2024-01-18T23:37:56,844 Created temporary directory: /tmp/pip-build-tracker-opys08u5 2024-01-18T23:37:56,846 Initialized build tracking at /tmp/pip-build-tracker-opys08u5 2024-01-18T23:37:56,846 Created build tracker: /tmp/pip-build-tracker-opys08u5 2024-01-18T23:37:56,847 Entered build tracker: /tmp/pip-build-tracker-opys08u5 2024-01-18T23:37:56,847 Created temporary directory: /tmp/pip-wheel-amc5s6rn 2024-01-18T23:37:56,851 Created temporary directory: /tmp/pip-ephem-wheel-cache-jt9xs8ba 2024-01-18T23:37:56,873 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-01-18T23:37:56,876 2 location(s) to search for versions of hydra-rbp: 2024-01-18T23:37:56,876 * https://pypi.org/simple/hydra-rbp/ 2024-01-18T23:37:56,876 * https://www.piwheels.org/simple/hydra-rbp/ 2024-01-18T23:37:56,877 Fetching project page and analyzing links: https://pypi.org/simple/hydra-rbp/ 2024-01-18T23:37:56,878 Getting page https://pypi.org/simple/hydra-rbp/ 2024-01-18T23:37:56,880 Found index url https://pypi.org/simple/ 2024-01-18T23:37:57,093 Fetched page https://pypi.org/simple/hydra-rbp/ as application/vnd.pypi.simple.v1+json 2024-01-18T23:37:57,097 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 2024-01-18T23:37:57,098 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 2024-01-18T23:37:57,099 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) 2024-01-18T23:37:57,100 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 2024-01-18T23:37:57,100 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) 2024-01-18T23:37:57,101 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 2024-01-18T23:37:57,102 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) 2024-01-18T23:37:57,103 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 2024-01-18T23:37:57,104 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) 2024-01-18T23:37:57,105 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 2024-01-18T23:37:57,105 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) 2024-01-18T23:37:57,107 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 2024-01-18T23:37:57,108 Fetching project page and analyzing links: https://www.piwheels.org/simple/hydra-rbp/ 2024-01-18T23:37:57,108 Getting page https://www.piwheels.org/simple/hydra-rbp/ 2024-01-18T23:37:57,109 Found index url https://www.piwheels.org/simple/ 2024-01-18T23:37:57,291 Fetched page https://www.piwheels.org/simple/hydra-rbp/ as text/html 2024-01-18T23:37:57,294 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) 2024-01-18T23:37:57,295 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) 2024-01-18T23:37:57,295 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) 2024-01-18T23:37:57,296 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) 2024-01-18T23:37:57,296 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) 2024-01-18T23:37:57,297 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) 2024-01-18T23:37:57,298 Skipping link: not a file: https://www.piwheels.org/simple/hydra-rbp/ 2024-01-18T23:37:57,298 Skipping link: not a file: https://pypi.org/simple/hydra-rbp/ 2024-01-18T23:37:57,318 Given no hashes to check 1 links for project 'hydra-rbp': discarding no candidates 2024-01-18T23:37:57,336 Collecting hydra-rbp==0.1.21.33 2024-01-18T23:37:57,339 Created temporary directory: /tmp/pip-unpack-o_inuxzx 2024-01-18T23:37:57,555 Downloading hydra_rbp-0.1.21.33.tar.gz (52.3 MB) 2024-01-18T23:38:15,823 Added hydra-rbp==0.1.21.33 from https://files.pythonhosted.org/packages/bc/87/28d107780077880671add84ac044599769995ea63ddafc2003421a8796de/hydra_rbp-0.1.21.33.tar.gz to build tracker '/tmp/pip-build-tracker-opys08u5' 2024-01-18T23:38:15,825 Running setup.py (path:/tmp/pip-wheel-amc5s6rn/hydra-rbp_e3246ad3ed554c51bb6e79dea99f33ef/setup.py) egg_info for package hydra-rbp 2024-01-18T23:38:15,826 Created temporary directory: /tmp/pip-pip-egg-info-tjhn470s 2024-01-18T23:38:15,827 Preparing metadata (setup.py): started 2024-01-18T23:38:15,828 Running command python setup.py egg_info 2024-01-18T23:38:16,535 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-01-18T23:38:16,536 !! 2024-01-18T23:38:16,537 ******************************************************************************** 2024-01-18T23:38:16,538 Requirements should be satisfied by a PEP 517 installer. 2024-01-18T23:38:16,538 If you are using pip, you can try `pip install --use-pep517`. 2024-01-18T23:38:16,539 ******************************************************************************** 2024-01-18T23:38:16,541 !! 