2024-05-10T01:02:38,904 Created temporary directory: /tmp/pip-build-tracker-amg84ie1 2024-05-10T01:02:38,905 Initialized build tracking at /tmp/pip-build-tracker-amg84ie1 2024-05-10T01:02:38,906 Created build tracker: /tmp/pip-build-tracker-amg84ie1 2024-05-10T01:02:38,906 Entered build tracker: /tmp/pip-build-tracker-amg84ie1 2024-05-10T01:02:38,907 Created temporary directory: /tmp/pip-wheel-8aj7hvmw 2024-05-10T01:02:38,910 Created temporary directory: /tmp/pip-ephem-wheel-cache-i1jsohyg 2024-05-10T01:02:38,932 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-10T01:02:38,936 2 location(s) to search for versions of hydra-rbp: 2024-05-10T01:02:38,936 * https://pypi.org/simple/hydra-rbp/ 2024-05-10T01:02:38,936 * https://www.piwheels.org/simple/hydra-rbp/ 2024-05-10T01:02:38,937 Fetching project page and analyzing links: https://pypi.org/simple/hydra-rbp/ 2024-05-10T01:02:38,937 Getting page https://pypi.org/simple/hydra-rbp/ 2024-05-10T01:02:38,939 Found index url https://pypi.org/simple/ 2024-05-10T01:02:39,156 Fetched page https://pypi.org/simple/hydra-rbp/ as application/vnd.pypi.simple.v1+json 2024-05-10T01:02:39,160 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 2024-05-10T01:02:39,161 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 2024-05-10T01:02:39,162 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) 2024-05-10T01:02:39,163 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 2024-05-10T01:02:39,164 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) 2024-05-10T01:02:39,165 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 2024-05-10T01:02:39,165 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) 2024-05-10T01:02:39,166 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 2024-05-10T01:02:39,167 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) 2024-05-10T01:02:39,168 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 2024-05-10T01:02:39,169 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) 2024-05-10T01:02:39,170 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 2024-05-10T01:02:39,171 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) 2024-05-10T01:02:39,172 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 2024-05-10T01:02:39,172 Fetching project page and analyzing links: https://www.piwheels.org/simple/hydra-rbp/ 2024-05-10T01:02:39,173 Getting page https://www.piwheels.org/simple/hydra-rbp/ 2024-05-10T01:02:39,174 Found index url https://www.piwheels.org/simple/ 2024-05-10T01:02:39,480 Fetched page https://www.piwheels.org/simple/hydra-rbp/ as text/html 2024-05-10T01:02:39,483 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) 2024-05-10T01:02:39,484 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) 2024-05-10T01:02:39,484 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) 2024-05-10T01:02:39,485 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) 2024-05-10T01:02:39,486 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) 2024-05-10T01:02:39,486 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) 2024-05-10T01:02:39,487 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) 2024-05-10T01:02:39,488 Skipping link: not a file: https://www.piwheels.org/simple/hydra-rbp/ 2024-05-10T01:02:39,488 Skipping link: not a file: https://pypi.org/simple/hydra-rbp/ 2024-05-10T01:02:39,508 Given no hashes to check 1 links for project 'hydra-rbp': discarding no candidates 2024-05-10T01:02:39,526 Collecting hydra-rbp==0.1.21.34 2024-05-10T01:02:39,528 Created temporary directory: /tmp/pip-unpack-swm8vktd 2024-05-10T01:02:39,747 Downloading hydra_rbp-0.1.21.34.tar.gz (52.3 MB) 2024-05-10T01:03:00,378 Added hydra-rbp==0.1.21.34 from https://files.pythonhosted.org/packages/12/84/4e08c0bc35387dfd2176c0136f91f3e4f2f0009606b3985fab1e652a1497/hydra_rbp-0.1.21.34.tar.gz to build tracker '/tmp/pip-build-tracker-amg84ie1' 2024-05-10T01:03:00,379 Running setup.py (path:/tmp/pip-wheel-8aj7hvmw/hydra-rbp_7736c1a1c2bf408dbde0659433a1e556/setup.py) egg_info for package hydra-rbp 2024-05-10T01:03:00,380 Created temporary directory: /tmp/pip-pip-egg-info-p7bybhj9 2024-05-10T01:03:00,381 Preparing metadata (setup.py): started 2024-05-10T01:03:00,383 Running command python setup.py egg_info 2024-05-10T01:03:01,148 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-05-10T01:03:01,148 !! 2024-05-10T01:03:01,149 ******************************************************************************** 2024-05-10T01:03:01,150 Requirements should be satisfied by a PEP 517 installer. 2024-05-10T01:03:01,150 If you are using pip, you can try `pip install --use-pep517`. 2024-05-10T01:03:01,151 ******************************************************************************** 2024-05-10T01:03:01,152 !! 