2023-12-15T05:58:22,053 Created temporary directory: /tmp/pip-build-tracker-uwk61p6q 2023-12-15T05:58:22,054 Initialized build tracking at /tmp/pip-build-tracker-uwk61p6q 2023-12-15T05:58:22,054 Created build tracker: /tmp/pip-build-tracker-uwk61p6q 2023-12-15T05:58:22,055 Entered build tracker: /tmp/pip-build-tracker-uwk61p6q 2023-12-15T05:58:22,056 Created temporary directory: /tmp/pip-wheel-grnnnts8 2023-12-15T05:58:22,059 Created temporary directory: /tmp/pip-ephem-wheel-cache-wa7etoee 2023-12-15T05:58:22,084 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-12-15T05:58:22,087 2 location(s) to search for versions of hydra-rbp: 2023-12-15T05:58:22,087 * https://pypi.org/simple/hydra-rbp/ 2023-12-15T05:58:22,087 * https://www.piwheels.org/simple/hydra-rbp/ 2023-12-15T05:58:22,088 Fetching project page and analyzing links: https://pypi.org/simple/hydra-rbp/ 2023-12-15T05:58:22,089 Getting page https://pypi.org/simple/hydra-rbp/ 2023-12-15T05:58:22,090 Found index url https://pypi.org/simple/ 2023-12-15T05:58:22,313 Fetched page https://pypi.org/simple/hydra-rbp/ as application/vnd.pypi.simple.v1+json 2023-12-15T05:58:22,316 Found link https://files.pythonhosted.org/packages/c5/09/447109100c21cdb2df7a02685baa6324ffad284da0f14a3cfb6ce4b64972/hydra_rbp-0.1.21.27.tar.gz (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6), version: 0.1.21.27 2023-12-15T05:58:22,317 Found link https://files.pythonhosted.org/packages/f3/d2/ff965058796232582106702bd93d72d0bdce3920bd9ae52773bfd8a8db71/hydra_rbp-0.1.21.28.tar.gz (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6), version: 0.1.21.28 2023-12-15T05:58:22,318 Skipping link: No binaries permitted for hydra-rbp: https://files.pythonhosted.org/packages/dd/03/db9334056fd0aeda9ecc38c591895e544b6f4530b5003a50dcdb3773bd05/hydra_rbp-0.1.21.29-py3-none-any.whl (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6) 2023-12-15T05:58:22,319 Found link https://files.pythonhosted.org/packages/49/44/f12c30956623421691997bd996a83708903dbf9f1a0aef3f06b3b209c780/hydra_rbp-0.1.21.29.tar.gz (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6), version: 0.1.21.29 2023-12-15T05:58:22,319 Skipping link: No binaries permitted for hydra-rbp: https://files.pythonhosted.org/packages/2b/eb/56bd5fd43ae21430c6fb8b13146c9f39e742ed414207aaadf1c3657266f3/hydra_rbp-0.1.21.30-py3-none-any.whl (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6) 2023-12-15T05:58:22,320 Found link https://files.pythonhosted.org/packages/83/7c/f7f088132d9ff564207a99897d2c0375b7a9663214d221f5a06fccfd32db/hydra_rbp-0.1.21.30.tar.gz (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6), version: 0.1.21.30 2023-12-15T05:58:22,321 Skipping link: No binaries permitted for hydra-rbp: https://files.pythonhosted.org/packages/e5/2d/54a09009e4b876ab35dce61dd20d809ec9823b128f6d918b68397d41f075/hydra_rbp-0.1.21.31-py3-none-any.whl (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6) 2023-12-15T05:58:22,322 Found link https://files.pythonhosted.org/packages/f7/dc/a9b087b4d2c0d4a9719f850141f5f3bd7d43e54f8494456ee8aaec507a62/hydra_rbp-0.1.21.31.tar.gz (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6), version: 0.1.21.31 2023-12-15T05:58:22,323 Skipping link: No binaries permitted for hydra-rbp: https://files.pythonhosted.org/packages/ed/14/bd88a23bf60ddc41af6967b180df6a81ca3a07e61a92caccd61004eb7bec/hydra_rbp-0.1.21.32-py3-none-any.whl (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6) 2023-12-15T05:58:22,324 Found link https://files.pythonhosted.org/packages/42/1a/4e011525c4acc37587aaeda8cb1a4a43c18024f828a7f2a944838804fd20/hydra_rbp-0.1.21.32.tar.gz (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6), version: 0.1.21.32 2023-12-15T05:58:22,325 Fetching project page and analyzing links: https://www.piwheels.org/simple/hydra-rbp/ 2023-12-15T05:58:22,325 Getting page https://www.piwheels.org/simple/hydra-rbp/ 2023-12-15T05:58:22,327 Found index url https://www.piwheels.org/simple/ 2023-12-15T05:58:22,499 Fetched page https://www.piwheels.org/simple/hydra-rbp/ as text/html 2023-12-15T05:58:22,501 Skipping link: No binaries permitted for hydra-rbp: https://www.piwheels.org/simple/hydra-rbp/hydra_rbp-0.1.21.31-py3-none-any.whl#sha256=176bbf98f3d5e29b7c9a5236b92d239567dab6b746703603818e840e0a7857db (from https://www.piwheels.org/simple/hydra-rbp/) (requires-python:>=3.6) 2023-12-15T05:58:22,502 Skipping link: No binaries permitted for hydra-rbp: https://www.piwheels.org/simple/hydra-rbp/hydra_rbp-0.1.21.30-py3-none-any.whl#sha256=997fd56e129174ba095b515d6883360d8b23cca3c8c83ddeb33c988e0bcc39c8 (from https://www.piwheels.org/simple/hydra-rbp/) (requires-python:>=3.6) 2023-12-15T05:58:22,503 Skipping link: No binaries permitted for hydra-rbp: https://www.piwheels.org/simple/hydra-rbp/hydra_rbp-0.1.21.29-py3-none-any.whl#sha256=e1ffbf05d3124e9af44781389df5f63a7ba227f3dcf8c98cbdb55b4eda436c9b (from https://www.piwheels.org/simple/hydra-rbp/) (requires-python:>=3.6) 2023-12-15T05:58:22,503 Skipping link: No binaries permitted for hydra-rbp: https://www.piwheels.org/simple/hydra-rbp/hydra_rbp-0.1.21.28-py3-none-any.whl#sha256=2dce1c5216cc6dfeb287ba82fc7ecc0f084574aebca3a134b3d2dd9c2c0bd3dc (from https://www.piwheels.org/simple/hydra-rbp/) (requires-python:>=3.6) 2023-12-15T05:58:22,504 Skipping link: No binaries permitted for hydra-rbp: https://www.piwheels.org/simple/hydra-rbp/hydra_rbp-0.1.21.27-py3-none-any.whl#sha256=c9ac5819931db90ef2e745d6179b24dc2bdc396044ae3c6ceaef7dbadbe6a45a (from https://www.piwheels.org/simple/hydra-rbp/) (requires-python:>=3.6) 2023-12-15T05:58:22,504 Skipping link: not a file: https://www.piwheels.org/simple/hydra-rbp/ 2023-12-15T05:58:22,505 Skipping link: not a file: https://pypi.org/simple/hydra-rbp/ 2023-12-15T05:58:22,523 Given no hashes to check 1 links for project 'hydra-rbp': discarding no candidates 2023-12-15T05:58:22,541 Collecting hydra-rbp==0.1.21.32 2023-12-15T05:58:22,543 Created temporary directory: /tmp/pip-unpack-5h245usd 2023-12-15T05:58:22,761 Downloading hydra_rbp-0.1.21.32.tar.gz (52.4 MB) 2023-12-15T05:58:40,903 Added hydra-rbp==0.1.21.32 from https://files.pythonhosted.org/packages/42/1a/4e011525c4acc37587aaeda8cb1a4a43c18024f828a7f2a944838804fd20/hydra_rbp-0.1.21.32.tar.gz to build tracker '/tmp/pip-build-tracker-uwk61p6q' 2023-12-15T05:58:40,905 Running setup.py (path:/tmp/pip-wheel-grnnnts8/hydra-rbp_d0194546b6744a2c9072e75aaf2eec8c/setup.py) egg_info for package hydra-rbp 2023-12-15T05:58:40,906 Created temporary directory: /tmp/pip-pip-egg-info-_8cs63fk 2023-12-15T05:58:40,907 Preparing metadata (setup.py): started 2023-12-15T05:58:40,908 Running command python setup.py egg_info 2023-12-15T05:58:41,610 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-12-15T05:58:41,610 !! 2023-12-15T05:58:41,612 ******************************************************************************** 2023-12-15T05:58:41,612 Requirements should be satisfied by a PEP 517 installer. 2023-12-15T05:58:41,613 If you are using pip, you can try `pip install --use-pep517`. 2023-12-15T05:58:41,613 ******************************************************************************** 2023-12-15T05:58:41,615 !! 2023-12-15T05:58:41,615 dist.fetch_build_eggs(dist.setup_requires) 2023-12-15T05:58:44,681 running egg_info 2023-12-15T05:58:44,683 creating /tmp/pip-pip-egg-info-_8cs63fk/hydra_rbp.egg-info 2023-12-15T05:58:44,711 writing /tmp/pip-pip-egg-info-_8cs63fk/hydra_rbp.egg-info/PKG-INFO 2023-12-15T05:58:44,714 writing dependency_links to /tmp/pip-pip-egg-info-_8cs63fk/hydra_rbp.egg-info/dependency_links.txt 2023-12-15T05:58:44,716 writing entry points to /tmp/pip-pip-egg-info-_8cs63fk/hydra_rbp.egg-info/entry_points.txt 2023-12-15T05:58:44,718 writing requirements to /tmp/pip-pip-egg-info-_8cs63fk/hydra_rbp.egg-info/requires.txt 2023-12-15T05:58:44,719 writing top-level names to /tmp/pip-pip-egg-info-_8cs63fk/hydra_rbp.egg-info/top_level.txt 2023-12-15T05:58:44,720 writing manifest file '/tmp/pip-pip-egg-info-_8cs63fk/hydra_rbp.egg-info/SOURCES.txt' 2023-12-15T05:58:44,834 reading manifest file '/tmp/pip-pip-egg-info-_8cs63fk/hydra_rbp.egg-info/SOURCES.txt' 2023-12-15T05:58:44,836 reading manifest template 'MANIFEST.in' 2023-12-15T05:58:44,839 adding license file 'LICENSE' 2023-12-15T05:58:44,844 writing manifest file '/tmp/pip-pip-egg-info-_8cs63fk/hydra_rbp.egg-info/SOURCES.txt' 2023-12-15T05:58:44,951 Preparing metadata (setup.py): finished with status 'done' 2023-12-15T05:58:44,955 Source in /tmp/pip-wheel-grnnnts8/hydra-rbp_d0194546b6744a2c9072e75aaf2eec8c has version 0.1.21.32, which satisfies requirement hydra-rbp==0.1.21.32 from https://files.pythonhosted.org/packages/42/1a/4e011525c4acc37587aaeda8cb1a4a43c18024f828a7f2a944838804fd20/hydra_rbp-0.1.21.32.tar.gz 2023-12-15T05:58:44,956 Removed hydra-rbp==0.1.21.32 from https://files.pythonhosted.org/packages/42/1a/4e011525c4acc37587aaeda8cb1a4a43c18024f828a7f2a944838804fd20/hydra_rbp-0.1.21.32.tar.gz from build tracker '/tmp/pip-build-tracker-uwk61p6q' 2023-12-15T05:58:44,962 Created temporary directory: /tmp/pip-unpack-7ql5od26 2023-12-15T05:58:44,963 Created temporary directory: /tmp/pip-unpack-fnk_k_4o 2023-12-15T05:58:44,976 Building wheels for collected packages: hydra-rbp 2023-12-15T05:58:44,980 Created temporary directory: /tmp/pip-wheel-90_cb8vt 2023-12-15T05:58:44,981 Building wheel for hydra-rbp (setup.py): started 2023-12-15T05:58:44,982 Destination directory: /tmp/pip-wheel-90_cb8vt 2023-12-15T05:58:44,982 Running command python setup.py bdist_wheel 2023-12-15T05:58:45,648 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-12-15T05:58:45,648 !! 2023-12-15T05:58:45,649 ******************************************************************************** 2023-12-15T05:58:45,650 Requirements should be satisfied by a PEP 517 installer. 2023-12-15T05:58:45,651 If you are using pip, you can try `pip install --use-pep517`. 2023-12-15T05:58:45,651 ******************************************************************************** 2023-12-15T05:58:45,652 !! 