Merge pull request #56 from jjjermiah/development

Development
jjjermiah · Jan 28, 2024 · fb09228 · fb09228
2 parents e20d4af + 1ba3d1e
commit fb09228
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -4,7 +4,7 @@ name: Unit Tests
 on:
   push:
     # push to any branch
-    branches: [ main ]
+    branches: [ main, development]
   pull_request:
     branches: [ main ]
 
@@ -31,20 +31,39 @@ jobs:
         run: |
           pip install -r requirements.txt
           poetry install
-          pytest --cov --cov-report=xml
+          pytest --cov --cov-report=xml:coverage-report/coverage.xml
+
+      - name: Build documentation
+        run: poetry run make html --directory docs/
+
+      - name: Upload coverage report
+        uses: actions/upload-artifact@v2
+        with:
+          name: coverage-report
+          path: coverage-report
+
+  Codecov:
+    needs: Continuous-Integration
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Download coverage.xml artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: coverage-report
+          path: coverage-report
 
       - name: Use Codecov to track coverage
         uses: codecov/codecov-action@v3
         with:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-          files: ./coverage.xml
-          fail_ci_if_error: true # optional (default = false)
-          verbose: true # optional (default = false)
+          files: ./coverage-report/coverage.xml
+          fail_ci_if_error: true
+          verbose: true
           name: codecov-umbrella
 
-      - name: Build documentation
-        run: poetry run make html --directory docs/
-
   Continuous-Deployment:
     permissions:
         contents: write
@@ -170,57 +189,30 @@ jobs:
           ghcr.io/${{ github.repository }}/nbiatoolkit:latest
         labels: ${{ steps.meta.outputs.labels }}
 
-    - name: Test Image
-      if: steps.release.outputs.released == 'true'
-      run: |
-        docker run --rm \
-          ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }} \
-          python -c "import nbiatoolkit; print(nbiatoolkit.__version__)"
-    # # - name: Publish package distributions to GitHub Releases
-    # - name: Build and Publish
-    #   uses: pypa/gh-action-pypi-publish@release/v1
-    #   with:
-    #     user: __token__
-    #     password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-    #     repository_url: https://test.pypi.org/legacy/
-    #     build: true
-    #     build_command: poetry build
-    #     build_command_postfix: dist/*
-
-    # - name: Publish package distributions to PyPI
-    #   id: pypi-publish
-
-
-
-    # - name: Publish package distributions to GitHub Releases
-    #   uses: python-semantic-release/upload-to-gh-release@main
-    #   if: steps.release.outputs.released == 'true'
-    #   with:
-    #     github_token: ${{ secrets.GITHUB_TOKEN }}
-    # - name: Publish to TestPyPI
-    #   uses: pypa/gh-action-pypi-publish@release/v1
-    #   with:
-    #     user: __token__
-    #     password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-    #     repository_url: https://test.pypi.org/legacy/
-
-    # - name: Test install from TestPyPI
-    #   run: |
-    #       pip install \
-    #       --index-url https://test.pypi.org/simple/ \
-    #       --extra-index-url https://pypi.org/simple \
-    #       nbiatoolkit
-
-    # - name: Publish to PyPI
-    #   uses: pypa/gh-action-pypi-publish@release/v1
-    #   with:
-    #     user: __token__
-    #     password: ${{ secrets.PYPI_API_TOKEN }}
-
-    # - name: Publish documentation
-    #   uses: maxheld83/ghpages@v0.2.1
-    #   with:
-    #     build_dir: docs/_build/html
-    #     target_branch: gh-pages
-    #     committer_name: "GitHub Actions"
-    #     committer_email: "jermiahjoseph98@gmail.com"
+  test_image_with_new_tag:
+    needs: Continuous-Deployment
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Test Image With new Tag
+        if: needs.build.result == 'success'
+        run: |
+          docker run --rm \
+            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }} \
+            python -c "import nbiatoolkit; print(nbiatoolkit.__version__)"
+
+  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
+        if: needs.build.result == 'success'
+        run: |
+          docker run --rm \
+            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest \
+            python -c "import nbiatoolkit; print(nbiatoolkit.__version__)"
diff --git a/src/nbiatoolkit/nbia.py b/src/nbiatoolkit/nbia.py
@@ -258,40 +258,4 @@ def parsePARAMS(self, params: dict) -> dict:
     pprint(all)
 
     sub = client.getCollections(prefix="aCrin")
-    pprint(sub)
-    # collections = client.getCollections()
-    # pprint(collections[0:5])
-    # seriesJSON = client.getSeries(Collection="4D-Lung")
-    # # first get a list of the SeriesInstanceUIDs
-    # seriesUIDS = [series['SeriesInstanceUID'] for series in seriesJSON]
-    # pprint(seriesUIDS[0:5])
-
-    # seriesUIDS = [
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.189721824525842725510380467695',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.336250251691987239290048605884',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.227929163446067537882961857921',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.925990093742075237571072608963',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.139116724721865252687455544825',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.364787732307640672278270360328',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.384197169742944248273003912317',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.149750833495190982103087204448',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.300347070051003027185063750283',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.317831614083862743715273480521',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.736089011729021729851027177073',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.133381852562664457904201355429',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.909088026336573109170906532418',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.953079890279542310843831057254',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.427052348021168186336245283790',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.295010883410722294053941635303',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.263257070197787007872578860295',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.672179203515231442641005032212',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.184961274239908956209701869504',
-    #     '1.3.6.1.4.1.14519.5.2.1.6834.5010.797307942821711099898506950104']
-
-    # downloadDir = "./data"
-    # os.makedirs(downloadDir, exist_ok=True)
-
-    # client.downloadSeries(
-    #     seriesUIDS, downloadDir, overwrite=True, nParallel=8)
-
-    # pprint(os.listdir(downloadDir))
+    pprint(sub)