2024-05-10T01:03:01,152 dist.fetch_build_eggs(dist.setup_requires) 2024-05-10T01:03:04,116 running egg_info 2024-05-10T01:03:04,117 creating /tmp/pip-pip-egg-info-p7bybhj9/hydra_rbp.egg-info 2024-05-10T01:03:04,144 writing /tmp/pip-pip-egg-info-p7bybhj9/hydra_rbp.egg-info/PKG-INFO 2024-05-10T01:03:04,147 writing dependency_links to /tmp/pip-pip-egg-info-p7bybhj9/hydra_rbp.egg-info/dependency_links.txt 2024-05-10T01:03:04,149 writing entry points to /tmp/pip-pip-egg-info-p7bybhj9/hydra_rbp.egg-info/entry_points.txt 2024-05-10T01:03:04,151 writing requirements to /tmp/pip-pip-egg-info-p7bybhj9/hydra_rbp.egg-info/requires.txt 2024-05-10T01:03:04,152 writing top-level names to /tmp/pip-pip-egg-info-p7bybhj9/hydra_rbp.egg-info/top_level.txt 2024-05-10T01:03:04,153 writing manifest file '/tmp/pip-pip-egg-info-p7bybhj9/hydra_rbp.egg-info/SOURCES.txt' 2024-05-10T01:03:04,265 reading manifest file '/tmp/pip-pip-egg-info-p7bybhj9/hydra_rbp.egg-info/SOURCES.txt' 2024-05-10T01:03:04,267 reading manifest template 'MANIFEST.in' 2024-05-10T01:03:04,270 adding license file 'LICENSE' 2024-05-10T01:03:04,275 writing manifest file '/tmp/pip-pip-egg-info-p7bybhj9/hydra_rbp.egg-info/SOURCES.txt' 2024-05-10T01:03:04,393 Preparing metadata (setup.py): finished with status 'done' 2024-05-10T01:03:04,398 Source in /tmp/pip-wheel-8aj7hvmw/hydra-rbp_7736c1a1c2bf408dbde0659433a1e556 has version 0.1.21.34, which satisfies requirement hydra-rbp==0.1.21.34 from https://files.pythonhosted.org/packages/12/84/4e08c0bc35387dfd2176c0136f91f3e4f2f0009606b3985fab1e652a1497/hydra_rbp-0.1.21.34.tar.gz 2024-05-10T01:03:04,399 Removed hydra-rbp==0.1.21.34 from https://files.pythonhosted.org/packages/12/84/4e08c0bc35387dfd2176c0136f91f3e4f2f0009606b3985fab1e652a1497/hydra_rbp-0.1.21.34.tar.gz from build tracker '/tmp/pip-build-tracker-amg84ie1' 2024-05-10T01:03:04,406 Created temporary directory: /tmp/pip-unpack-pki1_ro6 2024-05-10T01:03:04,407 Created temporary directory: /tmp/pip-unpack-dg1uk71b 2024-05-10T01:03:04,422 Building wheels for collected packages: hydra-rbp 2024-05-10T01:03:04,426 Created temporary directory: /tmp/pip-wheel-phcem6d8 2024-05-10T01:03:04,427 Building wheel for hydra-rbp (setup.py): started 2024-05-10T01:03:04,428 Destination directory: /tmp/pip-wheel-phcem6d8 2024-05-10T01:03:04,429 Running command python setup.py bdist_wheel 2024-05-10T01:03:05,162 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-05-10T01:03:05,162 !! 2024-05-10T01:03:05,164 ******************************************************************************** 2024-05-10T01:03:05,164 Requirements should be satisfied by a PEP 517 installer. 2024-05-10T01:03:05,165 If you are using pip, you can try `pip install --use-pep517`. 2024-05-10T01:03:05,166 ******************************************************************************** 2024-05-10T01:03:05,167 !! 2024-05-10T01:03:05,167 dist.fetch_build_eggs(dist.setup_requires) 2024-05-10T01:03:05,683 running bdist_wheel 2024-05-10T01:03:05,791 running build 2024-05-10T01:03:05,792 running build_py 2024-05-10T01:03:05,823 creating build 2024-05-10T01:03:05,824 creating build/lib 2024-05-10T01:03:05,825 creating build/lib/HydRa 2024-05-10T01:03:05,826 copying HydRa/HydRa_predict.py -> build/lib/HydRa 2024-05-10T01:03:05,828 copying HydRa/test_data_load.py -> build/lib/HydRa 2024-05-10T01:03:05,830 copying HydRa/__init__.py -> build/lib/HydRa 2024-05-10T01:03:05,832 copying HydRa/HydRa2_0_predict.py -> build/lib/HydRa 2024-05-10T01:03:05,835 creating build/lib/HydRa/preprocessing 2024-05-10T01:03:05,836 copying HydRa/preprocessing/PPI_feature_generation.py -> build/lib/HydRa/preprocessing 2024-05-10T01:03:05,838 copying HydRa/preprocessing/get_SVM_seq_features.py -> build/lib/HydRa/preprocessing 2024-05-10T01:03:05,840 copying HydRa/preprocessing/Get_All_selected_SVM_features.py -> build/lib/HydRa/preprocessing 2024-05-10T01:03:05,842 copying HydRa/preprocessing/predict_SS.py -> build/lib/HydRa/preprocessing 2024-05-10T01:03:05,844 copying HydRa/preprocessing/__init__.py -> build/lib/HydRa/preprocessing 2024-05-10T01:03:05,846 creating build/lib/HydRa/training 2024-05-10T01:03:05,847 copying HydRa/training/train_and_evaluate_HydRa_bk.py -> build/lib/HydRa/training 2024-05-10T01:03:05,850 copying HydRa/training/train_and_evaluate_HydRa2_0.py -> build/lib/HydRa/training 2024-05-10T01:03:05,853 copying HydRa/training/train_HydRa.py -> build/lib/HydRa/training 2024-05-10T01:03:05,855 copying HydRa/training/train_HydRa2_0.py -> build/lib/HydRa/training 2024-05-10T01:03:05,858 copying HydRa/training/train_and_evaluate_HydRa.py -> build/lib/HydRa/training 2024-05-10T01:03:05,861 copying HydRa/training/__init__.py -> build/lib/HydRa/training 2024-05-10T01:03:05,863 creating build/lib/HydRa/models 2024-05-10T01:03:05,864 copying HydRa/models/Sequence_class.py -> build/lib/HydRa/models 2024-05-10T01:03:05,867 copying HydRa/models/DNN_seq.py -> build/lib/HydRa/models 2024-05-10T01:03:05,871 copying HydRa/models/__init__.py -> build/lib/HydRa/models 2024-05-10T01:03:05,873 creating build/lib/HydRa/evaluation 2024-05-10T01:03:05,874 copying HydRa/evaluation/__init__.py -> build/lib/HydRa/evaluation 2024-05-10T01:03:05,875 copying HydRa/evaluation/ROC_PR_AUC_analysis.py -> build/lib/HydRa/evaluation 2024-05-10T01:03:05,878 creating build/lib/HydRa/predictions 2024-05-10T01:03:05,879 copying HydRa/predictions/Occlusion_1D_analysis_2.py -> build/lib/HydRa/predictions 2024-05-10T01:03:05,881 copying HydRa/predictions/Occlusion_map_v2.py -> build/lib/HydRa/predictions 2024-05-10T01:03:05,884 copying HydRa/predictions/Occlusion_map.py -> build/lib/HydRa/predictions 2024-05-10T01:03:05,887 copying HydRa/predictions/Occlusion_map_v2_HydRa2_0.py -> build/lib/HydRa/predictions 2024-05-10T01:03:05,891 copying HydRa/predictions/__init__.py -> build/lib/HydRa/predictions 2024-05-10T01:03:05,893 copying HydRa/predictions/Occlusion_map_v3_HydRa2_0.py -> build/lib/HydRa/predictions 2024-05-10T01:03:05,897 creating build/lib/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:05,898 copying HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:05,900 copying HydRa/preprocessing/Feature_generation/PPI_feature_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:05,902 copying HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:05,903 copying HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:05,906 copying HydRa/preprocessing/Feature_generation/kmer_table_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:05,907 copying HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:05,909 copying HydRa/preprocessing/Feature_generation/__init__.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:05,911 creating build/lib/HydRa/preprocessing/Feature_selection 2024-05-10T01:03:05,912 copying HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py -> build/lib/HydRa/preprocessing/Feature_selection 2024-05-10T01:03:05,914 copying HydRa/preprocessing/Feature_selection/__init__.py -> build/lib/HydRa/preprocessing/Feature_selection 2024-05-10T01:03:05,916 running egg_info 2024-05-10T01:03:05,968 writing hydra_rbp.egg-info/PKG-INFO 2024-05-10T01:03:05,971 writing dependency_links to hydra_rbp.egg-info/dependency_links.txt 2024-05-10T01:03:05,973 writing entry points to hydra_rbp.egg-info/entry_points.txt 2024-05-10T01:03:05,974 writing requirements to hydra_rbp.egg-info/requires.txt 2024-05-10T01:03:05,975 writing top-level names to hydra_rbp.egg-info/top_level.txt 2024-05-10T01:03:06,018 reading manifest file 'hydra_rbp.egg-info/SOURCES.txt' 2024-05-10T01:03:06,022 reading manifest template 'MANIFEST.in' 2024-05-10T01:03:06,024 adding license file 'LICENSE' 2024-05-10T01:03:06,029 writing manifest file 'hydra_rbp.egg-info/SOURCES.txt' 2024-05-10T01:03:06,032 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'HydRa.data' is absent from the `packages` configuration. 2024-05-10T01:03:06,032 !! 2024-05-10T01:03:06,033 ******************************************************************************** 2024-05-10T01:03:06,033 ############################ 2024-05-10T01:03:06,034 # Package would be ignored # 2024-05-10T01:03:06,034 ############################ 2024-05-10T01:03:06,035 Python recognizes 'HydRa.data' as an importable package[^1], 2024-05-10T01:03:06,035 but it is absent from setuptools' `packages` configuration. 2024-05-10T01:03:06,036 This leads to an ambiguous overall configuration. If you want to distribute this 2024-05-10T01:03:06,037 package, please make sure that 'HydRa.data' is explicitly added 2024-05-10T01:03:06,037 to the `packages` configuration field. 2024-05-10T01:03:06,038 Alternatively, you can also rely on setuptools' discovery methods 2024-05-10T01:03:06,039 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-05-10T01:03:06,039 instead of `find_packages(...)`/`find:`). 2024-05-10T01:03:06,040 You can read more about "package discovery" on setuptools documentation page: 2024-05-10T01:03:06,041 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-05-10T01:03:06,042 If you don't want 'HydRa.data' to be distributed and are 2024-05-10T01:03:06,043 already explicitly excluding 'HydRa.data' via 2024-05-10T01:03:06,043 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-05-10T01:03:06,044 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-05-10T01:03:06,045 combination with a more fine grained `package-data` configuration. 