Merge branch 'main' into 201-bugfix-remove-references-to-sites-where-…

…data-originated-from

.github/dependabot.yml

@@ -4,4 +4,4 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "daily"
+      interval: "monthly"

.github/workflows/deployment.yml → .github/workflows/publish_docker.yml

@@ -16,19 +16,19 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Log in to Docker Hub
-        uses: docker/login-action@42d299face0c5c43a0487c477f595ac9cf22f1a7
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@e5622373a38e60fb6d795a4421e56882f2d7a681
+        uses: docker/metadata-action@507c2f2dc502c992ad446e3d7a5dfbe311567a96
         with:
           images: gsttmriphysics/hazen
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@a66e35b9cbcf4ad0ea91ffcaf7bbad63ad9e0229
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
         with:
           context: .
           push: true

.github/workflows/publish_pypi.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test_cli.yml

@@ -0,0 +1,114 @@
+# Runs on pull request or release - checks CLI tools are working without raising exception
+
+
+name: CLI tests
+
+on:
+  pull_request:
+  release:
+
+jobs:
+ test_cli:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest ]
+        python-version: [ '3.9', '3.10' ]
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest pytest-cov
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+      - name: Install hazen
+        run: |
+          pip install .
+
+      - name: test snr
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen snr tests/data/snr/Siemens --report
+          hazen snr tests/data/snr/Siemens --measured_slice_width 5.0012 --report
+
+      - name: test_acr_snr
+        if: always() # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen acr_snr tests/data/acr/Siemens --report
+          hazen acr_snr tests/data/acr/Siemens --subtract tests/data/acr/Siemens2 --report
+
+      - name: test acr_uniformity
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen acr_uniformity tests/data/acr/Siemens --report
+      
+      - name: test acr_ghosting
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen acr_ghosting tests/data/acr/Siemens --report
+          
+      - name: test acr_slice_position
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen acr_slice_position tests/data/acr/Siemens --report
+
+      - name: test acr_slice_thickness
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen acr_slice_thickness tests/data/acr/Siemens --report
+
+      - name: test acr_geometric_accuracy
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen acr_geometric_accuracy tests/data/acr/Siemens --report
+
+      - name: test acr_spatial_resolution
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen acr_spatial_resolution tests/data/acr/SiemensMTF --report
+
+      - name: test slice_position
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen slice_position tests/data/slicepos/SLICEPOSITION --report
+
+      - name: test slice_width
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen slice_width tests/data/slicewidth/512_matrix --report
+          hazen slice_width tests/data/slicewidth/SLICEWIDTH --report
+
+      - name: test spatial_resolution
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen spatial_resolution tests/data/resolution/RESOLUTION/ --report
+
+      - name: test uniformity
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+           hazen uniformity tests/data/uniformity --report
+
+      - name: test ghosting
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen ghosting tests/data/ghosting/GHOSTING --report
+          hazen ghosting tests/data/ghosting/PE_COL_PHANTOM_BOTTOM_RIGHT --report
+
+      - name: test snr_map
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen snr_map tests/data/snr/Siemens --report
+
+      - name: test relaxometry
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen relaxometry tests/data/relaxometry/T1/site1_20200218/plate5 --calc_t1 --plate_number=5 --report
+

.github/workflows/tests_development.yml

@@ -18,30 +18,12 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-    # Service containers to run with `container-job`
-    services:
-      # Label used to access the service container
-      postgres:
-        # Docker Hub image
-        image: postgres
-        # Provide the password for postgres
-        ports:
-          - 5432:5432
-        env:
-          POSTGRES_DB: hazen_test
-          POSTGRES_USER: test_user
-          POSTGRES_PASSWORD: test_user_password
-        # Set health checks to wait until postgres has started
-        options: >-
-          --health-cmd pg_isready
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
+
     steps:
     - uses: actions/checkout@v2
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -76,45 +58,3 @@ jobs:
       with:
         pytest-coverage-path: ./pytest-coverage.txt
         junitxml-path: ./pytest.xml
-
-    - name: Update the coverage Badge
-      if: github.event.pull_request.base.ref == 'main'  # if pull request is merging into main
-      uses: schneegans/[email protected]
-      with:
-        auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }}
-        gistID: ba102d5f3e592fcd50451c2eff8a803d
-        filename: hazen_pytest-coverage-comment.json
-        label: Test coverage
-        message: ${{ steps.coverageComment.outputs.coverage }}
-        color: ${{ steps.coverageComment.outputs.color }}
-        namedLogo: python
-
-  test_cli:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ ubuntu-latest ]
-        python-version: [ '3.9', '3.10' ]
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install flake8 pytest pytest-cov
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-
-      - name: Install hazen
-        run: |
-          python setup.py install
-
-      - name: test snr
-        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
-        run: |
-          hazen snr tests/data/snr/Siemens --report

.github/workflows/tests_release.yml

@@ -17,31 +17,12 @@ jobs:
       matrix:
         os: [ ubuntu-latest ]
         python-version: [ '3.9', '3.10' ]
-    # Service containers to run with `container-job`
-    services:
-      # Label used to access the service container
-      postgres:
-        # Docker Hub image
-        image: postgres
-        # Provide the password for postgres
-        ports:
-          - 5432:5432
-        env:
-          POSTGRES_DB: hazen_test
-          POSTGRES_USER: test_user
-          POSTGRES_PASSWORD: test_user_password
-        # Set health checks to wait until postgres has started
-        options: >-
-          --health-cmd pg_isready
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
 
     steps:
     - uses: actions/checkout@v2
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -56,32 +37,20 @@ jobs:
         set -Eeuxo pipefail
         pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=hazenlib tests/ | tee pytest-coverage.txt ; echo $?
 
-  test_cli:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ ubuntu-latest ]
-        python-version: [ '3.9', '3.10' ]
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install flake8 pytest pytest-cov
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-
-      - name: Install hazen
-        run: |
-          python setup.py install
+    - name: Pytest coverage comment
+      id: coverageComment
+      uses: MishaKav/pytest-coverage-comment@main
+      with:
+        pytest-coverage-path: ./pytest-coverage.txt
+        junitxml-path: ./pytest.xml
 
-      - name: test snr
-        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
-        run: |
-          hazen snr tests/data/snr/Siemens --report
+    - name: Update the coverage Badge
+      uses: schneegans/[email protected]
+      with:
+        auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }}
+        gistID: ba102d5f3e592fcd50451c2eff8a803d
+        filename: hazen_pytest-coverage-comment.json
+        label: Test coverage
+        message: ${{ steps.coverageComment.outputs.coverage }}
+        color: ${{ steps.coverageComment.outputs.color }}
+        namedLogo: python