15:22:04,891   creating build/lib/protenix/openfold_local/utils/kernel
2024-11-29T15:22:04,892   copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel
2024-11-29T15:22:04,894   copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel
2024-11-29T15:22:04,897   creating build/lib/protenix/openfold_local/utils/geometry
2024-11-29T15:22:04,899   copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry
2024-11-29T15:22:04,901   copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry
2024-11-29T15:22:04,903   copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry
2024-11-29T15:22:04,906   copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry
2024-11-29T15:22:04,908   copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry
2024-11-29T15:22:04,910   copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry
2024-11-29T15:22:04,913   copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry
2024-11-29T15:22:04,915   running egg_info
2024-11-29T15:22:04,946   writing protenix.egg-info/PKG-INFO
2024-11-29T15:22:04,950   writing dependency_links to protenix.egg-info/dependency_links.txt
2024-11-29T15:22:04,952   writing entry points to protenix.egg-info/entry_points.txt
2024-11-29T15:22:04,954   writing requirements to protenix.egg-info/requires.txt
2024-11-29T15:22:04,955   writing top-level names to protenix.egg-info/top_level.txt
2024-11-29T15:22:05,003   reading manifest file 'protenix.egg-info/SOURCES.txt'
2024-11-29T15:22:05,012   adding license file 'LICENSE'
2024-11-29T15:22:05,019   writing manifest file 'protenix.egg-info/SOURCES.txt'
2024-11-29T15:22:05,023   /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.
2024-11-29T15:22:05,024   !!

2024-11-29T15:22:05,025           ********************************************************************************
2024-11-29T15:22:05,025           ############################
2024-11-29T15:22:05,026           # Package would be ignored #
2024-11-29T15:22:05,026           ############################
2024-11-29T15:22:05,027           Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1],
2024-11-29T15:22:05,027           but it is absent from setuptools' `packages` configuration.

2024-11-29T15:22:05,028           This leads to an ambiguous overall configuration. If you want to distribute this
2024-11-29T15:22:05,029           package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added
2024-11-29T15:22:05,030           to the `packages` configuration field.

2024-11-29T15:22:05,031           Alternatively, you can also rely on setuptools' discovery methods
2024-11-29T15:22:05,031           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-11-29T15:22:05,032           instead of `find_packages(...)`/`find:`).

2024-11-29T15:22:05,033           You can read more about "package discovery" on setuptools documentation page:

2024-11-29T15:22:05,034           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-11-29T15:22:05,035           If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are
2024-11-29T15:22:05,035           already explicitly excluding 'protenix.model.layer_norm.kernel' via
2024-11-29T15:22:05,036           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-11-29T15:22:05,037           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-11-29T15:22:05,037           combination with a more fine grained `package-data` configuration.

2024-11-29T15:22:05,038           You can read more about "package data files" on setuptools documentation page:

2024-11-29T15:22:05,039           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-11-29T15:22:05,041           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-11-29T15:22:05,042                 even if it does not contain any `.py` files.
2024-11-29T15:22:05,042                 On the other hand, currently there is no concept of package data
2024-11-29T15:22:05,043                 directory, all directories are treated like packages.
2024-11-29T15:22:05,043           ********************************************************************************

2024-11-29T15:22:05,044   !!
2024-11-29T15:22:05,045     check.warn(importable)
2024-11-29T15:22:05,045   creating build/lib/protenix/model/layer_norm/kernel
2024-11-29T15:22:05,046   copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel
2024-11-29T15:22:05,046   copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel
2024-11-29T15:22:05,047   copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel
2024-11-29T15:22:05,048   copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel
2024-11-29T15:22:05,088   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2024-11-29T15:22:05,089   !!

2024-11-29T15:22:05,090           ********************************************************************************
2024-11-29T15:22:05,090           Please avoid running ``setup.py`` directly.
2024-11-29T15:22:05,091           Instead, use pypa/build, pypa/installer or other
2024-11-29T15:22:05,092           standards-based tools.

