init

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  # - package-ecosystem: pip
+  #   directory: "/"
+  #   schedule:
+  #     interval: daily
+  - package-ecosystem: 'github-actions'
+    directory: '/'
+    schedule:
+      # Check for updates once a week
+      interval: 'weekly'

.github/workflows/ci.yaml

@@ -0,0 +1,67 @@
+name: CI
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 0 * * *' # Daily “At 00:00”
+  workflow_dispatch: # allows you to trigger manually
+
+jobs:
+  skip-duplicate-jobs:
+    runs-on: ubuntu-latest
+    if: |
+      github.repository == 'c-worthy-ocean/ocean-c-lab'
+    outputs:
+      should_skip: ${{ steps.skip_check.outputs.should_skip }}
+    steps:
+      - id: skip_check
+        uses: fkirc/[email protected]
+        with:
+          # For workflows which are triggered concurrently with the same
+          # contents, attempt to execute them exactly once.
+          concurrent_skipping: 'same_content_newer'
+          paths_ignore: '["**/doc/**"]'
+
+  build:
+    name: python-${{ matrix.python-version }}
+    needs: skip-duplicate-jobs
+    if: ${{ needs.skip-duplicate-jobs.outputs.should_skip != 'true' }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.8', '3.9', '3.10']
+    steps:
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+          activate-environment: c_worthy
+          auto-update-conda: false
+          python-version: ${{ matrix.python-version }}
+          environment-file: ci/environment.yml
+          mamba-version: '*'
+          use-mamba: true
+          miniforge-variant: Mambaforge
+
+      - name: Install ocean-c-lab
+        run: |
+          python -m pip install -e . --no-deps --force-reinstall
+          conda list
+
+      - name: Run Tests
+        run: |
+          python -m pytest
+
+      - name: Upload code coverage to Codecov
+        uses: codecov/[email protected]
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false

.github/workflows/pypi-release.yaml

@@ -0,0 +1,78 @@
+name: Build distribution
+on:
+  release:
+    types:
+      - published
+  push:
+
+jobs:
+  build-artifacts:
+    runs-on: ubuntu-latest
+    if: github.repository == 'c-worthy-ocean/ocean-c-lab'
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: actions/[email protected]
+        name: Install Python
+        with:
+          python-version: 3.8
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools setuptools-scm wheel twine check-manifest
+
+      - name: Build tarball and wheels
+        run: |
+          git clean -xdf
+          git restore -SW .
+          python -m build --sdist --wheel .
+
+      - name: Check built artifacts
+        run: |
+          python -m twine check dist/*
+          pwd
+          if [ -f dist/ocean-c-lab-0.0.0.tar.gz ]; then
+            echo "❌ INVALID VERSION NUMBER"
+            exit 1
+          else
+            echo "✅ Looks good"
+          fi
+      - uses: actions/upload-artifact@v3
+        with:
+          name: releases
+          path: dist
+
+  test-built-dist:
+    needs: build-artifacts
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+        name: Install Python
+        with:
+          python-version: 3.8
+      - uses: actions/download-artifact@v3
+        with:
+          name: releases
+          path: dist
+      - name: List contents of built dist
+        run: |
+          ls -ltrh
+          ls -ltrh dist
+
+  upload-to-pypi:
+    needs: test-built-dist
+    if: github.event_name == 'release'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: releases
+          path: dist
+      - name: Publish package to PyPI
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}
+          verbose: true

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

@@ -0,0 +1,89 @@
+name: Upstream CI
+on:
+  push:
+  schedule:
+    - cron: '0 0 * * *' # Daily “At 00:00” UTC
+  workflow_dispatch: # allows you to trigger the workflow run manually
+
+jobs:
+  upstream-dev:
+    name: upstream-dev
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10']
+    steps:
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        id: conda
+        with:
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+          activate-environment: c-worthy-upstream
+          auto-update-conda: false
+          python-version: ${{ matrix.python-version }}
+          environment-file: ci/upstream-dev-environment.yml
+          mamba-version: '*'
+          use-mamba: true
+          miniforge-variant: Mambaforge
+
+      - name: Install ocean-c-lab
+        id: install
+        run: |
+          python -m pip install -e . --no-deps --force-reinstall
+          conda list
+
+      - name: Run Tests
+        id: test
+        run: |
+          python -m pytest
+
+      - name: Report Status
+        if: |
+          always()
+          && (steps.conda.outcome != 'success' || steps.install.outcome != 'success' || steps.install.outcome != 'success')
+
+        uses: actions/github-script@v6
+        with:
+          script: |
+            const title = '⚠️ Upstream CI Failed ⚠️'
+            const creator = 'github-actions[bot]'
+            const issueLabel = 'CI'
+            const workflow_url = `https://github.com/${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')
+            }

.gitignore

@@ -0,0 +1,135 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Dask
+dask-worker-space/
+
+# Vscode
+.vscode/