2023-12-15T05:58:45,653 dist.fetch_build_eggs(dist.setup_requires) 2023-12-15T05:58:46,134 running bdist_wheel 2023-12-15T05:58:46,247 running build 2023-12-15T05:58:46,248 running build_py 2023-12-15T05:58:46,276 creating build 2023-12-15T05:58:46,276 creating build/lib 2023-12-15T05:58:46,277 creating build/lib/HydRa 2023-12-15T05:58:46,278 copying HydRa/test_data_load.py -> build/lib/HydRa 2023-12-15T05:58:46,280 copying HydRa/HydRa_predict.py -> build/lib/HydRa 2023-12-15T05:58:46,283 copying HydRa/HydRa2_0_predict.py -> build/lib/HydRa 2023-12-15T05:58:46,285 copying HydRa/__init__.py -> build/lib/HydRa 2023-12-15T05:58:46,288 creating build/lib/HydRa/models 2023-12-15T05:58:46,288 copying HydRa/models/DNN_seq.py -> build/lib/HydRa/models 2023-12-15T05:58:46,292 copying HydRa/models/Sequence_class.py -> build/lib/HydRa/models 2023-12-15T05:58:46,294 copying HydRa/models/__init__.py -> build/lib/HydRa/models 2023-12-15T05:58:46,297 creating build/lib/HydRa/predictions 2023-12-15T05:58:46,298 copying HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124.py -> build/lib/HydRa/predictions 2023-12-15T05:58:46,302 copying HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124_ensScore.py -> build/lib/HydRa/predictions 2023-12-15T05:58:46,304 copying HydRa/predictions/Occlusion_map_v3_HydRa2_0.py -> build/lib/HydRa/predictions 2023-12-15T05:58:46,308 copying HydRa/predictions/Occlusion_map_v2.py -> build/lib/HydRa/predictions 2023-12-15T05:58:46,311 copying HydRa/predictions/Occlusion_map_v2_HydRa2_0.py -> build/lib/HydRa/predictions 2023-12-15T05:58:46,316 copying HydRa/predictions/Occlusion_1D_analysis_2.py -> build/lib/HydRa/predictions 2023-12-15T05:58:46,318 copying HydRa/predictions/Occlusion_map.py -> build/lib/HydRa/predictions 2023-12-15T05:58:46,322 copying HydRa/predictions/__init__.py -> build/lib/HydRa/predictions 2023-12-15T05:58:46,324 creating build/lib/HydRa/preprocessing 2023-12-15T05:58:46,326 copying HydRa/preprocessing/get_SVM_seq_features.py -> build/lib/HydRa/preprocessing 2023-12-15T05:58:46,328 copying HydRa/preprocessing/Get_All_selected_SVM_features.py -> build/lib/HydRa/preprocessing 2023-12-15T05:58:46,330 copying HydRa/preprocessing/PPI_feature_generation.py -> build/lib/HydRa/preprocessing 2023-12-15T05:58:46,333 copying HydRa/preprocessing/__init__.py -> build/lib/HydRa/preprocessing 2023-12-15T05:58:46,335 copying HydRa/preprocessing/predict_SS.py -> build/lib/HydRa/preprocessing 2023-12-15T05:58:46,338 creating build/lib/HydRa/training 2023-12-15T05:58:46,339 copying HydRa/training/train_and_evaluate_HydRa_bk.py -> build/lib/HydRa/training 2023-12-15T05:58:46,342 copying HydRa/training/train_HydRa2_0.py -> build/lib/HydRa/training 2023-12-15T05:58:46,345 copying HydRa/training/train_and_evaluate_HydRa2_0.py -> build/lib/HydRa/training 2023-12-15T05:58:46,347 copying HydRa/training/train_and_evaluate_HydRa.py -> build/lib/HydRa/training 2023-12-15T05:58:46,350 copying HydRa/training/train_HydRa.py -> build/lib/HydRa/training 2023-12-15T05:58:46,353 copying HydRa/training/__init__.py -> build/lib/HydRa/training 2023-12-15T05:58:46,355 creating build/lib/HydRa/evaluation 2023-12-15T05:58:46,355 copying HydRa/evaluation/ROC_PR_AUC_analysis.py -> build/lib/HydRa/evaluation 2023-12-15T05:58:46,357 copying HydRa/evaluation/__init__.py -> build/lib/HydRa/evaluation 2023-12-15T05:58:46,359 creating build/lib/HydRa/preprocessing/Feature_selection 2023-12-15T05:58:46,360 copying HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py -> build/lib/HydRa/preprocessing/Feature_selection 2023-12-15T05:58:46,362 copying HydRa/preprocessing/Feature_selection/__init__.py -> build/lib/HydRa/preprocessing/Feature_selection 2023-12-15T05:58:46,365 creating build/lib/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:46,366 copying HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:46,367 copying HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:46,370 copying HydRa/preprocessing/Feature_generation/PPI_feature_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:46,372 copying HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:46,374 copying HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:46,375 copying HydRa/preprocessing/Feature_generation/kmer_table_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:46,377 copying HydRa/preprocessing/Feature_generation/__init__.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:46,379 running egg_info 2023-12-15T05:58:46,430 writing hydra_rbp.egg-info/PKG-INFO 2023-12-15T05:58:46,434 writing dependency_links to hydra_rbp.egg-info/dependency_links.txt 2023-12-15T05:58:46,436 writing entry points to hydra_rbp.egg-info/entry_points.txt 2023-12-15T05:58:46,437 writing requirements to hydra_rbp.egg-info/requires.txt 2023-12-15T05:58:46,438 writing top-level names to hydra_rbp.egg-info/top_level.txt 2023-12-15T05:58:46,480 reading manifest file 'hydra_rbp.egg-info/SOURCES.txt' 2023-12-15T05:58:46,484 reading manifest template 'MANIFEST.in' 2023-12-15T05:58:46,487 adding license file 'LICENSE' 2023-12-15T05:58:46,492 writing manifest file 'hydra_rbp.egg-info/SOURCES.txt' 2023-12-15T05:58:46,495 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'HydRa.data' is absent from the `packages` configuration. 2023-12-15T05:58:46,495 !! 2023-12-15T05:58:46,497 ******************************************************************************** 2023-12-15T05:58:46,497 ############################ 2023-12-15T05:58:46,497 # Package would be ignored # 2023-12-15T05:58:46,498 ############################ 2023-12-15T05:58:46,498 Python recognizes 'HydRa.data' as an importable package[^1], 2023-12-15T05:58:46,499 but it is absent from setuptools' `packages` configuration. 