Refactor PyCIEMSS to use ChiRho and remove stale functionality

.github/workflows/lint.yml

@@ -0,0 +1,38 @@
+name: Lint
+
+on:
+  push:
+    branches: [ main, staging-refactor ]
+  pull_request:
+    branches: [ main, staging-refactor ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: pip cache
+        uses: actions/cache@v1
+        with:
+          path: ~/.cache/pip
+          key: lint-pip-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            lint-pip-
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[tests]
+
+      - name: Lint
+        run: ./scripts/lint.sh

.github/workflows/test.yml

@@ -0,0 +1,53 @@
+name: Test
+
+on:
+  push:
+    branches: [ main, staging-refactor ]
+  pull_request:
+    branches: [ main, staging-refactor ]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.8, 3.9, '3.10']
+        os: [ubuntu-latest]  # , macos-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Ubuntu cache
+        uses: actions/cache@v1
+        if: startsWith(matrix.os, 'ubuntu')
+        with:
+          path: ~/.cache/pip
+          key:
+            ${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            ${{ matrix.os }}-${{ matrix.python-version }}-
+
+      - name: macOS cache
+        uses: actions/cache@v1
+        if: startsWith(matrix.os, 'macOS')
+        with:
+          path: ~/Library/Caches/pip
+          key:
+            ${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            ${{ matrix.os }}-${{ matrix.python-version }}-
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[tests]
+
+      - name: Test
+        shell: bash
+        run: |
+          pytest tests/ -s -n auto

.github/workflows/test_notebooks.yml

@@ -0,0 +1,40 @@
+name: Test notebooks
+
+on:
+    schedule:
+      - cron: '0 0 * * 6'  # Run at midnight on Saturdays
+    push:
+      branches: [ main, staging-refactor ]
+    pull_request: 
+      branches: [ main, staging-refactor ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    steps:
+        - uses: actions/checkout@v2
+
+        - name: pip cache
+          uses: actions/cache@v1
+          with:
+            path: ~/.cache/pip
+            key: lint-pip-${{ hashFiles('**/pyproject.toml') }}
+            restore-keys: |
+              lint-pip-
+
+        - name: Set up Python ${{ matrix.python-version }}
+          uses: actions/setup-python@v1
+          with:
+            python-version: ${{ matrix.python-version }}
+
+        - name: Install dependencies
+          run: |
+            python -m pip install --upgrade pip
+            pip install -e .[tests]
+
+        - name: Run Notebook Test
+          run: python -m pytest --nbval-lax docs/source/interfaces.ipynb

.gitignore

@@ -339,3 +339,4 @@ venv/
 *~
 *_schema.json
 *data_with_missing_entries.csv
+*.nix

Makefile

@@ -0,0 +1,10 @@
+lint: FORCE
+	./scripts/lint.sh
+
+format:
+	./scripts/clean.sh
+
+tests: lint FORCE
+	pytest -v tests -n auto
+
+FORCE:

docs/source/conf.py

@@ -19,7 +19,7 @@
 exclude_patterns = []
 
 extensions += ['sphinx.ext.autodoc', 'autoapi.extension']
-autoapi_dirs = ['../../src']
+autoapi_dirs = ['../../pyciemss']
 
 
 # -- Options for HTML output -------------------------------------------------