Update CI workflows (#105)

.github/workflows/ci.yaml

@@ -1,59 +1,51 @@
 name: CI
 on:
   push:
+    branches:
+      - main
   pull_request:
+  schedule:
+    - cron: '0 0 * * *' # Daily “At 00:00”
   workflow_dispatch: # allows you to trigger manually
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
-  pre-job:
-    runs-on: ubuntu-latest
-    outputs:
-      should_skip: ${{ steps.skip_check.outputs.should_skip }}
-    steps:
-      - id: skip_check
-        uses: fkirc/skip-duplicate-actions@master
-        with:
-          concurrent_skipping: 'same_content'
-          skip_after_successful_duplicate: 'false'
-          do_not_skip: '["pull_request", "workflow_dispatch", "schedule"]'
-          paths_ignore: '["**/docs/**"]'
   build:
-    needs: pre-job
-    if: ${{ needs.pre-job.outputs.should_skip != 'true' }}
     name: python-${{ matrix.python-version }}
+    if: github.repository == 'NCAR/ecgtools'
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.8', '3.9']
+        python-version: ['3.7', '3.8', '3.9', '3.10']
     steps:
-      - name: Cancel Previous Runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ github.token }}
       - uses: actions/checkout@v2
-        with:
-          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          channels: conda-forge,nodefaults
-          mamba-version: '*'
+          channels: conda-forge
+          channel-priority: strict
           activate-environment: ecgtools-dev
           auto-update-conda: false
           python-version: ${{ matrix.python-version }}
+          mamba-version: '*'
+          use-mamba: true
+          miniforge-variant: Mambaforge
           environment-file: ci/environment.yml
 
-      - name: Set up conda environment
+      - name: Install ecgtools
         run: |
-          python -m pip install -e .
+          python -m pip install -e . --no-deps --force-reinstall
           conda list
 
       - name: Run Tests
         run: |
-          python -m pytest --cov=./ --cov-report=xml --verbose
+          python -m pytest
 
       - name: Upload code coverage to Codecov
         uses: codecov/[email protected]

.github/workflows/pypi.yaml → .github/workflows/pypi-release.yaml

@@ -1,8 +1,9 @@
-name: Build and Upload ecgtools to PyPI
+name: Build distribution
 on:
   release:
     types:
       - published
+  push:
 
 jobs:
   build-artifacts:
@@ -60,6 +61,13 @@ jobs:
           ls -ltrh
           ls -ltrh dist
 
+      - name: Verify the built dist/wheel is valid
+        if: github.event_name == 'push'
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install dist/ecgtools*.whl
+          python -c "import ecgtools; print(ecgtools.__version__)"
+
   upload-to-pypi:
     needs: test-built-dist
     if: github.event_name == 'release'

.github/workflows/upstream-dev-ci.yaml

@@ -0,0 +1,95 @@
+name: Upstream CI
+on:
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: '0 0 * * *' # Daily “At 00:00” UTC
+  workflow_dispatch: # allows you to trigger the workflow run manually
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  upstream-dev:
+    name: upstream-dev
+    runs-on: ubuntu-latest
+    if: github.repository == 'NCAR/ecgtools'
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10']
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        id: conda
+        with:
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+          activate-environment: ecgtools-dev
+          auto-update-conda: false
+          python-version: ${{ matrix.python-version }}
+          environment-file: ci/environment-upstream-dev.yml
+          mamba-version: '*'
+          use-mamba: true
+          miniforge-variant: Mambaforge
+
+      - name: Install ecgtools
+        id: install
+        run: |
+          python -m pip install -e . --no-deps --force-reinstall
+          conda list
+
+      - name: Run Tests
+        id: test
+        run: |
+          python -m pytest
+
+      - name: Report Status
+        if: |
+          always()
+          && (steps.conda.outcome != 'success' || steps.install.outcome != 'success' || steps.install.outcome != 'success')
+        uses: actions/github-script@v5
+        with:
+          script: |
+            const title = '⚠️ Upstream CI Failed ⚠️'
+            const creator = 'github-actions[bot]'
+            const issueLabel = 'CI'
+            const workflow_url = `https://github.com/${process.env.GITHUB_REPOSITORY}/actions/runs/${process.env.GITHUB_RUN_ID}`
+            const issue_body = `[Workflow Run URL](${workflow_url})\n\n`
+            let foundIssue = false
+            const issues = await github.rest.issues.listForRepo({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+            })
+            for (let issue of issues.data) {
+              if (
+                issue.user.login === creator &&
+                issue.state === 'open' &&
+                issue.labels.some((label) => label.name === issueLabel)
+              ) {
+                github.rest.issues.update({
+                  owner: context.repo.owner,
+                  repo: context.repo.repo,
+                  issue_number: issue.number,
+                  body: issue_body,
+                })
+                core.info(`Updated an existing issue: ${issue.number}.`)
+                foundIssue = true
+                break
+              }
+            }
+            if (!foundIssue) {
+              await github.rest.issues.create({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                title: title,
+                body: issue_body,
+                labels: [issueLabel],
+              })
+              core.info('Opened a new issue')
+            }

ci/environment-upstream-dev.yml

@@ -0,0 +1,25 @@
+name: ecgtools-dev
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - cf_xarray
+  - codecov
+  - intake-esm
+  - joblib
+  - nbsphinx
+  - netcdf4
+  - numpydoc
+  - pip
+  - pre-commit
+  - pydantic
+  - pytest
+  - pytest-cov
+  - pytest-sugar
+  - pytest-xdist
+  - pyyaml
+  - typer
+  - xarray
+  - pip:
+      - git+https://github.com/xarray-contrib/cf-xarray
+      - git+https://github.com/intake/intake-esm

ci/environment.yml

@@ -4,7 +4,6 @@ channels:
   - nodefaults
 dependencies:
   - cf_xarray
-  - codecov
   - intake-esm
   - joblib
   - nbsphinx
@@ -20,3 +19,5 @@ dependencies:
   - pyyaml
   - typer
   - xarray
+  - pip:
+      - git+https://github.com/intake/intake-esm

readthedocs.yml

@@ -1,6 +1,6 @@
 version: 2
 conda:
-  environment: docs/environment.yml
+  environment: ci/environment-docs.yml
 build:
   os: 'ubuntu-20.04'
   tools: