sort repo for paper

classification/binary_classification.py

@@ -1317,7 +1317,6 @@ def main(
   output_path = figures_path / model_type
   output_path.mkdir(parents=True, exist_ok=True)
   # Run the classification with multiple seeds in parallel
-  """
   evaluation_seeds = multiple_seeds_classification_with_parallel(
       PRIMARY_SEED, n_iterations, model_type, processed_files, metadata_df,
       output_path, n_trials=50, n_jobs=-1
@@ -1328,7 +1327,6 @@ def main(
       PRIMARY_SEED, n_permutations, model_type, processed_files, metadata_df,
       output_path, permutation_output_path, n_jobs=-1
   )
-  """
   # Create the figures dir
   if not figures_path.exists():
     figures_path.mkdir(parents=True, exist_ok=True)

environment.yml

@@ -1,22 +1,151 @@
-name: tfgpu_jup
+name: nanobiopsy
+channels:
+  - bioconda
+  - pytorch
+  - conda-forge
+  - nvidia
+  - defaults
 dependencies:
-  - python = 3.9
-  - cudatoolkit
-  - cudnn
-  - tensorflow-gpu
-  - scikit-learn
-  - scikit-image
-  - numpy
-  - pandas
-  - seaborn
-  - matplotlib
-  - tqdm
-  - pip
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - _py-xgboost-mutex=2.0=cpu_0
+  - alembic=1.14.0=pyhd8ed1ab_0
+  - aom=3.9.1=hac33072_0
+  - blosc=1.21.6=hef167b5_0
+  - brotli=1.1.0=hb9d3cd8_2
+  - brotli-bin=1.1.0=hb9d3cd8_2
+  - brunsli=0.1=h9c3ff4c_0
+  - bzip2=1.0.8=h4bc722e_7
+  - c-blosc2=2.15.1=hc57e6cf_0
+  - ca-certificates=2024.8.30=hbcca054_0
+  - certifi=2024.8.30=pyhd8ed1ab_0
+  - charls=2.4.2=h59595ed_0
+  - cloudpickle=3.1.0=pyhd8ed1ab_1
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - colorlog=6.9.0=pyh707e725_0
+  - contourpy=1.3.1=py311hd18a35c_0
+  - cycler=0.12.1=pyhd8ed1ab_0
+  - dav1d=1.2.1=hd590300_0
+  - fonttools=4.55.0=py311h2dc5d0c_0
+  - freetype=2.12.1=h267a509_2
+  - giflib=5.2.2=hd590300_0
+  - greenlet=3.1.1=py311hfdbb021_0
+  - icu=75.1=he02047a_0
+  - imagecodecs=2024.9.22=py311h7d28041_0
+  - imageio=2.36.0=pyh12aca89_1
+  - importlib-metadata=8.5.0=pyha770c72_0
+  - importlib_resources=6.4.5=pyhd8ed1ab_0
+  - joblib=1.4.2=pyhd8ed1ab_0
+  - jxrlib=1.1=hd590300_3
+  - kiwisolver=1.4.7=py311hd18a35c_0
+  - lazy-loader=0.4=pyhd8ed1ab_1
+  - lazy_loader=0.4=pyhd8ed1ab_1
+  - lcms2=2.16=hb7c19ff_0
+  - ld_impl_linux-64=2.43=h712a8e2_2
+  - lerc=4.0.0=h27087fc_0
+  - libaec=1.1.3=h59595ed_0
+  - libavif16=1.1.1=h1909e37_2
+  - libblas=3.9.0=25_linux64_openblas
+  - libboost=1.84.0=hb8260a3_6
+  - libbrotlicommon=1.1.0=hb9d3cd8_2
+  - libbrotlidec=1.1.0=hb9d3cd8_2
+  - libbrotlienc=1.1.0=hb9d3cd8_2
+  - libcblas=3.9.0=25_linux64_openblas
+  - libdeflate=1.22=hb9d3cd8_0
+  - libexpat=2.6.4=h5888daf_0
+  - libffi=3.4.2=h7f98852_5
+  - libgcc=14.2.0=h77fa898_1
+  - libgcc-ng=14.2.0=h69a702a_1
+  - libgfortran=14.2.0=h69a702a_1
+  - libgfortran5=14.2.0=hd5240d6_1
+  - libgomp=14.2.0=h77fa898_1
+  - libhwy=1.1.0=h00ab1b0_0
+  - libjpeg-turbo=3.0.0=hd590300_1
+  - libjxl=0.11.0=hdb8da77_2
+  - liblapack=3.9.0=25_linux64_openblas
