Create python-app.yml

.github/workflows/python-app.yml

@@ -0,0 +1,63 @@
+name: Python package
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: macos-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.12.3" # Specify the version of Python to use
+
+      - name: Cache conda
+        uses: actions/cache@v2
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}
+          restore-keys: |
+            ${{ runner.os }}-conda-
+
+      - name: Install Miniconda
+        shell: bash
+        run: |
+          wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh
+          bash miniconda.sh -b -p $HOME/miniconda
+          source "$HOME/miniconda/etc/profile.d/conda.sh"
+          conda config --set always_yes yes --set changeps1 no
+          conda config --add pkgs_dirs ~/conda_pkgs_dir
+          conda update -q conda
+
+      - name: Add conda channels
+        shell: bash
+        run: |
+          source "$HOME/miniconda/etc/profile.d/conda.sh"
+          conda config --add channels conda-forge
+
+      - name: Create and activate conda environment
+        shell: bash
+        run: |
+          source "$HOME/miniconda/etc/profile.d/conda.sh"
+          conda env create -f environment.yml
+          conda activate protein-prediction
+        env:
+          CONDA_PKGS_DIRS: ~/conda_pkgs_dir
+
+      - name: Check Python version
+        shell: bash
+        run: |
+          source "$HOME/miniconda/etc/profile.d/conda.sh"
+          conda activate protein-prediction
+          python --version
+
+      - name: Run tests
+        shell: bash
+        run: |
+          source "$HOME/miniconda/etc/profile.d/conda.sh"
+          conda activate protein-prediction
+          pytest

