Merge pull request #33 from bioinfoUQAM/dev

Thesis PR

requirements.txt

@@ -1,95 +1,10 @@
-absl-py==1.4.0
-aiohttp==3.8.5
-aiohttp-cors==0.7.0
-aiosignal==1.3.1
-astunparse==1.6.3
-async-timeout==4.0.2
-attrs==23.1.0
-biopython==1.78
-blessed==1.20.0
-cachetools==5.3.1
-certifi==2023.7.22
-charset-normalizer==3.2.0
-click==8.1.6
-cloudpickle==2.2.1
-colorful==0.5.5
-Cython==3.0.0
-distlib==0.3.7
-filelock==3.12.2
-flatbuffers==23.5.26
-frozenlist==1.4.0
-future==0.18.3
-gast==0.4.0
-google-api-core==2.11.1
-google-auth==2.22.0
-google-auth-oauthlib==1.0.0
-google-pasta==0.2.0
-googleapis-common-protos==1.60.0
-gpustat==1.1
-grpcio==1.48.2
-h5py==3.9.0
-idna==3.4
-importlib-metadata==6.8.0
-importlib-resources==6.0.0
-InSilicoSeq==1.5.4
-joblib==1.3.1
-jsonschema==4.18.6
-jsonschema-specifications==2023.7.1
-keras==2.13.1
-libclang==16.0.6
-Markdown==3.4.4
-MarkupSafe==2.1.3
-msgpack==1.0.5
-multidict==6.0.4
-numpy==1.24.3
-nvidia-ml-py==12.535.77
-oauthlib==3.2.2
-opencensus==0.11.2
-opencensus-context==0.1.3
-opt-einsum==3.3.0
-packaging==23.1
-pandas==2.0.3
-pkgutil_resolve_name==1.3.10
-platformdirs==3.10.0
-prometheus-client==0.13.1
-protobuf==4.23.4
-psutil==5.9.5
-py-spy==0.3.14
-pyarrow==12.0.1
-pyasn1==0.5.0
-pyasn1-modules==0.3.0
-pydantic==1.10.12
-pysam==0.21.0
-python-dateutil==2.8.2
-pytz==2023.3
-PyYAML==6.0.1
+biopython>=1.79
+cloudpickle>=2.2.1
+InSilicoSeq==1.6.0
+keras==2.14
+numpy>=1.2
+pandas>=2.0
 ray==2.6.3
-referencing==0.30.2
-requests==2.31.0
-requests-oauthlib==1.3.1
-rpds-py==0.9.2
-rsa==4.9
 scikit-learn==1.3.0
-scipy==1.10.1
-six==1.16.0
-smart-open==6.3.0
-tabulate==0.9.0
-tensorboard==2.13.0
-tensorboard-data-server==0.7.1
-tensorboardX==2.6.2
-tensorflow==2.13.0
-tensorflow-estimator==2.13.0
-tensorflow-io-gcs-filesystem==0.33.0
-termcolor==2.3.0
-threadpoolctl==3.2.0
-tqdm==4.65.0
-tune-sklearn==0.4.6
-typing_extensions==4.5.0
-tzdata==2023.3
-urllib3==1.26.16
-virtualenv==20.24.2
-wcwidth==0.2.6
-Werkzeug==2.3.6
-wrapt==1.15.0
-yarl==1.9.2
-zipp==3.16.2
+tensorflow==2.14
+pyarrow==12.0.1

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Caribou
-version = 1.3.1
+version = 1.4.1
 url = https://github.com/bioinfoUQAM/Caribou/wiki
 author = Nicolas de Montigny
 author_email = de_montigny.nicolas@courrier.uqam.ca
@@ -11,29 +11,24 @@ long_description = file: README.md
 
 [options]
 install_requires =
-  setuptools
-  wheel
-  grpcio==1.48.2
-  ray[default]==2.6.3
-  pydantic<2
-  pyarrow>=6.0.1,!=7
-  keras>=2.0.0
-  tensorflow>=2.0.0
-  numpy>=1.16
-  pandas>=1.3.0
-  scikit-learn>=1.1.2
-  scipy
-  insilicoseq
-  biopython==1.78
-  tqdm
-  cloudpickle
-  tune-sklearn
+  ray==2.6.3
+  numpy>=1.2
+  pandas>=2.0
+  pyarrow==12.0.1
+  cloudpickle>=2.2.1
+  keras==2.14
+  tensorflow==2.14
+  scikit-learn==1.3.0
+  biopython>=1.79
+  InSilicoSeq==1.6.0
 include_package_data = True
 python_requires = >=3.8
 scripts =
   src/Caribou_pipeline.py
   src/Caribou_kmers.py
   src/Caribou_reduce_features.py
+  src/Caribou_simulate_test_val.py
+  src/Caribou_dimensions_decomposition.py
   src/Caribou_extraction.py
   src/Caribou_classification.py
   src/Caribou_extraction_train_cv.py