Add structured Sphinx-based documentation scaffold (issue #61)

.github/workflows/docs.yml

@@ -0,0 +1,22 @@
+name: Docs
+
+on: [push, pull_request]
+
+jobs:
+    build-docs:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+
+            - uses: actions/setup-python@v5
+              with:
+                python-version: "3.12"
+
+            - name: Install uv
+              uses: astral-sh/setup-uv@v5
+
+            - name: Install docs dependencies
+              run: uv sync --group docs
+
+            - name: Build docs
+              run: uv run sphinx-build -b html docs/source docs/build/html

.gitignore

@@ -88,3 +88,6 @@ __MACOSX
 # exclude pdm.lock file so that both cpu and gpu versions of torch will be accepted by pdm
 pdm.lock
 tests/test_outputs/
+
+### Sphinx ###
+docs/build/

.readthedocs.yaml

@@ -0,0 +1,17 @@
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+
+sphinx:
+  configuration: docs/source/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+    - requirements: docs/requirements.txt

docs/Makefile

@@ -0,0 +1,20 @@
+# 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/requirements.txt

@@ -0,0 +1,3 @@
+sphinx>=7.0
+furo>=2024.1.29
+myst-parser>=3.0

docs/source/api.rst

@@ -0,0 +1,57 @@
+API Reference
+=============
+
+Core Components
+---------------
+
+Interaction Network
+~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: neural_lam.interaction_net
+
+Metrics
+~~~~~~~
+
+.. automodule:: neural_lam.metrics
+
+Utilities
+~~~~~~~~~
+
+.. automodule:: neural_lam.utils
+
+Visualization
+~~~~~~~~~~~~~
+
+.. automodule:: neural_lam.vis
+
+
+Model Architecture
+------------------
+
+Models
+~~~~~~
+
+.. automodule:: neural_lam.models
+
+
+Data Handling
+-------------
+
+Datastore
+~~~~~~~~~
+
+.. automodule:: neural_lam.datastore
+
+Weather Dataset
+~~~~~~~~~~~~~~~
+
+.. automodule:: neural_lam.weather_dataset
+
+
+Training
+--------
+
+Training Utilities
+~~~~~~~~~~~~~~~~~~
+
+.. automodule:: neural_lam.train_model

docs/source/conf.py

@@ -0,0 +1,84 @@
+# 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
+
+# Standard library
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../../"))
+
+# Mock heavy scientific and ML dependencies so documentation
+# can be built without requiring the full runtime environment.
+MOCK_MODULES = [
+    "torch",
+    "torch.nn",
+    "torch.optim",
+    "torch.utils",
+    "torch_geometric",
+    "pytorch_lightning",
+    "mlflow",
+    "numpy",
+    "scipy",
+    "pandas",
+    "xarray",
+    "netCDF4",
+    "zarr",
+    "matplotlib",
+    "matplotlib.pyplot",
+    "seaborn",
+    "tueplots",
+    "wandb",
+    "sklearn",
+    "tqdm",
+    "yaml",
+    "loguru",
+    "dataclass_wizard",
+    "cartopy",
+    "cartopy.crs",
+    "mllam_data_prep",
+    "dask",
+    "parse",
+]
+
+project = "Neural-LAM"
+copyright = "2026, MLLAM Contributors"
+author = "MLLAM Contributors"
+release = "0.0.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "myst_parser",
+]
+
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+autosummary_generate = True
+autodoc_preserve_defaults = True
+autodoc_mock_imports = MOCK_MODULES
+suppress_warnings = ["autodoc.import_object"]
+
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": True,
+    "show-inheritance": True,
+}
+
+templates_path = ["_templates"]
+exclude_patterns: list[str] = []
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "furo"
+html_static_path = ["_static"]

docs/source/index.rst

@@ -0,0 +1,21 @@
+Neural-LAM Documentation
+========================
+
+Neural-LAM is a graph-based, research-oriented framework for
+Limited Area Model (LAM) data-driven weather forecasting.
+It combines graph neural network architectures with structured
+meteorological datasets to enable scalable regional forecasting
+experiments.
+
+For project details and research context, see the
+`Neural-LAM GitHub repository <https://github.com/mllam/neural-lam>`_.
+
+Contents
+--------
+
+.. toctree::
+   :maxdepth: 2
+
+   introduction
+   installation
+   api

docs/source/installation.rst

@@ -0,0 +1,54 @@
+Installation
+============
+
+Install from PyPI
+------------------
+
+For standard use:
+
+.. code-block:: bash
+
+   pip install neural_lam
+
+Basic Installation (Development)
+--------------------------------
+
+Neural-LAM uses `uv <https://github.com/astral-sh/uv>`_ for dependency management.
+
+Clone the repository:
+
+.. code-block:: bash
+
+   git clone https://github.com/mllam/neural-lam.git
+   cd neural-lam
+
+Install dependencies:
+
+.. code-block:: bash
+
+   uv sync
+
+Note
+----
+
+Neural-LAM depends on several scientific and machine learning
+libraries (e.g., PyTorch, Cartopy, Dask). Depending on your use
+case (training, visualization, data preparation), additional
+dependencies may be required.
+
+Refer to ``pyproject.toml`` for the full dependency list.
+
+Building the Documentation
+--------------------------
+
+To build the documentation locally, ensure the required documentation tools are installed (e.g., Sphinx, Furo, myst-parser).
+
+Then run:
+
+.. code-block:: bash
+
+   sphinx-build -b html docs/source docs/build
+
+The generated HTML files will be available in:
+
+``docs/build/html/``

docs/source/introduction.rst

@@ -0,0 +1,20 @@
+Introduction
+============
+
+Neural-LAM is a research framework designed for data-driven
+weather forecasting in Limited Area Models (LAMs).
+
+The project leverages graph neural networks to represent
+structured spatial relationships between meteorological grid
+points. This allows flexible modeling of regional weather systems
+while maintaining scalability.
+
+The repository includes:
+
+- Graph-based neural network architectures
+- Dataset abstractions for meteorological data
+- Training and evaluation utilities
+- Visualization tools for model diagnostics
+
+For full project background and research motivation,
+refer to the main README and associated publications.

pyproject.toml

@@ -41,6 +41,7 @@ requires-python = ">=3.10"
 
 [dependency-groups]
 dev = ["pre-commit>=3.8.0", "pytest>=8.3.2", "pooch>=1.8.2"]
+docs = ["sphinx>=7.0", "furo>=2024.1.29", "myst-parser>=3.0"]
 
 [tool.setuptools]
 py-modules = ["neural_lam"]