2024-06-01T00:49:24,317 Created temporary directory: /tmp/pip-build-tracker-khzi2075 2024-06-01T00:49:24,319 Initialized build tracking at /tmp/pip-build-tracker-khzi2075 2024-06-01T00:49:24,319 Created build tracker: /tmp/pip-build-tracker-khzi2075 2024-06-01T00:49:24,319 Entered build tracker: /tmp/pip-build-tracker-khzi2075 2024-06-01T00:49:24,320 Created temporary directory: /tmp/pip-wheel-rm35vqbn 2024-06-01T00:49:24,324 Created temporary directory: /tmp/pip-ephem-wheel-cache-hyriuxt4 2024-06-01T00:49:24,345 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-06-01T00:49:24,349 2 location(s) to search for versions of hydra-rbp: 2024-06-01T00:49:24,349 * https://pypi.org/simple/hydra-rbp/ 2024-06-01T00:49:24,349 * https://www.piwheels.org/simple/hydra-rbp/ 2024-06-01T00:49:24,350 Fetching project page and analyzing links: https://pypi.org/simple/hydra-rbp/ 2024-06-01T00:49:24,351 Getting page https://pypi.org/simple/hydra-rbp/ 2024-06-01T00:49:24,352 Found index url https://pypi.org/simple/ 2024-06-01T00:49:24,565 Fetched page https://pypi.org/simple/hydra-rbp/ as application/vnd.pypi.simple.v1+json 2024-06-01T00:49:24,569 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 2024-06-01T00:49:24,570 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 2024-06-01T00:49:24,570 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) 2024-06-01T00:49:24,571 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 2024-06-01T00:49:24,572 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) 2024-06-01T00:49:24,573 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 2024-06-01T00:49:24,574 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) 2024-06-01T00:49:24,575 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 2024-06-01T00:49:24,575 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) 2024-06-01T00:49:24,576 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 2024-06-01T00:49:24,577 Skipping link: No binaries permitted for hydra-rbp: https://files.pythonhosted.org/packages/88/57/b1d2918fe6e9988fdf1bc06b7e5c69a89acd7fde29e0a2c635c8439d774d/hydra_rbp-0.1.21.33-py3-none-any.whl (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6) 2024-06-01T00:49:24,578 Found link https://files.pythonhosted.org/packages/bc/87/28d107780077880671add84ac044599769995ea63ddafc2003421a8796de/hydra_rbp-0.1.21.33.tar.gz (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6), version: 0.1.21.33 2024-06-01T00:49:24,579 Skipping link: No binaries permitted for hydra-rbp: https://files.pythonhosted.org/packages/b9/ba/31dde9b6a647f4552395ac929d97f173aac1943c6807cbd056260e10028c/hydra_rbp-0.1.21.34-py3-none-any.whl (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6) 2024-06-01T00:49:24,580 Found link https://files.pythonhosted.org/packages/12/84/4e08c0bc35387dfd2176c0136f91f3e4f2f0009606b3985fab1e652a1497/hydra_rbp-0.1.21.34.tar.gz (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6), version: 0.1.21.34 2024-06-01T00:49:24,580 Skipping link: No binaries permitted for hydra-rbp: https://files.pythonhosted.org/packages/a2/61/2f9e31862f6e82e3db3a167ed96f11e18ad33f33543f0d08cad59011b77f/hydra_rbp-0.1.21.35-py3-none-any.whl (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6) 2024-06-01T00:49:24,581 Found link https://files.pythonhosted.org/packages/b6/7a/b3e1ea2088b4b45a70921acf27e86ca59f09dce53baebf193d7aeff71632/hydra_rbp-0.1.21.35.tar.gz (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6), version: 0.1.21.35 2024-06-01T00:49:24,582 Fetching project page and analyzing links: https://www.piwheels.org/simple/hydra-rbp/ 2024-06-01T00:49:24,583 Getting page https://www.piwheels.org/simple/hydra-rbp/ 2024-06-01T00:49:24,584 Found index url https://www.piwheels.org/simple/ 2024-06-01T00:49:24,767 Fetched page https://www.piwheels.org/simple/hydra-rbp/ as text/html 2024-06-01T00:49:24,771 Skipping link: No binaries permitted for hydra-rbp: https://www.piwheels.org/simple/hydra-rbp/hydra_rbp-0.1.21.34-py3-none-any.whl#sha256=19acfcf39c71eb20541e352df50ac02af84ab12973dba15bb2dce0b73a86fbc6 (from https://www.piwheels.org/simple/hydra-rbp/) (requires-python:>=3.6) 2024-06-01T00:49:24,772 Skipping link: No binaries permitted for hydra-rbp: https://www.piwheels.org/simple/hydra-rbp/hydra_rbp-0.1.21.33-py3-none-any.whl#sha256=bb44a445cfe2552b4ee79605c98945b5fd01b3902ae9f65ed3a7c644be59cad3 (from https://www.piwheels.org/simple/hydra-rbp/) (requires-python:>=3.6) 2024-06-01T00:49:24,772 Skipping link: No binaries permitted for hydra-rbp: https://www.piwheels.org/simple/hydra-rbp/hydra_rbp-0.1.21.32-py3-none-any.whl#sha256=f2c2dd36cbc56568123d1736387532a1e0cb29727a80e19ec147b7b32891ae63 (from https://www.piwheels.org/simple/hydra-rbp/) (requires-python:>=3.6) 2024-06-01T00:49:24,773 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) 2024-06-01T00:49:24,773 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) 2024-06-01T00:49:24,774 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) 