2024-01-18T23:38:16,541 dist.fetch_build_eggs(dist.setup_requires) 2024-01-18T23:38:19,309 running egg_info 2024-01-18T23:38:19,311 creating /tmp/pip-pip-egg-info-tjhn470s/hydra_rbp.egg-info 2024-01-18T23:38:19,339 writing /tmp/pip-pip-egg-info-tjhn470s/hydra_rbp.egg-info/PKG-INFO 2024-01-18T23:38:19,343 writing dependency_links to /tmp/pip-pip-egg-info-tjhn470s/hydra_rbp.egg-info/dependency_links.txt 2024-01-18T23:38:19,345 writing entry points to /tmp/pip-pip-egg-info-tjhn470s/hydra_rbp.egg-info/entry_points.txt 2024-01-18T23:38:19,347 writing requirements to /tmp/pip-pip-egg-info-tjhn470s/hydra_rbp.egg-info/requires.txt 2024-01-18T23:38:19,348 writing top-level names to /tmp/pip-pip-egg-info-tjhn470s/hydra_rbp.egg-info/top_level.txt 2024-01-18T23:38:19,350 writing manifest file '/tmp/pip-pip-egg-info-tjhn470s/hydra_rbp.egg-info/SOURCES.txt' 2024-01-18T23:38:19,466 reading manifest file '/tmp/pip-pip-egg-info-tjhn470s/hydra_rbp.egg-info/SOURCES.txt' 2024-01-18T23:38:19,468 reading manifest template 'MANIFEST.in' 2024-01-18T23:38:19,472 adding license file 'LICENSE' 2024-01-18T23:38:19,477 writing manifest file '/tmp/pip-pip-egg-info-tjhn470s/hydra_rbp.egg-info/SOURCES.txt' 2024-01-18T23:38:19,585 Preparing metadata (setup.py): finished with status 'done' 2024-01-18T23:38:19,589 Source in /tmp/pip-wheel-amc5s6rn/hydra-rbp_e3246ad3ed554c51bb6e79dea99f33ef has version 0.1.21.33, which satisfies requirement hydra-rbp==0.1.21.33 from https://files.pythonhosted.org/packages/bc/87/28d107780077880671add84ac044599769995ea63ddafc2003421a8796de/hydra_rbp-0.1.21.33.tar.gz 2024-01-18T23:38:19,590 Removed hydra-rbp==0.1.21.33 from https://files.pythonhosted.org/packages/bc/87/28d107780077880671add84ac044599769995ea63ddafc2003421a8796de/hydra_rbp-0.1.21.33.tar.gz from build tracker '/tmp/pip-build-tracker-opys08u5' 2024-01-18T23:38:19,597 Created temporary directory: /tmp/pip-unpack-0yhpzqy_ 2024-01-18T23:38:19,598 Created temporary directory: /tmp/pip-unpack-8wzondjm 2024-01-18T23:38:19,614 Building wheels for collected packages: hydra-rbp 2024-01-18T23:38:19,618 Created temporary directory: /tmp/pip-wheel-2yvjpi1e 2024-01-18T23:38:19,619 Building wheel for hydra-rbp (setup.py): started 2024-01-18T23:38:19,621 Destination directory: /tmp/pip-wheel-2yvjpi1e 2024-01-18T23:38:19,621 Running command python setup.py bdist_wheel 2024-01-18T23:38:20,320 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-01-18T23:38:20,321 !! 2024-01-18T23:38:20,322 ******************************************************************************** 2024-01-18T23:38:20,323 Requirements should be satisfied by a PEP 517 installer. 2024-01-18T23:38:20,323 If you are using pip, you can try `pip install --use-pep517`. 2024-01-18T23:38:20,324 ******************************************************************************** 2024-01-18T23:38:20,325 !! 2024-01-18T23:38:20,326 dist.fetch_build_eggs(dist.setup_requires) 2024-01-18T23:38:20,822 running bdist_wheel 2024-01-18T23:38:20,927 running build 2024-01-18T23:38:20,928 running build_py 2024-01-18T23:38:20,956 creating build 2024-01-18T23:38:20,957 creating build/lib 2024-01-18T23:38:20,958 creating build/lib/HydRa 2024-01-18T23:38:20,959 copying HydRa/test_data_load.py -> build/lib/HydRa 2024-01-18T23:38:20,961 copying HydRa/HydRa_predict.py -> build/lib/HydRa 2024-01-18T23:38:20,964 copying HydRa/__init__.py -> build/lib/HydRa 2024-01-18T23:38:20,966 copying HydRa/HydRa2_0_predict.py -> build/lib/HydRa 2024-01-18T23:38:20,970 creating build/lib/HydRa/preprocessing 2024-01-18T23:38:20,971 copying HydRa/preprocessing/get_SVM_seq_features.py -> build/lib/HydRa/preprocessing 2024-01-18T23:38:20,973 copying HydRa/preprocessing/__init__.py -> build/lib/HydRa/preprocessing 2024-01-18T23:38:20,975 copying HydRa/preprocessing/Get_All_selected_SVM_features.py -> build/lib/HydRa/preprocessing 2024-01-18T23:38:20,978 copying HydRa/preprocessing/predict_SS.py -> build/lib/HydRa/preprocessing 2024-01-18T23:38:20,979 copying HydRa/preprocessing/PPI_feature_generation.py -> build/lib/HydRa/preprocessing 2024-01-18T23:38:20,981 creating build/lib/HydRa/evaluation 2024-01-18T23:38:20,982 copying HydRa/evaluation/__init__.py -> build/lib/HydRa/evaluation 2024-01-18T23:38:20,984 copying HydRa/evaluation/ROC_PR_AUC_analysis.py -> build/lib/HydRa/evaluation 2024-01-18T23:38:20,987 creating build/lib/HydRa/training 2024-01-18T23:38:20,987 copying HydRa/training/train_and_evaluate_HydRa_bk.py -> build/lib/HydRa/training 2024-01-18T23:38:20,990 copying HydRa/training/train_and_evaluate_HydRa2_0.py -> build/lib/HydRa/training 2024-01-18T23:38:20,993 copying HydRa/training/train_HydRa2_0.py -> build/lib/HydRa/training 2024-01-18T23:38:20,996 copying HydRa/training/__init__.py -> build/lib/HydRa/training 2024-01-18T23:38:20,998 copying HydRa/training/train_and_evaluate_HydRa.py -> build/lib/HydRa/training 2024-01-18T23:38:21,001 copying HydRa/training/train_HydRa.py -> build/lib/HydRa/training 2024-01-18T23:38:21,004 creating build/lib/HydRa/predictions 2024-01-18T23:38:21,005 copying HydRa/predictions/Occlusion_map_v2.py -> build/lib/HydRa/predictions 2024-01-18T23:38:21,008 copying HydRa/predictions/Occlusion_map.py -> build/lib/HydRa/predictions 2024-01-18T23:38:21,011 copying HydRa/predictions/Occlusion_map_v3_HydRa2_0.py -> build/lib/HydRa/predictions 2024-01-18T23:38:21,015 copying HydRa/predictions/Occlusion_1D_analysis_2.py -> build/lib/HydRa/predictions 2024-01-18T23:38:21,017 copying HydRa/predictions/__init__.py -> build/lib/HydRa/predictions 2024-01-18T23:38:21,019 copying HydRa/predictions/Occlusion_map_v2_HydRa2_0.py -> build/lib/HydRa/predictions 2024-01-18T23:38:21,023 creating build/lib/HydRa/models 2024-01-18T23:38:21,024 copying HydRa/models/DNN_seq.py -> build/lib/HydRa/models 2024-01-18T23:38:21,029 copying HydRa/models/Sequence_class.py -> build/lib/HydRa/models 2024-01-18T23:38:21,032 copying HydRa/models/__init__.py -> build/lib/HydRa/models 2024-01-18T23:38:21,034 creating build/lib/HydRa/preprocessing/Feature_selection 2024-01-18T23:38:21,035 copying HydRa/preprocessing/Feature_selection/__init__.py -> build/lib/HydRa/preprocessing/Feature_selection 2024-01-18T23:38:21,037 copying HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py -> build/lib/HydRa/preprocessing/Feature_selection 2024-01-18T23:38:21,040 creating build/lib/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:21,041 copying HydRa/preprocessing/Feature_generation/kmer_table_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:21,043 copying HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:21,044 copying HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:21,046 copying HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:21,048 copying HydRa/preprocessing/Feature_generation/__init__.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:21,050 copying HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:21,052 copying HydRa/preprocessing/Feature_generation/PPI_feature_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:21,054 running egg_info 2024-01-18T23:38:21,106 writing hydra_rbp.egg-info/PKG-INFO 2024-01-18T23:38:21,109 writing dependency_links to hydra_rbp.egg-info/dependency_links.txt 2024-01-18T23:38:21,111 writing entry points to hydra_rbp.egg-info/entry_points.txt 2024-01-18T23:38:21,113 writing requirements to hydra_rbp.egg-info/requires.txt 2024-01-18T23:38:21,114 writing top-level names to hydra_rbp.egg-info/top_level.txt 2024-01-18T23:38:21,159 reading manifest file 'hydra_rbp.egg-info/SOURCES.txt' 2024-01-18T23:38:21,162 reading manifest template 'MANIFEST.in' 2024-01-18T23:38:21,165 adding license file 'LICENSE' 2024-01-18T23:38:21,170 writing manifest file 'hydra_rbp.egg-info/SOURCES.txt' 2024-01-18T23:38:21,172 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'HydRa.data' is absent from the `packages` configuration. 2024-01-18T23:38:21,173 !! 2024-01-18T23:38:21,174 ******************************************************************************** 2024-01-18T23:38:21,174 ############################ 2024-01-18T23:38:21,175 # Package would be ignored # 2024-01-18T23:38:21,175 ############################ 2024-01-18T23:38:21,176 Python recognizes 'HydRa.data' as an importable package[^1], 2024-01-18T23:38:21,176 but it is absent from setuptools' `packages` configuration. 2024-01-18T23:38:21,177 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-18T23:38:21,178 package, please make sure that 'HydRa.data' is explicitly added 2024-01-18T23:38:21,178 to the `packages` configuration field. 2024-01-18T23:38:21,179 Alternatively, you can also rely on setuptools' discovery methods 2024-01-18T23:38:21,179 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-18T23:38:21,180 instead of `find_packages(...)`/`find:`). 2024-01-18T23:38:21,181 You can read more about "package discovery" on setuptools documentation page: 2024-01-18T23:38:21,182 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-18T23:38:21,183 If you don't want 'HydRa.data' to be distributed and are 2024-01-18T23:38:21,183 already explicitly excluding 'HydRa.data' via 2024-01-18T23:38:21,184 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-18T23:38:21,184 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-18T23:38:21,185 combination with a more fine grained `package-data` configuration. 2024-01-18T23:38:21,186 You can read more about "package data files" on setuptools documentation page: 2024-01-18T23:38:21,188 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-18T23:38:21,190 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-18T23:38:21,191 even if it does not contain any `.py` files. 2024-01-18T23:38:21,198 On the other hand, currently there is no concept of package data 2024-01-18T23:38:21,204 directory, all directories are treated like packages. 2024-01-18T23:38:21,208 ******************************************************************************** 2024-01-18T23:38:21,209 !! 2024-01-18T23:38:21,210 check.warn(importable) 2024-01-18T23:38:21,210 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'HydRa.pre_trained' is absent from the `packages` configuration. 2024-01-18T23:38:21,211 !! 2024-01-18T23:38:21,212 ******************************************************************************** 2024-01-18T23:38:21,213 ############################ 2024-01-18T23:38:21,213 # Package would be ignored # 2024-01-18T23:38:21,214 ############################ 2024-01-18T23:38:21,214 Python recognizes 'HydRa.pre_trained' as an importable package[^1], 2024-01-18T23:38:21,215 but it is absent from setuptools' `packages` configuration. 2024-01-18T23:38:21,216 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-18T23:38:21,224 package, please make sure that 'HydRa.pre_trained' is explicitly added 2024-01-18T23:38:21,228 to the `packages` configuration field. 2024-01-18T23:38:21,229 Alternatively, you can also rely on setuptools' discovery methods 2024-01-18T23:38:21,230 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-18T23:38:21,230 instead of `find_packages(...)`/`find:`). 2024-01-18T23:38:21,234 You can read more about "package discovery" on setuptools documentation page: 2024-01-18T23:38:21,235 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-18T23:38:21,236 If you don't want 'HydRa.pre_trained' to be distributed and are 2024-01-18T23:38:21,237 already explicitly excluding 'HydRa.pre_trained' via 2024-01-18T23:38:21,237 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-18T23:38:21,238 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-18T23:38:21,238 combination with a more fine grained `package-data` configuration. 2024-01-18T23:38:21,239 You can read more about "package data files" on setuptools documentation page: 2024-01-18T23:38:21,240 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-18T23:38:21,242 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-18T23:38:21,242 even if it does not contain any `.py` files. 2024-01-18T23:38:21,243 On the other hand, currently there is no concept of package data 2024-01-18T23:38:21,243 directory, all directories are treated like packages. 2024-01-18T23:38:21,244 ******************************************************************************** 2024-01-18T23:38:21,245 !! 2024-01-18T23:38:21,245 check.warn(importable) 2024-01-18T23:38:21,246 creating build/lib/HydRa/data 2024-01-18T23:38:21,247 copying HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2024-01-18T23:38:21,247 copying HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2024-01-18T23:38:21,248 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls -> build/lib/HydRa/data 2024-01-18T23:38:21,353 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv -> build/lib/HydRa/data 2024-01-18T23:38:21,381 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv -> build/lib/HydRa/data 2024-01-18T23:38:21,421 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2024-01-18T23:38:21,628 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/lib/HydRa/data 2024-01-18T23:38:21,697 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk -> build/lib/HydRa/data 2024-01-18T23:38:21,884 copying HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2024-01-18T23:38:21,917 copying HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/lib/HydRa/data 2024-01-18T23:38:21,951 copying HydRa/data/Combined10RBPlist_uniprotID_20190716.txt -> build/lib/HydRa/data 2024-01-18T23:38:21,956 copying HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt -> build/lib/HydRa/data 2024-01-18T23:38:21,961 copying HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/lib/HydRa/data 2024-01-18T23:38:21,964 copying HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl -> build/lib/HydRa/data 2024-01-18T23:38:21,966 copying HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl -> build/lib/HydRa/data 2024-01-18T23:38:21,969 copying HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv -> build/lib/HydRa/data 2024-01-18T23:38:22,044 copying HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/lib/HydRa/data 2024-01-18T23:38:22,047 copying HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt -> build/lib/HydRa/data 2024-01-18T23:38:22,188 copying HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt -> build/lib/HydRa/data 2024-01-18T23:38:22,189 copying HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2024-01-18T23:38:22,191 copying HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2024-01-18T23:38:22,194 copying HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt -> build/lib/HydRa/data 2024-01-18T23:38:22,772 copying HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2024-01-18T23:38:22,774 copying HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2024-01-18T23:38:22,776 copying HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt -> build/lib/HydRa/data 2024-01-18T23:38:22,843 copying HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls -> build/lib/HydRa/data 2024-01-18T23:38:22,874 copying HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls -> build/lib/HydRa/data 2024-01-18T23:38:22,909 copying HydRa/data/protVec_100d_3grams.csv -> build/lib/HydRa/data 2024-01-18T23:38:23,032 creating build/lib/HydRa/pre_trained 2024-01-18T23:38:23,034 copying HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2024-01-18T23:38:23,062 copying HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2024-01-18T23:38:23,090 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 2024-01-18T23:38:23,093 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 2024-01-18T23:38:23,157 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 2024-01-18T23:38:23,160 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 2024-01-18T23:38:23,220 copying HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2024-01-18T23:38:23,223 copying HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2024-01-18T23:38:23,227 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 2024-01-18T23:38:23,248 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 2024-01-18T23:38:23,264 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 2024-01-18T23:38:27,338 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 2024-01-18T23:38:29,233 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-01-18T23:38:29,233 !! 2024-01-18T23:38:29,234 ******************************************************************************** 2024-01-18T23:38:29,235 Please avoid running ``setup.py`` directly. 2024-01-18T23:38:29,235 Instead, use pypa/build, pypa/installer or other 2024-01-18T23:38:29,236 standards-based tools. 2024-01-18T23:38:29,237 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-01-18T23:38:29,237 ******************************************************************************** 2024-01-18T23:38:29,238 !! 2024-01-18T23:38:29,239 self.initialize_options() 2024-01-18T23:38:29,261 installing to build/bdist.linux-armv7l/wheel 2024-01-18T23:38:29,262 running install 2024-01-18T23:38:29,286 running install_lib 2024-01-18T23:38:29,315 creating build/bdist.linux-armv7l 2024-01-18T23:38:29,315 creating build/bdist.linux-armv7l/wheel 2024-01-18T23:38:29,317 creating build/bdist.linux-armv7l/wheel/HydRa 2024-01-18T23:38:29,319 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-01-18T23:38:29,320 copying build/lib/HydRa/preprocessing/get_SVM_seq_features.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-01-18T23:38:29,323 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2024-01-18T23:38:29,324 copying build/lib/HydRa/preprocessing/Feature_selection/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2024-01-18T23:38:29,326 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 2024-01-18T23:38:29,328 copying build/lib/HydRa/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-01-18T23:38:29,330 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:29,331 copying build/lib/HydRa/preprocessing/Feature_generation/kmer_table_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:29,333 copying build/lib/HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:29,335 copying build/lib/HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:29,337 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 2024-01-18T23:38:29,339 copying build/lib/HydRa/preprocessing/Feature_generation/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:29,341 copying build/lib/HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:29,343 copying build/lib/HydRa/preprocessing/Feature_generation/PPI_feature_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2024-01-18T23:38:29,346 copying build/lib/HydRa/preprocessing/Get_All_selected_SVM_features.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-01-18T23:38:29,348 copying build/lib/HydRa/preprocessing/predict_SS.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-01-18T23:38:29,350 copying build/lib/HydRa/preprocessing/PPI_feature_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2024-01-18T23:38:29,353 copying build/lib/HydRa/test_data_load.py -> build/bdist.linux-armv7l/wheel/HydRa 2024-01-18T23:38:29,355 creating build/bdist.linux-armv7l/wheel/HydRa/evaluation 2024-01-18T23:38:29,356 copying build/lib/HydRa/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/evaluation 2024-01-18T23:38:29,358 copying build/lib/HydRa/evaluation/ROC_PR_AUC_analysis.py -> build/bdist.linux-armv7l/wheel/HydRa/evaluation 2024-01-18T23:38:29,361 creating build/bdist.linux-armv7l/wheel/HydRa/training 2024-01-18T23:38:29,361 copying build/lib/HydRa/training/train_and_evaluate_HydRa_bk.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-01-18T23:38:29,365 copying build/lib/HydRa/training/train_and_evaluate_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-01-18T23:38:29,368 copying build/lib/HydRa/training/train_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-01-18T23:38:29,371 copying build/lib/HydRa/training/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-01-18T23:38:29,373 copying build/lib/HydRa/training/train_and_evaluate_HydRa.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-01-18T23:38:29,376 copying build/lib/HydRa/training/train_HydRa.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2024-01-18T23:38:29,379 copying build/lib/HydRa/HydRa_predict.py -> build/bdist.linux-armv7l/wheel/HydRa 2024-01-18T23:38:29,382 copying build/lib/HydRa/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa 2024-01-18T23:38:29,384 creating build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-01-18T23:38:29,385 copying build/lib/HydRa/predictions/Occlusion_map_v2.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-01-18T23:38:29,389 copying build/lib/HydRa/predictions/Occlusion_map.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-01-18T23:38:29,392 copying build/lib/HydRa/predictions/Occlusion_map_v3_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-01-18T23:38:29,396 copying build/lib/HydRa/predictions/Occlusion_1D_analysis_2.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-01-18T23:38:29,398 copying build/lib/HydRa/predictions/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-01-18T23:38:29,400 copying build/lib/HydRa/predictions/Occlusion_map_v2_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2024-01-18T23:38:29,406 creating build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2024-01-18T23:38:29,407 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 2024-01-18T23:38:32,995 copying build/lib/HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2024-01-18T23:38:32,998 copying build/lib/HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2024-01-18T23:38:33,024 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 2024-01-18T23:38:33,041 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 2024-01-18T23:38:35,474 copying build/lib/HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2024-01-18T23:38:35,500 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 2024-01-18T23:38:35,503 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 2024-01-18T23:38:35,519 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 2024-01-18T23:38:35,522 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 2024-01-18T23:38:35,583 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 2024-01-18T23:38:35,585 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 2024-01-18T23:38:35,647 copying build/lib/HydRa/HydRa2_0_predict.py -> build/bdist.linux-armv7l/wheel/HydRa 2024-01-18T23:38:35,650 creating build/bdist.linux-armv7l/wheel/HydRa/models 2024-01-18T23:38:35,651 copying build/lib/HydRa/models/DNN_seq.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2024-01-18T23:38:35,655 copying build/lib/HydRa/models/Sequence_class.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2024-01-18T23:38:35,658 copying build/lib/HydRa/models/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2024-01-18T23:38:35,661 creating build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:35,663 copying build/lib/HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:35,733 copying build/lib/HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:35,769 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 2024-01-18T23:38:35,797 copying build/lib/HydRa/data/Combined10RBPlist_uniprotID_20190716.