Integrate Raphaels refactor, package structure, and documentation

.github/workflows/docs-pages.yml

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+name: Build & Deploy Docs (GitHub Pages)
+
+on:
+  push:
+    branches: [ "main" ]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .
+          pip install sphinx sphinx-rtd-theme
+
+      - name: Build Sphinx HTML
+        run: |
+          sphinx-build -b html docs docs/_build/html
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+    environment:
+      name: github-pages
+    steps:
+      - name: Deploy to GitHub Pages
+        uses: actions/deploy-pages@v4

.github/workflows/docs.yml

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+name: Build and Deploy Docs
+
+on:
+  push:
+    branches:
+      - main  # Or 'master', depending on your default branch name
+
+permissions:
+  contents: write
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+
+      - name: Install Pandoc # Required for nbsphinx
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc libgeos-dev libproj-dev proj-data
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install sphinx sphinx-rtd-theme nbsphinx
+          pip install .  # Installs your 'moaap' package so Sphinx can import it
+
+      - name: Build HTML
+        run: |
+          cd docs
+          make html
+
+      - name: Create .nojekyll to disable Jekyll processing
+        run: touch docs/build/html/.nojekyll
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/build/html

.gitignore

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+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Linker files
+*.ilk
+
+# Debugger Files
+*.pdb
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# debug information files
+*.dwo
+
+__pycache__/
+*.pyc
+
+20210701-04_MOAAP-Input_24h.nc
+moaap_output/
+images/
+outputs/synthetic_cells.nc
+data_cache/*
+
+Tracking_Functions_old.py
+
+docs/build/
+watershed_history*
+tracks/
+run_3d.py
+generate_shim.py
+logs/
+.vscode
+moaap.egg-info

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../'))  # Points to the project root
+
+project = 'MOAAP'
+copyright = '2025, Andreas F. Prein, Raphael Graf'
+author = 'Andreas F. Prein, Raphael Graf'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',  # Essential for specific docstring format!
+    'sphinx.ext.viewcode',  # adds links to source code
+    'nbsphinx',            # to include Jupyter Notebooks
+]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
+
+napoleon_custom_sections = [
+    ('Precipitation objects', 'params_style'),
+    ('Moisture streams', 'params_style'),
+    ('Cyclones & anticyclones', 'params_style'),
+    ('Frontal zones', 'params_style'),
+    ('Cloud tracking', 'params_style'),
+    ('Atmospheric rivers (AR)', 'params_style'),
+    ('Tropical cyclone detection', 'params_style'),
+    ('Mesoscale convective systems (MCS)', 'params_style'),
+    ('Jet streams & tropical waves', 'params_style'),
+    ('500 hPa cyclones/anticyclones', 'params_style'),
+    ('Equatorial waves', 'params_style'),
+]
+
+nbsphinx_execute = 'never' # Do not execute notebooks during doc build

docs/source/index.rst

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+.. MOAAP documentation master file, created by
+   sphinx-quickstart on Wed Dec 10 11:20:05 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to MOAAP's documentation!
+=================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+   tutorial
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

docs/source/modules.rst

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+MOAAP Reference
+===============
+
+Main Interface
+--------------
+
+.. automodule:: moaap.main
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: moaap.config
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Utils
+-----
+.. automodule:: moaap.utils.constants
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: moaap.utils.data_proc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. automodule:: moaap.utils.grid
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: moaap.utils.object_props
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. automodule:: moaap.utils.profiling
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. automodule:: moaap.utils.segmentation
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Trackers
+--------
+
+.. automodule:: moaap.trackers.atmospheric_rivers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: moaap.trackers.clouds
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: moaap.trackers.cyclones
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: moaap.trackers.fronts
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: moaap.trackers.jets
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: moaap.trackers.tropical_cyclones
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: moaap.trackers.waves
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tutorial.ipynb

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+../../tutorial.ipynb

moaap/__init__.py

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+# moaap/__init__.py
+
+from .main import moaap
+
+# Optional: Add version info
+__version__ = "1.0.0"