2024-06-01T00:49:24,775 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) 2024-06-01T00:49:24,775 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) 2024-06-01T00:49:24,776 Skipping link: not a file: https://www.piwheels.org/simple/hydra-rbp/ 2024-06-01T00:49:24,777 Skipping link: not a file: https://pypi.org/simple/hydra-rbp/ 2024-06-01T00:49:24,796 Given no hashes to check 1 links for project 'hydra-rbp': discarding no candidates 2024-06-01T00:49:24,814 Collecting hydra-rbp==0.1.21.35 2024-06-01T00:49:24,816 Created temporary directory: /tmp/pip-unpack-2zd2pa9i 2024-06-01T00:49:25,034 Downloading hydra_rbp-0.1.21.35.tar.gz (52.3 MB) 2024-06-01T00:49:42,356 Added hydra-rbp==0.1.21.35 from https://files.pythonhosted.org/packages/b6/7a/b3e1ea2088b4b45a70921acf27e86ca59f09dce53baebf193d7aeff71632/hydra_rbp-0.1.21.35.tar.gz to build tracker '/tmp/pip-build-tracker-khzi2075' 2024-06-01T00:49:42,359 Running setup.py (path:/tmp/pip-wheel-rm35vqbn/hydra-rbp_83674380a3554f07a1c1c52201efdfad/setup.py) egg_info for package hydra-rbp 2024-06-01T00:49:42,360 Created temporary directory: /tmp/pip-pip-egg-info-ag23oyqf 2024-06-01T00:49:42,360 Preparing metadata (setup.py): started 2024-06-01T00:49:42,361 Running command python setup.py egg_info 2024-06-01T00:49:43,161 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-06-01T00:49:43,162 !! 2024-06-01T00:49:43,163 ******************************************************************************** 2024-06-01T00:49:43,163 Requirements should be satisfied by a PEP 517 installer. 2024-06-01T00:49:43,163 If you are using pip, you can try `pip install --use-pep517`. 2024-06-01T00:49:43,164 ******************************************************************************** 2024-06-01T00:49:43,165 !! 2024-06-01T00:49:43,166 dist.fetch_build_eggs(dist.setup_requires) 2024-06-01T00:49:46,109 running egg_info 2024-06-01T00:49:46,110 creating /tmp/pip-pip-egg-info-ag23oyqf/hydra_rbp.egg-info 2024-06-01T00:49:46,136 writing /tmp/pip-pip-egg-info-ag23oyqf/hydra_rbp.egg-info/PKG-INFO 2024-06-01T00:49:46,140 writing dependency_links to /tmp/pip-pip-egg-info-ag23oyqf/hydra_rbp.egg-info/dependency_links.txt 2024-06-01T00:49:46,142 writing entry points to /tmp/pip-pip-egg-info-ag23oyqf/hydra_rbp.egg-info/entry_points.txt 2024-06-01T00:49:46,143 writing requirements to /tmp/pip-pip-egg-info-ag23oyqf/hydra_rbp.egg-info/requires.txt 2024-06-01T00:49:46,144 writing top-level names to /tmp/pip-pip-egg-info-ag23oyqf/hydra_rbp.egg-info/top_level.txt 2024-06-01T00:49:46,146 writing manifest file '/tmp/pip-pip-egg-info-ag23oyqf/hydra_rbp.egg-info/SOURCES.txt' 2024-06-01T00:49:46,259 reading manifest file '/tmp/pip-pip-egg-info-ag23oyqf/hydra_rbp.egg-info/SOURCES.txt' 2024-06-01T00:49:46,261 reading manifest template 'MANIFEST.in' 2024-06-01T00:49:46,265 adding license file 'LICENSE' 2024-06-01T00:49:46,270 writing manifest file '/tmp/pip-pip-egg-info-ag23oyqf/hydra_rbp.egg-info/SOURCES.txt' 2024-06-01T00:49:46,389 Preparing metadata (setup.py): finished with status 'done' 2024-06-01T00:49:46,422 Source in /tmp/pip-wheel-rm35vqbn/hydra-rbp_83674380a3554f07a1c1c52201efdfad has version 0.1.21.35, which satisfies requirement hydra-rbp==0.1.21.35 from https://files.pythonhosted.org/packages/b6/7a/b3e1ea2088b4b45a70921acf27e86ca59f09dce53baebf193d7aeff71632/hydra_rbp-0.1.21.35.tar.gz 2024-06-01T00:49:46,424 Removed hydra-rbp==0.1.21.35 from https://files.pythonhosted.org/packages/b6/7a/b3e1ea2088b4b45a70921acf27e86ca59f09dce53baebf193d7aeff71632/hydra_rbp-0.1.21.35.tar.gz from build tracker '/tmp/pip-build-tracker-khzi2075' 2024-06-01T00:49:46,431 Created temporary directory: /tmp/pip-unpack-7e1l6mi5 2024-06-01T00:49:46,432 Created temporary directory: /tmp/pip-unpack-oy0v7dtm 2024-06-01T00:49:46,450 Building wheels for collected packages: hydra-rbp 2024-06-01T00:49:46,459 Created temporary directory: /tmp/pip-wheel-ipogwkqi 2024-06-01T00:49:46,460 Building wheel for hydra-rbp (setup.py): started 2024-06-01T00:49:46,461 Destination directory: /tmp/pip-wheel-ipogwkqi 2024-06-01T00:49:46,462 Running command python setup.py bdist_wheel 2024-06-01T00:49:47,212 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-06-01T00:49:47,213 !! 2024-06-01T00:49:47,214 ******************************************************************************** 2024-06-01T00:49:47,214 Requirements should be satisfied by a PEP 517 installer. 2024-06-01T00:49:47,214 If you are using pip, you can try `pip install --use-pep517`. 2024-06-01T00:49:47,215 ******************************************************************************** 2024-06-01T00:49:47,216 !! 