Merge pull request #105 from bas-amop/github-pages-docs

Merge v2.3.0

Author: thomaszwagerman

.github/ISSUE_TEMPLATE/bug---issue-report.md

@@ -9,35 +9,11 @@ Version Number: <!--- Include version number of MeshiPhi the PR will be included
 ## Fixes # (issue)
 <!--- If this PR adds functionality or resolves problems associated with an issue on GitHub, please include a link to the issue -->
 
-# Testing
-To ensure that the functionality of the MeshiPhi codebase remains consistent throughout the development cycle a testing strategy has been developed, which can be viewed in the document `test/testing_strategy.md`. 
-This includes a collection of test files which should be run according to which part of the codebase has been altered in a pull request. Please consult the testing strategy to determine which tests need to be run. 
-
-- [ ] My changes have not altered any of the files listed in the testing strategy
-
-- [ ] My changes result in all required regression tests passing without the need to update test files.  
-  
-> *list which files have been altered and include a pytest.txt file for each of
-> the tests required to be run*
->
-> The files which have been changed during this PR can be listed using the command
-
-    git diff --name-only 2.2.x
-
-- [ ] My changes require one or more test files to be updated for all regression tests to pass.   
-
-> *include pytest.txt file showing which tests fail.*  
-> *include reasoning as to why your changes cause these tests to fail.* 
->
-> Should these changes be valid, relevant test files should be updated.  
-> *include pytest.txt file of test passing after test files have been updated.*
 
 # Checklist
 
-- [ ] My code follows [pep8](https://peps.python.org/pep-0008/) style guidelines.  
 - [ ] I have commented my code, particularly in hard-to-understand areas.  
 - [ ] I have updated the documentation of the codebase where required.  
-- [ ] My changes generate no new warnings.   
 - [ ] My PR has been made to the `2.2.x` branch (**DO NOT SUBMIT A PR TO MAIN**)  
 
 

.github/ISSUE_TEMPLATE/data-acquisition.md

@@ -0,0 +1,38 @@
+name: Build docs
+
+on:
+  push:
+    branches:
+        - main
+  pull_request:
+    branches:
+        - main
+    types: [opened, synchronize, reopened, ready_for_review]
+  workflow_dispatch:
+
+jobs:
+  build-docs:
+    if: github.event.pull_request.draft == false || github.event_name != 'pull_request'
+    permissions:
+        contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: 3.12
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[docs]
+      - name: Build documentation
+        run: |
+          cd docs
+          sphinx-build -b html source _build/html
+      - name: Deploy docs
+        if: ${{ github.event_name == 'push' }}
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: docs/_build/html

.github/ISSUE_TEMPLATE/feature-or-enhancement-request.md

@@ -0,0 +1,26 @@
+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
+    steps:
+      - uses: actions/checkout@v5
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[test]
+      - name: Run tests
+        run: pytest -m "not slow" -n auto

.github/pull_request_template.md

@@ -33,4 +33,10 @@ GRF_Plots/*
 tests/regression_tests/.outputs/*
 docs/doctrees
 docs/html/*
-docs/index.html
+docs/index.html
+
+# Coverage reports
+.coverage
+coverage.xml
+htmlcov/
+*.cover

.github/workflows/docs.yml

@@ -0,0 +1,21 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v6.0.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-added-large-files
+    - id: check-json
+    - id: check-toml
+    - id: check-merge-conflict
+    - id: debug-statements
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.14.10
+  hooks:
+    # Run the linter.
+    - id: ruff-check
+      args: [--fix]
+    # Run the formatter.
+    - id: ruff-format

.github/workflows/test.yml

@@ -0,0 +1,25 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [2.3.0] - YYYY-MM-DD
+
+### Added
+- Initial changelog entry
+- Modern Python package tooling improvements
+- Ruff configuration for consistent code formatting and linting
+- Type checking with mypy
+- Test coverage reporting
+- Enhanced CI/CD workflows with linting and type checking
+- Development dependencies section in pyproject.toml
+- Pre-commit hooks with comprehensive code quality checks
+- Dependabot configuration for automated dependency updates
+- Improved test fixtures using proper temporary file patterns
+
+[Unreleased]: https://github.com/bas-amop/MeshiPhi/compare/v2.3.0...HEAD
+[2.3.0]: https://github.com/bas-amop/MeshiPhi/releases/tag/v2.3.0

.gitignore

@@ -0,0 +1,33 @@
+cff-version: 1.2.0
+title: "MeshiPhi: Earth's digital twin mapped on a non-uniform mesh"
+authors:
+  - family-names: Smith
+    given-names: Jonathan D.
+  - family-names: Hall
+    given-names: Samuel
+  - family-names: Coombs
+    given-names: George
+  - family-names: Byrne
+    given-names: James
+  - family-names: Thorne
+    given-names: Michael A. S.
+  - family-names: Brearley
+    given-names: J. Alexander
+  - family-names: Long
+    given-names: Derek
+  - family-names: Meredith
+    given-names: Michael
+  - family-names: Wyld
+    given-names: David
+  - family-names: Zwagerman
+    given-names: Thomas
+  - family-names: Fox
+    given-names: Maria
+version: "2.3.0"
+doi: 10.48550/arXiv.2209.02389
+url: https://github.com/bas-amop/MeshiPhi
+repository-code: https://github.com/bas-amop/MeshiPhi
+date-released: 2022-09-06
+license: MIT
+message: "If you use this software, please cite our arXiv paper."
+citation: "Jonathan D. Smith, Samuel Hall, George Coombs, James Byrne, Michael A. S. Thorne,  J. Alexander Brearley, Derek Long, Michael Meredith, Maria Fox,  (2022), Autonomous Passage Planning for a Polar Vessel, arXiv, https://arxiv.org/abs/2209.02389"