2024-11-29T15:11:41,468 Created temporary directory: /tmp/pip-build-tracker-wl_t_okq 2024-11-29T15:11:41,469 Initialized build tracking at /tmp/pip-build-tracker-wl_t_okq 2024-11-29T15:11:41,470 Created build tracker: /tmp/pip-build-tracker-wl_t_okq 2024-11-29T15:11:41,470 Entered build tracker: /tmp/pip-build-tracker-wl_t_okq 2024-11-29T15:11:41,471 Created temporary directory: /tmp/pip-wheel-4jrtse24 2024-11-29T15:11:41,475 Created temporary directory: /tmp/pip-ephem-wheel-cache-og5kuoxc 2024-11-29T15:11:41,517 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-11-29T15:11:41,520 2 location(s) to search for versions of protenix: 2024-11-29T15:11:41,520 * https://pypi.org/simple/protenix/ 2024-11-29T15:11:41,520 * https://www.piwheels.org/simple/protenix/ 2024-11-29T15:11:41,521 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2024-11-29T15:11:41,522 Getting page https://pypi.org/simple/protenix/ 2024-11-29T15:11:41,523 Found index url https://pypi.org/simple/ 2024-11-29T15:11:41,744 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2024-11-29T15:11:41,746 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/) 2024-11-29T15:11:41,747 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/) 2024-11-29T15:11:41,747 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 2024-11-29T15:11:41,748 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) 2024-11-29T15:11:41,749 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 2024-11-29T15:11:41,749 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) 2024-11-29T15:11:41,751 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 2024-11-29T15:11:41,751 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2024-11-29T15:11:41,752 Getting page https://www.piwheels.org/simple/protenix/ 2024-11-29T15:11:41,754 Found index url https://www.piwheels.org/simple/ 2024-11-29T15:11:41,938 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2024-11-29T15:11:41,940 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/) 2024-11-29T15:11:41,941 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2024-11-29T15:11:41,942 Skipping link: not a file: https://pypi.org/simple/protenix/ 2024-11-29T15:11:41,959 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2024-11-29T15:11:41,961 Collecting protenix==0.1.0 2024-11-29T15:11:41,964 Created temporary directory: /tmp/pip-unpack-10qhtie4 2024-11-29T15:11:42,112 Downloading protenix-0.1.0.tar.gz (298 kB) 2024-11-29T15:11:42,717 Added protenix==0.1.0 from https://files.pythonhosted.org/packages/d5/61/cdea4397a181ca2b108c6df0aa4c30e7a6fc34c5b75ad69557569c44b61d/protenix-0.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-wl_t_okq' 2024-11-29T15:11:42,719 Running setup.py (path:/tmp/pip-wheel-4jrtse24/protenix_24fe50745ddf44f68190cebbbd2431cb/setup.py) egg_info for package protenix 2024-11-29T15:11:42,720 Created temporary directory: /tmp/pip-pip-egg-info-0wg2yh_y 2024-11-29T15:11:42,720 Preparing metadata (setup.py): started 2024-11-29T15:11:42,722 Running command python setup.py egg_info 2024-11-29T15:11:43,856 running egg_info 2024-11-29T15:11:44,097 creating /tmp/pip-pip-egg-info-0wg2yh_y/protenix.egg-info 2024-11-29T15:11:44,098 writing /tmp/pip-pip-egg-info-0wg2yh_y/protenix.egg-info/PKG-INFO 2024-11-29T15:11:44,103 writing dependency_links to /tmp/pip-pip-egg-info-0wg2yh_y/protenix.egg-info/dependency_links.txt 2024-11-29T15:11:44,105 writing entry points to /tmp/pip-pip-egg-info-0wg2yh_y/protenix.egg-info/entry_points.txt 2024-11-29T15:11:44,106 writing requirements to /tmp/pip-pip-egg-info-0wg2yh_y/protenix.egg-info/requires.txt 2024-11-29T15:11:44,108 writing top-level names to /tmp/pip-pip-egg-info-0wg2yh_y/protenix.egg-info/top_level.txt 2024-11-29T15:11:44,110 writing manifest file '/tmp/pip-pip-egg-info-0wg2yh_y/protenix.egg-info/SOURCES.txt' 2024-11-29T15:11:44,441 reading manifest file '/tmp/pip-pip-egg-info-0wg2yh_y/protenix.egg-info/SOURCES.txt' 2024-11-29T15:11:44,443 adding license file 'LICENSE' 2024-11-29T15:11:44,448 writing manifest file '/tmp/pip-pip-egg-info-0wg2yh_y/protenix.egg-info/SOURCES.txt' 2024-11-29T15:11:44,557 Preparing metadata (setup.py): finished with status 'done' 2024-11-29T15:11:44,562 Source in /tmp/pip-wheel-4jrtse24/protenix_24fe50745ddf44f68190cebbbd2431cb has version 0.1.0, which satisfies requirement protenix==0.1.0 from https://files.pythonhosted.org/packages/d5/61/cdea4397a181ca2b108c6df0aa4c30e7a6fc34c5b75ad69557569c44b61d/protenix-0.1.0.tar.gz 2024-11-29T15:11:44,563 Removed protenix==0.1.0 from https://files.pythonhosted.org/packages/d5/61/cdea4397a181ca2b108c6df0aa4c30e7a6fc34c5b75ad69557569c44b61d/protenix-0.