2024-06-01T00:49:47,216 dist.fetch_build_eggs(dist.setup_requires) 2024-06-01T00:49:47,741 running bdist_wheel 2024-06-01T00:49:47,851 running build 2024-06-01T00:49:47,852 running build_py 2024-06-01T00:49:47,882 creating build 2024-06-01T00:49:47,883 creating build/lib 2024-06-01T00:49:47,883 creating build/lib/HydRa 2024-06-01T00:49:47,885 copying HydRa/__init__.py -> build/lib/HydRa 2024-06-01T00:49:47,887 copying HydRa/test_data_load.py -> build/lib/HydRa 2024-06-01T00:49:47,888 copying HydRa/HydRa_predict.py -> build/lib/HydRa 2024-06-01T00:49:47,891 copying HydRa/HydRa2_0_predict.py -> build/lib/HydRa 2024-06-01T00:49:47,894 creating build/lib/HydRa/preprocessing 2024-06-01T00:49:47,895 copying HydRa/preprocessing/__init__.py -> build/lib/HydRa/preprocessing 2024-06-01T00:49:47,897 copying HydRa/preprocessing/PPI_feature_generation.py -> build/lib/HydRa/preprocessing 2024-06-01T00:49:47,899 copying HydRa/preprocessing/get_SVM_seq_features.py -> build/lib/HydRa/preprocessing 2024-06-01T00:49:47,901 copying HydRa/preprocessing/predict_SS.py -> build/lib/HydRa/preprocessing 2024-06-01T00:49:47,902 copying HydRa/preprocessing/Get_All_selected_SVM_features.py -> build/lib/HydRa/preprocessing 2024-06-01T00:49:47,905 creating build/lib/HydRa/training 2024-06-01T00:49:47,906 copying HydRa/training/train_and_evaluate_HydRa.py -> build/lib/HydRa/training 2024-06-01T00:49:47,909 copying HydRa/training/__init__.py -> build/lib/HydRa/training 2024-06-01T00:49:47,911 copying HydRa/training/train_and_evaluate_HydRa2_0.py -> build/lib/HydRa/training 2024-06-01T00:49:47,914 copying HydRa/training/train_and_evaluate_HydRa_bk.py -> build/lib/HydRa/training 2024-06-01T00:49:47,917 copying HydRa/training/train_HydRa.py -> build/lib/HydRa/training 2024-06-01T00:49:47,919 copying HydRa/training/train_HydRa2_0.py -> build/lib/HydRa/training 2024-06-01T00:49:47,923 creating build/lib/HydRa/models 2024-06-01T00:49:47,924 copying HydRa/models/__init__.py -> build/lib/HydRa/models 2024-06-01T00:49:47,926 copying HydRa/models/DNN_seq.py -> build/lib/HydRa/models 2024-06-01T00:49:47,929 copying HydRa/models/Sequence_class.py -> build/lib/HydRa/models 2024-06-01T00:49:47,932 creating build/lib/HydRa/evaluation 2024-06-01T00:49:47,933 copying HydRa/evaluation/__init__.py -> build/lib/HydRa/evaluation 2024-06-01T00:49:47,935 copying HydRa/evaluation/ROC_PR_AUC_analysis.py -> build/lib/HydRa/evaluation 2024-06-01T00:49:47,937 creating build/lib/HydRa/predictions 2024-06-01T00:49:47,938 copying HydRa/predictions/__init__.py -> build/lib/HydRa/predictions 2024-06-01T00:49:47,940 copying HydRa/predictions/Occlusion_map_v2.py -> build/lib/HydRa/predictions 2024-06-01T00:49:47,943 copying HydRa/predictions/Occlusion_map.py -> build/lib/HydRa/predictions 2024-06-01T00:49:47,946 copying HydRa/predictions/Occlusion_map_v2_HydRa2_0.py -> build/lib/HydRa/predictions 2024-06-01T00:49:47,986 copying HydRa/predictions/Occlusion_map_v3_HydRa2_0.py -> build/lib/HydRa/predictions 2024-06-01T00:49:48,042 copying HydRa/predictions/Occlusion_1D_analysis_2.py -> build/lib/HydRa/predictions 2024-06-01T00:49:48,050 creating build/lib/HydRa/preprocessing/Feature_selection 2024-06-01T00:49:48,052 copying HydRa/preprocessing/Feature_selection/__init__.py -> build/lib/HydRa/preprocessing/Feature_selection 2024-06-01T00:49:48,054 copying HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py -> build/lib/HydRa/preprocessing/Feature_selection 2024-06-01T00:49:48,058 creating build/lib/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:48,059 copying HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:48,063 copying HydRa/preprocessing/Feature_generation/__init__.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:48,065 copying HydRa/preprocessing/Feature_generation/PPI_feature_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:48,068 copying HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:48,071 copying HydRa/preprocessing/Feature_generation/kmer_table_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:48,074 copying HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:48,078 copying HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:48,081 running egg_info 2024-06-01T00:49:48,134 writing hydra_rbp.egg-info/PKG-INFO 2024-06-01T00:49:48,138 writing dependency_links to hydra_rbp.egg-info/dependency_links.txt 2024-06-01T00:49:48,140 writing entry points to hydra_rbp.egg-info/entry_points.txt 2024-06-01T00:49:48,141 writing requirements to hydra_rbp.egg-info/requires.txt 2024-06-01T00:49:48,142 writing top-level names to hydra_rbp.egg-info/top_level.txt 2024-06-01T00:49:48,185 reading manifest file 'hydra_rbp.egg-info/SOURCES.txt' 2024-06-01T00:49:48,189 reading manifest template 'MANIFEST.in' 2024-06-01T00:49:48,192 adding license file 'LICENSE' 2024-06-01T00:49:48,197 writing manifest file 'hydra_rbp.egg-info/SOURCES.txt' 2024-06-01T00:49:48,200 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'HydRa.data' is absent from the `packages` configuration. 2024-06-01T00:49:48,200 !! 