Merge pull request #54 from justinlaughlin/finsberg/jupyter-book

Use jupyterbook and github pages instead of pure sphinx and readthedocs

.github/workflows/build_docs.yml

@@ -0,0 +1,68 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches:
+    - "**"
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+
+  build:
+    runs-on: ubuntu-22.04
+    container: ghcr.io/scientificcomputing/fenics:2023-01-16
+    env:
+      DEB_PYTHON_INSTALL_LAYOUT: deb_system
+      PUBLISH_DIR: ./_build/html
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Install dependencies
+        run: python3 -m pip install --no-binary=h5py ".[docs,dev]"
+
+      - name: Build docs
+        run: jupyter book build .
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: ${{ env.PUBLISH_DIR }}
+
+  # Single deploy job since we're just deploying
+  deploy:
+    if: github.ref == 'refs/heads/development'
+    needs: build
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v2
+
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1

.github/workflows/test_fenics_stubs.yml

@@ -23,12 +23,13 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: "Install code"
-        run: python3 -m pip install --no-binary=h5py .[dev]
+        run: python3 -m pip install --no-binary=h5py .[dev] jupytext
 
       - name: Run example 1
         run: |
           cd examples/example1/
-          python3 example1_driver.py
+          jupytext example1.ipynb --to py
+          python3 example1.py
 
       # - name: Run tests
       #   run: |

.gitignore

@@ -1,3 +1,5 @@
+_build
+examples/example1/mesh/
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

_config.yml

@@ -0,0 +1,38 @@
+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: fenics-subs
+author: Justin Laughlin
+copyright: "2022"
+only_build_toc_files: true
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: cache
+  timeout: 3000
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/justinlaughlin/stubs # Online location of your book
+  branch: development
+
+
+html:
+  use_issues_button: true
+  use_repository_button: true
+
+parse:
+  myst_enable_extensions:
+    - amsmath
+    - dollarmath
+    - linkify
+
+sphinx:
+
+  extra_extensions:
+  - 'sphinx.ext.autodoc'
+  - 'sphinx.ext.napoleon'
+  - 'sphinx.ext.viewcode'
+  - 'sphinx.ext.autosummary'
+

_toc.yml

@@ -0,0 +1,15 @@
+format: jb-book
+root: docs/index
+
+parts:
+  - caption: Getting started
+    chapters:
+    - file: docs/install
+    - file: docs/math
+    - file: docs/faq
+  - caption: Demo
+    chapters:
+    - file: examples/example1/example1
+  - caption: API documentation
+    chapters:
+    - file: "docs/pystubs_verbose.rst"

docs/_pythonapi/stubs.common.rst

@@ -0,0 +1,65 @@
+stubs.common
+============
+
+.. automodule:: stubs.common
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      DemoCuboidsMesh
+      append_meshfunction_to_meshdomains
+      bmesh_to_parent
+      convert_xml_to_hdf5
+      cube_condition
+      data_path
+      empty_sbmodel
+      face_topology
+      find_steady_state
+      insert_dataframe_col
+      interp_limit_dy
+      json_to_ObjectContainer
+      mesh_vertex_to_dof
+      nan_to_none
+      np_smart_hstack
+      pint_quantity_to_unit
+      pint_unit_to_quantity
+      read_hdf5
+      read_sbmodel
+      round_to_n
+      sbmodel_from_locals
+      stubs_expressions
+      sub
+      submesh_dof_to_mesh_dof
+      submesh_dof_to_vertex
+      submesh_to_bmesh
+      sum_discrete_signals
+      write_mesh
+      write_sbmodel
+      zplane_condition
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      Stopwatch
+      ref
+
+
+
+
+
+
+
+
+

docs/_pythonapi/stubs.config.rst

@@ -0,0 +1,29 @@
+stubs.config
+============
+
+.. automodule:: stubs.config
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      Config
+
+
+
+
+
+
+
+
+

docs/_pythonapi/stubs.data_manipulation.rst

@@ -0,0 +1,31 @@
+stubs.data\_manipulation
+========================
+
+.. automodule:: stubs.data_manipulation
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      Data
+      PostProcessor
+      Probe
+
+
+
+
+
+
+
+
+

docs/_pythonapi/stubs.mesh.rst

@@ -0,0 +1,30 @@
+stubs.mesh
+==========
+
+.. automodule:: stubs.mesh
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      ChildMesh
+      ParentMesh
+
+
+
+
+
+
+
+
+

docs/_pythonapi/stubs.model.rst

@@ -0,0 +1,29 @@
+stubs.model
+===========
+
+.. automodule:: stubs.model
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      Model
+
+
+
+
+
+
+
+
+