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-wl_t_okq' 2024-11-29T15:11:44,574 Created temporary directory: /tmp/pip-unpack-_q9in5g1 2024-11-29T15:11:44,576 Created temporary directory: /tmp/pip-unpack-ncooxhnu 2024-11-29T15:11:44,577 Building wheels for collected packages: protenix 2024-11-29T15:11:44,804 Created temporary directory: /tmp/pip-wheel-l9zl0ada 2024-11-29T15:11:44,805 Building wheel for protenix (setup.py): started 2024-11-29T15:11:44,808 Destination directory: /tmp/pip-wheel-l9zl0ada 2024-11-29T15:11:44,810 Running command python setup.py bdist_wheel 2024-11-29T15:11:46,125 running bdist_wheel 2024-11-29T15:11:46,257 running build 2024-11-29T15:11:46,258 running build_py 2024-11-29T15:11:46,288 creating build/lib/configs 2024-11-29T15:11:46,291 copying configs/configs_inference.py -> build/lib/configs 2024-11-29T15:11:46,293 copying configs/configs_data.py -> build/lib/configs 2024-11-29T15:11:46,295 copying configs/__init__.py -> build/lib/configs 2024-11-29T15:11:46,298 copying configs/configs_base.py -> build/lib/configs 2024-11-29T15:11:46,301 creating build/lib/protenix 2024-11-29T15:11:46,302 copying protenix/__init__.py -> build/lib/protenix 2024-11-29T15:11:46,304 creating build/lib/runner 2024-11-29T15:11:46,305 copying runner/dumper.py -> build/lib/runner 2024-11-29T15:11:46,307 copying runner/__init__.py -> build/lib/runner 2024-11-29T15:11:46,309 copying runner/ema.py -> build/lib/runner 2024-11-29T15:11:46,311 copying runner/train.py -> build/lib/runner 2024-11-29T15:11:46,314 copying runner/inference.py -> build/lib/runner 2024-11-29T15:11:46,317 creating build/lib/protenix/data 2024-11-29T15:11:46,319 copying protenix/data/constants.py -> build/lib/protenix/data 2024-11-29T15:11:46,322 copying protenix/data/ccd.py -> build/lib/protenix/data 2024-11-29T15:11:46,325 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2024-11-29T15:11:46,328 copying protenix/data/utils.py -> build/lib/protenix/data 2024-11-29T15:11:46,331 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2024-11-29T15:11:46,333 copying protenix/data/parser.py -> build/lib/protenix/data 2024-11-29T15:11:46,337 copying protenix/data/dataloader.py -> build/lib/protenix/data 2024-11-29T15:11:46,339 copying protenix/data/dataset.py -> build/lib/protenix/data 2024-11-29T15:11:46,342 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2024-11-29T15:11:46,345 copying protenix/data/__init__.py -> build/lib/protenix/data 2024-11-29T15:11:46,347 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2024-11-29T15:11:46,349 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2024-11-29T15:11:46,352 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2024-11-29T15:11:46,355 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2024-11-29T15:11:46,358 copying protenix/data/featurizer.py -> build/lib/protenix/data 2024-11-29T15:11:46,361 copying protenix/data/json_parser.py -> build/lib/protenix/data 2024-11-29T15:11:46,364 creating build/lib/protenix/metrics 2024-11-29T15:11:46,365 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2024-11-29T15:11:46,368 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2024-11-29T15:11:46,370 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2024-11-29T15:11:46,372 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2024-11-29T15:11:46,375 creating build/lib/protenix/utils 2024-11-29T15:11:46,376 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2024-11-29T15:11:46,379 copying protenix/utils/logger.py -> build/lib/protenix/utils 2024-11-29T15:11:46,381 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2024-11-29T15:11:46,383 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2024-11-29T15:11:46,385 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2024-11-29T15:11:46,388 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2024-11-29T15:11:46,389 copying protenix/utils/training.py -> build/lib/protenix/utils 2024-11-29T15:11:46,392 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2024-11-29T15:11:46,394 copying protenix/utils/seed.py -> build/lib/protenix/utils 2024-11-29T15:11:46,396 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2024-11-29T15:11:46,399 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2024-11-29T15:11:46,401 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2024-11-29T15:11:46,404 creating build/lib/protenix/config 2024-11-29T15:11:46,405 copying protenix/config/extend_types.py -> build/lib/protenix/config 2024-11-29T15:11:46,407 copying protenix/config/config.py -> build/lib/protenix/config 2024-11-29T15:11:46,410 copying protenix/config/__init__.py -> build/lib/protenix/config 2024-11-29T15:11:46,412 creating build/lib/protenix/web_service 2024-11-29T15:11:46,414 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2024-11-29T15:11:46,416 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2024-11-29T15:11:46,418 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2024-11-29T15:11:46,421 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2024-11-29T15:11:46,423 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2024-11-29T15:11:46,425 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2024-11-29T15:11:46,428 creating build/lib/protenix/model 2024-11-29T15:11:46,429 copying protenix/model/utils.py -> build/lib/protenix/model 2024-11-29T15:11:46,432 copying