Migrate user_guide from jules-lsm.github.io

.github/workflows/user-guide.yaml

@@ -0,0 +1,72 @@
+name: User Guide
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    types: [opened, reopened, synchronize]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    env:
+      PYTHON_VRSN: '3.13'
+      VENV_PATH: 'doc/.venv'
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Setup uv with Python ${{ env.PYTHON_VRSN }}
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ env.PYTHON_VRSN }}
+
+      - name: Cache uv venv
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.VENV_PATH }}
+          key: ${{ runner.os }}-uv-${{ env.PYTHON_VRSN }}-${{ hashFiles('pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-uv-${{ env.PYTHON_VRSN }}-
+
+      - name: Install dependencies
+        working-directory: ./doc
+        run: uv sync
+
+      - name: Lint Sphinx docs
+        working-directory: ./doc
+        run: uv run sphinx-lint source
+
+      - name: Build HTML docs
+        working-directory: ./doc
+        run: uv run make clean html
+
+      - name: Minimize uv cache
+        run: uv cache prune --ci
+
+      # -- Deploy to GitHub Pages only on push to upstream main
+      - name: Setup GitHub Pages
+        if: ${{ github.ref_name == 'main' && (github.event_name == 'push' || github.event_name == 'merge_group') }}
+        uses: actions/configure-pages@v5
+
+      - name: Upload artifact to GitHub Pages
+        if: ${{ github.ref_name == 'main' && (github.event_name == 'push' || github.event_name == 'merge_group') }}
+        uses: actions/upload-pages-artifact@v4
+        with:
+          name: github-pages
+          path: doc/build/html
+          retention-days: 1
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        if: ${{ github.ref_name == 'main' && (github.event_name == 'push' || github.event_name == 'merge_group') }}
+        uses: actions/deploy-pages@v4

.gitignore

@@ -0,0 +1,28 @@
+*~
+__pycache__/
+results/*.png
+results/*.txt
+processed_data/*.dat
+.*.sw?
+
+# ignore build output
+*build/
+*_build/
+user_guide/doc/_build
+user_guide/doc/build
+
+# ignore VS Code files
+/.idea
+
+# ignore envs
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# UV
+*uv.lock
+.python-version

README.md

@@ -0,0 +1,4 @@
+# JULES - Joint UK Land Environment Simulator
+
+The Joint UK Land Environment Simulator (JULES) is a computer model that
+simulates many soil and vegetation processes.

doc/Makefile

@@ -0,0 +1,28 @@
+# 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
+
+REPO := $(notdir $(shell git rev-parse --show-toplevel))
+BRANCH := $(shell git rev-parse --abbrev-ref HEAD)
+DEPLOYDIR  = $(HOME)/public_html
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(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) $(O)
+
+deploy:
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(DEPLOYDIR)/$(REPO)/$(BRANCH)" $(SPHINXOPTS) $(O)
+

doc/README.md

@@ -0,0 +1,29 @@
+# Building the JULES User Guide
+
+This README describes how to build the JULES User Guide.
+
+For first time users, please create a virtual environment to build the docs.
+
+From the `jules/doc` folder of the repository run:
+
+```sh
+conda env create -f environment.yml
+```
+
+Activate the environment:
+
+```sh
+conda activate jules-user-guide
+```
+
+Build the documentation:
+
+```sh
+make clean html
+```
+
+View the documentation:
+
+```sh
+firefox build/html/index.html
+```

doc/environment.yaml

@@ -0,0 +1,11 @@
+name: jules-user-guide
+
+channels:
+  - conda-forge
+
+dependencies:
+  - python=3.13.2
+  - doc8>=2.0.0
+  - sphinx-lint==1.0.1
+  - sphinx==8.2.3
+

doc/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
+
+if "%1" == "" goto help
+
+%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
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/pyproject.toml

@@ -0,0 +1,11 @@
+[project]
+name = "jules"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.13"
+dependencies = [
+    "doc8>=2.0.0",
+    "sphinx==8.2.3",
+    "sphinx-lint==1.0.1",
+]