2024-12-11T18:19:15,689 Created temporary directory: /tmp/pip-build-tracker-ljutlwtb 2024-12-11T18:19:15,690 Initialized build tracking at /tmp/pip-build-tracker-ljutlwtb 2024-12-11T18:19:15,691 Created build tracker: /tmp/pip-build-tracker-ljutlwtb 2024-12-11T18:19:15,691 Entered build tracker: /tmp/pip-build-tracker-ljutlwtb 2024-12-11T18:19:15,692 Created temporary directory: /tmp/pip-wheel-zvl77kpe 2024-12-11T18:19:15,696 Created temporary directory: /tmp/pip-ephem-wheel-cache-4yj_ygue 2024-12-11T18:19:15,740 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-12-11T18:19:15,742 2 location(s) to search for versions of protenix: 2024-12-11T18:19:15,742 * https://pypi.org/simple/protenix/ 2024-12-11T18:19:15,742 * https://www.piwheels.org/simple/protenix/ 2024-12-11T18:19:15,743 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2024-12-11T18:19:15,744 Getting page https://pypi.org/simple/protenix/ 2024-12-11T18:19:15,745 Found index url https://pypi.org/simple/ 2024-12-11T18:19:15,967 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2024-12-11T18:19:15,970 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/a8/ea/bbe375d1a89b5e3cbe5e07e56184e29a7b779f964a8ea910337a0746af5e/Protenix-0.0.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) 2024-12-11T18:19:15,971 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/35/f6/105b3517490c13d23880689ef3b4477d072d117ca4cc6f805bad9ee16391/protenix-0.0.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) 2024-12-11T18:19:15,971 Found link https://files.pythonhosted.org/packages/63/d5/22a2098752b2b8c95f2ced18d38918883aa9a5ac8cee9df5174aadfee19c/protenix-0.0.1.tar.gz (from https://pypi.org/simple/protenix/), version: 0.0.1 2024-12-11T18:19:15,972 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/85/33/10bb83edcf222b7cd05cc94d453ac7edfa86f09c7100db8c62fcc894745c/protenix-0.1.0-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2024-12-11T18:19:15,973 Found link https://files.pythonhosted.org/packages/d5/61/cdea4397a181ca2b108c6df0aa4c30e7a6fc34c5b75ad69557569c44b61d/protenix-0.1.0.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.1.0 2024-12-11T18:19:15,974 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/28/00/2206a6a3a02d45eeb6e16c6ffcacff6789f11489238acd07ad5127219741/protenix-0.1.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2024-12-11T18:19:15,975 Found link https://files.pythonhosted.org/packages/2b/7b/20fe2818e890f5d25a892ba31a24b910d0cf34e9f86b990c042c3f91fd05/protenix-0.1.1.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.1.1 2024-12-11T18:19:15,975 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/f5/3f/993181bd5478dccf62a5265df701cc9762d257ac04ea6aec26f2e0ec6b0e/protenix-0.1.2-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:<3.12,>=3.10) 2024-12-11T18:19:15,977 Found link https://files.pythonhosted.org/packages/18/ff/8a30b1df6d1bc731a8b4075a077421e306d85976cae82e758a5f15cef4fd/protenix-0.1.2.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:<3.12,>=3.10), version: 0.1.2 2024-12-11T18:19:15,977 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/c3/31/3b2b20aafa4471bcda6389257ad5348c7762374fe725b0552f836dc13ef6/protenix-0.1.3-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2024-12-11T18:19:15,978 Found link https://files.pythonhosted.org/packages/2c/1c/0788760bb4cd6bae9edc74ef1341e9cc74ad6190b8b5dbd972a361184b97/protenix-0.1.3.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.1.3 2024-12-11T18:19:15,979 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2024-12-11T18:19:15,980 Getting page https://www.piwheels.org/simple/protenix/ 2024-12-11T18:19:15,981 Found index url https://www.piwheels.org/simple/ 2024-12-11T18:19:16,181 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2024-12-11T18:19:16,183 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.1-py3-none-any.whl#sha256=aa7a8c0ad8f38f5430cb145bb56675e2b0deb861589bbb05ec6eb09dd95c5f57 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2024-12-11T18:19:16,184 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.0-py3-none-any.whl#sha256=95dd14c125ff66c76135ed8525ede80d6be803880749ec813036bb317ca23e6e (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2024-12-11T18:19:16,184 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/Protenix-0.0.1-py3-none-any.whl#sha256=5b251c54ef00f26ee302a294be031208ca73350e41e88d05368f4146cdb01794 (from https://www.piwheels.org/simple/protenix/) 2024-12-11T18:19:16,185 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2024-12-11T18:19:16,185 Skipping link: not a file: https://pypi.org/simple/protenix/ 2024-12-11T18:19:16,204 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2024-12-11T18:19:16,206 Collecting protenix==0.1.2 2024-12-11T18:19:16,208 Created temporary directory: /tmp/pip-unpack-zv8upn48 2024-12-11T18:19:16,350 Downloading protenix-0.1.2.tar.gz (309 kB) 2024-12-11T18:19:16,717 Added protenix==0.1.2 from https://files.pythonhosted.org/packages/18/ff/8a30b1df6d1bc731a8b4075a077421e306d85976cae82e758a5f15cef4fd/protenix-0.1.2.tar.gz to build tracker '/tmp/pip-build-tracker-ljutlwtb' 2024-12-11T18:19:16,719 Running setup.py (path:/tmp/pip-wheel-zvl77kpe/protenix_89519b6245df4f3899eaf187cabe259f/setup.py) egg_info for package protenix 2024-12-11T18:19:16,719 