2024-06-01T00:49:48,202 ******************************************************************************** 2024-06-01T00:49:48,202 ############################ 2024-06-01T00:49:48,203 # Package would be ignored # 2024-06-01T00:49:48,204 ############################ 2024-06-01T00:49:48,204 Python recognizes 'HydRa.data' as an importable package[^1], 2024-06-01T00:49:48,205 but it is absent from setuptools' `packages` configuration. 2024-06-01T00:49:48,206 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-01T00:49:48,207 package, please make sure that 'HydRa.data' is explicitly added 2024-06-01T00:49:48,207 to the `packages` configuration field. 2024-06-01T00:49:48,209 Alternatively, you can also rely on setuptools' discovery methods 2024-06-01T00:49:48,209 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-01T00:49:48,210 instead of `find_packages(...)`/`find:`). 2024-06-01T00:49:48,211 You can read more about "package discovery" on setuptools documentation page: 2024-06-01T00:49:48,212 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-01T00:49:48,213 If you don't want 'HydRa.data' to be distributed and are 2024-06-01T00:49:48,213 already explicitly excluding 'HydRa.data' via 2024-06-01T00:49:48,214 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-01T00:49:48,215 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-01T00:49:48,215 combination with a more fine grained `package-data` configuration. 2024-06-01T00:49:48,216 You can read more about "package data files" on setuptools documentation page: 2024-06-01T00:49:48,217 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-01T00:49:48,219 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-01T00:49:48,219 even if it does not contain any `.py` files. 2024-06-01T00:49:48,219 On the other hand, currently there is no concept of package data 2024-06-01T00:49:48,220 directory, all directories are treated like packages. 2024-06-01T00:49:48,220 ******************************************************************************** 2024-06-01T00:49:48,221 !! 2024-06-01T00:49:48,221 check.warn(importable) 2024-06-01T00:49:48,222 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'HydRa.pre_trained' is absent from the `packages` configuration. 2024-06-01T00:49:48,222 !! 2024-06-01T00:49:48,223 ******************************************************************************** 2024-06-01T00:49:48,224 ############################ 2024-06-01T00:49:48,224 # Package would be ignored # 2024-06-01T00:49:48,225 ############################ 2024-06-01T00:49:48,225 Python recognizes 'HydRa.pre_trained' as an importable package[^1], 2024-06-01T00:49:48,225 but it is absent from setuptools' `packages` configuration. 2024-06-01T00:49:48,226 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-01T00:49:48,227 package, please make sure that 'HydRa.pre_trained' is explicitly added 2024-06-01T00:49:48,227 to the `packages` configuration field. 2024-06-01T00:49:48,229 Alternatively, you can also rely on setuptools' discovery methods 2024-06-01T00:49:48,229 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-01T00:49:48,230 instead of `find_packages(...)`/`find:`). 2024-06-01T00:49:48,231 You can read more about "package discovery" on setuptools documentation page: 2024-06-01T00:49:48,233 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-01T00:49:48,237 If you don't want 'HydRa.pre_trained' to be distributed and are 2024-06-01T00:49:48,237 already explicitly excluding 'HydRa.pre_trained' via 2024-06-01T00:49:48,238 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-01T00:49:48,239 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-01T00:49:48,240 combination with a more fine grained `package-data` configuration. 2024-06-01T00:49:48,241 You can read more about "package data files" on setuptools documentation page: 2024-06-01T00:49:48,243 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-01T00:49:48,245 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-01T00:49:48,246 even if it does not contain any `.py` files. 2024-06-01T00:49:48,247 On the other hand, currently there is no concept of package data 2024-06-01T00:49:48,247 directory, all directories are treated like packages. 2024-06-01T00:49:48,248 ******************************************************************************** 2024-06-01T00:49:48,250 !! 2024-06-01T00:49:48,250 check.warn(importable) 2024-06-01T00:49:48,251 creating build/lib/HydRa/data 2024-06-01T00:49:48,252 copying HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2024-06-01T00:49:48,258 copying HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2024-06-01T00:49:48,287 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls -> build/lib/HydRa/data 2024-06-01T00:49:48,438 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv -> build/lib/HydRa/data 2024-06-01T00:49:48,465 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv -> build/lib/HydRa/data 2024-06-01T00:49:48,519 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2024-06-01T00:49:48,719 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/lib/HydRa/data 2024-06-01T00:49:48,787 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk -> build/lib/HydRa/data 2024-06-01T00:49:48,960 copying HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2024-06-01T00:49:48,993 copying HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/lib/HydRa/data 2024-06-01T00:49:49,028 copying HydRa/data/Combined10RBPlist_uniprotID_20190716.txt -> build/lib/HydRa/data 2024-06-01T00:49:49,077 copying HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt -> build/lib/HydRa/data 2024-06-01T00:49:49,081 copying HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/lib/HydRa/data 2024-06-01T00:49:49,083 copying HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl -> build/lib/HydRa/data 2024-06-01T00:49:49,085 copying HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl -> build/lib/HydRa/data 2024-06-01T00:49:49,087 copying HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv -> build/lib/HydRa/data 2024-06-01T00:49:49,226 copying HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/lib/HydRa/data 2024-06-01T00:49:49,228 copying HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt -> build/lib/HydRa/data 2024-06-01T00:49:49,380 copying HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt -> build/lib/HydRa/data 2024-06-01T00:49:49,382 copying HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2024-06-01T00:49:49,384 copying HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2024-06-01T00:49:49,386 copying HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt -> build/lib/HydRa/data 2024-06-01T00:49:49,945 copying HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2024-06-01T00:49:49,947 copying HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2024-06-01T00:49:49,949 copying HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt -> build/lib/HydRa/data 2024-06-01T00:49:50,018 copying HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls -> build/lib/HydRa/data 2024-06-01T00:49:50,051 copying HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls -> build/lib/HydRa/data 2024-06-01T00:49:50,138 copying HydRa/data/protVec_100d_3grams.csv -> build/lib/HydRa/data 2024-06-01T00:49:50,269 creating build/lib/HydRa/pre_trained 2024-06-01T00:49:50,270 copying HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2024-06-01T00:49:50,297 copying HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2024-06-01T00:49:50,321 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 2024-06-01T00:49:50,324 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 2024-06-01T00:49:50,380 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 2024-06-01T00:49:50,383 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 2024-06-01T00:49:50,442 copying HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2024-06-01T00:49:50,446 copying HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2024-06-01T00:49:50,449 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 2024-06-01T00:49:50,469 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 2024-06-01T00:49:50,485 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 2024-06-01T00:49:53,540 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 2024-06-01T00:49:55,273 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-06-01T00:49:55,274 !! 2024-06-01T00:49:55,275 ******************************************************************************** 2024-06-01T00:49:55,276 Please avoid running ``setup.py`` directly. 2024-06-01T00:49:55,277 Instead, use pypa/build, pypa/installer or other 2024-06-01T00:49:55,277 standards-based tools. 2024-06-01T00:49:55,278 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-06-01T00:49:55,279 ******************************************************************************** 2024-06-01T00:49:55,280 !! 2024-06-01T00:49:55,281 self.initialize_options() 2024-06-01T00:49:55,301 installing to build/bdist.linux-armv7l/wheel 2024-06-01T00:49:55,301 running install 2024-06-01T00:49:55,326 running install_lib 2024-06-01T00:49:55,352 creating build/bdist.linux-armv7l 2024-06-01T00:49:55,353 creating build/bdist.linux-armv7l/wheel 2024-06-01T00:49:55,354 creating build/bdist.linux-armv7l/wheel/HydRa 2024-06-01T00:49:55,355 copying build/lib/HydRa/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa 2024-06-01T00:49:55,358 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-06-01T00:49:55,359 copying build/lib/HydRa/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-06-01T00:49:55,361 copying build/lib/HydRa/preprocessing/PPI_feature_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-06-01T00:49:55,364 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2024-06-01T00:49:55,365 copying build/lib/HydRa/preprocessing/Feature_selection/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2024-06-01T00:49:55,367 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 2024-06-01T00:49:55,369 copying build/lib/HydRa/preprocessing/get_SVM_seq_features.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-06-01T00:49:55,371 copying build/lib/HydRa/preprocessing/predict_SS.