2024-05-10T01:03:06,046 You can read more about "package data files" on setuptools documentation page: 2024-05-10T01:03:06,047 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-05-10T01:03:06,048 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-05-10T01:03:06,054 even if it does not contain any `.py` files. 2024-05-10T01:03:06,060 On the other hand, currently there is no concept of package data 2024-05-10T01:03:06,066 directory, all directories are treated like packages. 2024-05-10T01:03:06,067 ******************************************************************************** 2024-05-10T01:03:06,068 !! 2024-05-10T01:03:06,068 check.warn(importable) 2024-05-10T01:03:06,069 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'HydRa.pre_trained' is absent from the `packages` configuration. 2024-05-10T01:03:06,070 !! 2024-05-10T01:03:06,071 ******************************************************************************** 2024-05-10T01:03:06,071 ############################ 2024-05-10T01:03:06,072 # Package would be ignored # 2024-05-10T01:03:06,072 ############################ 2024-05-10T01:03:06,073 Python recognizes 'HydRa.pre_trained' as an importable package[^1], 2024-05-10T01:03:06,073 but it is absent from setuptools' `packages` configuration. 2024-05-10T01:03:06,074 This leads to an ambiguous overall configuration. If you want to distribute this 2024-05-10T01:03:06,075 package, please make sure that 'HydRa.pre_trained' is explicitly added 2024-05-10T01:03:06,075 to the `packages` configuration field. 2024-05-10T01:03:06,076 Alternatively, you can also rely on setuptools' discovery methods 2024-05-10T01:03:06,077 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-05-10T01:03:06,078 instead of `find_packages(...)`/`find:`). 2024-05-10T01:03:06,079 You can read more about "package discovery" on setuptools documentation page: 2024-05-10T01:03:06,081 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-05-10T01:03:06,083 If you don't want 'HydRa.pre_trained' to be distributed and are 2024-05-10T01:03:06,083 already explicitly excluding 'HydRa.pre_trained' via 2024-05-10T01:03:06,084 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-05-10T01:03:06,085 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-05-10T01:03:06,086 combination with a more fine grained `package-data` configuration. 2024-05-10T01:03:06,087 You can read more about "package data files" on setuptools documentation page: 2024-05-10T01:03:06,089 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-05-10T01:03:06,093 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-05-10T01:03:06,094 even if it does not contain any `.py` files. 2024-05-10T01:03:06,096 On the other hand, currently there is no concept of package data 2024-05-10T01:03:06,098 directory, all directories are treated like packages. 2024-05-10T01:03:06,100 ******************************************************************************** 2024-05-10T01:03:06,100 !! 2024-05-10T01:03:06,101 check.warn(importable) 2024-05-10T01:03:06,102 creating build/lib/HydRa/data 2024-05-10T01:03:06,102 copying HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2024-05-10T01:03:06,103 copying HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2024-05-10T01:03:06,103 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls -> build/lib/HydRa/data 2024-05-10T01:03:06,242 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv -> build/lib/HydRa/data 2024-05-10T01:03:06,274 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv -> build/lib/HydRa/data 2024-05-10T01:03:06,319 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2024-05-10T01:03:06,593 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/lib/HydRa/data 2024-05-10T01:03:06,691 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk -> build/lib/HydRa/data 2024-05-10T01:03:06,888 copying HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2024-05-10T01:03:06,936 copying HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/lib/HydRa/data 2024-05-10T01:03:06,974 copying HydRa/data/Combined10RBPlist_uniprotID_20190716.txt -> build/lib/HydRa/data 2024-05-10T01:03:06,979 copying HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt -> build/lib/HydRa/data 2024-05-10T01:03:06,984 copying HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/lib/HydRa/data 2024-05-10T01:03:06,986 copying HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl -> build/lib/HydRa/data 2024-05-10T01:03:06,988 copying HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl -> build/lib/HydRa/data 2024-05-10T01:03:06,990 copying HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv -> build/lib/HydRa/data 2024-05-10T01:03:07,087 copying HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/lib/HydRa/data 