Created temporary directory: /tmp/pip-pip-egg-info-730512nl 2024-12-11T18:19:16,720 Preparing metadata (setup.py): started 2024-12-11T18:19:16,722 Running command python setup.py egg_info 2024-12-11T18:19:17,793 running egg_info 2024-12-11T18:19:17,820 creating /tmp/pip-pip-egg-info-730512nl/protenix.egg-info 2024-12-11T18:19:17,827 writing /tmp/pip-pip-egg-info-730512nl/protenix.egg-info/PKG-INFO 2024-12-11T18:19:17,830 writing dependency_links to /tmp/pip-pip-egg-info-730512nl/protenix.egg-info/dependency_links.txt 2024-12-11T18:19:17,832 writing entry points to /tmp/pip-pip-egg-info-730512nl/protenix.egg-info/entry_points.txt 2024-12-11T18:19:17,834 writing requirements to /tmp/pip-pip-egg-info-730512nl/protenix.egg-info/requires.txt 2024-12-11T18:19:17,835 writing top-level names to /tmp/pip-pip-egg-info-730512nl/protenix.egg-info/top_level.txt 2024-12-11T18:19:17,837 writing manifest file '/tmp/pip-pip-egg-info-730512nl/protenix.egg-info/SOURCES.txt' 2024-12-11T18:19:17,947 reading manifest file '/tmp/pip-pip-egg-info-730512nl/protenix.egg-info/SOURCES.txt' 2024-12-11T18:19:17,948 adding license file 'LICENSE' 2024-12-11T18:19:17,954 writing manifest file '/tmp/pip-pip-egg-info-730512nl/protenix.egg-info/SOURCES.txt' 2024-12-11T18:19:18,063 Preparing metadata (setup.py): finished with status 'done' 2024-12-11T18:19:18,068 Source in /tmp/pip-wheel-zvl77kpe/protenix_89519b6245df4f3899eaf187cabe259f has version 0.1.2, which satisfies requirement protenix==0.1.2 from https://files.pythonhosted.org/packages/18/ff/8a30b1df6d1bc731a8b4075a077421e306d85976cae82e758a5f15cef4fd/protenix-0.1.2.tar.gz 2024-12-11T18:19:18,069 Removed protenix==0.1.2 from https://files.pythonhosted.org/packages/18/ff/8a30b1df6d1bc731a8b4075a077421e306d85976cae82e758a5f15cef4fd/protenix-0.1.2.tar.gz from build tracker '/tmp/pip-build-tracker-ljutlwtb' 2024-12-11T18:19:18,078 Created temporary directory: /tmp/pip-unpack-czouar1h 2024-12-11T18:19:18,080 Created temporary directory: /tmp/pip-unpack-4oucj8u4 2024-12-11T18:19:18,080 Building wheels for collected packages: protenix 2024-12-11T18:19:18,085 Created temporary directory: /tmp/pip-wheel-yl49nwq7 2024-12-11T18:19:18,086 Building wheel for protenix (setup.py): started 2024-12-11T18:19:18,087 Destination directory: /tmp/pip-wheel-yl49nwq7 2024-12-11T18:19:18,087 Running command python setup.py bdist_wheel 2024-12-11T18:19:19,111 running bdist_wheel 2024-12-11T18:19:19,244 running build 2024-12-11T18:19:19,245 running build_py 2024-12-11T18:19:19,275 creating build/lib/runner 2024-12-11T18:19:19,277 copying runner/__init__.py -> build/lib/runner 2024-12-11T18:19:19,278 copying runner/inference.py -> build/lib/runner 2024-12-11T18:19:19,281 copying runner/batch_inference.py -> build/lib/runner 2024-12-11T18:19:19,283 copying runner/ema.py -> build/lib/runner 2024-12-11T18:19:19,285 copying runner/dumper.py -> build/lib/runner 2024-12-11T18:19:19,288 copying runner/train.py -> build/lib/runner 2024-12-11T18:19:19,290 creating build/lib/protenix 2024-12-11T18:19:19,291 copying protenix/__init__.py -> build/lib/protenix 2024-12-11T18:19:19,294 creating build/lib/configs 2024-12-11T18:19:19,295 copying configs/__init__.py -> build/lib/configs 2024-12-11T18:19:19,296 copying configs/configs_base.py -> build/lib/configs 2024-12-11T18:19:19,299 copying configs/configs_inference.py -> build/lib/configs 2024-12-11T18:19:19,300 copying configs/configs_data.py -> build/lib/configs 2024-12-11T18:19:19,303 creating build/lib/protenix/config 2024-12-11T18:19:19,304 copying protenix/config/__init__.py -> build/lib/protenix/config 2024-12-11T18:19:19,306 copying protenix/config/extend_types.py -> build/lib/protenix/config 2024-12-11T18:19:19,308 copying protenix/config/config.py -> build/lib/protenix/config 2024-12-11T18:19:19,311 creating build/lib/protenix/web_service 2024-12-11T18:19:19,312 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2024-12-11T18:19:19,315 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2024-12-11T18:19:19,316 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2024-12-11T18:19:19,319 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2024-12-11T18:19:19,321 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2024-12-11T18:19:19,323 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2024-12-11T18:19:19,326 creating build/lib/protenix/openfold_local 2024-12-11T18:19:19,327 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2024-12-11T18:19:19,330 creating build/lib/protenix/data 2024-12-11T18:19:19,331 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2024-12-11T18:19:19,334 copying protenix/data/__init__.py -> build/lib/protenix/data 2024-12-11T18:19:19,336 copying protenix/data/json_parser.py -> build/lib/protenix/data 2024-12-11T18:19:19,339 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2024-12-11T18:19:19,341 copying protenix/data/parser.py -> build/lib/protenix/data 2024-12-11T18:19:19,345 copying protenix/data/ccd.py -> build/lib/protenix/data 2024-12-11T18:19:19,347 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2024-12-11T18:19:19,350 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2024-12-11T18:19:19,352 copying protenix/data/featurizer.py -> build/lib/protenix/data 2024-12-11T18:19:19,355 