protenix/model/__init__.py -> build/lib/protenix/model 2024-11-29T15:11:46,434 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2024-11-29T15:11:46,437 copying protenix/model/protenix.py -> build/lib/protenix/model 2024-11-29T15:11:46,440 copying protenix/model/loss.py -> build/lib/protenix/model 2024-11-29T15:11:46,445 copying protenix/model/generator.py -> build/lib/protenix/model 2024-11-29T15:11:46,448 creating build/lib/protenix/openfold_local 2024-11-29T15:11:46,449 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2024-11-29T15:11:46,452 creating build/lib/protenix/utils/permutation 2024-11-29T15:11:46,453 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2024-11-29T15:11:46,455 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2024-11-29T15:11:46,457 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2024-11-29T15:11:46,460 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2024-11-29T15:11:46,463 creating build/lib/protenix/utils/permutation/chain_permutation 2024-11-29T15:11:46,464 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-11-29T15:11:46,467 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-11-29T15:11:46,469 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-11-29T15:11:46,472 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2024-11-29T15:11:46,475 creating build/lib/protenix/model/layer_norm 2024-11-29T15:11:46,476 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2024-11-29T15:11:46,478 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2024-11-29T15:11:46,480 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2024-11-29T15:11:46,483 creating build/lib/protenix/model/modules 2024-11-29T15:11:46,484 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2024-11-29T15:11:46,486 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2024-11-29T15:11:46,489 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2024-11-29T15:11:46,491 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2024-11-29T15:11:46,494 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2024-11-29T15:11:46,496 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2024-11-29T15:11:46,498 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2024-11-29T15:11:46,501 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2024-11-29T15:11:46,504 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2024-11-29T15:11:46,507 creating build/lib/protenix/openfold_local/data 2024-11-29T15:11:46,508 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2024-11-29T15:11:46,511 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2024-11-29T15:11:46,514 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2024-11-29T15:11:46,517 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2024-11-29T15:11:46,519 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2024-11-29T15:11:46,521 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2024-11-29T15:11:46,524 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2024-11-29T15:11:46,527 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2024-11-29T15:11:46,531 creating build/lib/protenix/openfold_local/utils 2024-11-29T15:11:46,532 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2024-11-29T15:11:46,536 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2024-11-29T15:11:46,539 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2024-11-29T15:11:46,541 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2024-11-29T15:11:46,543 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2024-11-29T15:11:46,546 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2024-11-29T15:11:46,548 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2024-11-29T15:11:46,551 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2024-11-29T15:11:46,555 creating build/lib/protenix/openfold_local/np 2024-11-29T15:11:46,556 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2024-11-29T15:11:46,558 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2024-11-29T15:11:46,563 creating build/lib/protenix/openfold_local/model 2024-11-29T15:11:46,564 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2024-11-29T15:11:46,567 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2024-11-29T15:11:46,570 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2024-11-29T15:11:46,572 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2024-11-29T15:11:46,576 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2024-11-29T15:11:46,579 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2024-11-29T15:11:46,582 creating build/lib/protenix/openfold_local/data/tools 2024-11-29T15:11:46,584 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2024-11-29T15:11:46,586 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2024-11-29T15:11:46,588 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2024-11-29T15:11:46,592 creating build/lib/protenix/openfold_local/utils/geometry 2024-11-29T15:11:46,593 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-11-29T15:11:46,596 