environment.yml

@@ -1,75 +1,78 @@
 name: protein-prediction
 channels:
+  - conda-forge
   - defaults
-  - https://conda.anaconda.org/gurobi
 dependencies:
-  - blas=1.0=openblas
-  - bottleneck=1.3.7=py312h32608ca_0
-  - brotli=1.0.9=h6c40b1e_8
-  - brotli-bin=1.0.9=h6c40b1e_8
-  - bzip2=1.0.8=h6c40b1e_6
-  - ca-certificates=2024.3.11=hecd8cb5_0
-  - colorama=0.4.6=py312hecd8cb5_0
-  - contourpy=1.2.0=py312ha357a0b_0
-  - cycler=0.11.0=pyhd3eb1b0_0
-  - expat=2.6.2=hcec6c5f_0
-  - fonttools=4.51.0=py312h6c40b1e_0
-  - freetype=2.12.1=hd8bbffd_0
-  - intel-openmp=2023.1.0=ha357a0b_43548
-  - joblib=1.4.0=py312hecd8cb5_0
-  - jpeg=9e=h6c40b1e_1
-  - kiwisolver=1.4.4=py312hcec6c5f_0
-  - lcms2=2.12=hf1fd2bf_0
-  - lerc=3.0=he9d5cce_0
-  - libbrotlicommon=1.0.9=h6c40b1e_8
-  - libbrotlidec=1.0.9=h6c40b1e_8
-  - libbrotlienc=1.0.9=h6c40b1e_8
-  - libcxx=14.0.6=h9765a3e_0
-  - libdeflate=1.17=hb664fd8_1
-  - libffi=3.4.4=hecd8cb5_1
-  - libgfortran=5.0.0=11_3_0_hecd8cb5_28
-  - libgfortran5=11.3.0=h9dfd629_28
-  - libopenblas=0.3.21=h54e7dc3_0
-  - libpng=1.6.39=h6c40b1e_0
-  - libtiff=4.5.1=hcec6c5f_0
-  - libwebp-base=1.3.2=h6c40b1e_0
-  - llvm-openmp=14.0.6=h0dcd299_0
-  - lz4-c=1.9.4=hcec6c5f_1
-  - matplotlib=3.8.4=py312hecd8cb5_0
-  - matplotlib-base=3.8.4=py312h7f12edd_0
-  - mkl=2023.1.0=h8e150cf_43560
-  - mkl-service=2.4.0=py312h6c40b1e_1
-  - ncurses=6.4=hcec6c5f_0
-  - networkx=3.1=py312hecd8cb5_0
-  - numexpr=2.8.7=py312h7d6adbd_0
-  - numpy=1.26.4=py312h7d6adbd_0
-  - numpy-base=1.26.4=py312hbb3573c_0
-  - openjpeg=2.4.0=h66ea3da_0
-  - openssl=3.0.13=hca72f7f_1
-  - packaging=23.2=py312hecd8cb5_0
-  - pandas=2.2.1=py312he282a81_0
-  - pathlib=1.0.1=pyhd3eb1b0_1
-  - pillow=10.3.0=py312h6c40b1e_0
-  - pip=24.0=py312hecd8cb5_0
-  - pybind11-abi=5=hd3eb1b0_0
-  - pyparsing=3.0.9=py312hecd8cb5_0
-  - python=3.12.3=hd58486a_1
-  - python-dateutil=2.9.0post0=py312hecd8cb5_0
-  - python-tzdata=2023.3=pyhd3eb1b0_0
-  - pytz=2024.1=py312hecd8cb5_0
-  - readline=8.2=hca72f7f_0
-  - scikit-learn=1.4.2=py312he282a81_1
-  - scipy=1.13.0=py312hba6221a_0
-  - setuptools=69.5.1=py312hecd8cb5_0
-  - six=1.16.0=pyhd3eb1b0_1
-  - sqlite=3.45.3=h6c40b1e_0
-  - tbb=2021.8.0=ha357a0b_0
-  - threadpoolctl=2.2.0=pyh0d69192_0
-  - tk=8.6.14=h4d00af3_0
-  - tornado=6.3.3=py312h6c40b1e_0
-  - tzdata=2024a=h04d1e81_0
-  - unicodedata2=15.1.0=py312h6c40b1e_0
-  - wheel=0.43.0=py312hecd8cb5_0
-  - xz=5.4.6=h6c40b1e_1
-  - zlib=1.2.13=h4b97444_1
-  - zstd=1.5.5=hc035e20_2
+  - brotli=1.1.0=h0dc2134_1
+  - brotli-bin=1.1.0=h0dc2134_1
+  - bzip2=1.0.8=h10d778d_5
+  - ca-certificates=2024.6.2=h8857fd0_0
+  - certifi=2024.2.2=pyhd8ed1ab_0
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - contourpy=1.2.1=py312h9230928_0
+  - cycler=0.12.1=pyhd8ed1ab_0
+  - exceptiongroup=1.2.0=pyhd8ed1ab_2
+  - fonttools=4.53.0=py312hbd25219_0
+  - freetype=2.12.1=h60636b9_2
+  - iniconfig=2.0.0=pyhd8ed1ab_0
+  - joblib=1.4.2=pyhd8ed1ab_0
+  - kiwisolver=1.4.5=py312h49ebfd2_1
+  - lcms2=2.16=ha2f27b4_0
+  - lerc=4.0.0=hb486fe8_0
+  - libblas=3.9.0=22_osx64_openblas
+  - libbrotlicommon=1.1.0=h0dc2134_1
+  - libbrotlidec=1.1.0=h0dc2134_1
+  - libbrotlienc=1.1.0=h0dc2134_1
+  - libcblas=3.9.0=22_osx64_openblas
+  - libcxx=17.0.6=h88467a6_0
+  - libdeflate=1.20=h49d49c5_0
+  - libexpat=2.6.2=h73e2aa4_0
+  - libffi=3.4.2=h0d85af4_5
+  - libgfortran=5.0.0=13_2_0_h97931a8_3
+  - libgfortran5=13.2.0=h2873a65_3
+  - libjpeg-turbo=3.0.0=h0dc2134_1
+  - liblapack=3.9.0=22_osx64_openblas
+  - libopenblas=0.3.27=openmp_hfef2a42_0
+  - libpng=1.6.43=h92b6c6a_0
+  - libsqlite=3.45.3=h92b6c6a_0
+  - libtiff=4.6.0=h129831d_3
+  - libwebp-base=1.4.0=h10d778d_0
+  - libxcb=1.15=hb7f2c08_0
+  - libzlib=1.3.1=h87427d6_1
+  - llvm-openmp=18.1.6=h15ab845_0
+  - matplotlib=3.8.4=py312hb401068_2
+  - matplotlib-base=3.8.4=py312hb6d62fa_2
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - ncurses=6.5=h5846eda_0
+  - networkx=3.3=pyhd8ed1ab_1
+  - numpy=1.26.4=py312he3a82b2_0
+  - openjpeg=2.5.2=h7310d3a_0
+  - openssl=3.3.1=h87427d6_0
+  - packaging=24.0=pyhd8ed1ab_0
+  - pandas=2.2.2=py312h1171441_1
+  - pillow=10.3.0=py312h0c923fa_0
+  - pip=24.0=pyhd8ed1ab_0
+  - pluggy=1.5.0=pyhd8ed1ab_0
+  - pthread-stubs=0.4=hc929b4f_1001
+  - pyparsing=3.1.2=pyhd8ed1ab_0
+  - pytest=8.2.2=pyhd8ed1ab_0
+  - python=3.12.3=h1411813_0_cpython
+  - python-dateutil=2.9.0=pyhd8ed1ab_0
+  - python-tzdata=2024.1=pyhd8ed1ab_0
+  - python_abi=3.12=4_cp312
+  - pytz=2024.1=pyhd8ed1ab_0
+  - readline=8.2=h9e318b2_1
+  - scikit-learn=1.5.0=py312hc214ba5_1
+  - scipy=1.13.1=py312hb9702fa_0
+  - setuptools=70.0.0=pyhd8ed1ab_0
+  - six=1.16.0=pyh6c4a22f_0
+  - threadpoolctl=3.5.0=pyhc1e730c_0
+  - tk=8.6.13=h1abcd95_1
+  - tomli=2.0.1=pyhd8ed1ab_0
+  - tornado=6.4=py312h41838bb_0
+  - tzdata=2024a=h0c530f3_0
+  - wheel=0.43.0=pyhd8ed1ab_1
+  - xorg-libxau=1.0.11=h0dc2134_0
+  - xorg-libxdmcp=1.1.3=h35c211d_0
+  - xz=5.2.6=h775f41a_0
+  - zstd=1.5.6=h915ae27_0

tests/test_pytest.py

@@ -14,6 +14,8 @@
     import_graph_from_pickle,
 )
 from tools.workflow import run_workflow
+import os
+
 
 
 def test_algorithm_attributes():
@@ -47,6 +49,15 @@ def test_algorithm_inherits_class():
 
 
 def test_algorithm_workflow():
+    if not os.path.exists("output"):
+        os.makedirs("output")
+    if not os.path.exists("output/dataset"):
+        os.makedirs("output/dataset")
+    if not os.path.exists("output/data"):
+        os.makedirs("output/data")
+    if not os.path.exists("output/images"):
+        os.makedirs("output/images")
+
     output_data_path = Path("./output/data/")
     output_image_path = Path("./output/images/")
     input_directory_path = Path("./tests/testing-dataset/")