copying protenix/data/json_maker.py -> build/lib/protenix/data 2024-12-11T18:19:19,358 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2024-12-11T18:19:19,360 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2024-12-11T18:19:19,363 copying protenix/data/dataset.py -> build/lib/protenix/data 2024-12-11T18:19:19,366 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2024-12-11T18:19:19,369 copying protenix/data/dataloader.py -> build/lib/protenix/data 2024-12-11T18:19:19,371 copying protenix/data/filter.py -> build/lib/protenix/data 2024-12-11T18:19:19,374 copying protenix/data/constants.py -> build/lib/protenix/data 2024-12-11T18:19:19,376 copying protenix/data/utils.py -> build/lib/protenix/data 2024-12-11T18:19:19,379 creating build/lib/protenix/utils 2024-12-11T18:19:19,380 copying protenix/utils/logger.py -> build/lib/protenix/utils 2024-12-11T18:19:19,382 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2024-12-11T18:19:19,384 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2024-12-11T18:19:19,386 copying protenix/utils/training.py -> build/lib/protenix/utils 2024-12-11T18:19:19,388 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2024-12-11T18:19:19,390 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2024-12-11T18:19:19,391 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2024-12-11T18:19:19,393 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2024-12-11T18:19:19,395 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2024-12-11T18:19:19,398 copying protenix/utils/seed.py -> build/lib/protenix/utils 2024-12-11T18:19:19,399 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2024-12-11T18:19:19,402 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2024-12-11T18:19:19,405 creating build/lib/protenix/metrics 2024-12-11T18:19:19,406 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2024-12-11T18:19:19,407 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2024-12-11T18:19:19,410 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2024-12-11T18:19:19,412 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2024-12-11T18:19:19,414 creating build/lib/protenix/model 2024-12-11T18:19:19,415 copying protenix/model/protenix.py -> build/lib/protenix/model 2024-12-11T18:19:19,418 copying protenix/model/__init__.py -> build/lib/protenix/model 2024-12-11T18:19:19,420 copying protenix/model/loss.py -> build/lib/protenix/model 2024-12-11T18:19:19,424 copying protenix/model/generator.py -> build/lib/protenix/model 2024-12-11T18:19:19,426 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2024-12-11T18:19:19,429 copying protenix/model/utils.py -> build/lib/protenix/model 2024-12-11T18:19:19,432 creating build/lib/protenix/openfold_local/data 2024-12-11T18:19:19,433 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:19:19,435 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:19:19,438 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:19:19,439 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:19:19,442 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:19:19,444 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:19:19,447 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:19:19,449 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2024-12-11T18:19:19,452 creating build/lib/protenix/openfold_local/utils 2024-12-11T18:19:19,454 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:19:19,456 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:19:19,459 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:19:19,461 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:19:19,464 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:19:19,466 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:19:19,468 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:19:19,470 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2024-12-11T18:19:19,474 creating build/lib/protenix/openfold_local/np 2024-12-11T18:19:19,476 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2024-12-11T18:19:19,478 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2024-12-11T18:19:19,481 creating build/lib/protenix/openfold_local/model 2024-12-11T18:19:19,483 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2024-12-11T18:19:19,486 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2024-12-11T18:19:19,488 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2024-12-11T18:19:19,490 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2024-12-11T18:19:19,492 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2024-12-11T18:19:19,496 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2024-12-11T18:19:19,499 creating build/lib/protenix/openfold_local/data/tools 2024-12-11T18:19:19,501 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2024-12-11T18:19:19,502 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2024-12-11T18:19:19,505 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2024-12-11T18:19:19,508 creating build/lib/protenix/openfold_local/utils/kernel 2024-12-11T18:19:19,509 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2024-12-11T18:19:19,511 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2024-12-11T18:19:19,514 creating build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,515 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,518 