2024-05-10T01:03:07,089 copying HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt -> build/lib/HydRa/data 2024-05-10T01:03:07,276 copying HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt -> build/lib/HydRa/data 2024-05-10T01:03:07,278 copying HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2024-05-10T01:03:07,280 copying HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2024-05-10T01:03:07,283 copying HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt -> build/lib/HydRa/data 2024-05-10T01:03:08,496 copying HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2024-05-10T01:03:08,499 copying HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2024-05-10T01:03:08,501 copying HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt -> build/lib/HydRa/data 2024-05-10T01:03:08,582 copying HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls -> build/lib/HydRa/data 2024-05-10T01:03:08,613 copying HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls -> build/lib/HydRa/data 2024-05-10T01:03:08,664 copying HydRa/data/protVec_100d_3grams.csv -> build/lib/HydRa/data 2024-05-10T01:03:08,890 creating build/lib/HydRa/pre_trained 2024-05-10T01:03:08,892 copying HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2024-05-10T01:03:08,922 copying HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2024-05-10T01:03:08,954 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 2024-05-10T01:03:08,957 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 2024-05-10T01:03:09,046 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 2024-05-10T01:03:09,049 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 2024-05-10T01:03:09,139 copying HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2024-05-10T01:03:09,142 copying HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2024-05-10T01:03:09,146 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 2024-05-10T01:03:09,166 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 2024-05-10T01:03:09,187 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 2024-05-10T01:03:15,455 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 2024-05-10T01:03:16,658 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-05-10T01:03:16,658 !! 2024-05-10T01:03:16,660 ******************************************************************************** 2024-05-10T01:03:16,660 Please avoid running ``setup.py`` directly. 2024-05-10T01:03:16,661 Instead, use pypa/build, pypa/installer or other 2024-05-10T01:03:16,661 standards-based tools. 2024-05-10T01:03:16,663 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-05-10T01:03:16,663 ******************************************************************************** 2024-05-10T01:03:16,664 !! 2024-05-10T01:03:16,665 self.initialize_options() 2024-05-10T01:03:16,686 installing to build/bdist.linux-armv7l/wheel 2024-05-10T01:03:16,687 running install 2024-05-10T01:03:16,711 running install_lib 2024-05-10T01:03:16,738 creating build/bdist.linux-armv7l 2024-05-10T01:03:16,738 creating build/bdist.linux-armv7l/wheel 2024-05-10T01:03:16,740 creating build/bdist.linux-armv7l/wheel/HydRa 2024-05-10T01:03:16,741 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-05-10T01:03:16,743 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:16,744 copying build/lib/HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:16,746 copying build/lib/HydRa/preprocessing/Feature_generation/PPI_feature_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:16,748 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 2024-05-10T01:03:16,751 copying build/lib/HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:16,753 copying build/lib/HydRa/preprocessing/Feature_generation/kmer_table_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:16,755 copying build/lib/HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:16,757 copying build/lib/HydRa/preprocessing/Feature_generation/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-05-10T01:03:16,759 copying build/lib/HydRa/preprocessing/PPI_feature_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-05-10T01:03:16,761 copying build/lib/HydRa/preprocessing/get_SVM_seq_features.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-05-10T01:03:16,763 copying build/lib/HydRa/preprocessing/Get_All_selected_SVM_features.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-05-10T01:03:16,765 copying build/lib/HydRa/preprocessing/predict_SS.