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-11-29T15:11:46,599 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2024-11-29T15:11:46,602 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2024-11-29T15:11:46,604 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2024-11-29T15:11:46,606 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2024-11-29T15:11:46,609 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2024-11-29T15:11:46,612 creating build/lib/protenix/openfold_local/utils/kernel 2024-11-29T15:11:46,614 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2024-11-29T15:11:46,617 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2024-11-29T15:11:46,619 running egg_info 2024-11-29T15:11:46,650 writing protenix.egg-info/PKG-INFO 2024-11-29T15:11:46,654 writing dependency_links to protenix.egg-info/dependency_links.txt 2024-11-29T15:11:46,655 writing entry points to protenix.egg-info/entry_points.txt 2024-11-29T15:11:46,657 writing requirements to protenix.egg-info/requires.txt 2024-11-29T15:11:46,658 writing top-level names to protenix.egg-info/top_level.txt 2024-11-29T15:11:46,706 reading manifest file 'protenix.egg-info/SOURCES.txt' 2024-11-29T15:11:46,714 adding license file 'LICENSE' 2024-11-29T15:11:46,722 writing manifest file 'protenix.egg-info/SOURCES.txt' 2024-11-29T15:11:46,725 /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. 2024-11-29T15:11:46,725 !! 2024-11-29T15:11:46,726 ******************************************************************************** 2024-11-29T15:11:46,726 ############################ 2024-11-29T15:11:46,727 # Package would be ignored # 2024-11-29T15:11:46,727 ############################ 2024-11-29T15:11:46,728 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2024-11-29T15:11:46,728 but it is absent from setuptools' `packages` configuration. 2024-11-29T15:11:46,729 This leads to an ambiguous overall configuration. If you want to distribute this 2024-11-29T15:11:46,730 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2024-11-29T15:11:46,730 to the `packages` configuration field. 2024-11-29T15:11:46,731 Alternatively, you can also rely on setuptools' discovery methods 2024-11-29T15:11:46,732 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-11-29T15:11:46,732 instead of `find_packages(...)`/`find:`). 2024-11-29T15:11:46,733 You can read more about "package discovery" on setuptools documentation page: 2024-11-29T15:11:46,734 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-11-29T15:11:46,736 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2024-11-29T15:11:46,736 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2024-11-29T15:11:46,737 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-11-29T15:11:46,737 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-11-29T15:11:46,738 combination with a more fine grained `package-data` configuration. 2024-11-29T15:11:46,739 You can read more about "package data files" on setuptools documentation page: 2024-11-29T15:11:46,740 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-11-29T15:11:46,742 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-11-29T15:11:46,743 even if it does not contain any `.py` files. 2024-11-29T15:11:46,743 On the other hand, currently there is no concept of package data 2024-11-29T15:11:46,744 directory, all directories are treated like packages. 2024-11-29T15:11:46,744 ******************************************************************************** 2024-11-29T15:11:46,746 !! 2024-11-29T15:11:46,746 check.warn(importable) 2024-11-29T15:11:46,747 creating build/lib/protenix/model/layer_norm/kernel 2024-11-29T15:11:46,748 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2024-11-29T15:11:46,748 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2024-11-29T15:11:46,749 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2024-11-29T15:11:46,750 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2024-11-29T15:11:46,791 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-11-29T15:11:46,791 !! 2024-11-29T15:11:46,792 ******************************************************************************** 2024-11-29T15:11:46,793 Please avoid running ``setup.py`` directly. 2024-11-29T15:11:46,793 Instead, use pypa/build, pypa/installer or other 2024-11-29T15:11:46,794 standards-based tools. 2024-11-29T15:11:46,795 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-11-29T15:11:46,795 ******************************************************************************** 2024-11-29T15:11:46,796 !! 