Merge pull request #3 from scientificcomputing/finsberg/updates

Restructure repo and add workflow for reproducing results

.dockerignore

@@ -2,6 +2,7 @@
 data/*
 code/results/*
 code/figures/*
+_build
 
 
 ### Python ###

.github/workflows/build_docs.yml

@@ -1,6 +1,9 @@
-name: Github Pages
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
 
 on:
+  push:
+    branches: ["main"]
   pull_request:
     branches: ["main"]
 
@@ -16,22 +19,54 @@ jobs:
       PUBLISH_DIR: ./_build/html
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
           python-version: "3.10"
 
+      - 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 documentation as artifact
-        uses: actions/upload-artifact@v3
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v2
         with:
-          name: documentation
           path: ${{ env.PUBLISH_DIR }}
-          if-no-files-found: error
+
+  # Single deploy job since we're just deploying
+  deploy:
+    if: github.ref == 'refs/heads/main'
+    needs: build
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

.github/workflows/docker-image.yml

@@ -25,29 +25,29 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@v4
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: .
           push: true

.github/workflows/pre-commit.yml

@@ -0,0 +1,21 @@
+name: Pre-commit
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+
+
+jobs:
+  check-code:
+    runs-on: ubuntu-22.04
+    steps:
+      # This action sets the current path to the root of your github repo
+      - uses: actions/checkout@v4
+
+      - name: Install pre-commit
+        run: python3 -m pip install pre-commit
+
+      - name: Run hooks
+        run: pre-commit run --all

.github/workflows/reproduce_results.yml

@@ -0,0 +1,59 @@
+# 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
+    env:
+      # Directory that will be published on github pages
+      DATAPATH: ./artifacts/data/data.json
+      FIGDIR: ./artifacts/figures
+      RESULTDIR: ./artifacts/results
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - 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: Run pre-processing
+        run: python3 code/pre_processing.py --datapath=${{ env.DATAPATH }}
+
+      - name: Run simulation
+        run: python3 code/run_all.py --resultdir=${{ env.RESULTDIR }}
+
+      - name: Postprocess
+        run: python3 code/postprocess.py --resultdir=${{ env.RESULTDIR }} --datapath=${{ env.DATAPATH }} --figdir=${{ env.FIGDIR }}
+
+      - name: Upload artifact
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          path: ./artifacts
+          if-no-files-found: error

.gitignore

@@ -1,6 +1,8 @@
+_build
 code/results
-data/data.txt
+data/data.json
 code/figures
+.DS_Store
 # Created by https://www.toptal.com/developers/gitignore/api/python,visualstudiocode
 # Edit at https://www.toptal.com/developers/gitignore?templates=python,visualstudiocode
 

.pre-commit-config.yaml

@@ -1,41 +1,40 @@
 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
 
-  - 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

README.md

@@ -3,15 +3,15 @@
 
 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
 Provide the abstract of the paper
 
 ## Getting started
 
-We provide a pre-build Docker image which can be used to run the the code in this repository. First thing you need to do is in ensure that you have [docker installed](https://docs.docker.com/get-docker/).
+We provide a pre-build Docker image which can be used to run the the code in this repository. First thing you need to do is to ensure that you have [docker installed](https://docs.docker.com/get-docker/).
 
 To start an interactive docker container you can execute the following command
 

_config.yml

@@ -2,9 +2,10 @@
 # Learn more at https://jupyterbook.org/customize/config.html
 
 title: Example paper
-author: Henrik Finsberg
+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
@@ -30,13 +31,24 @@ parse:
     - dollarmath
     - linkify
 
+
 sphinx:
   config:
     bibtex_bibfiles: ["docs/refs.bib"]
+    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/*"]

_toc.yml

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