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:35,802 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 2024-01-18T23:38:35,824 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 2024-01-18T23:38:35,826 copying build/lib/HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:35,828 copying build/lib/HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:35,859 copying build/lib/HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:35,892 copying build/lib/HydRa/data/protVec_100d_3grams.csv -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:36,014 copying build/lib/HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:36,016 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 2024-01-18T23:38:36,018 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 2024-01-18T23:38:36,086 copying build/lib/HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:37,338 copying build/lib/HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:37,529 copying build/lib/HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:37,594 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 2024-01-18T23:38:37,769 copying build/lib/HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:37,771 copying build/lib/HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:37,773 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 2024-01-18T23:38:37,775 copying build/lib/HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:37,778 copying build/lib/HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:37,779 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 2024-01-18T23:38:37,802 copying build/lib/HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:37,807 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 2024-01-18T23:38:37,934 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 2024-01-18T23:38:38,091 copying build/lib/HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2024-01-18T23:38:38,122 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 2024-01-18T23:38:38,153 running install_egg_info 2024-01-18T23:38:38,182 Copying hydra_rbp.egg-info to build/bdist.linux-armv7l/wheel/hydra_rbp-0.1.21.33-py3.11.egg-info 2024-01-18T23:38:38,196 running install_scripts 2024-01-18T23:38:38,215 creating build/bdist.linux-armv7l/wheel/hydra_rbp-0.1.21.33.dist-info/WHEEL 2024-01-18T23:38:38,218 creating '/tmp/pip-wheel-2yvjpi1e/hydra_rbp-0.1.21.33-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-01-18T23:38:38,224 adding 'HydRa/HydRa2_0_predict.py' 2024-01-18T23:38:38,229 adding 'HydRa/HydRa_predict.py' 2024-01-18T23:38:38,232 adding 'HydRa/__init__.py' 2024-01-18T23:38:38,234 adding 'HydRa/test_data_load.py' 2024-01-18T23:38:38,651 adding 'HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv' 2024-01-18T23:38:39,014 adding 'HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv' 2024-01-18T23:38:41,164 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls' 2024-01-18T23:38:41,718 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv' 2024-01-18T23:38:42,458 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv' 2024-01-18T23:38:45,791 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv' 2024-01-18T23:38:46,968 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv' 2024-01-18T23:38:50,317 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk' 2024-01-18T23:38:50,944 adding 'HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv' 2024-01-18T23:38:51,682 adding 'HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv' 2024-01-18T23:38:51,740 adding 'HydRa/data/Combined10RBPlist_uniprotID_20190716.txt' 2024-01-18T23:38:51,785 adding 'HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt' 2024-01-18T23:38:51,788 adding 'HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl' 2024-01-18T23:38:51,789 adding 'HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl' 2024-01-18T23:38:51,791 adding 'HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl' 2024-01-18T23:38:52,899 adding 'HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv' 2024-01-18T23:38:52,930 adding 'HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl' 2024-01-18T23:38:54,599 adding 'HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt' 2024-01-18T23:38:54,662 adding 'HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt' 2024-01-18T23:38:54,664 adding 'HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2024-01-18T23:38:54,666 adding 'HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2024-01-18T23:38:57,906 adding 'HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt' 2024-01-18T23:38:58,152 adding 'HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2024-01-18T23:38:58,154 adding 'HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2024-01-18T23:38:59,612 adding 'HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt' 2024-01-18T23:39:00,120 adding 'HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls' 2024-01-18T23:39:00,692 adding 'HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls' 