2024-11-29T15:11:46,796 self.initialize_options() 2024-11-29T15:11:46,819 installing to build/bdist.linux-armv7l/wheel 2024-11-29T15:11:46,820 running install 2024-11-29T15:11:46,845 running install_lib 2024-11-29T15:11:46,873 creating build/bdist.linux-armv7l/wheel 2024-11-29T15:11:46,875 creating build/bdist.linux-armv7l/wheel/configs 2024-11-29T15:11:46,876 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2024-11-29T15:11:46,878 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2024-11-29T15:11:46,880 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2024-11-29T15:11:46,882 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2024-11-29T15:11:46,885 creating build/bdist.linux-armv7l/wheel/protenix 2024-11-29T15:11:46,886 creating build/bdist.linux-armv7l/wheel/protenix/data 2024-11-29T15:11:46,888 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,891 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,893 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,895 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,898 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,900 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,903 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,905 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,908 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,911 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,912 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,914 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,917 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,920 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,922 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,925 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2024-11-29T15:11:46,928 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2024-11-29T15:11:46,929 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-11-29T15:11:46,932 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-11-29T15:11:46,934 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-11-29T15:11:46,936 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2024-11-29T15:11:46,939 creating build/bdist.linux-armv7l/wheel/protenix/utils 2024-11-29T15:11:46,940 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-11-29T15:11:46,943 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-11-29T15:11:46,944 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-11-29T15:11:46,947 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-11-29T15:11:46,948 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-11-29T15:11:46,951 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-11-29T15:11:46,952 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-11-29T15:11:46,955 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-11-29T15:11:46,956 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-11-29T15:11:46,958 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-11-29T15:11:46,961 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-11-29T15:11:46,963 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2024-11-29T15:11:46,965 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2024-11-29T15:11:46,967 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2024-11-29T15:11:46,969 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-11-29T15:11:46,971 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-11-29T15:11:46,973 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-11-29T15:11:46,976 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2024-11-29T15:11:46,979 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-11-29T15:11:46,981 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-11-29T15:11:46,983 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-11-29T15:11:46,986 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2024-11-29T15:11:46,989 creating build/bdist.linux-armv7l/wheel/protenix/config 2024-11-29T15:11:46,990 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-11-29T15:11:46,992 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-11-29T15:11:46,995 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2024-11-29T15:11:46,998 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2024-11-29T15:11:46,999 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-11-29T15:11:47,001 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-11-29T15:11:47,003 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-11-29T15:11:47,006 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-11-29T15:11:47,008 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-11-29T15:11:47,010 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2024-11-29T15:11:47,014 creating build/bdist.linux-armv7l/wheel/protenix/model 2024-11-29T15:11:47,015 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-11-29T15:11:47,018 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-11-29T15:11:47,019 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-11-29T15:11:47,023 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2024-11-29T15:11:47,024 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2024-11-29T15:11:47,026 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-11-29T15:11:47,028 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-11-29T15:11:47,030 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-11-29T15:11:47,032 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2024-11-29T15:11:47,035 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-11-29T15:11:47,037 