2023-12-15T05:58:46,500 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-15T05:58:46,500 package, please make sure that 'HydRa.data' is explicitly added 2023-12-15T05:58:46,500 to the `packages` configuration field. 2023-12-15T05:58:46,501 Alternatively, you can also rely on setuptools' discovery methods 2023-12-15T05:58:46,501 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-15T05:58:46,502 instead of `find_packages(...)`/`find:`). 2023-12-15T05:58:46,503 You can read more about "package discovery" on setuptools documentation page: 2023-12-15T05:58:46,504 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-15T05:58:46,505 If you don't want 'HydRa.data' to be distributed and are 2023-12-15T05:58:46,505 already explicitly excluding 'HydRa.data' via 2023-12-15T05:58:46,506 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-15T05:58:46,506 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-15T05:58:46,507 combination with a more fine grained `package-data` configuration. 2023-12-15T05:58:46,508 You can read more about "package data files" on setuptools documentation page: 2023-12-15T05:58:46,509 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-15T05:58:46,511 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-15T05:58:46,511 even if it does not contain any `.py` files. 2023-12-15T05:58:46,512 On the other hand, currently there is no concept of package data 2023-12-15T05:58:46,513 directory, all directories are treated like packages. 2023-12-15T05:58:46,513 ******************************************************************************** 2023-12-15T05:58:46,517 !! 2023-12-15T05:58:46,519 check.warn(importable) 2023-12-15T05:58:46,525 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'HydRa.pre_trained' is absent from the `packages` configuration. 2023-12-15T05:58:46,529 !! 2023-12-15T05:58:46,531 ******************************************************************************** 2023-12-15T05:58:46,531 ############################ 2023-12-15T05:58:46,532 # Package would be ignored # 2023-12-15T05:58:46,533 ############################ 2023-12-15T05:58:46,533 Python recognizes 'HydRa.pre_trained' as an importable package[^1], 2023-12-15T05:58:46,534 but it is absent from setuptools' `packages` configuration. 2023-12-15T05:58:46,535 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-15T05:58:46,535 package, please make sure that 'HydRa.pre_trained' is explicitly added 2023-12-15T05:58:46,536 to the `packages` configuration field. 2023-12-15T05:58:46,537 Alternatively, you can also rely on setuptools' discovery methods 2023-12-15T05:58:46,538 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-15T05:58:46,543 instead of `find_packages(...)`/`find:`). 2023-12-15T05:58:46,548 You can read more about "package discovery" on setuptools documentation page: 2023-12-15T05:58:46,552 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-15T05:58:46,553 If you don't want 'HydRa.pre_trained' to be distributed and are 2023-12-15T05:58:46,553 already explicitly excluding 'HydRa.pre_trained' via 2023-12-15T05:58:46,561 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-15T05:58:46,561 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-15T05:58:46,562 combination with a more fine grained `package-data` configuration. 2023-12-15T05:58:46,563 You can read more about "package data files" on setuptools documentation page: 2023-12-15T05:58:46,564 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-15T05:58:46,565 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-15T05:58:46,566 even if it does not contain any `.py` files. 2023-12-15T05:58:46,566 On the other hand, currently there is no concept of package data 2023-12-15T05:58:46,566 directory, all directories are treated like packages. 2023-12-15T05:58:46,567 ******************************************************************************** 2023-12-15T05:58:46,568 !! 2023-12-15T05:58:46,568 check.warn(importable) 2023-12-15T05:58:46,574 creating build/lib/HydRa/data 2023-12-15T05:58:46,575 copying HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2023-12-15T05:58:46,575 copying HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2023-12-15T05:58:46,576 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls -> build/lib/HydRa/data 2023-12-15T05:58:46,663 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv -> build/lib/HydRa/data 2023-12-15T05:58:46,688 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv -> build/lib/HydRa/data 2023-12-15T05:58:46,725 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2023-12-15T05:58:46,886 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/lib/HydRa/data 2023-12-15T05:58:46,992 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk -> build/lib/HydRa/data 2023-12-15T05:58:47,185 copying HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2023-12-15T05:58:47,229 copying HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/lib/HydRa/data 2023-12-15T05:58:47,274 copying HydRa/data/Combined10RBPlist_uniprotID_20190716.txt -> build/lib/HydRa/data 2023-12-15T05:58:47,280 copying HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt -> build/lib/HydRa/data 2023-12-15T05:58:47,287 copying HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/lib/HydRa/data 2023-12-15T05:58:47,290 copying HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl -> build/lib/HydRa/data 2023-12-15T05:58:47,292 copying HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl -> build/lib/HydRa/data 2023-12-15T05:58:47,294 copying HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv -> build/lib/HydRa/data 2023-12-15T05:58:47,461 copying HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/lib/HydRa/data 2023-12-15T05:58:47,464 copying HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt -> build/lib/HydRa/data 2023-12-15T05:58:47,787 copying HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt -> build/lib/HydRa/data 2023-12-15T05:58:47,790 copying HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2023-12-15T05:58:47,794 copying HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2023-12-15T05:58:47,798 copying HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt -> build/lib/HydRa/data 2023-12-15T05:58:48,407 copying HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2023-12-15T05:58:48,409 copying HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2023-12-15T05:58:48,411 copying HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt -> build/lib/HydRa/data 2023-12-15T05:58:48,474 copying HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls -> build/lib/HydRa/data 2023-12-15T05:58:48,503 copying HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls -> build/lib/HydRa/data 2023-12-15T05:58:48,546 copying HydRa/data/protVec_100d_3grams.csv -> build/lib/HydRa/data 2023-12-15T05:58:48,676 creating build/lib/HydRa/pre_trained 2023-12-15T05:58:48,677 copying HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2023-12-15T05:58:48,707 copying HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2023-12-15T05:58:48,737 copying HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_structure.json -> build/lib/HydRa/pre_trained 2023-12-15T05:58:48,740 copying HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_weights.h5 -> build/lib/HydRa/pre_trained 2023-12-15T05:58:48,804 copying HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_structure.json -> build/lib/HydRa/pre_trained 2023-12-15T05:58:48,807 copying HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_weights.h5 -> build/lib/HydRa/pre_trained 2023-12-15T05:58:48,868 copying HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2023-12-15T05:58:48,872 copying HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2023-12-15T05:58:48,875 copying HydRa/pre_trained/SVM_PPI_MB-S_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl -> build/lib/HydRa/pre_trained 2023-12-15T05:58:48,897 copying HydRa/pre_trained/SVM_PPI_MB_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl -> build/lib/HydRa/pre_trained 2023-12-15T05:58:48,915 copying HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pickle.pkl -> build/lib/HydRa/pre_trained 2023-12-15T05:58:51,880 copying HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_ModelFile.pickle.pkl -> build/lib/HydRa/pre_trained 2023-12-15T05:58:52,820 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-12-15T05:58:52,820 !! 2023-12-15T05:58:52,821 ******************************************************************************** 2023-12-15T05:58:52,822 Please avoid running ``setup.py`` directly. 2023-12-15T05:58:52,822 Instead, use pypa/build, pypa/installer or other 2023-12-15T05:58:52,823 standards-based tools. 2023-12-15T05:58:52,824 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-12-15T05:58:52,824 ******************************************************************************** 2023-12-15T05:58:52,825 !! 2023-12-15T05:58:52,825 self.initialize_options() 2023-12-15T05:58:52,848 installing to build/bdist.linux-armv7l/wheel 2023-12-15T05:58:52,848 running install 2023-12-15T05:58:52,873 running install_lib 2023-12-15T05:58:52,900 creating build/bdist.linux-armv7l 2023-12-15T05:58:52,900 creating build/bdist.linux-armv7l/wheel 2023-12-15T05:58:52,902 creating build/bdist.linux-armv7l/wheel/HydRa 2023-12-15T05:58:52,904 creating build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:52,905 copying build/lib/HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:52,946 copying build/lib/HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,055 copying build/lib/HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,077 copying build/lib/HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,229 copying build/lib/HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,231 copying build/lib/HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,234 copying build/lib/HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,239 copying build/lib/HydRa/data/protVec_100d_3grams.csv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,366 copying build/lib/HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,442 copying build/lib/HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,444 copying build/lib/HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,471 copying build/lib/HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,473 copying build/lib/HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,541 copying build/lib/HydRa/data/Combined10RBPlist_uniprotID_20190716.