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-05-10T01:03:16,767 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2024-05-10T01:03:16,768 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 2024-05-10T01:03:16,771 copying build/lib/HydRa/preprocessing/Feature_selection/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2024-05-10T01:03:16,772 copying build/lib/HydRa/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-05-10T01:03:16,775 creating build/bdist.linux-armv7l/wheel/HydRa/training 2024-05-10T01:03:16,775 copying build/lib/HydRa/training/train_and_evaluate_HydRa_bk.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-05-10T01:03:16,779 copying build/lib/HydRa/training/train_and_evaluate_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-05-10T01:03:16,782 copying build/lib/HydRa/training/train_HydRa.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-05-10T01:03:16,785 copying build/lib/HydRa/training/train_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-05-10T01:03:16,788 copying build/lib/HydRa/training/train_and_evaluate_HydRa.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-05-10T01:03:16,791 copying build/lib/HydRa/training/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-05-10T01:03:16,794 copying build/lib/HydRa/HydRa_predict.py -> build/bdist.linux-armv7l/wheel/HydRa 2024-05-10T01:03:16,798 creating build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:16,799 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 2024-05-10T01:03:16,999 copying build/lib/HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:17,070 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 2024-05-10T01:03:17,100 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 2024-05-10T01:03:17,103 copying build/lib/HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:18,024 copying build/lib/HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:18,073 copying build/lib/HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:18,117 copying build/lib/HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:18,169 copying build/lib/HydRa/data/protVec_100d_3grams.csv -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:18,383 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 2024-05-10T01:03:18,618 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 2024-05-10T01:03:18,620 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 2024-05-10T01:03:18,649 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 2024-05-10T01:03:18,684 copying build/lib/HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:18,686 copying build/lib/HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:18,688 copying build/lib/HydRa/data/Combined10RBPlist_uniprotID_20190716.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:18,694 copying build/lib/HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:18,725 copying build/lib/HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:18,727 copying build/lib/HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:18,729 copying build/lib/HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:18,928 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 2024-05-10T01:03:19,065 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 2024-05-10T01:03:19,068 copying build/lib/HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:19,077 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 2024-05-10T01:03:19,117 copying build/lib/HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:19,203 copying build/lib/HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:19,205 copying build/lib/HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-05-10T01:03:19,206 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 2024-05-10T01:03:19,291 copying build/lib/HydRa/test_data_load.py -> build/bdist.linux-armv7l/wheel/HydRa 2024-05-10T01:03:19,293 creating build/bdist.linux-armv7l/wheel/HydRa/models 2024-05-10T01:03:19,294 copying build/lib/HydRa/models/Sequence_class.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2024-05-10T01:03:19,298 copying build/lib/HydRa/models/DNN_seq.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2024-05-10T01:03:19,301 copying build/lib/HydRa/models/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2024-05-10T01:03:19,303 creating build/bdist.linux-armv7l/wheel/HydRa/evaluation 2024-05-10T01:03:19,304 copying build/lib/HydRa/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/evaluation 2024-05-10T01:03:19,306 copying build/lib/HydRa/evaluation/ROC_PR_AUC_analysis.py -> build/bdist.linux-armv7l/wheel/HydRa/evaluation 2024-05-10T01:03:19,308 copying build/lib/HydRa/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa 2024-05-10T01:03:19,310 creating build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2024-05-10T01:03:19,311 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 2024-05-10T01:03:19,314 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 