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-11-29T15:11:47,039 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2024-11-29T15:11:47,042 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2024-11-29T15:11:47,043 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-11-29T15:11:47,045 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-11-29T15:11:47,047 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-11-29T15:11:47,049 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-11-29T15:11:47,051 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-11-29T15:11:47,053 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-11-29T15:11:47,056 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-11-29T15:11:47,059 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-11-29T15:11:47,062 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2024-11-29T15:11:47,064 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-11-29T15:11:47,067 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-11-29T15:11:47,070 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2024-11-29T15:11:47,073 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2024-11-29T15:11:47,075 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2024-11-29T15:11:47,077 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2024-11-29T15:11:47,078 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-11-29T15:11:47,080 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-11-29T15:11:47,083 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-11-29T15:11:47,086 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-11-29T15:11:47,087 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-11-29T15:11:47,090 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2024-11-29T15:11:47,091 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-11-29T15:11:47,093 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-11-29T15:11:47,094 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2024-11-29T15:11:47,097 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-11-29T15:11:47,099 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-11-29T15:11:47,101 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2024-11-29T15:11:47,104 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2024-11-29T15:11:47,106 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2024-11-29T15:11:47,107 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-11-29T15:11:47,109 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-11-29T15:11:47,111 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-11-29T15:11:47,114 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-11-29T15:11:47,115 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-11-29T15:11:47,117 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-11-29T15:11:47,119 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2024-11-29T15:11:47,122 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2024-11-29T15:11:47,123 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-11-29T15:11:47,125 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2024-11-29T15:11:47,127 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-11-29T15:11:47,130 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-11-29T15:11:47,132 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-11-29T15:11:47,134 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-11-29T15:11:47,136 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-11-29T15:11:47,138 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-11-29T15:11:47,140 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-11-29T15:11:47,141 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2024-11-29T15:11:47,144 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2024-11-29T15:11:47,146 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-11-29T15:11:47,147 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2024-11-29T15:11:47,151 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2024-11-29T15:11:47,152 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-11-29T15:11:47,154 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-11-29T15:11:47,157 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-11-29T15:11:47,158 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-11-29T15:11:47,162 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-11-29T15:11:47,164 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2024-11-29T15:11:47,166 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2024-11-29T15:11:47,168 creating build/bdist.linux-armv7l/wheel/runner 2024-11-29T15:11:47,170 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2024-11-29T15:11:47,172 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2024-11-29T15:11:47,174 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2024-11-29T15:11:47,176 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2024-11-29T15:11:47,179 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2024-11-29T15:11:47,181 running