Development

.github/workflows/main.yml

@@ -13,10 +13,11 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # os: [ubuntu-latest]
-        # python-version: ["3.12"]
         os: [ubuntu-latest, macos-latest, macos-14]
-        python-version: ["3.12", "3.11"]
+        python-version: ["3.12", "3.11", "3.10"]
+        # include:
+        #   - os: ubuntu-latest
+        #     python-version: "3.9"
 
     steps:
       - uses: actions/checkout@v3
@@ -122,12 +123,6 @@ jobs:
       with:
         fetch-depth: 0
 
-    - name: Install poetry
-      uses: snok/install-poetry@v1
-
-    - name: Install package
-      run: poetry install
-
    # This action uses Python Semantic Release v8
    # What this action does:
    # - Determines the next version number based on the commit history
@@ -140,154 +135,97 @@ jobs:
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
 
-    - name: Test Outputs of semantic release step
-      run: |
-        echo "${{ steps.release.outputs.released }}"
-        echo "${{ steps.release.outputs.version }}"
-        echo "${{ steps.release.outputs.tag }}"
-
-    - name: Install packaging-related tool
-      run:
-        python3 -m pip install build twine
-
-    # Build Package step:
-    # After semantic release, we should have a new tag if the commit history
-    # has been updated. If there isnt a new tag, then we dont need to build
-    # a new package. If there is a new tag, then we need to build a new package
-    # and publish it to PyPI
-    - name: Build package
-      if: steps.release.outputs.released == 'true'
-      run: |
-        poetry version ${{ steps.release.outputs.version }}
-        python -m build --sdist --wheel --outdir dist/ .
-
-    - name: Publish package distributions to PyPI
-      if: steps.release.outputs.released == 'true'
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        verbose: true
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
-
-    - name: Set up QEMU
-      if: steps.release.outputs.released == 'true'
-      uses: docker/setup-qemu-action@v3
-
-    - name: Set up Docker Buildx
-      if: steps.release.outputs.released == 'true'
-      uses: docker/setup-buildx-action@v3
-
-    - name: Login to Docker Hub
-      if: steps.release.outputs.released == 'true'
-      uses: docker/login-action@v3
-      with:
-        username: ${{ secrets.DOCKERHUB_USERNAME }}
-        password: ${{ secrets.DOCKERHUB_TOKEN }}
-
-    - name: Login to the GitHub Container Registry
-      if: steps.release.outputs.released == 'true'
-      uses: docker/login-action@v3
-      with:
-        registry: ghcr.io
-        username: ${{ github.actor }}
-        password: ${{ secrets.GITHUB_TOKEN }}
-
-    - name: Extract metadata (tags, labels) for Docker
-      id: meta
-      uses: docker/metadata-action@v3
-      with:
-        images: |
-          ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ steps.release.outputs.tag }}
-          ghcr.io/${{ github.repository }}/nbiatoolkit:${{ steps.release.outputs.tag }}
-
-    - name: Build
-      if: steps.release.outputs.released == 'true'
-      uses: docker/build-push-action@v5
-      with:
-        context: .
-        platforms: linux/amd64,linux/arm64
-        file: ./Dockerfile
-        push: true
-        tags: |
-          ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ steps.release.outputs.tag }}
-          ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest
-          ghcr.io/${{ github.repository }}/nbiatoolkit:${{ steps.release.outputs.tag }}
-          ghcr.io/${{ github.repository }}/nbiatoolkit:latest
-        labels: ${{ steps.meta.outputs.labels }}
-
-  test_install_withPyPi:
+  Publish-To-PyPi:
     needs: Continuous-Deployment
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest, macos-latest, macos-14]
-        python-version: ["3.12", "3.11", "3.10"]
-
+    if: needs.Continuous-Deployment.outputs.released == 'true'
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout code
+        uses: actions/checkout@v3
 
