merging three workflows-install,run PyTest and run Colab notebook

.github/workflows/install_test_testcolab.yml

@@ -0,0 +1,204 @@
+name: Install, Run PyTest and Test Colab Notebook
+
+on:
+  pull_request:
+    branches: [ master ]
+  push:
+    branches: [ master ]
+  workflow_dispatch:
+
+jobs:
+  install-ersilia:
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install Ersilia
+      run: |
+        python -m pip install git+https://github.com/ersilia-os/bentoml-ersilia.git
+        python -m pip install -e .
+    - name: Test help command
+      run: |
+        ersilia --help
+        ersilia --version
+
+  test-docker:
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install Ersilia without pre-installing BentoML
+      run: |
+        python -m pip install -e .
+    - name: Test help command again
+      run: |
+        ersilia --help
+        ersilia --version
+    - name: Fetch molecular weight model from DockerHub
+      run: |
+        ersilia -v fetch molecular-weight --from_dockerhub
+
+  test-os:
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.platform }}
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # pin@v3.5.3
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: "3.10.10"
+
+      - name: Install dependencies
+        run: |
+          conda install git-lfs -c conda-forge
+          git-lfs install
+          conda install gh -c conda-forge
+
+      - name: Install ersilia from source
+        run: |
+          python --version
+          python -m pip install -e .
+
+      - name: Ersilia help
+        run: |
+          ersilia --help
+
+
+
+
+  run-pytest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # pin@v3.5.3
+
+      - name: Add conda to system path
+        run: echo $CONDA/bin >> $GITHUB_PATH
+
+      - name: Source conda
+        run: source $CONDA/etc/profile.d/conda.sh
+
+      - name: Set Python to 3.10.10
+        run:
+         conda install -y python=3.10.10  
+
+      - name: Install dependencies
+        run: |
+          source activate
+          conda init
+          conda install git-lfs -c conda-forge
+          git-lfs install
+          conda install gh -c conda-forge
+
+      - name: Install ersilia
+        run: |
+          source activate
+          python --version
+          echo "After conda init"
+          conda init
+          python -m pip install -e .[test]
+
+      - name: Run pytest
+        run: |
+          source activate          
+          pip install pytest
+          pytest
+
+  # update-model-request_template:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+
+  #     - name: Path Filter
+  #       id: filter
+  #       uses: dorny/paths-filter@v3
+  #       with:
+  #         filters: |
+  #           tag-file:
+  #             - 'ersilia/hub/content/metadata/tag.txt'
+
+  #     - name: Set up Python
+  #       if: steps.filter.outputs.tag-file == 'true'
+  #       uses: actions/setup-python@v4
+  #       with:
+  #         python-version: '3.10'
+
+  #     - name: Install dependencies
+  #       if: steps.filter.outputs.tag-file == 'true'
+  #       run: |
+  #         python -m pip install --upgrade pip
+  #         pip install pyyaml
+
+  #     - name: Run update_model_request_template.py
+  #       if: steps.filter.outputs.tag-file == 'true'
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  #       run: python .github/scripts/update_model_request_template.py
+
+  #     - name: Commit and push changes
+  #       if: steps.filter.outputs.tag-file == 'true'
+  #       uses: actions-js/push@5a7cbd780d82c0c937b5977586e641b2fd94acc5 # pin@v1.5
+  #       with:
+  #         author_name: "ersilia-bot"
+  #         author_email: "ersilia-bot@users.noreply.github.com"
+  #         message: "Update model_request.yml with new tags from tag.txt"
+  #         directory: .
+  #         repository: "ersilia-os/ersilia"
+  #         github_token: ${{ secrets.GITHUB_TOKEN }}
+  #         force: true
+
+
+  test-colab-notebook:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # pin@v3.5.3
+      - name: Add conda to system path
+        run: echo $CONDA/bin >> $GITHUB_PATH
+
+      - name: Source conda
+        run: source $CONDA/etc/profile.d/conda.sh
+
+      - name: Set Python to 3.10.10
+        run:
+         conda install -y python=3.10.10 
+
+      - name: Install dependencies
+        run: |
+          source activate
+          conda init
+          conda install google-colab -c conda-forge
+          jupyter --version
+          pip install --upgrade nbconvert nbformat jsonschema pandas
+
+      - name: Test Google Colab Notebook with CLI shell commands
+        run: |
+          jupyter nbconvert --to notebook --execute notebooks/test-colab-notebook-cli.ipynb --output=output-cli.ipynb --ExecutePreprocessor.timeout=-1
+
+      - name: Test Google Colab Notebook with Python API commands
+        run: |
+          echo "Skipping Python API notebook due to unresolved issue"
+          #jupyter nbconvert --to notebook --execute notebooks/test-colab-notebook-python-api.ipynb --output=output-python-api.ipynb --ExecutePreprocessor.timeout=-1
+
+      - name: Upload Output of the Google Colab Notebook CLI
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # pin@v4.3.3
+        with:
+          name: output-cli.ipynb
+          path: notebooks/output-cli.ipynb
+          retention-days: 7