Merge pull request #7 from scientificcomputing/finsberg/updates

A bunch of updates

Author: finsberg

.flake8

@@ -23,27 +23,44 @@ jobs:
   build:
     runs-on: ubuntu-22.04
     container:
-      image: finsberg/fenics-gmsh:latest
+      image: ghcr.io/scientificcomputing/fenics-gmsh:2023-08-16
 
     env:
       # Directory that will be published on github pages
       PUBLISH_DIR: ./_build/html
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install dependencies
-        run: python3 -m pip install -r requirements.txt
+        run: python3 -m pip install -r requirements-docs.txt
+
+      - name: Build docs
+        run: jupyter book build -W .
+
+
+      - name: Cache
+        id: cache
+        uses: actions/cache@v3
+        with:
+          path: |
+            ~/.cache/pip
+            ~/_build
+          key: cache_v1
+          restore-keys: |
+            cache_v1
+
+      - name: Install dependencies
+        run: python3 -m pip install -r requirements-docs.txt
 
       - name: Build docs
         run: jupyter book build .
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v2
         with:
           path: ${{ env.PUBLISH_DIR }}
 
-
   # Single deploy job since we're just deploying
   deploy:
     if: github.ref == 'refs/heads/main'
@@ -53,13 +70,15 @@ jobs:
       url: ${{ steps.deployment.outputs.page_url }}
 
     runs-on: ubuntu-latest
+
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Pages
-        uses: actions/configure-pages@v2
+        uses: actions/configure-pages@v3
+
 
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v1
+        uses: actions/deploy-pages@v2

.github/workflows/build_docs.yml

@@ -0,0 +1,56 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Reproduce results
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+
+    # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+  workflow_call:
+
+
+jobs:
+  run:
+    runs-on: ubuntu-22.04
+    container:
+      image: ghcr.io/scientificcomputing/fenics-gmsh:2023-08-16
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Cache
+        id: cache
+        uses: actions/cache@v3
+        with:
+          path: |
+            ~/.cache/pip
+          key: cache_v1
+          restore-keys: |
+            cache_v1
+
+      - name: Install dependencies
+        run: python3 -m pip install -r requirements.txt
+
+      - name: Download data
+        run: cd data && bash download_data.sh && cd ..
+
+      - name: Run pre-processing
+        run: cd code && python3 pre_processing.py && cd ..
+
+      - name: Run simulation
+        run: cd code && python3 run_fiber_generation.py && cd ..
+
+      - name: Postprocess
+        run: cd code && python3 postprocess.py && cd ..
+
+      - name: Upload artifact
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          path: |
+            ./data/mesh
+            ./code/results
+          if-no-files-found: error

.github/workflows/reproduce_results.yml

@@ -1,10 +1,9 @@
-data/data.tar
-data/mesh
-data/._mesh
-data/*.json
-data/*.h5
-code/results/*.h5
-code/results/*.xdmf
+data.tar
+mesh
+._mesh
+*.json
+*.h5
+*.xdmf
 
 # Created by https://www.toptal.com/developers/gitignore/api/python,visualstudiocode
 # Edit at https://www.toptal.com/developers/gitignore?templates=python,visualstudiocode

.gitignore

@@ -1,41 +1,42 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.5.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-docstring-first
       - id: debug-statements
       - id: requirements-txt-fixer
+      - id: check-added-large-files
+      - id: check-toml
 
-  - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.8.3
+  - repo: https://github.com/asottile/add-trailing-comma
+    rev: v3.1.0
     hooks:
-      - id: reorder-python-imports
+      - id: add-trailing-comma
 
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 23.10.1
     hooks:
       - id: black
 
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.0.0
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    # Ruff version.
+    rev: 'v0.1.4'
     hooks:
-      - id: flake8
+      - id: ruff
 
-  - repo: https://github.com/asottile/add-trailing-comma
-    rev: v2.3.0
-    hooks:
-      - id: add-trailing-comma
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.982
+    rev: v1.6.1
     hooks:
       - id: mypy
+        additional_dependencies:
+          - types-requests
 
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.1.0
+  - repo: https://github.com/streetsidesoftware/cspell-cli
+    rev: v7.3.2
     hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
+      - id: cspell
+        files: docs/(.+).md|README.md|code/demo.py

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 
 This repository contains supplementary code for the paper
 > Finsberg, H., Dokken, J. 2022.
-> Title of paper, Journal of blabla, volume, page, url
+> Title of paper, Journal of ..., volume, page, url
 
 
 ## Abstract

README.md

@@ -1,10 +1,11 @@
 # Book settings
 # Learn more at https://jupyterbook.org/customize/config.html
 
-title: Example FEniCS paper
-author: Henrik Finsberg
+title: Example paper FEniCS
+author: Henrik Finsberg and Jørgen Dokken
 logo: "docs/logo.png"
-copyright: "2022"
+copyright: "2023"
+only_build_toc_files: true
 
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
@@ -14,12 +15,11 @@ execute:
 # Information about where the book exists on the web
 repository:
   url: https://github.com/scientificcomputing/example-paper-fenics # Online location of your book
-  branch: main
+  branch: main  # Which branch of the repository should be used when creating links (optional)
 
 launch_buttons:
   notebook_interface: "jupyterlab" # The interface interactive links will activate ["classic", "jupyterlab"]
   binderhub_url: "https://mybinder.org"
-  thebe: true
 
 html:
   use_issues_button: true
@@ -31,13 +31,25 @@ parse:
     - dollarmath
     - linkify
 
+
 sphinx:
   config:
     bibtex_bibfiles: ["docs/refs.bib"]
     suppress_warnings: ["bibtex.duplicate_citation"] # If the same paper is cited in multiple files
+    nb_execution_show_tb: True
+    html_theme_options:
+      navigation_with_keys: false
+    html_last_updated_fmt: "%b %d, %Y"
+    nb_custom_formats:  # https://jupyterbook.org/en/stable/file-types/jupytext.html#file-types-custom
+        .py:
+            - jupytext.reads
+            - fmt: py
 
   extra_extensions:
   - 'sphinx.ext.autodoc'
   - 'sphinx.ext.napoleon'
   - 'sphinx.ext.viewcode'
   - "sphinxcontrib.bibtex"
+
+
+exclude_patterns: [".pytest_cache/*", ".github/*"]

_config.yml

@@ -1,5 +1,5 @@
 format: jb-book
-root: index
+root: README
 
 chapters:
   - file: docs/abstract