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: 3.12
 
-      - name: Install using PyPi
-        run: |
-          pip install  nbiatoolkit;
-          NBIAToolkit
+      - name: Install Package-Building Tool
+        run:
+          python3 -m pip install build twine
 
+      - name: Build package
+        run:
+          python3 -m build --sdist --wheel --outdir dist/
 
-  test_image_with_new_tag:
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+
+  Build-Docker-Images:
     needs: Continuous-Deployment
+    if: needs.Continuous-Deployment.outputs.released == 'true'
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
 
-      - name: Test Image With new Tag
-        run: |
-          # test image with latest tag
-          docker run --rm \
-            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }} \
-            NBIAToolkit
+      - name: Set up QEMU
+        if: steps.release.outputs.released == 'true'
+        uses: docker/setup-qemu-action@v3
 
+      - name: Set up Docker Buildx
+        if: steps.release.outputs.released == 'true'
+        uses: docker/setup-buildx-action@v3
 
-  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: Login to Docker Hub
+        if: steps.release.outputs.released == 'true'
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
 
-  Update-README:
-    needs: Continuous-Deployment
-    runs-on: ubuntu-latest
-    # if: jobs.Continuous-Deployment.outputs.released == 'true'
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v3
+      - name: Login to the GitHub Container Registry
+        if: steps.release.outputs.released == 'true'
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Get Current branch
-        run: |
-          echo "Current branch is: ${{ github.ref }}"
-          echo "Current branch is: ${{ github.head_ref }}"
-          echo "Current branch is: ${{ github.base_ref }}"
-          echo "Current branch is: ${{ github.event_name }}"
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v3
+        with:
+          images: |
+            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}
+            ghcr.io/${{ github.repository }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}
 
-          # if main, then git pull main
-          if [ "${{ github.ref }}" == "refs/heads/main" ]; then
-              git pull origin main
-          fi
+      - name: Build and push Docker images
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          file: ./Dockerfile
+          push: true
+          tags: |
+            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}
+            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest
+            ghcr.io/${{ github.repository }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}
+            ghcr.io/${{ github.repository }}/nbiatoolkit:latest
+          labels: ${{ steps.meta.outputs.labels }}
+
+  Test-PyPi-Install:
+    needs: Publish-To-PyPi
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, macos-14]
+        python-version: ["3.12", "3.11", "3.10"]
 
-          # fix diverged branch
-          git fetch origin ${{ github.head_ref }}
-          git checkout ${{ github.head_ref }}
+    steps:
+      - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
@@ -296,57 +234,21 @@ jobs:
 
       - name: Install using PyPi
         run: |
-          # update pip
-          pip install .
+          pip install  nbiatoolkit;
           NBIAToolkit
 
-      - name: Update README code block
-        run: |
-          awk '/``` bash NBIAToolkit-Output/ {
-            print "``` bash NBIAToolkit-Output";
-            print "> NBIAToolkit --version";
-            system("NBIAToolkit --version");
-            f=1;
-            next
-            } f && /```/ {
-              print "```";
-              f=0;
-              next
-            } !f' README.md > temp && mv temp README.md
-
-      - name: Commit and push changes
+  Test-Docker-Image:
+    needs: Build-Docker-Images
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        docker_tag: ["latest", "${{ needs.Continuous-Deployment.outputs.tag }}"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install using Docker
         run: |
-          LATEST_TAG=$(curl -s \
-              "https://api.github.com/repos/${{ github.repository }}/releases/latest" \
-              | jq -r .tag_name | sed 's/^v//')
-          echo "LATEST_TAG=${LATEST_TAG}"
-          # Check for changes
-          if [[ $(git status --porcelain) ]]; then
-              # Changes are present
-              echo "Changes found. Committing and pushing..."
-
-              git config --global user.name 'jjjermiah'
-              git config --global user.email 'jjjermiah@users.noreply.github.com'
-
-              # Add all changes
-              git add .
-
-              # Commit with a timestamp
-              git commit -m "chore: Update README: $LATEST_TAG"
-
-              # Push changes to the remote repository
-              # if github.head_ref is not null
-              # then push to the branch
-              # else push to the base branch
-              if [ -n "${{ github.head_ref }}" ]; then
-                  git push origin HEAD:${{ github.head_ref }}
-              else
-                  git push origin HEAD:${{ github.ref }}
-              fi
-
-
-              echo "Changes committed and pushed successfully."
-          else
-              # No changes
-              echo "No changes found. Nothing to commit or push."
-          fi
+          docker pull ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ matrix.docker_tag }};
+          docker run --rm ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ matrix.docker_tag }} NBIAToolkit