install_data 2024-11-29T15:11:47,209 creating build/bdist.linux-armv7l/wheel/protenix-0.1.0.data/data 2024-11-29T15:11:47,210 warning: install_data: setup script did not provide a directory for 'requirements.txt' -- installing right in 'build/bdist.linux-armv7l/wheel/protenix-0.1.0.data/data' 2024-11-29T15:11:47,212 copying requirements.txt -> build/bdist.linux-armv7l/wheel/protenix-0.1.0.data/data 2024-11-29T15:11:47,213 running install_egg_info 2024-11-29T15:11:47,246 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.1.0-py3.11.egg-info 2024-11-29T15:11:47,258 running install_scripts 2024-11-29T15:11:47,278 creating build/bdist.linux-armv7l/wheel/protenix-0.1.0.dist-info/WHEEL 2024-11-29T15:11:47,281 creating '/tmp/pip-wheel-l9zl0ada/protenix-0.1.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-11-29T15:11:47,283 adding 'configs/__init__.py' 2024-11-29T15:11:47,285 adding 'configs/configs_base.py' 2024-11-29T15:11:47,287 adding 'configs/configs_data.py' 2024-11-29T15:11:47,288 adding 'configs/configs_inference.py' 2024-11-29T15:11:47,291 adding 'protenix/__init__.py' 2024-11-29T15:11:47,292 adding 'protenix/config/__init__.py' 2024-11-29T15:11:47,294 adding 'protenix/config/config.py' 2024-11-29T15:11:47,296 adding 'protenix/config/extend_types.py' 2024-11-29T15:11:47,298 adding 'protenix/data/__init__.py' 2024-11-29T15:11:47,300 adding 'protenix/data/ccd.py' 2024-11-29T15:11:47,304 adding 'protenix/data/constants.py' 2024-11-29T15:11:47,307 adding 'protenix/data/data_pipeline.py' 2024-11-29T15:11:47,309 adding 'protenix/data/dataloader.py' 2024-11-29T15:11:47,314 adding 'protenix/data/dataset.py' 2024-11-29T15:11:47,318 adding 'protenix/data/featurizer.py' 2024-11-29T15:11:47,319 adding 'protenix/data/infer_data_pipeline.py' 2024-11-29T15:11:47,322 adding 'protenix/data/json_parser.py' 2024-11-29T15:11:47,324 adding 'protenix/data/json_to_feature.py' 2024-11-29T15:11:47,329 adding 'protenix/data/msa_featurizer.py' 2024-11-29T15:11:47,334 adding 'protenix/data/msa_utils.py' 2024-11-29T15:11:47,338 adding 'protenix/data/parser.py' 2024-11-29T15:11:47,340 adding 'protenix/data/substructure_perms.py' 2024-11-29T15:11:47,341 adding 'protenix/data/tokenizer.py' 2024-11-29T15:11:47,344 adding 'protenix/data/utils.py' 2024-11-29T15:11:47,345 adding 'protenix/metrics/__init__.py' 2024-11-29T15:11:47,347 adding 'protenix/metrics/clash.py' 2024-11-29T15:11:47,349 adding 'protenix/metrics/lddt_metrics.py' 2024-11-29T15:11:47,350 adding 'protenix/metrics/rmsd.py' 2024-11-29T15:11:47,352 adding 'protenix/model/__init__.py' 2024-11-29T15:11:47,354 adding 'protenix/model/generator.py' 2024-11-29T15:11:47,360 adding 'protenix/model/loss.py' 2024-11-29T15:11:47,363 adding 'protenix/model/protenix.py' 2024-11-29T15:11:47,366 adding 'protenix/model/sample_confidence.py' 2024-11-29T15:11:47,369 adding 'protenix/model/utils.py' 2024-11-29T15:11:47,371 adding 'protenix/model/layer_norm/__init__.py' 2024-11-29T15:11:47,372 adding 'protenix/model/layer_norm/layer_norm.py' 2024-11-29T15:11:47,373 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2024-11-29T15:11:47,375 adding 'protenix/model/layer_norm/kernel/compat.h' 2024-11-29T15:11:47,377 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2024-11-29T15:11:47,379 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2024-11-29T15:11:47,381 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2024-11-29T15:11:47,383 adding 'protenix/model/modules/__init__.py' 2024-11-29T15:11:47,385 adding 'protenix/model/modules/confidence.py' 2024-11-29T15:11:47,387 adding 'protenix/model/modules/diffusion.py' 2024-11-29T15:11:47,389 adding 'protenix/model/modules/embedders.py' 2024-11-29T15:11:47,390 adding 'protenix/model/modules/frames.py' 2024-11-29T15:11:47,392 adding 'protenix/model/modules/head.py' 2024-11-29T15:11:47,395 adding 'protenix/model/modules/pairformer.py' 2024-11-29T15:11:47,398 adding 'protenix/model/modules/primitives.py' 2024-11-29T15:11:47,402 adding 'protenix/model/modules/transformer.py' 2024-11-29T15:11:47,404 adding 'protenix/openfold_local/__init__.py' 2024-11-29T15:11:47,405 adding 'protenix/openfold_local/data/__init__.py' 2024-11-29T15:11:47,407 adding 'protenix/openfold_local/data/data_transforms.py' 2024-11-29T15:11:47,408 adding 'protenix/openfold_local/data/errors.py' 2024-11-29T15:11:47,411 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2024-11-29T15:11:47,413 adding 'protenix/openfold_local/data/msa_identifiers.py' 2024-11-29T15:11:47,415 adding 'protenix/openfold_local/data/msa_pairing.py' 2024-11-29T15:11:47,419 adding 'protenix/openfold_local/data/parsers.py' 2024-11-29T15:11:47,422 adding 'protenix/openfold_local/data/templates.py' 2024-11-29T15:11:47,424 adding 'protenix/openfold_local/data/tools/__init__.py' 2024-11-29T15:11:47,425 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2024-11-29T15:11:47,426 adding 'protenix/openfold_local/data/tools/utils.py' 2024-11-29T15:11:47,428 adding 'protenix/openfold_local/model/__init__.py' 