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,546 copying build/lib/HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,578 copying build/lib/HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,580 copying build/lib/HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,582 copying build/lib/HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,652 copying build/lib/HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,684 copying build/lib/HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:53,849 copying build/lib/HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:54,388 copying build/lib/HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:54,421 copying build/lib/HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:54,424 copying build/lib/HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:54,426 copying build/lib/HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:54,596 copying build/lib/HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:54,627 copying build/lib/HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:54,662 copying build/lib/HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-12-15T05:58:54,664 copying build/lib/HydRa/test_data_load.py -> build/bdist.linux-armv7l/wheel/HydRa 2023-12-15T05:58:54,666 creating build/bdist.linux-armv7l/wheel/HydRa/models 2023-12-15T05:58:54,667 copying build/lib/HydRa/models/DNN_seq.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2023-12-15T05:58:54,670 copying build/lib/HydRa/models/Sequence_class.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2023-12-15T05:58:54,673 copying build/lib/HydRa/models/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2023-12-15T05:58:54,675 creating build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-12-15T05:58:54,676 copying build/lib/HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-12-15T05:58:54,679 copying build/lib/HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124_ensScore.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-12-15T05:58:54,681 copying build/lib/HydRa/predictions/Occlusion_map_v3_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-12-15T05:58:54,685 copying build/lib/HydRa/predictions/Occlusion_map_v2.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-12-15T05:58:54,688 copying build/lib/HydRa/predictions/Occlusion_map_v2_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-12-15T05:58:54,692 copying build/lib/HydRa/predictions/Occlusion_1D_analysis_2.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-12-15T05:58:54,694 copying build/lib/HydRa/predictions/Occlusion_map.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-12-15T05:58:54,696 copying build/lib/HydRa/predictions/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-12-15T05:58:54,698 copying build/lib/HydRa/HydRa_predict.py -> build/bdist.linux-armv7l/wheel/HydRa 2023-12-15T05:58:54,701 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-12-15T05:58:54,702 copying build/lib/HydRa/preprocessing/get_SVM_seq_features.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-12-15T05:58:54,704 copying build/lib/HydRa/preprocessing/Get_All_selected_SVM_features.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-12-15T05:58:54,706 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2023-12-15T05:58:54,707 copying build/lib/HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2023-12-15T05:58:54,709 copying build/lib/HydRa/preprocessing/Feature_selection/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2023-12-15T05:58:54,711 copying build/lib/HydRa/preprocessing/PPI_feature_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-12-15T05:58:54,713 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:54,714 copying build/lib/HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:54,716 copying build/lib/HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:54,718 copying build/lib/HydRa/preprocessing/Feature_generation/PPI_feature_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:54,721 copying build/lib/HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:54,722 copying build/lib/HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:54,724 copying build/lib/HydRa/preprocessing/Feature_generation/kmer_table_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:54,726 copying build/lib/HydRa/preprocessing/Feature_generation/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-12-15T05:58:54,728 copying build/lib/HydRa/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-12-15T05:58:54,730 copying build/lib/HydRa/preprocessing/predict_SS.