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,520 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,522 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,525 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,527 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,530 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,532 creating build/lib/protenix/utils/permutation 2024-12-11T18:19:19,534 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2024-12-11T18:19:19,536 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2024-12-11T18:19:19,539 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2024-12-11T18:19:19,541 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2024-12-11T18:19:19,544 creating build/lib/protenix/utils/permutation/chain_permutation 2024-12-11T18:19:19,545 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-11T18:19:19,548 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-11T18:19:19,550 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-11T18:19:19,553 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-12-11T18:19:19,556 creating build/lib/protenix/model/modules 2024-12-11T18:19:19,557 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2024-12-11T18:19:19,559 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2024-12-11T18:19:19,562 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2024-12-11T18:19:19,565 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2024-12-11T18:19:19,566 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2024-12-11T18:19:19,569 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2024-12-11T18:19:19,571 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2024-12-11T18:19:19,574 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2024-12-11T18:19:19,576 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2024-12-11T18:19:19,579 creating build/lib/protenix/model/layer_norm 2024-12-11T18:19:19,580 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2024-12-11T18:19:19,582 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2024-12-11T18:19:19,584 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2024-12-11T18:19:19,586 running egg_info 2024-12-11T18:19:19,616 writing protenix.egg-info/PKG-INFO 2024-12-11T18:19:19,620 writing dependency_links to protenix.egg-info/dependency_links.txt 2024-12-11T18:19:19,621 writing entry points to protenix.egg-info/entry_points.txt 2024-12-11T18:19:19,623 writing requirements to protenix.egg-info/requires.txt 2024-12-11T18:19:19,624 writing top-level names to protenix.egg-info/top_level.txt 2024-12-11T18:19:19,672 reading manifest file 'protenix.egg-info/SOURCES.txt' 2024-12-11T18:19:19,680 adding license file 'LICENSE' 2024-12-11T18:19:19,688 writing manifest file 'protenix.egg-info/SOURCES.txt' 2024-12-11T18:19:19,691 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'protenix.model.layer_norm.kernel' is absent from the `packages` configuration. 2024-12-11T18:19:19,692 !! 2024-12-11T18:19:19,693 ******************************************************************************** 2024-12-11T18:19:19,694 ############################ 2024-12-11T18:19:19,694 # Package would be ignored # 2024-12-11T18:19:19,695 ############################ 2024-12-11T18:19:19,696 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2024-12-11T18:19:19,696 but it is absent from setuptools' `packages` configuration. 2024-12-11T18:19:19,697 This leads to an ambiguous overall configuration. If you want to distribute this 2024-12-11T18:19:19,698 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2024-12-11T18:19:19,698 to the `packages` configuration field. 2024-12-11T18:19:19,700 Alternatively, you can also rely on setuptools' discovery methods 2024-12-11T18:19:19,700 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-12-11T18:19:19,701 instead of `find_packages(...)`/`find:`). 2024-12-11T18:19:19,702 You can read more about "package discovery" on setuptools documentation page: 2024-12-11T18:19:19,704 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-12-11T18:19:19,705 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2024-12-11T18:19:19,705 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2024-12-11T18:19:19,705 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-12-11T18:19:19,706 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-12-11T18:19:19,706 combination with a more fine grained `package-data` configuration. 2024-12-11T18:19:19,707 You can read more about "package data files" on setuptools documentation page: 2024-12-11T18:19:19,708 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-12-11T18:19:19,709 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-12-11T18:19:19,710 even if it does not contain any `.py` files. 2024-12-11T18:19:19,711 On the other hand, currently there is no concept of package data 2024-12-11T18:19:19,711 directory, all directories are treated like packages. 2024-12-11T18:19:19,711 ******************************************************************************** 2024-12-11T18:19:19,713 !! 