create documentation

.github/workflows/deploy-docs.yml

@@ -0,0 +1,68 @@
+# (C) Crown Copyright 2025, Met Office.
+# The LICENSE file contains full licensing details.
+name: Build and deploy the documentation
+
+on:
+  # Runs on pushes targeting the default branch.
+  push:
+    branches: ["profsea-climate"]
+
+  # Allows you to run this workflow manually from the Actions tab.
+  workflow_dispatch:
+
+# Use a login shell so the Conda environment is activated.
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages.
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment,
+# skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs
+# as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Setup GitHub Pages
+        uses: actions/configure-pages@v6
+
+      - uses: mamba-org/setup-micromamba@v3
+        with:
+          environment-file: environment.yml
+          environment-name: profsea-climate-docs
+          cache-environment: true
+          cache-environment-key: env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('environment.yml') }}
+
+      - name: Build with Sphinx
+        run:  make --directory=docs html
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v4
+        with:
+          path: docs/build/html
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v5

.gitignore

@@ -2,4 +2,6 @@
 *__pycache__*
 profsea.egg-info
 data/
+# Ignore the documentation build directory
+docs/build
 *.DS_Store

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/source/api_reference.rst

@@ -0,0 +1,25 @@
+API Reference
+=============
+
+This page exposes selected Python API docs generated from in-code docstrings.
+
+Spatial Projections Module
+--------------------------
+
+.. automodule:: profsea.spatial_projections
+   :no-members:
+
+calc_future_sea_level
+~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: profsea.spatial_projections.calc_future_sea_level
+
+calculate_global_components
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: profsea.spatial_projections.calculate_global_components
+
+calculate_sl_components
+~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: profsea.spatial_projections.calculate_sl_components

docs/source/conf.py

@@ -0,0 +1,72 @@
+# 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
+
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'profsea-climate'
+copyright = '2026, MetOffice'
+author = 'isabellaascione'
+release = '1.0.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+]
+
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = True
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
+
+autodoc_mock_imports = [
+    "dask",
+    "matplotlib",
+    "netCDF4",
+    "numpy",
+    "pandas",
+    "profsea.config",
+    "profsea.directories",
+    "profsea.emulator",
+    "profsea.plotting_libraries",
+    "profsea.slr_pkg",
+    "profsea.utils",
+    "rich",
+    "scipy",
+    "xarray",
+]
+
+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 = 'pydata_sphinx_theme'
+html_theme_options = {
+    'show_nav_level': 2,
+    'secondary_sidebar_items': [],
+}
+html_sidebars = {
+    "**": ["search-field", "sidebar-nav-bs", "page-toc"],
+}
+html_static_path = ['_static']

docs/source/development_guidelines.rst

@@ -0,0 +1,63 @@
+.. _development_guidelines:
+
+Development Guidelines
+======================
+
+This is the Development Guidelines page.
+
+.. _open-an-issue:
+
+Open an Issue
+-------------
+Before forking the repository, open an issue in the main repository to describe the changes you plan to make. This helps maintainers track contributions and provide feedback early.
+
+.. _fork-the-repository:
+
+Fork the Repository
+-------------------
+First, create a fork of the repository in your GitHub account:
+
+1. Go to the repository page on GitHub.
+2. Click the **Fork** button in the top-right corner.
+3. Select your GitHub account as the destination for the fork.
+
+.. _clone-your-fork:
+
+Clone Your Fork
+---------------
+Clone your forked repository and switch to the `profsea-climate` branch:
+
+.. code-block:: bash
+
+   git clone git@github.com:<your-username>/ProFSea-tool.git
+   cd ProFSea-tool
+   git checkout profsea-climate
+
+Replace ``<your-username>`` with your GitHub username.
+
+.. _commit-changes-to-your-fork:
+
+Commit Changes to Your Fork
+---------------------------
+Once you are satisfied with your changes, commit and push them to your fork:
+
+.. code-block:: bash
+
+   git add .
+   git commit -m "Adding feature: <brief description of changes>"
+   git push origin profsea-climate
+
+Replace ``<brief description of changes>`` with a short summary of your updates.
+
+.. _create-a-pull-request:
+
+Create a Pull Request
+---------------------
+To contribute your changes to the main repository:
+
+1. Go to your forked repository on GitHub.
+2. Click the **Pull Request** button.
+3. Select the ``profsea-climate`` branch of the main repository as the base branch.
+4. Select the ``profsea-climate`` branch of your fork as the compare branch.
+5. Add a title and description for your pull request.
+6. Click **Create Pull Request**.

docs/source/documentation.rst

@@ -0,0 +1,82 @@
+How to update the documentation
+========================================
+
+This is the page describing how to update the documentation.
+
+If you want to update the documentation, follow these steps to ensure that your changes are tested locally before contributing:
+
+1. Initial Steps
+-----------------------------------
+First of all you need to open an issue, fork and clone the repository. For detailed instructions, refer to the following sections in the :ref:`Development Guidelines <development_guidelines>` page:
+
+- :ref:`Open an Issue <open-an-issue>`
+- :ref:`Fork the Repository <fork-the-repository>`
+- :ref:`Clone Your Fork <clone-your-fork>`
+
+2. Set Up the Environment
+-------------------------
+Ensure you have the required dependencies installed to build the documentation.
+
+2.1 Create a Conda Environment
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+If you are using Conda, create the environment from the ``environment.yml`` file:
+
+.. code-block:: bash
+
+   conda env create -f environment.yml
+   conda activate profsea-climate-docs
+
+2.2 Install Dependencies with Pip (Optional)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+If you are not using Conda, install the dependencies with ``pip``:
+
+.. code-block:: bash
+
+   pip install sphinx pydata-sphinx-theme
+
+3. Make Changes to the Documentation
+-------------------------------------
+Edit or add ``.rst`` files in the ``docs/source`` directory. For example:
+
+- Update ``index.rst`` to include new pages.
+- Modify existing ``.rst`` files to update content.
+- Add new ``.rst`` files for additional sections.
+
+4. Build the Documentation Locally
+-----------------------------------
+Before committing your changes, build the documentation locally to ensure there are no errors:
+
+.. code-block:: bash
+
+   cd docs
+   make html
+
+This will generate the HTML files in the ``docs/build/html`` directory. Open the ``index.html`` file in your browser to preview the changes:
+
+.. code-block:: bash
+
+   xdg-open build/html/index.html
+
+5. Test the Documentation
+--------------------------
+- Verify that all links work correctly.
+- Ensure the side menu and table of contents are updated.
+- Check for any warnings or errors in the terminal output during the build process.
+
+6. Commit Changes and Create a Pull Request
+---------------------------------------------
+Once you are satisfied with your changes, commit and push them to your fork. For detailed instructions,
+refer to the following sections in the :ref:`Development Guidelines <development_guidelines>` page:
+- :ref:`Commit Changes to Your Fork <commit-changes-to-your-fork>`
+- :ref:`Create a Pull Request <create-a-pull-request>`
+
+7. Verify Deployment
+---------------------
+After your pull request is merged, the GitHub Actions workflow will automatically build and deploy the updated documentation. Verify that the changes are live on GitHub Pages:
+
+1. Go to the **Actions** tab in the main repository.
+2. Check the logs for the ``deploy-docs.yml`` workflow to ensure it completed successfully.
+3. Visit the GitHub Pages URL to confirm the updates.
+
+Notes
+-----