Updates to GitHub Actions/Workflows (#151)

- Updates to GH Actions and pre-commit hooks
- Enable caching of pip reqs
- Enable code coverage generation and reporting
- Removed unused workflow files
- Update README to add badges
- Re-enable pip-compile hook; regenerate requirements.txt
- Remove requirements_dev.txt; not used

.github/workflows/ci.yml

@@ -0,0 +1,86 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: CI
+on:
+  push:
+    branches:
+      - "main"
+      - "release*"
+      - "*-devel"
+      - "*_devel"
+      - "*-ci"
+      - "*_ci"
+  pull_request:  # Run on all pull requests
+  workflow_dispatch:  # needed for "Run" button to show up in action
+env:
+  FORCE_COLOR: "1" # Make tools pretty.
+  PIP_DISABLE_PIP_VERSION_CHECK: "1"
+  PIP_NO_PYTHON_VERSION_WARNING: "1"
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      # Ensure that if even if a build in the matrix fails, the others continue
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          # Enable caching of pip packages between workflow jobs. This can speed things up dramatically, _if_
+          # jobs are executed fairly close together in time
+          # See: https://github.com/actions/setup-python/blob/main/docs/advanced-usage.md#caching-packages
+          cache: 'pip'
+          cache-dependency-path: 'requirements.txt'
+      - name: Install dependencies
+        run: |
+          # Install requirements, as compiled by pip-compile
+          pip install -r requirements.txt
+          # Install dysh itself, in editable mode (which is required to avoid breaking the caching mechanism above)
+          pip install -e .
+      - name: Test with pytest
+        run: |
+          # Write coverage data files, namespaced using matrix info
+          coverage run --data-file=".coverage.${{ matrix.os }}.${{ matrix.python-version }}" -m pytest
+      - name: Upload coverage data
+        # Upload only ubuntu results, since we are only running the coverage step on ubuntu
+        if: matrix.os == 'ubuntu-latest'
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-data
+          path: ".coverage.ubuntu-latest*"
+  coverage:
+    needs: tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+          cache: pip
+      - run: pip install --upgrade coverage[toml]
+      - uses: actions/download-artifact@v3
+        with:
+          name: coverage-data
+      - name: Combine coverage
+        run: |
+          coverage combine
+          coverage html --skip-covered --skip-empty
+
+          # Report and write to summary.
+          coverage report | sed 's/^/    /' >> $GITHUB_STEP_SUMMARY
+
+          # Report again and fail if under 100%.
+          # coverage report --fail-under=100
+      - name: Upload HTML report
+        uses: actions/upload-artifact@v3
+        with:
+          name: html-report
+          path: htmlcov

.github/workflows/release.yml

@@ -11,25 +11,22 @@ jobs:
     environment: release
     permissions:
       # IMPORTANT: this permission is mandatory for trusted publishing
+      # See: https://github.com/pypa/gh-action-pypi-publish#trusted-publishing
       id-token: write
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest]
-        python-version: ["3.x"]
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python
       uses: actions/setup-python@v3
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: '3.9'  # Should always be the minimum supported Python version
+        cache: 'pip'
+        cache-dependency-path': 'requirements.txt'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
-        pip install -e .
     - name: Build with hatch
       run: |
-        hatch build -c
+        hatch build --clean
     - name: upload release to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -1,39 +1,36 @@
 ---
 # See https://pre-commit.com for more information
 default_language_version:
-  python: python3.10
+  python: python3.9
 
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: 'https://github.com/pre-commit/pre-commit-hooks'
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
         exclude: '(notebooks|attic|benchmark|testdata)/.*'
       - id: end-of-file-fixer
         exclude: LICENSE
       - id: check-yaml
+      - id: check-toml
       - id: check-added-large-files
         args:
           - '--maxkb=1024'
       - id: debug-statements
+      - id: detect-private-key
       - id: mixed-line-ending
         args:
           - '--fix=lf'
       - id: check-docstring-first
+      - id: check-case-conflict # Check for files with names that would conflict on a case-insensitive filesystem
   - repo: https://github.com/pycqa/isort
     rev: 5.12.0
     hooks:
       - id: isort
         exclude: '(notebooks|attic|benchmark|testdata)/.*'
   - repo: 'https://github.com/psf/black'
-    rev: 23.1.0
+    rev: 23.11.0
     hooks:
       - id: black
         exclude: '(notebooks|attic|benchmark|testdata)/.*'
-#  - repo: https://github.com/jazzband/pip-tools
-#    rev: 6.12.3
-#    hooks:
-#      - id: pip-compile
-#        args:
-#          - '--resolver=backtracking'

README.md

@@ -1,4 +1,6 @@
 [![Documentation Status](https://readthedocs.org/projects/dysh/badge/?version=latest)](https://dysh.readthedocs.io/en/latest/?badge=latest)
+[![pre-commit.ci Status](https://results.pre-commit.ci/badge/github/GreenBankObservatory/dysh/main.svg)](https://results.pre-commit.ci/latest/github/GreenBankObservatory/dysh/main)
+[![CI Workflow Build Status](https://github.com/GreenBankObservatory/dysh/actions/workflows/ci.yml/badge.svg)](https://github.com/GreenBankObservatory/dysh/actions/workflows/ci.yml)
 
 # dysh
 

pyproject.toml

@@ -35,6 +35,7 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
+  "coverage[toml]",
   "ipdb",
   "numpydoc",
   "pytest",
@@ -81,7 +82,7 @@ docs-build = "sphinx-build {root}/docs/source {root}/docs/build -b html {args}"
 # run via: $ hatch run test:<script>
 [tool.hatch.envs.test.scripts]
 matrix = "pytest {args}"
-cov = "pytest --cov-report=term-missing --cov-config=pyproject.toml --cov=src/dysh --cov=tests {args}"
+cov = "pytest --cov-report=xml --cov-config=pyproject.toml --cov=src/dysh --cov=tests {args}"
 
 # Run tests across all supported version of Python
 [[tool.hatch.envs.test.matrix]]
@@ -105,10 +106,16 @@ exclude = [
 packages = ["src/dysh"]
 
 [tool.coverage.run]
+
 branch = true
+source = [
+  "src/"
+]
 parallel = true
 omit = [
   "src/dysh/__about__.py",
+  "*/tests/*",
+  "test_*.py"
 ]
 
 [tool.coverage.report]
@@ -154,6 +161,7 @@ ignore = [
   "E741",  # ambiguous-variable-name
 ]
 line-length = 120
+src = ["src", "benchmark", "notebooks"]
 
 [tool.ruff.per-file-ignores]
 # Ignore  in all `__init__.py` files
@@ -169,6 +177,15 @@ filterwarnings = [
     "ignore::DeprecationWarning"
 ]
 
+[tool.pip-tools]
+src_files = ["pyproject.toml"]
+extra = ["nb", "dev"]
+resolver = "backtracking"
+output_file= "requirements.txt"
+no_strip_extras = true
+quiet = true
+no_emit_trusted_host = true
+
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"