Merge pull request #401 from ImperialCollegeLondon/release/0.1.0

Publish version `0.1.0a0`

Author: davidorme

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,33 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+
+- OS: [e.g. iOS]
+- Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,23 @@
+# Description
+
+Please include a summary of the change and which issue is fixed. Please also include
+relevant motivation and context. List any dependencies that are required for this
+change.
+
+Fixes # (issue)
+
+## Type of change
+
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Optimization (back-end change that speeds up the code)
+- [ ] Bug fix (non-breaking change which fixes an issue)
+
+## Key checklist
+
+- [ ] Make sure you've run the `pre-commit` checks: `$ pre-commit run -a`
+- [ ] All tests pass: `$ poetry run pytest`
+
+## Further checks
+
+- [ ] Code is commented, particularly in hard-to-understand areas
+- [ ] Tests added that prove fix is effective or that feature works

.github/dependabot.yml

@@ -0,0 +1,17 @@
+
+
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/ci.yml

@@ -0,0 +1,80 @@
+name: Test and build
+
+on: [push, pull_request, release]
+
+jobs:
+  qa:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - uses: pre-commit/[email protected]
+
+  test:
+    needs: qa
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, macos-latest, windows-latest ]
+        python-version: [ "3.10", "3.11" ]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Poetry
+      uses: abatilo/[email protected]
+      with:
+        poetry-version: 1.5.1
+
+    - name: Install dependencies
+      run: poetry install
+
+    - name: Run tests
+      run: poetry run pytest --cov-report xml
+
+    - name: Upload coverage to Codecov
+      if: (matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10')
+      uses: codecov/codecov-action@v4
+      with:
+        fail_ci_if_error: true
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true
+  docs_build:
+    needs: qa
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install Poetry
+        uses: abatilo/[email protected]
+        with:
+          poetry-version: 1.5.1
+
+      - 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
+          poetry run sphinx-build -W --keep-going source build
+      
+      - name: Archive built docs for error checking on failure
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: built-docs
+          path: docs/build
+          retention-days: 2

.gitignore

@@ -50,6 +50,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+reports
 
 # Translations
 *.mo
@@ -75,7 +76,9 @@ docs/_build/
 target/
 
 # Jupyter Notebook
+# - deliberately excluding ipynb files. Using Jupytext to maintain paired Myst Markdown with only MD under version control
 .ipynb_checkpoints
+*.ipynb
 
 # IPython
 profile_default/

.markdownlint.yaml

@@ -0,0 +1,4 @@
+# MD013/line-length - Line length
+MD013:
+  # Number of characters
+  line_length: 88

.mdformat.toml

@@ -0,0 +1,9 @@
+# .mdformat.toml
+#
+# This file shows the default values and is equivalent to having
+# no configuration file at all. Change the values for non-default
+# behavior.
+#
+wrap = 88           # possible values: {"keep", "no", INTEGER}
+number = false      # possible values: {false, true}
+end_of_line = "lf"  # possible values: {"lf", "crlf"}

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-merge-conflict
+      - id: debug-statements
+  - repo: https://github.com/PyCQA/isort
+    rev: "5.13.2"
+    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]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.8.0"
+    hooks:
+      - id: mypy
+        additional_dependencies: [types-jsonschema, xarray]
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.39.0
+    hooks:
+    - id: markdownlint
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.1
+    hooks:
+      - id: pyupgrade
+        args: [--py310-plus]

.readthedocs.yaml

@@ -0,0 +1,41 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
+  jobs:
+    post_create_environment:
+      # Install poetry
+      # https://python-poetry.org/docs/#installing-manually
+      - pip install poetry
+    
+    post_install:
+      # Install dependencies with 'docs' dependency group
+      # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
+      # 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:
+   configuration: docs/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+# These are installed as dev requirements via poetry (but note that this will need to be
+# updated for poetry 1.2).
+#
+# python:
+#    install:
+#    - requirements: docs/requirements.txt