Merge pull request #549 from ImperialCollegeLondon/release/0.1.1a5

Release/0.1.1a5

.github/PULL_REQUEST_TEMPLATE.md

@@ -21,3 +21,4 @@ Fixes # (issue)
 
 - [ ] Code is commented, particularly in hard-to-understand areas
 - [ ] Tests added that prove fix is effective or that feature works
+- [ ] Relevant documentation reviewed and updated

.github/workflows/ci.yml

@@ -1,6 +1,13 @@
 name: Test and build
 
-on: [push, pull_request, release]
+# When does this run - new, reopened or updated PRs, pushes to main or develop and when
+# the workflow is called by another workflow, such as the publishing actions.
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+  push:
+    branches: [main, develop]
+  workflow_call:
 
 jobs:
   qa:
@@ -19,7 +26,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ "3.10", "3.11" ]
+        python-version: [ "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -63,9 +70,6 @@ jobs:
       - name: Install dependencies
         run: poetry install
 
-      - name: Set ipython kernel
-        run: poetry run python -m ipykernel install --user --name=vr_python3
-
       - name: Build docs using sphinx
         run: |
           cd docs

.github/workflows/publish.yml

@@ -0,0 +1,103 @@
+name: Publishing
+
+on: 
+  release:
+    types: [published]
+
+jobs:
+  # First, run the standard test suite - for this to work correctly, the workflow needs
+  # to inherit the organisation secrets used to authenticate to CodeCov.
+  # https://github.com/actions/runner/issues/1413
+  test:
+    uses: ./.github/workflows/ci.yml
+    secrets: inherit
+
+  # Next, build the package wheel and source releases and add them to the release assets
+  build-wheel:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      # Build the package - this could use `poetry build` directly but pyproject.toml 
+      # already has the build-system configured to use poetry so `pip` should pick that
+      # up automatically.
+      - name: Build sdist
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+
+      # Upload the build outputs as job artifacts - these will be two files with x.y.z
+      # version numbers:
+      # - virtual_ecosystem-x.y.z-py3-none-any.whl
+      # - virtual_ecosystem-x.y.z.tar.gz
+      - uses: actions/upload-artifact@v4
+        with:
+          path: dist/virtual_ecosystem*
+
+      # Add the built files to the release assets, alongside the repo archives 
+      # automatically added by GitHub. These files should then match exactly to the
+      # published files on PyPI.
+      - uses: softprops/action-gh-release@v1
+        with:
+          files: dist/virtual_ecosystem*
+
+  # Now attempt to publish the package to the TestPyPI site, where the virtual_ecosystem
+  # project has been configured to allow trusted publishing from this repo and workflow.
+  #
+  # The skip-existing option allows the publication step to pass even when the release
+  # files already exists on PyPI. That suggests something has gone wrong with the
+  # release or the build file staging and the release should not be allowed to continue
+  # to publish on PyPI.
+
+  publish-TestPyPI:
+    needs: build-wheel
+    name: Publish virtual_ecosystem to TestPyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+
+    steps:
+      # Download the built package files from the job artifacts
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: artifact
+          path: dist
+
+      # Information step to show the contents of the job artifacts
+      - name: Display structure of downloaded files
+        run: ls -R dist
+
+      # Use trusted publishing to release the files downloaded into dist to TestPyPI
+      - name: Publish package distributions to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          # skip-existing: true
+
+  # The final job in the workflow is to publish to the real PyPI as long as the release
+  # name does not contain the tag 'test-pypi-only'
+  publish-PyPI:
+    if: ${{ ! contains(github.event.release.name, 'test-pypi-only')}}
+    needs: publish-TestPyPI
+    name: Publish virtual_ecosystem to PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+
+    steps:
+      # Download the built package files from the job artifacts
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: artifact
+          path: dist
+
+      # Information step to show the contents of the job artifacts
+      - name: Display structure of downloaded files
+        run: ls -R dist
+
+      # Use trusted publishing to release the files downloaded into dist to PyPI
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -122,6 +122,8 @@ venv.bak/
 
 # mkdocs documentation
 /site
+docs/source/variables.rst
+docs/jupyter_execute/*.png
 
 # mypy
 .mypy_cache/
@@ -134,6 +136,5 @@ dmypy.json
 # Mac DS Store files
 .DS_Store
 
-# PYPI credentials
+# Local PyPI authentication tokens
 .pypirc
-

.pre-commit-config.yaml

@@ -1,34 +1,22 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
-  - repo: https://github.com/PyCQA/isort
-    rev: "5.13.2"
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.2
     hooks:
-      - id: isort
-        additional_dependencies: [toml]
-  - repo: https://github.com/psf/black
-    rev: "24.2.0"
-    hooks:
-      - id: black
-  - repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
-    hooks:
-      - id: flake8
-        additional_dependencies: [flake8-docstrings]
+      - id: ruff        #  Run the linter.
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format #  Run the formatter.
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.8.0"
+    rev: "v1.11.2"
     hooks:
       - id: mypy
-        additional_dependencies: [types-jsonschema, xarray]
+        additional_dependencies: [types-jsonschema, xarray, types-tabulate, numpy]
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.39.0
+    rev: v0.41.0
     hooks:
     - id: markdownlint
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.1
-    hooks:
-      - id: pyupgrade
-        args: [--py310-plus]
+

.readthedocs.yaml

@@ -22,7 +22,6 @@ build:
       # VIRTUAL_ENV needs to be set manually for now.
       # See https://github.com/readthedocs/readthedocs.org/pull/11152/
       - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
-      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry run python -m ipykernel install --user --name=vr_python3
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

.vscode/extensions.json

@@ -2,11 +2,11 @@
     "recommendations": [
         "Gruntfuggly.todo-tree",
         "ms-python.python",
-        "ms-python.vscode-pylance",
         "ms-toolsai.jupyter",
         "ms-toolsai.jupyter-keymap",
         "ms-toolsai.jupyter-renderers",
         "ms-vsliveshare.vsliveshare",
-        "stkb.rewrap"
+        "stkb.rewrap",
+        "charliermarsh.ruff"
     ]
 }

.vscode/settings.json

@@ -1,8 +1,4 @@
 {
-    "python.linting.flake8Enabled": true,
-    "python.linting.mypyEnabled": true,
-    "python.linting.enabled": true,
-    "python.formatting.provider": "none",
     "editor.formatOnSave": true,
     "editor.rulers": [
         88
@@ -18,8 +14,7 @@
     "workbench.editorAssociations": {
         "*.ipynb": "jupyter-notebook"
     },
-    "cSpell.words": [],
     "[python]": {
-        "editor.defaultFormatter": "ms-python.black-formatter"
+        "editor.defaultFormatter": "charliermarsh.ruff"
     },
 }