2024-12-11T18:19:19,713 check.warn(importable) 2024-12-11T18:19:19,714 creating build/lib/protenix/model/layer_norm/kernel 2024-12-11T18:19:19,714 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2024-12-11T18:19:19,715 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2024-12-11T18:19:19,715 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2024-12-11T18:19:19,716 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2024-12-11T18:19:19,756 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-12-11T18:19:19,757 !! 2024-12-11T18:19:19,758 ******************************************************************************** 2024-12-11T18:19:19,759 Please avoid running ``setup.py`` directly. 2024-12-11T18:19:19,759 Instead, use pypa/build, pypa/installer or other 2024-12-11T18:19:19,760 standards-based tools. 2024-12-11T18:19:19,761 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-12-11T18:19:19,762 ******************************************************************************** 2024-12-11T18:19:19,763 !! 2024-12-11T18:19:19,764 self.initialize_options() 2024-12-11T18:19:19,784 installing to build/bdist.linux-armv7l/wheel 2024-12-11T18:19:19,785 running install 2024-12-11T18:19:19,810 running install_lib 2024-12-11T18:19:19,837 creating build/bdist.linux-armv7l/wheel 2024-12-11T18:19:19,839 creating build/bdist.linux-armv7l/wheel/runner 2024-12-11T18:19:19,840 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-11T18:19:19,842 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-11T18:19:19,844 copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-11T18:19:19,847 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-11T18:19:19,849 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-11T18:19:19,851 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2024-12-11T18:19:19,854 creating build/bdist.linux-armv7l/wheel/protenix 2024-12-11T18:19:19,856 creating build/bdist.linux-armv7l/wheel/protenix/config 2024-12-11T18:19:19,857 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-11T18:19:19,859 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-11T18:19:19,861 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-12-11T18:19:19,864 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2024-12-11T18:19:19,865 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-11T18:19:19,868 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-11T18:19:19,870 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-11T18:19:19,872 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-11T18:19:19,874 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-11T18:19:19,876 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-12-11T18:19:19,879 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2024-12-11T18:19:19,880 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2024-12-11T18:19:19,883 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2024-12-11T18:19:19,884 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:19:19,886 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:19:19,890 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2024-12-11T18:19:19,891 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-11T18:19:19,892 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-11T18:19:19,895 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-12-11T18:19:19,896 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:19:19,898 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:19:19,900 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:19:19,902 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:19:19,905 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:19:19,907 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-12-11T18:19:19,910 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2024-12-11T18:19:19,911 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:19:19,913 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:19:19,915 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:19:19,917 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:19:19,919 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:19:19,921 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:19:19,924 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2024-12-11T18:19:19,925 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-12-11T18:19:19,927 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-12-11T18:19:19,929 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,931 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,933 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,935 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,937 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,939 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,941 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,943 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-12-11T18:19:19,945 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:19:19,947 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-12-11T18:19:19,951 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2024-12-11T18:19:19,952 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-12-11T18:19:19,954 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-12-11T18:19:19,957 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2024-12-11T18:19:19,958 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-11T18:19:19,961 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-11T18:19:19,963 