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-06-01T00:49:55,373 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:55,374 copying build/lib/HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:55,377 copying build/lib/HydRa/preprocessing/Feature_generation/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:55,378 copying build/lib/HydRa/preprocessing/Feature_generation/PPI_feature_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:55,380 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 2024-06-01T00:49:55,382 copying build/lib/HydRa/preprocessing/Feature_generation/kmer_table_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:55,384 copying build/lib/HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:55,386 copying build/lib/HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-06-01T00:49:55,387 copying build/lib/HydRa/preprocessing/Get_All_selected_SVM_features.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-06-01T00:49:55,390 creating build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:55,391 copying build/lib/HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:55,393 copying build/lib/HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:55,963 copying build/lib/HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:55,965 copying build/lib/HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:55,966 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 2024-06-01T00:49:55,992 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 2024-06-01T00:49:55,994 copying build/lib/HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:56,023 copying build/lib/HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:56,025 copying build/lib/HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:56,064 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 2024-06-01T00:49:56,178 copying build/lib/HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:56,180 copying build/lib/HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:56,301 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 2024-06-01T00:49:56,323 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 2024-06-01T00:49:56,325 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 2024-06-01T00:49:56,362 copying build/lib/HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:56,400 copying build/lib/HydRa/data/protVec_100d_3grams.csv -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:56,539 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 2024-06-01T00:49:56,558 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 2024-06-01T00:49:56,629 copying build/lib/HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:56,634 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 2024-06-01T00:49:56,802 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 2024-06-01T00:49:56,968 copying build/lib/HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:56,970 copying build/lib/HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:57,122 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 2024-06-01T00:49:57,123 copying build/lib/HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:57,155 copying build/lib/HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:57,221 copying build/lib/HydRa/data/Combined10RBPlist_uniprotID_20190716.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-06-01T00:49:57,226 creating build/bdist.linux-armv7l/wheel/HydRa/training 2024-06-01T00:49:57,227 copying build/lib/HydRa/training/train_and_evaluate_HydRa.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-06-01T00:49:57,230 copying build/lib/HydRa/training/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-06-01T00:49:57,232 copying build/lib/HydRa/training/train_and_evaluate_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-06-01T00:49:57,235 copying build/lib/HydRa/training/train_and_evaluate_HydRa_bk.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-06-01T00:49:57,238 copying build/lib/HydRa/training/train_HydRa.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-06-01T00:49:57,241 copying build/lib/HydRa/training/train_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-06-01T00:49:57,244 copying build/lib/HydRa/test_data_load.py -> build/bdist.linux-armv7l/wheel/HydRa 2024-06-01T00:49:57,246 creating build/bdist.linux-armv7l/wheel/HydRa/models 2024-06-01T00:49:57,247 copying build/lib/HydRa/models/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2024-06-01T00:49:57,249 copying build/lib/HydRa/models/DNN_seq.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2024-06-01T00:49:57,252 copying build/lib/HydRa/models/Sequence_class.