2024-11-29T15:22:05,093           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2024-11-29T15:22:05,093           ********************************************************************************

2024-11-29T15:22:05,094   !!
2024-11-29T15:22:05,095     self.initialize_options()
2024-11-29T15:22:05,118   installing to build/bdist.linux-armv7l/wheel
2024-11-29T15:22:05,118   running install
2024-11-29T15:22:05,143   running install_lib
2024-11-29T15:22:05,170   creating build/bdist.linux-armv7l/wheel
2024-11-29T15:22:05,173   creating build/bdist.linux-armv7l/wheel/runner
2024-11-29T15:22:05,174   copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner
2024-11-29T15:22:05,176   copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner
2024-11-29T15:22:05,178   copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner
2024-11-29T15:22:05,181   copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner
2024-11-29T15:22:05,183   copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner
2024-11-29T15:22:05,185   creating build/bdist.linux-armv7l/wheel/configs
2024-11-29T15:22:05,186   copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs
2024-11-29T15:22:05,188   copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs
2024-11-29T15:22:05,190   copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs
2024-11-29T15:22:05,193   copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs
2024-11-29T15:22:05,195   creating build/bdist.linux-armv7l/wheel/protenix
2024-11-29T15:22:05,196   creating build/bdist.linux-armv7l/wheel/protenix/data
2024-11-29T15:22:05,198   copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,200   copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,203   copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,206   copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,209   copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,212   copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,214   copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,216   copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,218   copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,221   copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,223   copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,226   copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,228   copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,230   copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,232   copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,234   copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data
2024-11-29T15:22:05,238   creating build/bdist.linux-armv7l/wheel/protenix/web_service
2024-11-29T15:22:05,239   copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service
2024-11-29T15:22:05,241   copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service
2024-11-29T15:22:05,243   copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service
2024-11-29T15:22:05,246   copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service
2024-11-29T15:22:05,248   copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service
2024-11-29T15:22:05,250   copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service
2024-11-29T15:22:05,253   creating build/bdist.linux-armv7l/wheel/protenix/model
2024-11-29T15:22:05,254   copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model
2024-11-29T15:22:05,256   copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model
2024-11-29T15:22:05,259   copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model
2024-11-29T15:22:05,263   creating build/bdist.linux-armv7l/wheel/protenix/model/modules
2024-11-29T15:22:05,264   copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-11-29T15:22:05,266   copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-11-29T15:22:05,269   copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-11-29T15:22:05,271   copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-11-29T15:22:05,273   copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-11-29T15:22:05,276   copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-11-29T15:22:05,278   copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-11-29T15:22:05,280   copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-11-29T15:22:05,283   copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules
2024-11-29T15:22:05,285   creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm
2024-11-29T15:22:05,287   copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm
2024-11-29T15:22:05,289   copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm
2024-11-29T15:22:05,292   creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel
2024-11-29T15:22:05,293   copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel
2024-11-29T15:22:05,295   copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel
2024-11-29T15:22:05,298   copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel
2024-11-29T15:22:05,300   copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel
2024-11-29T15:22:05,302   copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm
2024-11-29T15:22:05,303   copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model
2024-11-29T15:22:05,306   copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model
2024-11-29T15:22:05,308   copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model
2024-11-29T15:22:05,310   creating build/bdist.linux-armv7l/wheel/protenix/config
2024-11-29T15:22:05,311   copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config
2024-11-29T15:22:05,314   copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config
2024-11-29T15:22:05,316   copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config
2024-11-29T15:22:05,318   creating build/bdist.linux-armv7l/wheel/protenix/utils
