Refactor (#3)

* Start code refactoring

* Update ruff version

* Add SVI

* Exclude LuxRep

* Add new line

* Use init_loc_fn

* Split notebooks

* Exclude LuxRep

* Update documentation

* Add docstrings

* Improve testing

- add pytest-cov
- improve test coverage

* Update project template

* Fix tests.yaml

* Update docstrings

* Bump version

.github/workflows/tests.yaml

@@ -0,0 +1,49 @@
+name: tests
+
+on:
+  push:
+    branches:
+      - "**"
+  pull_request:
+    types: [opened]
+    branches:
+      - "**"
+
+jobs:
+  unit-testing:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          uv venv
+          uv pip install nox
+      - name: Run tests
+        run: |
+          uv run --no-project nox --python ${{ matrix.python-version }}
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          uv venv
+          uv pip install nox
+      - name: Lint the code
+        run: uv run --no-project nox -e lint

.gitignore

@@ -0,0 +1,140 @@
+# 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/
+
+# poetry
+/poetry.toml
+/releases/*
+poetry/core/*
+
+# Mac OS X
+.DS_Store
+
+# ruff
+.ruff_cache/

.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+ci:
+  autoupdate_schedule: monthly
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: "^LuxRep"
+      - id: end-of-file-fixer
+        exclude_types: [json, binary]
+        exclude: "^LuxRep"
+      - id: mixed-line-ending
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.0
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.11.2"
+    hooks:
+      - id: mypy
+        exclude: |
+          (?x)(
+              LuxRep/
+          )