Rewrite Visualisation

.github/workflows/deptry.yml

@@ -0,0 +1,27 @@
+name: Deptry Dependency Check
+
+on: [pull_request]
+
+jobs:
+  dependencies:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      # Setup the minimum required python distribution
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+      # Install deptry
+      - run: pip install deptry
+      # Remove testing related packages
+      - run: sed -e '/hypothesis*/d' -e '/pytest*/d' -i requirements.txt
+      # Install all other packages
+      - run: pip install -r requirements.txt
+      # Remove pyproject.toml so that deptry doesn't get confused
+      - run: rm pyproject.toml
+      # Remove the pytest modules because they are for testing only.
+      - run: sed -i -e '/pytest/d' -e '/hypothesis/d' -e '/diffimg/d' requirements.txt
+      # Install requirements
+      - run: pip install -r requirements.txt
+      # Run deptry to check that all dependencies are present.
+      - run: deptry .

.github/workflows/git-extension.yml

@@ -0,0 +1,18 @@
+name: Check requirements.txt git URLs are properly formatted
+
+on: pull_request
+
+permissions:
+  contents: read
+  pull-requests: write
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: sed -ri '/git\+/ { /\.git(@\w+)?$/! s/(@\w+)?$/.git\1/ }' requirements.txt
+      - uses: parkerbxyz/suggest-changes@v2
+        with:
+          comment: 'Please change the following dependencies for consistency.'
+          event: 'REQUEST_CHANGES'

.github/workflows/numpydoc.yml

@@ -0,0 +1,36 @@
+name: Numpydoc Lint
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  numpydoc-lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - uses: awalsh128/cache-apt-pkgs-action@latest
+        with:
+          packages: fd-find
+          version: 1.0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'  # Adjust version as needed
+
+      - name: Install dependencies
+        run: |
+          pip install numpydoc
+          sudo apt-get install
+
+      - name: Run Numpydoc Lint
+        run: |
+          fdfind . visualisation/ -E "__init__.py" -E ccldpy.py --extension py -x numpydoc lint

.github/workflows/ruff.yml

@@ -0,0 +1,8 @@
+name: Ruff
+on: [pull_request]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1

.github/workflows/wiki.yml

@@ -0,0 +1,16 @@
+# .github/workflows/deploy-wiki.yml
+name: deploy-wiki
+on:
+  push:
+    branches: "master"
+    paths: wiki/**
+  workflow_dispatch:
+jobs:
+  deploy-wiki:
+    permissions:
+      contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: perl -i -pe 's;(\[.*?\])\((?!https:\/\/)(.*?)\.md\);\1(\2);g' wiki/*.md
+      - uses: actions4gh/deploy-wiki@v1

.gitignore

@@ -1,18 +1,176 @@
-*.csv
-*.info
-*.srf
-*.ll
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
 
-*.pyc
-*.idea
-*.egg-info/
+### Python ###
+# 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/
+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
 
-# params_plot.py* will be generated by calling plot_station.py if no output dir is given to plot_station.py so needs to be ignored
-*params_plot.py*
+# 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/
-**/__pycache__
-**/sample1/output/
-**/.cache/
-**/.coverage
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python