2024-11-29T15:22:05,319   copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-11-29T15:22:05,321   copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-11-29T15:22:05,323   copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-11-29T15:22:05,325   copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-11-29T15:22:05,327   copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-11-29T15:22:05,329   copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-11-29T15:22:05,331   copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-11-29T15:22:05,334   copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-11-29T15:22:05,336   copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-11-29T15:22:05,338   copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-11-29T15:22:05,340   copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-11-29T15:22:05,342   copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils
2024-11-29T15:22:05,344   creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation
2024-11-29T15:22:05,345   copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation
2024-11-29T15:22:05,348   creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation
2024-11-29T15:22:05,349   copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation
2024-11-29T15:22:05,351   copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation
2024-11-29T15:22:05,354   copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation
2024-11-29T15:22:05,357   copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation
2024-11-29T15:22:05,360   copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation
2024-11-29T15:22:05,362   copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation
2024-11-29T15:22:05,365   copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation
2024-11-29T15:22:05,367   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local
2024-11-29T15:22:05,369   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np
2024-11-29T15:22:05,370   copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np
2024-11-29T15:22:05,373   copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np
2024-11-29T15:22:05,375   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data
2024-11-29T15:22:05,376   copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-11-29T15:22:05,378   copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-11-29T15:22:05,380   copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-11-29T15:22:05,382   copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-11-29T15:22:05,384   copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-11-29T15:22:05,387   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools
2024-11-29T15:22:05,388   copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools
2024-11-29T15:22:05,390   copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools
2024-11-29T15:22:05,392   copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools
2024-11-29T15:22:05,394   copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-11-29T15:22:05,396   copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-11-29T15:22:05,399   copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data
2024-11-29T15:22:05,401   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model
2024-11-29T15:22:05,402   copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model
2024-11-29T15:22:05,404   copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model
2024-11-29T15:22:05,407   copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model
2024-11-29T15:22:05,409   copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model
2024-11-29T15:22:05,412   copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model
2024-11-29T15:22:05,414   copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model
2024-11-29T15:22:05,416   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils
2024-11-29T15:22:05,417   copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-11-29T15:22:05,420   copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-11-29T15:22:05,422   copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-11-29T15:22:05,424   copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-11-29T15:22:05,426   copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-11-29T15:22:05,428   copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-11-29T15:22:05,431   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel
2024-11-29T15:22:05,433   copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel
2024-11-29T15:22:05,435   copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel
2024-11-29T15:22:05,436   copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-11-29T15:22:05,438   copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils
2024-11-29T15:22:05,440   creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry
2024-11-29T15:22:05,441   copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-11-29T15:22:05,443   copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-11-29T15:22:05,445   copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-11-29T15:22:05,447   copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-11-29T15:22:05,449   copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-11-29T15:22:05,451   copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-11-29T15:22:05,453   copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry
2024-11-29T15:22:05,455   copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local
2024-11-29T15:22:05,457   copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix
2024-11-29T15:22:05,459   creating build/bdist.linux-armv7l/wheel/protenix/metrics
2024-11-29T15:22:05,460   copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics
2024-11-29T15:22:05,462   copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics
2024-11-29T15:22:05,465   copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics
2024-11-29T15:22:05,467   copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics
2024-11-29T15:22:05,468   running install_data
2024-11-29T15:22:05,496   creating build/bdist.linux-armv7l/wheel/protenix-0.1.1.data/data
2024-11-29T15:22:05,498   warning: install_data: setup script did not provide a directory for 'requirements.txt' -- installing right in 'build/bdist.linux-armv7l/wheel/protenix-0.1.1.data/data'