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-11T18:19:19,965 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-11T18:19:19,966 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-11T18:19:19,969 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-12-11T18:19:19,972 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2024-12-11T18:19:19,974 creating build/bdist.linux-armv7l/wheel/protenix/data 2024-12-11T18:19:19,975 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:19,978 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:19,979 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:19,982 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:19,984 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:19,987 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:19,990 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:19,992 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:19,994 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:19,997 copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:19,999 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:20,001 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:20,003 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:20,006 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:20,009 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:20,011 copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:20,013 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:20,016 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-12-11T18:19:20,019 creating build/bdist.linux-armv7l/wheel/protenix/utils 2024-12-11T18:19:20,020 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:19:20,022 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:19:20,024 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:19:20,026 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:19:20,028 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:19:20,031 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2024-12-11T18:19:20,032 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-11T18:19:20,035 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2024-12-11T18:19:20,036 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-11T18:19:20,038 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-11T18:19:20,041 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-11T18:19:20,044 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-12-11T18:19:20,046 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-11T18:19:20,048 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-11T18:19:20,051 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-12-11T18:19:20,053 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:19:20,054 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:19:20,056 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:19:20,058 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:19:20,060 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:19:20,062 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:19:20,064 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-12-11T18:19:20,067 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2024-12-11T18:19:20,068 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-11T18:19:20,070 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-11T18:19:20,072 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-11T18:19:20,074 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-12-11T18:19:20,077 creating build/bdist.linux-armv7l/wheel/protenix/model 2024-12-11T18:19:20,078 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-11T18:19:20,081 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2024-12-11T18:19:20,083 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:19:20,085 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:19:20,088 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:19:20,090 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:19:20,092 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:19:20,094 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:19:20,097 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:19:20,099 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:19:20,101 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-12-11T18:19:20,105 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2024-12-11T18:19:20,106 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-11T18:19:20,108 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-11T18:19:20,110 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2024-12-11T18:19:20,112 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-11T18:19:20,114 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-11T18:19:20,117 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-11T18:19:20,119 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-12-11T18:19:20,121 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-12-11T18:19:20,123 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-11T18:19:20,125 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-11T18:19:20,128 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-11T18:19:20,131 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-11T18:19:20,133 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-12-11T18:19:20,136 