README.md

@@ -16,11 +16,11 @@
 ![GitHub repo size](https://img.shields.io/github/repo-size/jjjermiah/nbia-toolkit)
 [![Docker Pulls](https://img.shields.io/docker/pulls/jjjermiah/nbiatoolkit)](https://hub.docker.com/r/jjjermiah/nbiatoolkit)
 
-![GitHub milestone details](https://img.shields.io/github/milestones/progress-percent/jjjermiah/nbia-toolkit/1?style=flat-square&label=1.0.0%20Stable%20Release%20Milestone&link=https%3A%2F%2Fgithub.com%2Fjjjermiah%2Fnbia-toolkit%2Fmilestone%2F1)![GitHub milestone details](https://img.shields.io/github/milestones/progress/jjjermiah/nbia-toolkit/1?style=flat-square&label=%20&link=https%3A%2F%2Fgithub.com%2Fjjjermiah%2Fnbia-toolkit%2Fmilestone%2F1)
 [![GitHub issues](https://img.shields.io/github/issues/jjjermiah/nbia-toolkit)](https://github.com/jjjermiah/nbia-toolkit/issues)
 ![GitHub last commit](https://img.shields.io/github/last-commit/jjjermiah/nbia-toolkit)
 
 ## Table of Contents
+
 - [Features](#features)
 - [Installation](#installation)
 - [Python Usage](#python-usage)
@@ -43,7 +43,7 @@
   - ***Validate doownloads with MD5 checksums*** for downloaded images
   - **Auto-sort** DICOM files using a user-defined pattern of DICOM tags with specialized ***DICOMSorter class***
 
-![SequenceDiagram](https://www.mermaidchart.com/raw/ce7f489f-bf58-4827-aedb-e379ed7bffd3?theme=dark&version=v0.1&format=svg)
+See [Developer Notes](devnotes/README.md) for more details on the features and the development process.
 
 ## Installation
 
@@ -93,10 +93,10 @@ For quick access to the NBIA, the toolkit also provides a command line interface
       /  |/ / __  |/ // /| | / / / __ \/ __ \/ / //_/ / __/
      / /|  / /_/ // // ___ |/ / / /_/ / /_/ / / ,< / / /_
     /_/ |_/_____/___/_/  |_/_/  \____/\____/_/_/|_/_/\__/
-    
+
 Version: 1.0.1
 
-Available CLI tools: 
+Available CLI tools:
 
 getCollections [-h] [-u USERNAME] [-pw PASSWORD] [-p PREFIX]
                [-o OUTPUTFILE] [--version]

devnotes/CI-CD_2024-03-17.md

@@ -0,0 +1,14 @@
+# Continuous Integration and Continuous Deployment Diagram
+
+```mermaid
+graph LR
+  A[Push or Pull Request\nto main] --> B[Unit-Tests]
+  B --> C[Codecov]
+  B --> D[Continuous-Deployment]
+  D --> E[Publish-To-PyPi]
+  D --> F[Build-Docker-Images]
+  E --> G[Test-PyPi-Install]
+  F --> H[Test-Docker-Image]
+  A --> I[Build-Documentation]
+
+```

devnotes/README.md

@@ -0,0 +1,4 @@
+# Developer Notes
+
+[CI-CD](CI-CD_2024-03-17.md)
+[Sequence Diagram](Sequence-diagram_2024-03-17.md)