+  - liblightgbm=4.5.0=cpu_h155599f_3
+  - libllvm14=14.0.6=hcd5def8_4
+  - libnsl=2.0.1=hd590300_0
+  - libopenblas=0.3.28=pthreads_h94d23a6_1
+  - libpng=1.6.44=hadc24fc_0
+  - libsqlite=3.47.0=hadc24fc_1
+  - libstdcxx=14.2.0=hc0a3c3a_1
+  - libstdcxx-ng=14.2.0=h4852527_1
+  - libtiff=4.7.0=he137b08_1
+  - libuuid=2.38.1=h0b41bf4_0
+  - libwebp-base=1.4.0=hd590300_0
+  - libxcb=1.17.0=h8a09558_0
+  - libxcrypt=4.4.36=hd590300_1
+  - libxgboost=2.1.2=cpu_h3a1dfae_1
+  - libzlib=1.3.1=hb9d3cd8_2
+  - libzopfli=1.0.3=h9c3ff4c_0
+  - lightgbm=4.5.0=cpu_py_3
+  - llvmlite=0.43.0=py311h9c9ff8c_1
+  - lz4-c=1.9.4=hcb278e6_0
+  - mako=1.3.6=pyhff2d567_0
+  - markupsafe=3.0.2=py311h2dc5d0c_0
+  - matplotlib-base=3.9.2=py311h2b939e6_2
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - ncurses=6.5=he02047a_1
+  - networkx=3.4.2=pyh267e887_2
+  - numba=0.60.0=py311h4bc866e_0
+  - numpy=2.0.2=py311h71ddf71_1
+  - ocl-icd=2.3.2=hd590300_1
+  - openjpeg=2.5.2=h488ebb8_0
+  - openssl=3.4.0=hb9d3cd8_0
+  - optuna=4.1.0=pyhd8ed1ab_0
+  - packaging=24.2=pyhff2d567_1
+  - pandas=2.2.3=py311h7db5c69_1
+  - patsy=1.0.1=pyhff2d567_0
+  - pillow=11.0.0=py311h49e9ac3_0
+  - pip=24.3.1=pyh8b19718_0
+  - plotly=5.24.1=pyhd8ed1ab_0
+  - pthread-stubs=0.4=hb9d3cd8_1002
+  - py-xgboost=2.1.2=cpu_pyhd3de297_1
+  - pymzml=2.5.10=pyhdfd78af_0
+  - pyparsing=3.2.0=pyhd8ed1ab_1
+  - python=3.11.10=hc5c86c4_3_cpython
+  - python-dateutil=2.9.0.post0=pyhff2d567_0
+  - python-tzdata=2024.2=pyhd8ed1ab_0
+  - python_abi=3.11=5_cp311
+  - pytz=2024.1=pyhd8ed1ab_0
+  - pywavelets=1.7.0=py311h9f3472d_2
+  - pyyaml=6.0.2=py311h9ecbd09_1
+  - qhull=2020.2=h434a139_5
+  - rav1e=0.6.6=he8a937b_2
+  - readline=8.2=h8228510_1
+  - regex=2024.11.6=py311h9ecbd09_0
+  - scikit-image=0.24.0=py311h7db5c69_3
+  - scikit-learn=1.5.2=py311h57cc02b_1
+  - scipy=1.14.1=py311he9a78e4_1
+  - seaborn=0.13.2=hd8ed1ab_2
+  - seaborn-base=0.13.2=pyhd8ed1ab_2
+  - setuptools=75.6.0=pyhff2d567_0
+  - shap=0.46.0=cpu_py311h92109a2_1
+  - six=1.16.0=pyh6c4a22f_0
+  - slicer=0.0.8=pyhd8ed1ab_0
+  - snappy=1.2.1=ha2e4443_0
+  - sqlalchemy=2.0.36=py311h9ecbd09_0
+  - statsmodels=0.14.4=py311h9f3472d_0
+  - svt-av1=2.3.0=h5888daf_0
+  - tenacity=9.0.0=pyhd8ed1ab_0
+  - threadpoolctl=3.5.0=pyhc1e730c_0
+  - tifffile=2024.9.20=pyhd8ed1ab_0
+  - tk=8.6.13=noxft_h4845f30_101
+  - tqdm=4.67.0=pyhd8ed1ab_0
+  - typing-extensions=4.12.2=hd8ed1ab_0
+  - typing_extensions=4.12.2=pyha770c72_0
+  - tzdata=2024b=hc8b5060_0
+  - unicodedata2=15.1.0=py311h9ecbd09_1
+  - wheel=0.45.1=pyhd8ed1ab_0
+  - xorg-libxau=1.0.11=hb9d3cd8_1
+  - xorg-libxdmcp=1.1.5=hb9d3cd8_0
+  - xz=5.2.6=h166bdaf_0
+  - yaml=0.2.5=h7f98852_2
+  - zfp=1.0.1=h5888daf_2
+  - zipp=3.21.0=pyhd8ed1ab_0
+  - zlib-ng=2.2.2=h5888daf_0
+  - zstd=1.5.6=ha6fb4c9_0
   - pip:
-    - pyimzml
-  - jupyterlab
-  - ipykernel
-  - ipywidgets
-  - jupyter-resource-usage
-  - nodejs
-  - widgetsnbextension
+      - pyimzml==1.5.5
+      - wheezy-template==3.2.3