creating build/bdist.linux-armv7l/wheel/configs 2024-12-11T18:19:20,137 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-11T18:19:20,139 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-11T18:19:20,141 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-11T18:19:20,143 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2024-12-11T18:19:20,145 running install_data 2024-12-11T18:19:20,173 creating build/bdist.linux-armv7l/wheel/protenix-0.1.2.data/data 2024-12-11T18:19:20,174 warning: install_data: setup script did not provide a directory for 'requirements.txt' -- installing right in 'build/bdist.linux-armv7l/wheel/protenix-0.1.2.data/data' 2024-12-11T18:19:20,175 copying requirements.txt -> build/bdist.linux-armv7l/wheel/protenix-0.1.2.data/data 2024-12-11T18:19:20,177 running install_egg_info 2024-12-11T18:19:20,210 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.1.2-py3.11.egg-info 2024-12-11T18:19:20,222 running install_scripts 2024-12-11T18:19:20,243 creating build/bdist.linux-armv7l/wheel/protenix-0.1.2.dist-info/WHEEL 2024-12-11T18:19:20,245 creating '/tmp/pip-wheel-yl49nwq7/protenix-0.1.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-12-11T18:19:20,247 adding 'configs/__init__.py' 2024-12-11T18:19:20,249 adding 'configs/configs_base.py' 2024-12-11T18:19:20,251 adding 'configs/configs_data.py' 2024-12-11T18:19:20,252 adding 'configs/configs_inference.py' 2024-12-11T18:19:20,254 adding 'protenix/__init__.py' 2024-12-11T18:19:20,256 adding 'protenix/config/__init__.py' 2024-12-11T18:19:20,258 adding 'protenix/config/config.py' 2024-12-11T18:19:20,259 adding 'protenix/config/extend_types.py' 2024-12-11T18:19:20,261 adding 'protenix/data/__init__.py' 2024-12-11T18:19:20,264 adding 'protenix/data/ccd.py' 2024-12-11T18:19:20,268 adding 'protenix/data/constants.py' 2024-12-11T18:19:20,270 adding 'protenix/data/data_pipeline.py' 2024-12-11T18:19:20,272 adding 'protenix/data/dataloader.py' 2024-12-11T18:19:20,278 adding 'protenix/data/dataset.py' 2024-12-11T18:19:20,282 adding 'protenix/data/featurizer.py' 2024-12-11T18:19:20,283 adding 'protenix/data/filter.py' 2024-12-11T18:19:20,285 adding 'protenix/data/infer_data_pipeline.py' 2024-12-11T18:19:20,287 adding 'protenix/data/json_maker.py' 2024-12-11T18:19:20,290 adding 'protenix/data/json_parser.py' 2024-12-11T18:19:20,292 adding 'protenix/data/json_to_feature.py' 2024-12-11T18:19:20,296 adding 'protenix/data/msa_featurizer.py' 2024-12-11T18:19:20,302 adding 'protenix/data/msa_utils.py' 2024-12-11T18:19:20,308 adding 'protenix/data/parser.py' 2024-12-11T18:19:20,310 adding 'protenix/data/substructure_perms.py' 2024-12-11T18:19:20,311 adding 'protenix/data/tokenizer.py' 2024-12-11T18:19:20,314 adding 'protenix/data/utils.py' 2024-12-11T18:19:20,316 adding 'protenix/metrics/__init__.py' 2024-12-11T18:19:20,318 adding 'protenix/metrics/clash.py' 2024-12-11T18:19:20,320 adding 'protenix/metrics/lddt_metrics.py' 2024-12-11T18:19:20,321 adding 'protenix/metrics/rmsd.py' 2024-12-11T18:19:20,323 adding 'protenix/model/__init__.py' 2024-12-11T18:19:20,325 adding 'protenix/model/generator.py' 2024-12-11T18:19:20,331 adding 'protenix/model/loss.py' 2024-12-11T18:19:20,334 adding 'protenix/model/protenix.py' 2024-12-11T18:19:20,337 adding 'protenix/model/sample_confidence.py' 2024-12-11T18:19:20,339 adding 'protenix/model/utils.py' 2024-12-11T18:19:20,341 adding 'protenix/model/layer_norm/__init__.py' 2024-12-11T18:19:20,343 adding 'protenix/model/layer_norm/layer_norm.py' 2024-12-11T18:19:20,344 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2024-12-11T18:19:20,346 adding 'protenix/model/layer_norm/kernel/compat.h' 2024-12-11T18:19:20,347 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2024-12-11T18:19:20,349 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2024-12-11T18:19:20,351 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2024-12-11T18:19:20,352 adding 'protenix/model/modules/__init__.py' 2024-12-11T18:19:20,354 adding 'protenix/model/modules/confidence.py' 2024-12-11T18:19:20,357 adding 'protenix/model/modules/diffusion.py' 2024-12-11T18:19:20,359 adding 'protenix/model/modules/embedders.py' 2024-12-11T18:19:20,360 adding 'protenix/model/modules/frames.py' 2024-12-11T18:19:20,361 adding 'protenix/model/modules/head.py' 2024-12-11T18:19:20,364 adding 'protenix/model/modules/pairformer.py' 2024-12-11T18:19:20,368 adding 'protenix/model/modules/primitives.py' 2024-12-11T18:19:20,371 adding 'protenix/model/modules/transformer.py' 2024-12-11T18:19:20,373 adding 'protenix/openfold_local/__init__.py' 2024-12-11T18:19:20,375 adding 'protenix/openfold_local/data/__init__.py' 2024-12-11T18:19:20,376 adding 'protenix/openfold_local/data/data_transforms.py' 2024-12-11T18:19:20,378 adding 'protenix/openfold_local/data/errors.py' 2024-12-11T18:19:20,380 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2024-12-11T18:19:20,382 adding 'protenix/openfold_local/data/msa_identifiers.py' 2024-12-11T18:19:20,384 adding 'protenix/openfold_local/data/msa_pairing.py' 2024-12-11T18:19:20,388 adding 'protenix/openfold_local/data/parsers.py' 2024-12-11T18:19:20,391 adding 'protenix/openfold_local/data/templates.py' 2024-12-11T18:19:20,393 adding 'protenix/openfold_local/data/tools/__init__.py' 