2024-11-29T15:22:05,499   copying requirements.txt -> build/bdist.linux-armv7l/wheel/protenix-0.1.1.data/data
2024-11-29T15:22:05,500   running install_egg_info
2024-11-29T15:22:05,534   Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.1.1-py3.11.egg-info
2024-11-29T15:22:05,546   running install_scripts
2024-11-29T15:22:05,565   creating build/bdist.linux-armv7l/wheel/protenix-0.1.1.dist-info/WHEEL
2024-11-29T15:22:05,567   creating '/tmp/pip-wheel-uueractf/protenix-0.1.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-11-29T15:22:05,569   adding 'configs/__init__.py'
2024-11-29T15:22:05,571   adding 'configs/configs_base.py'
2024-11-29T15:22:05,573   adding 'configs/configs_data.py'
2024-11-29T15:22:05,574   adding 'configs/configs_inference.py'
2024-11-29T15:22:05,576   adding 'protenix/__init__.py'
2024-11-29T15:22:05,578   adding 'protenix/config/__init__.py'
2024-11-29T15:22:05,579   adding 'protenix/config/config.py'
2024-11-29T15:22:05,581   adding 'protenix/config/extend_types.py'
2024-11-29T15:22:05,583   adding 'protenix/data/__init__.py'
2024-11-29T15:22:05,585   adding 'protenix/data/ccd.py'
2024-11-29T15:22:05,589   adding 'protenix/data/constants.py'
2024-11-29T15:22:05,591   adding 'protenix/data/data_pipeline.py'
2024-11-29T15:22:05,593   adding 'protenix/data/dataloader.py'
2024-11-29T15:22:05,598   adding 'protenix/data/dataset.py'
2024-11-29T15:22:05,602   adding 'protenix/data/featurizer.py'
2024-11-29T15:22:05,604   adding 'protenix/data/infer_data_pipeline.py'
2024-11-29T15:22:05,606   adding 'protenix/data/json_parser.py'
2024-11-29T15:22:05,608   adding 'protenix/data/json_to_feature.py'
2024-11-29T15:22:05,613   adding 'protenix/data/msa_featurizer.py'
2024-11-29T15:22:05,618   adding 'protenix/data/msa_utils.py'
2024-11-29T15:22:05,622   adding 'protenix/data/parser.py'
2024-11-29T15:22:05,624   adding 'protenix/data/substructure_perms.py'
2024-11-29T15:22:05,626   adding 'protenix/data/tokenizer.py'
2024-11-29T15:22:05,628   adding 'protenix/data/utils.py'
2024-11-29T15:22:05,630   adding 'protenix/metrics/__init__.py'
2024-11-29T15:22:05,632   adding 'protenix/metrics/clash.py'
2024-11-29T15:22:05,634   adding 'protenix/metrics/lddt_metrics.py'
2024-11-29T15:22:05,635   adding 'protenix/metrics/rmsd.py'
2024-11-29T15:22:05,637   adding 'protenix/model/__init__.py'
2024-11-29T15:22:05,639   adding 'protenix/model/generator.py'
2024-11-29T15:22:05,645   adding 'protenix/model/loss.py'
2024-11-29T15:22:05,649   adding 'protenix/model/protenix.py'
2024-11-29T15:22:05,652   adding 'protenix/model/sample_confidence.py'
2024-11-29T15:22:05,654   adding 'protenix/model/utils.py'
2024-11-29T15:22:05,656   adding 'protenix/model/layer_norm/__init__.py'
2024-11-29T15:22:05,658   adding 'protenix/model/layer_norm/layer_norm.py'
2024-11-29T15:22:05,659   adding 'protenix/model/layer_norm/torch_ext_compile.py'
2024-11-29T15:22:05,661   adding 'protenix/model/layer_norm/kernel/compat.h'
2024-11-29T15:22:05,662   adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp'
2024-11-29T15:22:05,665   adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu'
2024-11-29T15:22:05,666   adding 'protenix/model/layer_norm/kernel/type_shim.h'
2024-11-29T15:22:05,668   adding 'protenix/model/modules/__init__.py'
2024-11-29T15:22:05,670   adding 'protenix/model/modules/confidence.py'