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2024-06-01T00:49:57,255 copying build/lib/HydRa/HydRa_predict.py -> build/bdist.linux-armv7l/wheel/HydRa 2024-06-01T00:49:57,258 creating build/bdist.linux-armv7l/wheel/HydRa/evaluation 2024-06-01T00:49:57,259 copying build/lib/HydRa/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/evaluation 2024-06-01T00:49:57,260 copying build/lib/HydRa/evaluation/ROC_PR_AUC_analysis.py -> build/bdist.linux-armv7l/wheel/HydRa/evaluation 2024-06-01T00:49:57,263 creating build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2024-06-01T00:49:57,263 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 2024-06-01T00:49:57,279 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 2024-06-01T00:50:00,318 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 2024-06-01T00:50:00,320 copying build/lib/HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2024-06-01T00:50:00,345 copying build/lib/HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2024-06-01T00:50:00,348 copying build/lib/HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2024-06-01T00:50:00,374 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 2024-06-01T00:50:00,443 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 2024-06-01T00:50:00,506 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 2024-06-01T00:50:00,508 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 2024-06-01T00:50:00,525 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 2024-06-01T00:50:01,430 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 2024-06-01T00:50:01,434 copying build/lib/HydRa/HydRa2_0_predict.py -> build/bdist.linux-armv7l/wheel/HydRa 2024-06-01T00:50:01,441 creating build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-06-01T00:50:01,442 copying build/lib/HydRa/predictions/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-06-01T00:50:01,444 copying build/lib/HydRa/predictions/Occlusion_map_v2.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-06-01T00:50:01,447 copying build/lib/HydRa/predictions/Occlusion_map.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-06-01T00:50:01,450 copying build/lib/HydRa/predictions/Occlusion_map_v2_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-06-01T00:50:01,454 copying build/lib/HydRa/predictions/Occlusion_map_v3_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-06-01T00:50:01,458 copying build/lib/HydRa/predictions/Occlusion_1D_analysis_2.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-06-01T00:50:01,460 running install_egg_info 2024-06-01T00:50:01,491 Copying hydra_rbp.egg-info to build/bdist.linux-armv7l/wheel/hydra_rbp-0.1.21.35-py3.11.egg-info 2024-06-01T00:50:01,504 running install_scripts 2024-06-01T00:50:01,522 creating build/bdist.linux-armv7l/wheel/hydra_rbp-0.1.21.35.dist-info/WHEEL 2024-06-01T00:50:01,525 creating '/tmp/pip-wheel-ipogwkqi/hydra_rbp-0.1.21.35-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-06-01T00:50:01,530 adding 'HydRa/HydRa2_0_predict.py' 2024-06-01T00:50:01,534 adding 'HydRa/HydRa_predict.py' 2024-06-01T00:50:01,536 adding 'HydRa/__init__.py' 2024-06-01T00:50:01,537 adding 'HydRa/test_data_load.py' 2024-06-01T00:50:01,926 adding 'HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv' 2024-06-01T00:50:02,298 adding 'HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv' 2024-06-01T00:50:04,476 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls' 2024-06-01T00:50:05,038 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv' 2024-06-01T00:50:05,785 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv' 2024-06-01T00:50:09,170 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv' 2024-06-01T00:50:10,365 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv' 2024-06-01T00:50:13,767 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk' 2024-06-01T00:50:14,407 adding 'HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv' 2024-06-01T00:50:14,985 adding 'HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv' 2024-06-01T00:50:15,043 adding 'HydRa/data/Combined10RBPlist_uniprotID_20190716.txt' 2024-06-01T00:50:15,088 adding 'HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt' 2024-06-01T00:50:15,090 adding 'HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl' 2024-06-01T00:50:15,092 adding 'HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl' 2024-06-01T00:50:15,093 adding 'HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl' 2024-06-01T00:50:16,219 adding 'HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv' 2024-06-01T00:50:16,251 adding 'HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl' 2024-06-01T00:50:17,958 adding 'HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt' 2024-06-01T00:50:18,020 adding 'HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt' 2024-06-01T00:50:18,021 adding 'HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2024-06-01T00:50:18,023 adding 'HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2024-06-01T00:50:21,364 adding 'HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt' 2024-06-01T00:50:21,613 adding 'HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2024-06-01T00:50:21,614 adding 'HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2024-06-01T00:50:23,089 adding 'HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt' 2024-06-01T00:50:23,597 adding 'HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls' 2024-06-01T00:50:24,182 adding 'HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls' 2024-06-01T00:50:26,564 adding 'HydRa/data/protVec_100d_3grams.csv' 2024-06-01T00:50:26,613 adding 'HydRa/evaluation/ROC_PR_AUC_analysis.py' 2024-06-01T00:50:26,614 adding 'HydRa/evaluation/__init__.py' 2024-06-01T00:50:26,619 adding 'HydRa/models/DNN_seq.py' 2024-06-01T00:50:26,623 adding 'HydRa/models/Sequence_class.py' 2024-06-01T00:50:26,624 adding 'HydRa/models/__init__.py' 2024-06-01T00:50:26,854 adding 'HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5' 2024-06-01T00:50:27,090 adding 'HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5' 2024-06-01T00:50:27,101 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_structure.json' 2024-06-01T00:50:27,718 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_weights.h5' 2024-06-01T00:50:27,744 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_structure.json' 2024-06-01T00:50:28,357 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_weights.h5' 2024-06-01T00:50:28,388 adding 'HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5' 2024-06-01T00:50:28,395 adding 'HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5' 2024-06-01T00:50:28,493 adding 'HydRa/pre_trained/SVM_PPI_MB-S_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl' 2024-06-01T00:50:28,601 adding 'HydRa/pre_trained/SVM_PPI_MB_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl' 2024-06-01T00:50:33,576 adding 'HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pickle.pkl' 2024-06-01T00:50:36,920 adding 'HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_ModelFile.pickle.pkl' 2024-06-01T00:50:37,333 adding 'HydRa/predictions/Occlusion_1D_analysis_2.py' 2024-06-01T00:50:37,338 adding 'HydRa/predictions/Occlusion_map.py' 2024-06-01T00:50:37,344 adding 'HydRa/predictions/Occlusion_map_v2.py' 2024-06-01T00:50:37,353 adding 'HydRa/predictions/Occlusion_map_v2_HydRa2_0.py' 2024-06-01T00:50:37,363 adding 'HydRa/predictions/Occlusion_map_v3_HydRa2_0.py' 2024-06-01T00:50:37,365 adding 'HydRa/predictions/__init__.py' 2024-06-01T00:50:37,367 adding 'HydRa/preprocessing/Get_All_selected_SVM_features.py' 2024-06-01T00:50:37,368 adding 'HydRa/preprocessing/PPI_feature_generation.py' 2024-06-01T00:50:37,369 adding 'HydRa/preprocessing/__init__.py' 2024-06-01T00:50:37,370 adding 'HydRa/preprocessing/get_SVM_seq_features.py' 2024-06-01T00:50:37,372 adding 'HydRa/preprocessing/predict_SS.py' 2024-06-01T00:50:37,373 adding 'HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py' 2024-06-01T00:50:37,375 adding 'HydRa/preprocessing/Feature_generation/PPI_feature_generation.py' 2024-06-01T00:50:37,376 adding 'HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py' 2024-06-01T00:50:37,377 adding 'HydRa/preprocessing/Feature_generation/__init__.py' 2024-06-01T00:50:37,379 adding 'HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py' 2024-06-01T00:50:37,380 adding 'HydRa/preprocessing/Feature_generation/kmer_table_generation.py' 2024-06-01T00:50:37,381 adding 'HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py' 2024-06-01T00:50:37,383 adding 'HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py' 2024-06-01T00:50:37,384 adding 'HydRa/preprocessing/Feature_selection/__init__.py' 2024-06-01T00:50:37,386 adding 'HydRa/training/__init__.py' 2024-06-01T00:50:37,390 adding 'HydRa/training/train_HydRa.py' 2024-06-01T00:50:37,394 adding 'HydRa/training/train_HydRa2_0.py' 2024-06-01T00:50:37,399 adding 'HydRa/training/train_and_evaluate_HydRa.py' 2024-06-01T00:50:37,405 adding 'HydRa/training/train_and_evaluate_HydRa2_0.py' 2024-06-01T00:50:37,409 adding 'HydRa/training/train_and_evaluate_HydRa_bk.py' 2024-06-01T00:50:37,412 adding 'hydra_rbp-0.1.21.35.dist-info/LICENSE' 2024-06-01T00:50:37,414 adding 'hydra_rbp-0.1.21.35.dist-info/METADATA' 2024-06-01T00:50:37,415 adding 'hydra_rbp-0.1.21.35.dist-info/WHEEL' 2024-06-01T00:50:37,416 adding 'hydra_rbp-0.1.21.35.dist-info/entry_points.txt' 2024-06-01T00:50:37,417 adding 'hydra_rbp-0.1.21.35.dist-info/top_level.txt' 2024-06-01T00:50:37,419 adding 'hydra_rbp-0.1.21.35.dist-info/RECORD' 2024-06-01T00:50:37,455 removing build/bdist.linux-armv7l/wheel 2024-06-01T00:50:37,733 Building wheel for hydra-rbp (setup.py): finished with status 'done' 2024-06-01T00:50:38,267 Created wheel for hydra-rbp: filename=hydra_rbp-0.1.21.35-py3-none-any.whl size=53763632 sha256=6c3ec66bd534af4362c37423aa91f92ad02101d732b94cbdf28eb56ab8b57c65 2024-06-01T00:50:38,270 Stored in directory: /tmp/pip-ephem-wheel-cache-hyriuxt4/wheels/1c/f9/6f/c170ee9c6bb94eaee517df8f4531a5d80d9a20da3f52aa14d2 2024-06-01T00:50:38,300 Successfully built hydra-rbp 2024-06-01T00:50:39,618 Removed build tracker: '/tmp/pip-build-tracker-khzi2075'