2024-11-29T15:11:47,429 adding 'protenix/openfold_local/model/dropout.py' 2024-11-29T15:11:47,430 adding 'protenix/openfold_local/model/outer_product_mean.py' 2024-11-29T15:11:47,433 adding 'protenix/openfold_local/model/primitives.py' 2024-11-29T15:11:47,435 adding 'protenix/openfold_local/model/triangular_attention.py' 2024-11-29T15:11:47,437 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2024-11-29T15:11:47,439 adding 'protenix/openfold_local/np/__init__.py' 2024-11-29T15:11:47,444 adding 'protenix/openfold_local/np/residue_constants.py' 2024-11-29T15:11:47,446 adding 'protenix/openfold_local/utils/__init__.py' 2024-11-29T15:11:47,448 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2024-11-29T15:11:47,450 adding 'protenix/openfold_local/utils/checkpointing.py' 2024-11-29T15:11:47,452 adding 'protenix/openfold_local/utils/chunk_utils.py' 2024-11-29T15:11:47,454 adding 'protenix/openfold_local/utils/feats.py' 2024-11-29T15:11:47,455 adding 'protenix/openfold_local/utils/precision_utils.py' 2024-11-29T15:11:47,459 adding 'protenix/openfold_local/utils/rigid_utils.py' 2024-11-29T15:11:47,461 adding 'protenix/openfold_local/utils/tensor_utils.py' 2024-11-29T15:11:47,463 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2024-11-29T15:11:47,464 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2024-11-29T15:11:47,466 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2024-11-29T15:11:47,467 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2024-11-29T15:11:47,469 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2024-11-29T15:11:47,470 adding 'protenix/openfold_local/utils/geometry/utils.py' 2024-11-29T15:11:47,471 adding 'protenix/openfold_local/utils/geometry/vector.py' 2024-11-29T15:11:47,473 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2024-11-29T15:11:47,475 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2024-11-29T15:11:47,476 adding 'protenix/utils/__init__.py' 2024-11-29T15:11:47,480 adding 'protenix/utils/cropping.py' 2024-11-29T15:11:47,481 adding 'protenix/utils/distributed.py' 2024-11-29T15:11:47,483 adding 'protenix/utils/file_io.py' 2024-11-29T15:11:47,484 adding 'protenix/utils/geometry.py' 2024-11-29T15:11:47,486 adding 'protenix/utils/logger.py' 2024-11-29T15:11:47,487 adding 'protenix/utils/lr_scheduler.py' 2024-11-29T15:11:47,489 adding 'protenix/utils/metrics.py' 2024-11-29T15:11:47,490 adding 'protenix/utils/scatter_utils.py' 2024-11-29T15:11:47,492 adding 'protenix/utils/seed.py' 2024-11-29T15:11:47,493 adding 'protenix/utils/torch_utils.py' 2024-11-29T15:11:47,495 adding 'protenix/utils/training.py' 2024-11-29T15:11:47,496 adding 'protenix/utils/permutation/__init__.py' 2024-11-29T15:11:47,500 adding 'protenix/utils/permutation/atom_permutation.py' 2024-11-29T15:11:47,503 adding 'protenix/utils/permutation/permutation.py' 2024-11-29T15:11:47,504 adding 'protenix/utils/permutation/utils.py' 2024-11-29T15:11:47,506 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2024-11-29T15:11:47,511 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2024-11-29T15:11:47,513 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2024-11-29T15:11:47,514 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2024-11-29T15:11:47,516 adding 'protenix/web_service/__init__.py' 2024-11-29T15:11:47,518 adding 'protenix/web_service/colab_request_parser.py' 2024-11-29T15:11:47,520 adding 'protenix/web_service/colab_request_utils.py' 2024-11-29T15:11:47,521 adding 'protenix/web_service/dependency_url.py' 2024-11-29T15:11:47,523 adding 'protenix/web_service/prediction_visualization.py' 2024-11-29T15:11:47,525 adding 'protenix/web_service/viewer.py' 2024-11-29T15:11:47,527 adding 'protenix-0.1.0.data/data/requirements.txt' 2024-11-29T15:11:47,529 adding 'runner/__init__.py' 2024-11-29T15:11:47,531 adding 'runner/dumper.py' 2024-11-29T15:11:47,532 adding 'runner/ema.py' 2024-11-29T15:11:47,534 adding 'runner/inference.py' 2024-11-29T15:11:47,536 adding 'runner/train.py' 2024-11-29T15:11:47,539 adding 'protenix-0.1.0.dist-info/LICENSE' 2024-11-29T15:11:47,540 adding 'protenix-0.1.0.dist-info/METADATA' 2024-11-29T15:11:47,541 adding 'protenix-0.1.0.dist-info/WHEEL' 2024-11-29T15:11:47,542 adding 'protenix-0.1.0.dist-info/entry_points.txt' 2024-11-29T15:11:47,543 adding 'protenix-0.1.0.dist-info/top_level.txt' 2024-11-29T15:11:47,545 adding 'protenix-0.1.0.dist-info/RECORD' 2024-11-29T15:11:47,551 removing build/bdist.linux-armv7l/wheel 2024-11-29T15:11:47,696 Building wheel for protenix (setup.py): finished with status 'done' 2024-11-29T15:11:47,702 Created wheel for protenix: filename=protenix-0.1.0-py3-none-any.whl size=368085 sha256=95dd14c125ff66c76135ed8525ede80d6be803880749ec813036bb317ca23e6e 2024-11-29T15:11:47,704 Stored in directory: /tmp/pip-ephem-wheel-cache-og5kuoxc/wheels/58/2e/9e/c4933467326dc1572d9b75afa5b7e5dc299ea13def9d1bac79 2024-11-29T15:11:47,718 Successfully built protenix 2024-11-29T15:11:47,734 Removed build tracker: '/tmp/pip-build-tracker-wl_t_okq'