2024-11-29T15:22:05,672   adding 'protenix/model/modules/diffusion.py'
2024-11-29T15:22:05,674   adding 'protenix/model/modules/embedders.py'
2024-11-29T15:22:05,675   adding 'protenix/model/modules/frames.py'
2024-11-29T15:22:05,677   adding 'protenix/model/modules/head.py'
2024-11-29T15:22:05,680   adding 'protenix/model/modules/pairformer.py'
2024-11-29T15:22:05,684   adding 'protenix/model/modules/primitives.py'
2024-11-29T15:22:05,687   adding 'protenix/model/modules/transformer.py'
2024-11-29T15:22:05,689   adding 'protenix/openfold_local/__init__.py'
2024-11-29T15:22:05,690   adding 'protenix/openfold_local/data/__init__.py'
2024-11-29T15:22:05,692   adding 'protenix/openfold_local/data/data_transforms.py'
2024-11-29T15:22:05,694   adding 'protenix/openfold_local/data/errors.py'
2024-11-29T15:22:05,696   adding 'protenix/openfold_local/data/mmcif_parsing.py'
2024-11-29T15:22:05,698   adding 'protenix/openfold_local/data/msa_identifiers.py'
2024-11-29T15:22:05,700   adding 'protenix/openfold_local/data/msa_pairing.py'
2024-11-29T15:22:05,704   adding 'protenix/openfold_local/data/parsers.py'
2024-11-29T15:22:05,707   adding 'protenix/openfold_local/data/templates.py'
2024-11-29T15:22:05,708   adding 'protenix/openfold_local/data/tools/__init__.py'
2024-11-29T15:22:05,710   adding 'protenix/openfold_local/data/tools/jackhmmer.py'
2024-11-29T15:22:05,711   adding 'protenix/openfold_local/data/tools/utils.py'
2024-11-29T15:22:05,713   adding 'protenix/openfold_local/model/__init__.py'
2024-11-29T15:22:05,714   adding 'protenix/openfold_local/model/dropout.py'
2024-11-29T15:22:05,715   adding 'protenix/openfold_local/model/outer_product_mean.py'
2024-11-29T15:22:05,718   adding 'protenix/openfold_local/model/primitives.py'
2024-11-29T15:22:05,720   adding 'protenix/openfold_local/model/triangular_attention.py'
2024-11-29T15:22:05,723   adding 'protenix/openfold_local/model/triangular_multiplicative_update.py'
2024-11-29T15:22:05,725   adding 'protenix/openfold_local/np/__init__.py'
2024-11-29T15:22:05,729   adding 'protenix/openfold_local/np/residue_constants.py'
2024-11-29T15:22:05,731   adding 'protenix/openfold_local/utils/__init__.py'
2024-11-29T15:22:05,734   adding 'protenix/openfold_local/utils/all_atom_multimer.py'
2024-11-29T15:22:05,735   adding 'protenix/openfold_local/utils/checkpointing.py'
2024-11-29T15:22:05,737   adding 'protenix/openfold_local/utils/chunk_utils.py'
2024-11-29T15:22:05,739   adding 'protenix/openfold_local/utils/feats.py'
2024-11-29T15:22:05,740   adding 'protenix/openfold_local/utils/precision_utils.py'
2024-11-29T15:22:05,745   adding 'protenix/openfold_local/utils/rigid_utils.py'
2024-11-29T15:22:05,746   adding 'protenix/openfold_local/utils/tensor_utils.py'
2024-11-29T15:22:05,748   adding 'protenix/openfold_local/utils/geometry/__init__.py'
2024-11-29T15:22:05,750   adding 'protenix/openfold_local/utils/geometry/quat_rigid.py'
2024-11-29T15:22:05,751   adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py'
2024-11-29T15:22:05,753   adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py'
2024-11-29T15:22:05,754   adding 'protenix/openfold_local/utils/geometry/test_utils.py'
2024-11-29T15:22:05,755   adding 'protenix/openfold_local/utils/geometry/utils.py'
2024-11-29T15:22:05,757   adding 'protenix/openfold_local/utils/geometry/vector.py'
2024-11-29T15:22:05,758   adding 'protenix/openfold_local/utils/kernel/__init__.py'
