Merge pull request #80 from jjjermiah/development

test:

.github/workflows/main.yml

@@ -67,56 +67,56 @@ jobs:
 
 
 
-  Continuous-Deployment:
-    permissions:
-        contents: write
-        packages: write
-        issues: write
-        pull-requests: write
+  # Continuous-Deployment:
+  #   permissions:
+  #       contents: write
+  #       packages: write
+  #       issues: write
+  #       pull-requests: write
 
-    # needs: Continuous-Integration
+  #   # needs: Continuous-Integration
 
-    # if pulling to main, deploy to PyPI
-    # if: github.ref == 'refs/heads/main'
+  #   # if pulling to main, deploy to PyPI
+  #   # if: github.ref == 'refs/heads/main'
 
-    # Set up operating system
-    runs-on: ubuntu-latest
+  #   # Set up operating system
+  #   runs-on: ubuntu-latest
 
-    # Define job steps
-    steps:
-    - name: Set up Python 3.12
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.12
+  #   # Define job steps
+  #   steps:
+  #   - name: Set up Python 3.12
+  #     uses: actions/setup-python@v2
+  #     with:
+  #       python-version: 3.12
 
-    - name: Check-out repository
-      uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
+  #   - name: Check-out repository
+  #     uses: actions/checkout@v2
+  #     with:
+  #       fetch-depth: 0
 
-    - name: Install poetry
-      uses: snok/install-poetry@v1
+  #   - name: Install poetry
+  #     uses: snok/install-poetry@v1
 
-    - name: Install package
-      run: poetry install
+  #   - name: Install package
+  #     run: poetry install
 
 
-    # Existing jobs...
+  #   # Existing jobs...
 
 
 
-   # This action uses Python Semantic Release v8
-   # What this action does:
-   # - Determines the next version number based on the commit history
-    # - Creates a new tag with the new version number
-    # - Pushes the new tag to GitHub
-    # - Creates a GitHub release with the new version number
-    - name: Python Semantic Release
-      id: release
-      uses: python-semantic-release/python-semantic-release@master
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        git_commit_message: 'chore(release): release ${next_version}'
+  #  # This action uses Python Semantic Release v8
+  #  # What this action does:
+  #  # - Determines the next version number based on the commit history
+  #   # - Creates a new tag with the new version number
+  #   # - Pushes the new tag to GitHub
+  #   # - Creates a GitHub release with the new version number
+  #   - name: Python Semantic Release
+  #     id: release
+  #     uses: python-semantic-release/python-semantic-release@master
+  #     with:
+  #       github_token: ${{ secrets.GITHUB_TOKEN }}
+  #       git_commit_message: 'chore(release): release ${next_version}'
 
   #   - name: Install packaging-related tool
   #     run:
@@ -241,21 +241,21 @@ jobs:
   #           NBIAToolkit
 
 
-  test_image_with_latest_tag:
-    needs: Continuous-Deployment
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v2
+  # test_image_with_latest_tag:
+  #   needs: Continuous-Deployment
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Checkout code
+  #       uses: actions/checkout@v2
 
-      - name: Test Image with "latest" Tag
-        run: |
-          docker run --rm \
-            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest \
-            NBIAToolkit
+  #     - name: Test Image with "latest" Tag
+  #       run: |
+  #         docker run --rm \
+  #           ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest \
+  #           NBIAToolkit
 
   Update-README:
-    needs: Continuous-Deployment
+    # needs: Continuous-Deployment
     runs-on: ubuntu-latest
     # if: github.ref == 'refs/heads/development'
     steps:
@@ -269,6 +269,11 @@ jobs:
           echo "Current branch is: ${{ github.base_ref }}"
           echo "Current branch is: ${{ github.event_name }}"
 
+          # if main, then git pull main
+          if [ "${{ github.ref }}" == "refs/heads/main" ]; then
+              git pull origin main
+          fi
+
           # fix diverged branch
           git fetch origin ${{ github.head_ref }}
           git checkout ${{ github.head_ref }}
@@ -281,10 +286,7 @@ jobs:
       - name: Install using PyPi
         run: |
           # update pip
-          pip install --upgrade pip
-
-          # make sure pypi packages are up to date
-          pip install --upgrade nbiatoolkit
+          pip install .
           NBIAToolkit
 
       - name: Update README code block