Convert to cookiecutter template

.editorconfig

@@ -0,0 +1 @@
+{{ cookiecutter.project_slug }}/.editorconfig

.markdownlint.yaml

@@ -0,0 +1 @@
+{{ cookiecutter.project_slug }}/.markdownlint.yaml

.pre-commit-config.yaml

@@ -3,7 +3,6 @@ repos:
     rev: v4.6.0
     hooks:
       - id: check-merge-conflict
-      - id: debug-statements
       - id: trailing-whitespace
       - id: end-of-file-fixer
   - repo: https://github.com/python-jsonschema/check-jsonschema
@@ -17,16 +16,6 @@ repos:
         # Prettier supports many other file formats (e.g., JavaScript, HTML; see
         # https://prettier.io for list). Add other types here.
         types_or: [yaml, json]
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.4.4"
-    hooks:
-      - id: ruff
-        args: [--fix, --exit-non-zero-on-fix]
-      - id: ruff-format
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.10.0"
-    hooks:
-      - id: mypy
   - repo: https://github.com/igorshubovych/markdownlint-cli
     rev: v0.40.0
     hooks:

.vscode

@@ -0,0 +1 @@
+{{ cookiecutter.project_slug }}/.vscode

cookiecutter.json

@@ -0,0 +1,8 @@
+{
+    "project_name": "My Project",
+    "project_slug": "{{ cookiecutter.project_name.lower().replace(' ', '_') }}",
+    "project_description": "",
+    "author": "Jane Doe",
+    "author_email": "jane_doe@imperial.ac.uk",
+    "_copy_without_render": [".github"]
+}

{{ cookiecutter.project_slug }}/.editorconfig

@@ -0,0 +1,21 @@
+root = true
+
+[*]
+charset = utf-8
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_style = space
+indent_size = 4
+max_line_length = 88
+
+[*.md]
+indent_size = 2
+
+[*.yaml]
+indent_size = 2
+
+[*.yml]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

{{ cookiecutter.project_slug }}/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,26 @@
+# Description
+
+_Please include a summary of the change and which issue is fixed (if any). Please also
+include relevant motivation and context. List any dependencies that are required for
+this change._
+
+Fixes # (issue)
+
+## Type of change
+
+- [ ] Documentation (non-breaking change that adds or improves the documentation)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Optimization (non-breaking, back-end change that speeds up the code)
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] Breaking change (whatever its nature)
+
+## Key checklist
+
+- [ ] All tests pass (eg. `python -m pytest`)
+- [ ] The documentation builds and looks OK (eg. `python -m sphinx -b html docs docs/build`)
+- [ ] Pre-commit hooks run successfully (eg. `pre-commit run --all-files`)
+
+## Further checks
+
+- [ ] Code is commented, particularly in hard-to-understand areas
+- [ ] Tests added or an issue has been opened to tackle that in the future. (Indicate issue here: # (issue))

{{ cookiecutter.project_slug }}/.github/dependabot.yml

@@ -0,0 +1,15 @@
+# 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"

{{ cookiecutter.project_slug }}/.github/workflows/check-links.yml

@@ -0,0 +1,14 @@
+name: Check links in Markdown files
+on:
+  schedule:
+    - cron: "0 0 * * 1" # midnight every Monday
+
+jobs:
+  check-links:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: gaurav-nelson/github-action-markdown-link-check@v1
+        with:
+          use-quiet-mode: "yes"
+          use-verbose-mode: "yes"

{{ cookiecutter.project_slug }}/.github/workflows/ci.yml

@@ -0,0 +1,47 @@
+name: Test and build
+
+on: [push, pull_request, workflow_call]
+
+jobs:
+  qa:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pre-commit/action@v3.0.1
+
+  check-links:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: gaurav-nelson/github-action-markdown-link-check@v1
+        name: Check links in markdown files
+        with:
+          use-quiet-mode: "yes"
+          use-verbose-mode: "yes"
+
+  test:
+    needs: qa
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [windows-latest, ubuntu-latest, macos-latest]
+        python-version: ["3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        uses: abatilo/actions-poetry@v3.0.0
+        with:
+          poetry-version: 1.2.2
+
+      - name: Install dependencies
+        run: poetry install
+
+      - name: Run tests
+        run: poetry run pytest

{{ cookiecutter.project_slug }}/.github/workflows/pre-commit_autoupdate.yml

@@ -0,0 +1,20 @@
+name: Pre-commit auto-update
+
+on:
+  schedule:
+    - cron: "0 0 * * 1" # midnight every Monday
+
+jobs:
+  auto-update:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - uses: browniebroke/pre-commit-autoupdate-action@main
+      - uses: peter-evans/create-pull-request@v6
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: update/pre-commit-hooks
+          title: Update pre-commit hooks
+          commit-message: "chore: update pre-commit hooks"
+          body: Update versions of pre-commit hooks to latest version.

{{ cookiecutter.project_slug }}/.github/workflows/publish.yml

@@ -0,0 +1,27 @@
+on: [release]
+
+jobs:
+  test:
+    uses: ./.github/workflows/ci.yml
+
+  # publish:
+  #   runs-on: ubuntu-latest
+  #   needs: test
+  #   # The following steps to build a Docker image and publish to the GitHub container registry on release. Alternatively, can replace with other publising steps (ie. publishing to PyPI, deploying documentation etc.)
+  #   steps:
+  #     - name: Login to GitHub Container Registry
+  #       uses: docker/login-action@v3
+  #       with:
+  #         registry: ghcr.io
+  #         username: ${{ github.actor }}
+  #         password: ${{ secrets.GITHUB_TOKEN }}
+  #     - name: Get image metadata
+  #       id: meta
+  #       uses: docker/metadata-action@v5
+  #       with:
+  #         images: ghcr.io/${{ github.repository }}
+  #     - name: Build and push Docker image
+  #       uses: docker/build-push-action@v5
+  #       with:
+  #         push: true
+  #         tags: ${{ steps.meta.outputs.tags }}

{{ cookiecutter.project_slug }}/.gitignore

@@ -0,0 +1,129 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

{{ cookiecutter.project_slug }}/.markdownlint.yaml

@@ -0,0 +1,3 @@
+---
+# Disable checks here
+MD013: false