2024-11-29T15:22:05,760   adding 'protenix/openfold_local/utils/kernel/attention_core.py'
2024-11-29T15:22:05,761   adding 'protenix/utils/__init__.py'
2024-11-29T15:22:05,765   adding 'protenix/utils/cropping.py'
2024-11-29T15:22:05,766   adding 'protenix/utils/distributed.py'
2024-11-29T15:22:05,768   adding 'protenix/utils/file_io.py'
2024-11-29T15:22:05,769   adding 'protenix/utils/geometry.py'
2024-11-29T15:22:05,770   adding 'protenix/utils/logger.py'
2024-11-29T15:22:05,772   adding 'protenix/utils/lr_scheduler.py'
2024-11-29T15:22:05,773   adding 'protenix/utils/metrics.py'
2024-11-29T15:22:05,775   adding 'protenix/utils/scatter_utils.py'
2024-11-29T15:22:05,776   adding 'protenix/utils/seed.py'
2024-11-29T15:22:05,777   adding 'protenix/utils/torch_utils.py'
2024-11-29T15:22:05,779   adding 'protenix/utils/training.py'
2024-11-29T15:22:05,780   adding 'protenix/utils/permutation/__init__.py'
2024-11-29T15:22:05,784   adding 'protenix/utils/permutation/atom_permutation.py'
2024-11-29T15:22:05,787   adding 'protenix/utils/permutation/permutation.py'
2024-11-29T15:22:05,788   adding 'protenix/utils/permutation/utils.py'
2024-11-29T15:22:05,790   adding 'protenix/utils/permutation/chain_permutation/__init__.py'
2024-11-29T15:22:05,795   adding 'protenix/utils/permutation/chain_permutation/heuristic.py'
2024-11-29T15:22:05,797   adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py'
2024-11-29T15:22:05,798   adding 'protenix/utils/permutation/chain_permutation/utils.py'
2024-11-29T15:22:05,800   adding 'protenix/web_service/__init__.py'
2024-11-29T15:22:05,802   adding 'protenix/web_service/colab_request_parser.py'
2024-11-29T15:22:05,804   adding 'protenix/web_service/colab_request_utils.py'
2024-11-29T15:22:05,805   adding 'protenix/web_service/dependency_url.py'
2024-11-29T15:22:05,806   adding 'protenix/web_service/prediction_visualization.py'
2024-11-29T15:22:05,808   adding 'protenix/web_service/viewer.py'
2024-11-29T15:22:05,811   adding 'protenix-0.1.1.data/data/requirements.txt'
2024-11-29T15:22:05,813   adding 'runner/__init__.py'
2024-11-29T15:22:05,814   adding 'runner/dumper.py'
2024-11-29T15:22:05,816   adding 'runner/ema.py'
2024-11-29T15:22:05,817   adding 'runner/inference.py'
2024-11-29T15:22:05,820   adding 'runner/train.py'
2024-11-29T15:22:05,823   adding 'protenix-0.1.1.dist-info/LICENSE'
2024-11-29T15:22:05,824   adding 'protenix-0.1.1.dist-info/METADATA'
2024-11-29T15:22:05,825   adding 'protenix-0.1.1.dist-info/WHEEL'
2024-11-29T15:22:05,826   adding 'protenix-0.1.1.dist-info/entry_points.txt'
2024-11-29T15:22:05,827   adding 'protenix-0.1.1.dist-info/top_level.txt'
2024-11-29T15:22:05,829   adding 'protenix-0.1.1.dist-info/RECORD'
2024-11-29T15:22:05,835   removing build/bdist.linux-armv7l/wheel
2024-11-29T15:22:05,981   Building wheel for protenix (setup.py): finished with status 'done'
2024-11-29T15:22:05,987   Created wheel for protenix: filename=protenix-0.1.1-py3-none-any.whl size=367905 sha256=aa7a8c0ad8f38f5430cb145bb56675e2b0deb861589bbb05ec6eb09dd95c5f57
2024-11-29T15:22:05,988   Stored in directory: /tmp/pip-ephem-wheel-cache-14r43fhv/wheels/49/6f/7f/e05d572049e5fb7672b34c1592fa09ef250a30eacb33f59c4c
2024-11-29T15:22:06,002 Successfully built protenix
2024-11-29T15:22:06,020 Removed build tracker: '/tmp/pip-build-tracker-tknbflpb'