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-12-15T05:58:54,732 copying build/lib/HydRa/HydRa2_0_predict.py -> build/bdist.linux-armv7l/wheel/HydRa 2023-12-15T05:58:54,735 creating build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:54,736 copying build/lib/HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:54,739 copying build/lib/HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_ModelFile.pickle.pkl -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:55,669 copying build/lib/HydRa/pre_trained/SVM_PPI_MB_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:55,686 copying build/lib/HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pickle.pkl -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:58,806 copying build/lib/HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:58,829 copying build/lib/HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:58,856 copying build/lib/HydRa/pre_trained/SVM_PPI_MB-S_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:58,874 copying build/lib/HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_weights.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:58,942 copying build/lib/HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_structure.json -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:58,944 copying build/lib/HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_structure.json -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:58,946 copying build/lib/HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:58,949 copying build/lib/HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_weights.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-12-15T05:58:59,010 creating build/bdist.linux-armv7l/wheel/HydRa/training 2023-12-15T05:58:59,011 copying build/lib/HydRa/training/train_and_evaluate_HydRa_bk.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-12-15T05:58:59,014 copying build/lib/HydRa/training/train_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-12-15T05:58:59,016 copying build/lib/HydRa/training/train_and_evaluate_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-12-15T05:58:59,019 copying build/lib/HydRa/training/train_and_evaluate_HydRa.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-12-15T05:58:59,022 copying build/lib/HydRa/training/train_HydRa.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-12-15T05:58:59,025 copying build/lib/HydRa/training/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-12-15T05:58:59,027 copying build/lib/HydRa/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa 2023-12-15T05:58:59,029 creating build/bdist.linux-armv7l/wheel/HydRa/evaluation 2023-12-15T05:58:59,030 copying build/lib/HydRa/evaluation/ROC_PR_AUC_analysis.py -> build/bdist.linux-armv7l/wheel/HydRa/evaluation 2023-12-15T05:58:59,032 copying build/lib/HydRa/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/evaluation 2023-12-15T05:58:59,034 running install_egg_info 2023-12-15T05:58:59,061 Copying hydra_rbp.egg-info to build/bdist.linux-armv7l/wheel/hydra_rbp-0.1.21.32-py3.11.egg-info 2023-12-15T05:58:59,073 running install_scripts 2023-12-15T05:58:59,090 creating build/bdist.linux-armv7l/wheel/hydra_rbp-0.1.21.32.dist-info/WHEEL 2023-12-15T05:58:59,093 creating '/tmp/pip-wheel-90_cb8vt/hydra_rbp-0.1.21.32-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-12-15T05:58:59,098 adding 'HydRa/HydRa2_0_predict.py' 2023-12-15T05:58:59,102 adding 'HydRa/HydRa_predict.py' 2023-12-15T05:58:59,103 adding 'HydRa/__init__.py' 2023-12-15T05:58:59,105 adding 'HydRa/test_data_load.py' 2023-12-15T05:58:59,493 adding 'HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv' 2023-12-15T05:58:59,870 adding 'HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv' 2023-12-15T05:59:02,044 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls' 2023-12-15T05:59:02,601 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv' 2023-12-15T05:59:03,345 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv' 2023-12-15T05:59:06,710 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv' 2023-12-15T05:59:07,897 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv' 2023-12-15T05:59:11,281 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk' 2023-12-15T05:59:11,911 adding 'HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv' 2023-12-15T05:59:12,491 adding 'HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv' 2023-12-15T05:59:12,546 adding 'HydRa/data/Combined10RBPlist_uniprotID_20190716.txt' 2023-12-15T05:59:12,589 adding 'HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt' 2023-12-15T05:59:12,593 adding 'HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl' 2023-12-15T05:59:12,594 adding 'HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl' 2023-12-15T05:59:12,596 adding 'HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl' 2023-12-15T05:59:13,714 adding 'HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv' 2023-12-15T05:59:13,746 adding 'HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl' 2023-12-15T05:59:15,438 adding 'HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt' 2023-12-15T05:59:15,501 adding 'HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt' 2023-12-15T05:59:15,503 adding 'HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2023-12-15T05:59:15,505 adding 'HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2023-12-15T05:59:18,819 adding 'HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt' 2023-12-15T05:59:19,065 adding 'HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2023-12-15T05:59:19,067 