2024-05-10T01:03:19,317 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 2024-05-10T01:03:19,344 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 2024-05-10T01:03:19,362 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 2024-05-10T01:03:19,717 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 2024-05-10T01:03:19,720 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 2024-05-10T01:03:21,685 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 2024-05-10T01:03:21,785 copying build/lib/HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2024-05-10T01:03:21,830 copying build/lib/HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2024-05-10T01:03:21,834 copying build/lib/HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2024-05-10T01:03:21,868 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 2024-05-10T01:03:27,431 creating build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-05-10T01:03:27,432 copying build/lib/HydRa/predictions/Occlusion_1D_analysis_2.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-05-10T01:03:27,434 copying build/lib/HydRa/predictions/Occlusion_map_v2.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-05-10T01:03:27,438 copying build/lib/HydRa/predictions/Occlusion_map.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-05-10T01:03:27,441 copying build/lib/HydRa/predictions/Occlusion_map_v2_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-05-10T01:03:27,445 copying build/lib/HydRa/predictions/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-05-10T01:03:27,447 copying build/lib/HydRa/predictions/Occlusion_map_v3_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-05-10T01:03:27,451 copying build/lib/HydRa/HydRa2_0_predict.py -> build/bdist.linux-armv7l/wheel/HydRa 2024-05-10T01:03:27,454 running install_egg_info 2024-05-10T01:03:27,485 Copying hydra_rbp.egg-info to build/bdist.linux-armv7l/wheel/hydra_rbp-0.1.21.34-py3.11.egg-info 2024-05-10T01:03:27,499 running install_scripts 2024-05-10T01:03:27,518 creating build/bdist.linux-armv7l/wheel/hydra_rbp-0.1.21.34.dist-info/WHEEL 2024-05-10T01:03:27,520 creating '/tmp/pip-wheel-phcem6d8/hydra_rbp-0.1.21.34-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-05-10T01:03:27,526 adding 'HydRa/HydRa2_0_predict.py' 2024-05-10T01:03:27,530 adding 'HydRa/HydRa_predict.py' 2024-05-10T01:03:27,531 adding 'HydRa/__init__.py' 2024-05-10T01:03:27,533 adding 'HydRa/test_data_load.py' 2024-05-10T01:03:27,918 adding 'HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv' 2024-05-10T01:03:28,282 adding 'HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv' 2024-05-10T01:03:30,451 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls' 2024-05-10T01:03:31,008 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv' 2024-05-10T01:03:31,748 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv' 2024-05-10T01:03:35,101 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv' 2024-05-10T01:03:36,281 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv' 2024-05-10T01:03:39,645 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk' 2024-05-10T01:03:40,275 adding 'HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv' 2024-05-10T01:03:40,848 adding 'HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv' 2024-05-10T01:03:40,906 adding 'HydRa/data/Combined10RBPlist_uniprotID_20190716.txt' 2024-05-10T01:03:40,950 adding 'HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt' 2024-05-10T01:03:40,953 adding 'HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl' 2024-05-10T01:03:40,954 adding 'HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl' 2024-05-10T01:03:40,956 adding 'HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl' 2024-05-10T01:03:42,067 adding 'HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv' 2024-05-10T01:03:42,098 adding 'HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl' 2024-05-10T01:03:43,783 adding 'HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt' 2024-05-10T01:03:43,845 adding 'HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt' 2024-05-10T01:03:43,847 adding 'HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2024-05-10T01:03:43,849 adding 'HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2024-05-10T01:03:47,154 adding 'HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt' 2024-05-10T01:03:47,400 adding 'HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2024-05-10T01:03:47,401 adding 'HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2024-05-10T01:03:48,863 adding 'HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt' 2024-05-10T01:03:49,366 adding 'HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls' 2024-05-10T01:03:49,940 adding 'HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls' 2024-05-10T01:03:52,292 adding 'HydRa/data/protVec_100d_3grams.csv' 2024-05-10T01:03:52,346 adding 'HydRa/evaluation/ROC_PR_AUC_analysis.py' 2024-05-10T01:03:52,347 adding 'HydRa/evaluation/__init__.py' 2024-05-10T01:03:52,352 adding 'HydRa/models/DNN_seq.py' 2024-05-10T01:03:52,355 adding 'HydRa/models/Sequence_class.py' 2024-05-10T01:03:52,357 adding 'HydRa/models/__init__.py' 2024-05-10T01:03:52,585 adding 'HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5' 2024-05-10T01:03:52,819 adding 'HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5' 2024-05-10T01:03:52,830 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_structure.json' 2024-05-10T01:03:53,438 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_weights.h5' 2024-05-10T01:03:53,463 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_structure.json' 2024-05-10T01:03:54,078 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_weights.h5' 2024-05-10T01:03:54,150 adding 'HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5' 2024-05-10T01:03:54,194 adding 'HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5' 2024-05-10T01:03:54,304 adding 'HydRa/pre_trained/SVM_PPI_MB-S_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl' 2024-05-10T01:03:54,408 adding 'HydRa/pre_trained/SVM_PPI_MB_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl' 2024-05-10T01:04:01,154 adding 'HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pickle.pkl' 2024-05-10T01:04:05,500 adding 'HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_ModelFile.pickle.pkl' 2024-05-10T01:04:05,915 adding 'HydRa/predictions/Occlusion_1D_analysis_2.py' 2024-05-10T01:04:05,920 adding 'HydRa/predictions/Occlusion_map.py' 2024-05-10T01:04:05,927 adding 'HydRa/predictions/Occlusion_map_v2.py' 2024-05-10T01:04:05,935 adding 'HydRa/predictions/Occlusion_map_v2_HydRa2_0.py' 2024-05-10T01:04:05,946 adding 'HydRa/predictions/Occlusion_map_v3_HydRa2_0.py' 2024-05-10T01:04:05,948 adding 'HydRa/predictions/__init__.py' 2024-05-10T01:04:05,952 adding 'HydRa/preprocessing/Get_All_selected_SVM_features.py' 2024-05-10T01:04:05,954 adding 'HydRa/preprocessing/PPI_feature_generation.py' 2024-05-10T01:04:05,955 adding 'HydRa/preprocessing/__init__.py' 2024-05-10T01:04:05,957 adding 'HydRa/preprocessing/get_SVM_seq_features.py' 2024-05-10T01:04:05,959 adding 'HydRa/preprocessing/predict_SS.py' 2024-05-10T01:04:05,961 adding 'HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py' 2024-05-10T01:04:05,963 adding 'HydRa/preprocessing/Feature_generation/PPI_feature_generation.py' 2024-05-10T01:04:05,964 adding 'HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py' 2024-05-10T01:04:05,966 adding 'HydRa/preprocessing/Feature_generation/__init__.py' 2024-05-10T01:04:05,967 adding 'HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py' 2024-05-10T01:04:05,969 adding 'HydRa/preprocessing/Feature_generation/kmer_table_generation.py' 2024-05-10T01:04:05,970 adding 'HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py' 2024-05-10T01:04:05,973 adding 'HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py' 2024-05-10T01:04:05,974 adding 'HydRa/preprocessing/Feature_selection/__init__.py' 2024-05-10T01:04:05,976 adding 'HydRa/training/__init__.py' 2024-05-10T01:04:05,980 adding 'HydRa/training/train_HydRa.py' 2024-05-10T01:04:05,985 adding 'HydRa/training/train_HydRa2_0.py' 2024-05-10T01:04:05,990 adding 'HydRa/training/train_and_evaluate_HydRa.py' 2024-05-10T01:04:05,996 adding 'HydRa/training/train_and_evaluate_HydRa2_0.py' 2024-05-10T01:04:06,001 adding 'HydRa/training/train_and_evaluate_HydRa_bk.py' 2024-05-10T01:04:06,004 adding 'hydra_rbp-0.1.21.34.dist-info/LICENSE' 2024-05-10T01:04:06,007 adding 'hydra_rbp-0.1.21.34.dist-info/METADATA' 2024-05-10T01:04:06,008 adding 'hydra_rbp-0.1.21.34.dist-info/WHEEL' 2024-05-10T01:04:06,009 adding 'hydra_rbp-0.1.21.34.dist-info/entry_points.txt' 2024-05-10T01:04:06,011 adding 'hydra_rbp-0.1.21.34.dist-info/top_level.txt' 2024-05-10T01:04:06,013 adding 'hydra_rbp-0.1.21.34.dist-info/RECORD' 2024-05-10T01:04:06,132 removing build/bdist.linux-armv7l/wheel 2024-05-10T01:04:06,395 Building wheel for hydra-rbp (setup.py): finished with status 'done' 2024-05-10T01:04:08,025 Created wheel for hydra-rbp: filename=hydra_rbp-0.1.21.34-py3-none-any.whl size=53763611 sha256=19acfcf39c71eb20541e352df50ac02af84ab12973dba15bb2dce0b73a86fbc6 2024-05-10T01:04:08,026 Stored in directory: /tmp/pip-ephem-wheel-cache-i1jsohyg/wheels/23/86/af/febc7f65270ac3a57e43706a102e1e323ff7bda211ac563952 2024-05-10T01:04:08,057 Successfully built hydra-rbp 2024-05-10T01:04:10,251 Removed build tracker: '/tmp/pip-build-tracker-amg84ie1'