Merge pull request #23 from danielfromearth/develop

update `main`

.github/pull_request_template.md

@@ -0,0 +1,19 @@
+GitHub Issue: #NUM _(replace NUM with GitHub issue number)_
+
+### Description
+
+A short description of the changes in this PR.
+
+### Local test steps
+
+_Summarize testing and verification you've done. This includes unit tests or testing with specific data_
+
+### Overview of integration done
+
+_Explain how this change was integration tested. Provide screenshots or logs if appropriate. An example of this would be a local Harmony deployment._
+
+## PR Acceptance Checklist
+* [ ] Unit tests added/updated and passing.
+* [ ] Integration testing
+* [ ] `CHANGELOG.md` updated
+* [ ] Documentation updated (if needed).

.github/workflows/pull_request.yml

@@ -11,28 +11,5 @@ on:
       - issues/**
 
 jobs:
-  build:
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-
-    - name: Install Poetry
-      uses: abatilo/[email protected]
-      with:
-        poetry-version: 1.3.2
-
-    - name: Install stitchee
-      run: poetry install
-
-    - name: Lint
-      run: |
-        poetry run ruff concatenator
-
-    - name: Test with pytest
-      run: |
-        poetry run pytest tests/test_group_handling.py
-      # TODO: expand tests to include full concatenation runs, i.e., don't just run test_group_handling.py
+  build_and_test:
+    uses: ./.github/workflows/run_tests.yml

.github/workflows/push.yml

@@ -10,13 +10,19 @@ on:
   workflow_dispatch:
 
 jobs:
-  build-linux:
-    name: Lint and Test
-    runs-on: ubuntu-latest
+  run_tests:
+    uses: ./.github/workflows/run_tests.yml
+
+  bump_version:
+    needs: run_tests
+    runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
+    - name: Retrieve repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
       with:
         python-version: '3.10'
 
@@ -70,25 +76,25 @@ jobs:
       if: ${{ startsWith(github.ref, 'refs/heads/main') }}
       env:
         CURRENT_VERSION: ${{ steps.get-version.outputs.current_version }}
+        # True if the version already has a 'rc' pre-release identifier
+        BUMP_RC: ${{ contains(steps.get-version.outputs.current_version, 'rc') }}
+        # True if the version already has a 'alpha' pre-release identifier
+        BUMP_A: ${{ contains(steps.get-version.outputs.current_version, 'a') }}
+        # True if the version already has a 'beta' pre-release identifier
+        BUMP_B: ${{ contains(steps.get-version.outputs.current_version, 'b') }}
       # Remove rc* from end of version string
       # The ${string%%substring} syntax below deletes the longest match of $substring from back of $string.
       run: |
-        poetry version ${CURRENT_VERSION%%rc*}
+        if [ "$BUMP_RC" = true ]; then
+          poetry version ${CURRENT_VERSION%%rc*}
+        elif [ "$BUMP_B" = true ]; then
+          poetry version ${CURRENT_VERSION%%b*}
+        elif [ "$BUMP_A" = true ]; then
+          poetry version ${CURRENT_VERSION%%a*}
+        fi
         echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
         echo "venue=ops" >> $GITHUB_ENV
 
-    - name: Install stitchee
-      run: poetry install
-
-    - name: Lint
-      run: |
-        poetry run ruff concatenator
-
-    - name: Test with pytest
-      run: |
-        poetry run pytest tests/test_group_handling.py
-      # TODO: expand tests to include full concatenation runs, i.e., don't just run test_group_handling.py
-
 #    - name: Commit Version Bump
 #      # If building develop, a release branch, or main then we commit the version bump back to the repo
 #      if: |

.github/workflows/run_tests.yml

@@ -0,0 +1,67 @@
+# This workflow will install Python dependencies, run tests,
+# and report test results and code coverage as artifacts. It will
+# be called by the workflow that run tests against new PRs and as
+# a first step in the workflow that publishes new Docker images.
+
+name: A reusable workflow to build and run the unit test suite
+
+on:
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  build_and_test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Retrieve repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Set up Poetry
+        uses: abatilo/[email protected]
+        with:
+          poetry-version: 1.3.2
+
+      - name: Install package
+        run: poetry install
+
+      - name: Run linting
+        run: |
+          poetry run ruff concatenator
+
+      - name: Run tests with coverage
+        run: |
+          poetry run coverage run -m pytest tests/test_group_handling.py >& test_results.txt
+        # TODO: expand tests to include full concatenation runs, i.e., don't just run test_group_handling.py
+
+      - name: Generate coverage report
+        if: ${{ always() }}
+        run: |
+          poetry run coverage report -m >& coverage_report.txt
+          poetry run coverage html --dir htmlcov
+
+      - name: Archive test results
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: test result
+          path: test_results.txt
+
+      - name: Archive code coverage report (plain text)
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: code coverage report (plain text)
+          path: coverage_report.txt
+
+      - name: Archive code coverage report (HTML)
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: code coverage report (HTML)
+          path: htmlcov/*

concatenator/stitchee.py

@@ -24,6 +24,7 @@ def stitchee(
     write_tmp_flat_concatenated: bool = False,
     keep_tmp_files: bool = True,
     concat_dim: str = "",
+    concat_kwargs: dict | None = None,
     logger: Logger = default_logger,
 ) -> str:
     """Concatenate netCDF data files along an existing dimension.
@@ -89,8 +90,15 @@ def stitchee(
     #                                 coords='minimal',
     #                                 compat='override')
 
+    if concat_kwargs is None:
+        concat_kwargs = {}
+
     combined_ds = xr.concat(
-        xrdataset_list, dim=GROUP_DELIM + concat_dim, data_vars="minimal", coords="minimal"
+        xrdataset_list,
+        dim=GROUP_DELIM + concat_dim,
+        data_vars="minimal",
+        coords="minimal",
+        **concat_kwargs,
     )
 
     benchmark_log["concatenating"] = time.time() - start_time