Add coverage report as new step in CI

.github/.dependabot.yml

@@ -0,0 +1,7 @@
+# Maintain dependencies for GitHub Actions
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/ci.yml

@@ -31,12 +31,20 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
   tests:
     runs-on: [self-hosted, x64, Linux, ubuntu, generic]
+    permissions:
+      # Gives the action the necessary permissions for publishing new
+      # comments in pull requests.
+      pull-requests: write
+      # Gives the action the necessary permissions for pushing data to the
+      # python-coverage-comment-action branch, and for editing existing
+      # comments (to avoid publishing multiple comments in the same PR)
+      contents: write
     strategy:
       max-parallel: 1
       matrix:
@@ -47,7 +55,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -64,8 +72,10 @@ jobs:
           pip install build
           python -m build
 
-      - name: Install the package
-        run: pip install .[test]
+      - name: Install the package and coverage library
+        run: |
+          pip install .[test]
+          python -Im pip install --upgrade coverage[toml]
 
       - name: Install the package in editable mode with all additional dependencies
         run: pip install --editable .[all]
@@ -87,8 +97,23 @@ jobs:
           ls -lh $HOME/.astrometry_cache/5200/index-5200-00.fits
           ls -lh $HOME/iop4testdata.$TESTDATA_MD5SUM.tar.gz
 
-      - name: Run tests (with -o log_cli=true -o log_cli_level=DEBUG to debug CI actions)
-        run: pytest -o log_cli=true -o log_cli_level=DEBUG -vxs tests
+      - name: Run tests with coverage report (with -o log_cli=true -o log_cli_level=DEBUG to debug CI actions)
+        run: pytest -o log_cli=true -o log_cli_level=DEBUG -vxs --cov=iop4lib tests
+
+      - name: Coverage comment
+        id: coverage_comment
+        uses: py-cov-action/python-coverage-comment-action@v3.24
+        with:
+          GITHUB_TOKEN: ${{ github.token }}
+
+      - name: Store Pull Request comment to be posted
+        uses: actions/upload-artifact@v4
+        if: steps.coverage_comment.outputs.COMMENT_FILE_WRITTEN == 'true'
+        with:
+          # If you use a different name, update COMMENT_ARTIFACT_NAME accordingly
+          name: python-coverage-comment-action
+          # If you use a different name, update COMMENT_FILENAME accordingly
+          path: python-coverage-comment-action.txt
 
 
   docs:
@@ -105,7 +130,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/coverage.yml

@@ -0,0 +1,36 @@
+# .github/workflows/coverage.yml
+name: Post coverage comment
+
+on:
+  workflow_run:
+    workflows: ["CI"]
+    types:
+      - completed
+
+jobs:
+  test:
+    name: Run tests & display coverage
+    runs-on: ubuntu-latest
+    if: github.event.workflow_run.event == 'pull_request' && github.event.workflow_run.conclusion == 'success'
+    permissions:
+      # Gives the action the necessary permissions for publishing new
+      # comments in pull requests.
+      pull-requests: write
+      # Gives the action the necessary permissions for editing existing
+      # comments (to avoid publishing multiple comments in the same PR)
+      contents: write
+      # Gives the action the necessary permissions for looking up the
+      # workflow that launched this workflow, and download the related
+      # artifact that contains the comment to be published
+      actions: read
+    steps:
+      # DO NOT run actions/checkout here, for security reasons
+      # For details, refer to https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
+      - name: Post comment
+        uses: py-cov-action/python-coverage-comment-action@v3
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_RUN_ID: ${{ github.event.workflow_run.id }}
+          # Update those if you changed the default values:
+          # COMMENT_ARTIFACT_NAME: python-coverage-comment-action
+          # COMMENT_FILENAME: python-coverage-comment-action.txt

.github/workflows/deploy_pypi.yml

@@ -14,7 +14,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

.github/workflows/docs.yml

@@ -37,7 +37,7 @@ jobs:
         run: git fetch --tags --force origin
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 

.github/workflows/release-drafter.yml

@@ -15,6 +15,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Drafts your next Release notes as Pull Requests are merged into "main"
-      - uses: release-drafter/release-drafter@v5
+      - uses: release-drafter/release-drafter@v6
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

iop4lib/config.example.yaml

@@ -8,11 +8,11 @@
 datadir: ~/.iop4data/ # <str> Path to iop4data data folder.
 set_rawdata_readonly: False # <bool> True / False (sets raw fits file to readonly when downloading them or creating a RawFit object).
 db_path: ~/.iop4data/iop4.db # Path to iop4 sqlite database file.
-astrometry_cache_path: ~/.astrometry_cache/ # <tr> Path to store the astromery index files.
+astrometry_cache_path: ~/.astrometry_cache/ # <str> Path to store the astrometry index files.
 nthreads: 4 # <int> Number of threads / processes to use (e.g. 4).
 astrometry_timeout: 20 # <int> Timeout in minutes for astrometry solving.
 astrometry_allsky_allow: false # <bool> Whether to allow all sky searches in the astrometry.net solver. If there are many all-sky images and nthreads is too high, it might cause very high memory consumption.
-astrometry_allsky_septhreshold: 25 # <int> Threshold of detected poinint mismatch to trigger an all-sky search.
+astrometry_allsky_septhreshold: 25 # <int> Threshold of detected pointing mismatch to trigger an all-sky search.
 
 ################
 ### GRAPHICS ###
@@ -54,7 +54,7 @@ osn_t150_password: null # <yourosnpassword>
 
 osn_source_list_path: null # <path/to/osn/source/list>
 
-# List of (case insentitive) regex patterns.
+# List of (case insensitive) regex patterns.
 # Files matching any of these patterns will be downloaded from OSN. 
 # For example, (^BLLac.*\.fits?$) will match file names starting with BLLac 
 # and ending in .fit, .fits, or .fts. You can include your initials here, 

tests/test_caha_cafos.py

@@ -19,13 +19,12 @@
 from .fixtures import load_test_catalog
 
 
-
 @pytest.mark.django_db(transaction=True)
 def test_build_multi_proc_photopol(load_test_catalog):
     """ Test the whole building process of reduced fits through multiprocessing 
 
     Also tests here relative photometry and polarimetry results and their 
-    quality (value + uncertainties) (to avoud losing time reducing them
+    quality (value + uncertainties) (to avoid losing time reducing them
     in another test function).
     """