adding 'HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2023-12-15T05:59:20,532 adding 'HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt' 2023-12-15T05:59:21,039 adding 'HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls' 2023-12-15T05:59:21,617 adding 'HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls' 2023-12-15T05:59:23,980 adding 'HydRa/data/protVec_100d_3grams.csv' 2023-12-15T05:59:24,035 adding 'HydRa/evaluation/ROC_PR_AUC_analysis.py' 2023-12-15T05:59:24,036 adding 'HydRa/evaluation/__init__.py' 2023-12-15T05:59:24,041 adding 'HydRa/models/DNN_seq.py' 2023-12-15T05:59:24,045 adding 'HydRa/models/Sequence_class.py' 2023-12-15T05:59:24,047 adding 'HydRa/models/__init__.py' 2023-12-15T05:59:24,276 adding 'HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5' 2023-12-15T05:59:24,512 adding 'HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5' 2023-12-15T05:59:24,524 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_structure.json' 2023-12-15T05:59:25,136 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_weights.h5' 2023-12-15T05:59:25,162 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_structure.json' 2023-12-15T05:59:25,774 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_weights.h5' 2023-12-15T05:59:25,805 adding 'HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5' 2023-12-15T05:59:25,812 adding 'HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5' 2023-12-15T05:59:25,909 adding 'HydRa/pre_trained/SVM_PPI_MB-S_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl' 2023-12-15T05:59:26,014 adding 'HydRa/pre_trained/SVM_PPI_MB_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl' 2023-12-15T05:59:30,957 adding 'HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pickle.pkl' 2023-12-15T05:59:34,324 adding 'HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_ModelFile.pickle.pkl' 2023-12-15T05:59:34,737 adding 'HydRa/predictions/Occlusion_1D_analysis_2.py' 2023-12-15T05:59:34,742 adding 'HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124.py' 2023-12-15T05:59:34,744 adding 'HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124_ensScore.py' 2023-12-15T05:59:34,749 adding 'HydRa/predictions/Occlusion_map.py' 2023-12-15T05:59:34,756 adding 'HydRa/predictions/Occlusion_map_v2.py' 2023-12-15T05:59:34,765 adding 'HydRa/predictions/Occlusion_map_v2_HydRa2_0.py' 2023-12-15T05:59:34,775 adding 'HydRa/predictions/Occlusion_map_v3_HydRa2_0.py' 2023-12-15T05:59:34,777 adding 'HydRa/predictions/__init__.py' 2023-12-15T05:59:34,780 adding 'HydRa/preprocessing/Get_All_selected_SVM_features.py' 2023-12-15T05:59:34,781 adding 'HydRa/preprocessing/PPI_feature_generation.py' 2023-12-15T05:59:34,783 adding 'HydRa/preprocessing/__init__.py' 2023-12-15T05:59:34,784 adding 'HydRa/preprocessing/get_SVM_seq_features.py' 2023-12-15T05:59:34,786 adding 'HydRa/preprocessing/predict_SS.py' 2023-12-15T05:59:34,788 adding 'HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py' 2023-12-15T05:59:34,790 adding 'HydRa/preprocessing/Feature_generation/PPI_feature_generation.py' 2023-12-15T05:59:34,791 adding 'HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py' 2023-12-15T05:59:34,793 adding 'HydRa/preprocessing/Feature_generation/__init__.py' 2023-12-15T05:59:34,794 adding 'HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py' 2023-12-15T05:59:34,796 adding 'HydRa/preprocessing/Feature_generation/kmer_table_generation.py' 2023-12-15T05:59:34,798 adding 'HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py' 2023-12-15T05:59:34,800 adding 'HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py' 2023-12-15T05:59:34,801 adding 'HydRa/preprocessing/Feature_selection/__init__.py' 2023-12-15T05:59:34,803 adding 'HydRa/training/__init__.py' 2023-12-15T05:59:34,807 adding 'HydRa/training/train_HydRa.py' 2023-12-15T05:59:34,813 adding 'HydRa/training/train_HydRa2_0.py' 2023-12-15T05:59:34,818 adding 'HydRa/training/train_and_evaluate_HydRa.py' 2023-12-15T05:59:34,824 adding 'HydRa/training/train_and_evaluate_HydRa2_0.py' 2023-12-15T05:59:34,829 adding 'HydRa/training/train_and_evaluate_HydRa_bk.py' 2023-12-15T05:59:34,832 adding 'hydra_rbp-0.1.21.32.dist-info/LICENSE' 2023-12-15T05:59:34,834 adding 'hydra_rbp-0.1.21.32.dist-info/METADATA' 2023-12-15T05:59:34,835 adding 'hydra_rbp-0.1.21.32.dist-info/WHEEL' 2023-12-15T05:59:34,836 adding 'hydra_rbp-0.1.21.32.dist-info/entry_points.txt' 2023-12-15T05:59:34,837 adding 'hydra_rbp-0.1.21.32.dist-info/top_level.txt' 2023-12-15T05:59:34,840 adding 'hydra_rbp-0.1.21.32.dist-info/RECORD' 2023-12-15T05:59:34,883 removing build/bdist.linux-armv7l/wheel 2023-12-15T05:59:35,125 Building wheel for hydra-rbp (setup.py): finished with status 'done' 2023-12-15T05:59:36,191 Created wheel for hydra-rbp: filename=hydra_rbp-0.1.21.32-py3-none-any.whl size=53775149 sha256=f2c2dd36cbc56568123d1736387532a1e0cb29727a80e19ec147b7b32891ae63 2023-12-15T05:59:36,192 Stored in directory: /tmp/pip-ephem-wheel-cache-wa7etoee/wheels/c3/85/fa/3a444e694f3a3662a17e8d3d147244d8a58cb97486048113de 2023-12-15T05:59:36,222 Successfully built hydra-rbp 2023-12-15T05:59:37,524 Removed build tracker: '/tmp/pip-build-tracker-uwk61p6q'