2024-01-18T23:39:03,039 adding 'HydRa/data/protVec_100d_3grams.csv' 2024-01-18T23:39:03,100 adding 'HydRa/evaluation/ROC_PR_AUC_analysis.py' 2024-01-18T23:39:03,107 adding 'HydRa/evaluation/__init__.py' 2024-01-18T23:39:03,112 adding 'HydRa/models/DNN_seq.py' 2024-01-18T23:39:03,116 adding 'HydRa/models/Sequence_class.py' 2024-01-18T23:39:03,118 adding 'HydRa/models/__init__.py' 2024-01-18T23:39:03,359 adding 'HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5' 2024-01-18T23:39:03,593 adding 'HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5' 2024-01-18T23:39:03,605 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_structure.json' 2024-01-18T23:39:04,204 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_weights.h5' 2024-01-18T23:39:04,230 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_structure.json' 2024-01-18T23:39:04,834 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_weights.h5' 2024-01-18T23:39:04,968 adding 'HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5' 2024-01-18T23:39:04,974 adding 'HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5' 2024-01-18T23:39:05,071 adding 'HydRa/pre_trained/SVM_PPI_MB-S_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl' 2024-01-18T23:39:05,175 adding 'HydRa/pre_trained/SVM_PPI_MB_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl' 2024-01-18T23:39:11,637 adding 'HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pickle.pkl' 2024-01-18T23:39:14,943 adding 'HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_ModelFile.pickle.pkl' 2024-01-18T23:39:15,360 adding 'HydRa/predictions/Occlusion_1D_analysis_2.py' 2024-01-18T23:39:15,365 adding 'HydRa/predictions/Occlusion_map.py' 2024-01-18T23:39:15,372 adding 'HydRa/predictions/Occlusion_map_v2.py' 2024-01-18T23:39:15,381 adding 'HydRa/predictions/Occlusion_map_v2_HydRa2_0.py' 2024-01-18T23:39:15,392 adding 'HydRa/predictions/Occlusion_map_v3_HydRa2_0.py' 2024-01-18T23:39:15,394 adding 'HydRa/predictions/__init__.py' 2024-01-18T23:39:15,398 adding 'HydRa/preprocessing/Get_All_selected_SVM_features.py' 2024-01-18T23:39:15,401 adding 'HydRa/preprocessing/PPI_feature_generation.py' 2024-01-18T23:39:15,402 adding 'HydRa/preprocessing/__init__.py' 2024-01-18T23:39:15,403 adding 'HydRa/preprocessing/get_SVM_seq_features.py' 2024-01-18T23:39:15,405 adding 'HydRa/preprocessing/predict_SS.py' 2024-01-18T23:39:15,407 adding 'HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py' 2024-01-18T23:39:15,408 adding 'HydRa/preprocessing/Feature_generation/PPI_feature_generation.py' 2024-01-18T23:39:15,410 adding 'HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py' 2024-01-18T23:39:15,411 adding 'HydRa/preprocessing/Feature_generation/__init__.py' 2024-01-18T23:39:15,412 adding 'HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py' 2024-01-18T23:39:15,414 adding 'HydRa/preprocessing/Feature_generation/kmer_table_generation.py' 2024-01-18T23:39:15,415 adding 'HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py' 2024-01-18T23:39:15,417 adding 'HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py' 2024-01-18T23:39:15,419 adding 'HydRa/preprocessing/Feature_selection/__init__.py' 2024-01-18T23:39:15,421 adding 'HydRa/training/__init__.py' 2024-01-18T23:39:15,425 adding 'HydRa/training/train_HydRa.py' 2024-01-18T23:39:15,429 adding 'HydRa/training/train_HydRa2_0.py' 2024-01-18T23:39:15,434 adding 'HydRa/training/train_and_evaluate_HydRa.py' 2024-01-18T23:39:15,440 adding 'HydRa/training/train_and_evaluate_HydRa2_0.py' 2024-01-18T23:39:15,445 adding 'HydRa/training/train_and_evaluate_HydRa_bk.py' 2024-01-18T23:39:15,450 adding 'hydra_rbp-0.1.21.33.dist-info/LICENSE' 2024-01-18T23:39:15,452 adding 'hydra_rbp-0.1.21.33.dist-info/METADATA' 2024-01-18T23:39:15,453 adding 'hydra_rbp-0.1.21.33.dist-info/WHEEL' 2024-01-18T23:39:15,454 adding 'hydra_rbp-0.1.21.33.dist-info/entry_points.txt' 2024-01-18T23:39:15,455 adding 'hydra_rbp-0.1.21.33.dist-info/top_level.txt' 2024-01-18T23:39:15,457 adding 'hydra_rbp-0.1.21.33.dist-info/RECORD' 2024-01-18T23:39:15,535 removing build/bdist.linux-armv7l/wheel 2024-01-18T23:39:15,784 Building wheel for hydra-rbp (setup.py): finished with status 'done' 2024-01-18T23:39:17,016 Created wheel for hydra-rbp: filename=hydra_rbp-0.1.21.33-py3-none-any.whl size=53763603 sha256=bb44a445cfe2552b4ee79605c98945b5fd01b3902ae9f65ed3a7c644be59cad3 2024-01-18T23:39:17,017 Stored in directory: /tmp/pip-ephem-wheel-cache-jt9xs8ba/wheels/82/c9/b0/b25d926110bb04373b3f78f7331e0e33aa314126066eaf4b18 2024-01-18T23:39:17,048 Successfully built hydra-rbp 2024-01-18T23:39:18,449 Removed build tracker: '/tmp/pip-build-tracker-opys08u5'