2024-12-11T18:19:20,394 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2024-12-11T18:19:20,396 adding 'protenix/openfold_local/data/tools/utils.py' 2024-12-11T18:19:20,397 adding 'protenix/openfold_local/model/__init__.py' 2024-12-11T18:19:20,399 adding 'protenix/openfold_local/model/dropout.py' 2024-12-11T18:19:20,400 adding 'protenix/openfold_local/model/outer_product_mean.py' 2024-12-11T18:19:20,403 adding 'protenix/openfold_local/model/primitives.py' 2024-12-11T18:19:20,405 adding 'protenix/openfold_local/model/triangular_attention.py' 2024-12-11T18:19:20,407 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2024-12-11T18:19:20,409 adding 'protenix/openfold_local/np/__init__.py' 2024-12-11T18:19:20,414 adding 'protenix/openfold_local/np/residue_constants.py' 2024-12-11T18:19:20,416 adding 'protenix/openfold_local/utils/__init__.py' 2024-12-11T18:19:20,419 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2024-12-11T18:19:20,420 adding 'protenix/openfold_local/utils/checkpointing.py' 2024-12-11T18:19:20,423 adding 'protenix/openfold_local/utils/chunk_utils.py' 2024-12-11T18:19:20,424 adding 'protenix/openfold_local/utils/feats.py' 2024-12-11T18:19:20,426 adding 'protenix/openfold_local/utils/precision_utils.py' 2024-12-11T18:19:20,430 adding 'protenix/openfold_local/utils/rigid_utils.py' 2024-12-11T18:19:20,432 adding 'protenix/openfold_local/utils/tensor_utils.py' 2024-12-11T18:19:20,434 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2024-12-11T18:19:20,435 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2024-12-11T18:19:20,436 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2024-12-11T18:19:20,438 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2024-12-11T18:19:20,439 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2024-12-11T18:19:20,440 adding 'protenix/openfold_local/utils/geometry/utils.py' 2024-12-11T18:19:20,442 adding 'protenix/openfold_local/utils/geometry/vector.py' 2024-12-11T18:19:20,443 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2024-12-11T18:19:20,444 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2024-12-11T18:19:20,446 adding 'protenix/utils/__init__.py' 2024-12-11T18:19:20,450 adding 'protenix/utils/cropping.py' 2024-12-11T18:19:20,451 adding 'protenix/utils/distributed.py' 2024-12-11T18:19:20,452 adding 'protenix/utils/file_io.py' 2024-12-11T18:19:20,454 adding 'protenix/utils/geometry.py' 2024-12-11T18:19:20,455 adding 'protenix/utils/logger.py' 2024-12-11T18:19:20,456 adding 'protenix/utils/lr_scheduler.py' 2024-12-11T18:19:20,458 adding 'protenix/utils/metrics.py' 2024-12-11T18:19:20,459 adding 'protenix/utils/scatter_utils.py' 2024-12-11T18:19:20,461 adding 'protenix/utils/seed.py' 2024-12-11T18:19:20,462 adding 'protenix/utils/torch_utils.py' 2024-12-11T18:19:20,463 adding 'protenix/utils/training.py' 2024-12-11T18:19:20,465 adding 'protenix/utils/permutation/__init__.py' 2024-12-11T18:19:20,469 adding 'protenix/utils/permutation/atom_permutation.py' 2024-12-11T18:19:20,471 adding 'protenix/utils/permutation/permutation.py' 2024-12-11T18:19:20,473 adding 'protenix/utils/permutation/utils.py' 2024-12-11T18:19:20,475 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2024-12-11T18:19:20,479 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2024-12-11T18:19:20,481 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2024-12-11T18:19:20,482 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2024-12-11T18:19:20,484 adding 'protenix/web_service/__init__.py' 2024-12-11T18:19:20,486 adding 'protenix/web_service/colab_request_parser.py' 2024-12-11T18:19:20,488 adding 'protenix/web_service/colab_request_utils.py' 2024-12-11T18:19:20,489 adding 'protenix/web_service/dependency_url.py' 2024-12-11T18:19:20,491 adding 'protenix/web_service/prediction_visualization.py' 2024-12-11T18:19:20,493 adding 'protenix/web_service/viewer.py' 2024-12-11T18:19:20,495 adding 'protenix-0.1.2.data/data/requirements.txt' 2024-12-11T18:19:20,498 adding 'runner/__init__.py' 2024-12-11T18:19:20,500 adding 'runner/batch_inference.py' 2024-12-11T18:19:20,502 adding 'runner/dumper.py' 2024-12-11T18:19:20,503 adding 'runner/ema.py' 2024-12-11T18:19:20,505 adding 'runner/inference.py' 2024-12-11T18:19:20,508 adding 'runner/train.py' 2024-12-11T18:19:20,511 adding 'protenix-0.1.2.dist-info/LICENSE' 2024-12-11T18:19:20,512 adding 'protenix-0.1.2.dist-info/METADATA' 2024-12-11T18:19:20,513 adding 'protenix-0.1.2.dist-info/WHEEL' 2024-12-11T18:19:20,514 adding 'protenix-0.1.2.dist-info/entry_points.txt' 2024-12-11T18:19:20,515 adding 'protenix-0.1.2.dist-info/top_level.txt' 2024-12-11T18:19:20,517 adding 'protenix-0.1.2.dist-info/RECORD' 2024-12-11T18:19:20,524 removing build/bdist.linux-armv7l/wheel 2024-12-11T18:19:20,670 Building wheel for protenix (setup.py): finished with status 'done' 2024-12-11T18:19:20,677 Created wheel for protenix: filename=protenix-0.1.2-py3-none-any.whl size=383227 sha256=10909020be81638dbfe8da0ff0bc107ad732dc3dc8e420d09aa3e346c53ac527 2024-12-11T18:19:20,678 Stored in directory: /tmp/pip-ephem-wheel-cache-4yj_ygue/wheels/87/0a/e7/8616c89dacbac822f933dcb2f43ca04b0852a6b983c38f37c4 2024-12-11T18:19:20,692 Successfully built protenix 2024-12-11T18:19:20,704 Removed build tracker: '/tmp/pip-build-tracker-ljutlwtb'