Restructure files

Author: finsberg

.dockerignore

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

.flake8

@@ -1,18 +1,35 @@
-name: Github Pages
+# 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:
-      - main
+    - "**"
+
+  # 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:
-  deploy:
+  build:
     runs-on: ubuntu-22.04
     env:
       # Directory that will be published on github pages
       PUBLISH_DIR: ./docs/_build/html
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v4
@@ -23,19 +40,31 @@ jobs:
         run: python3 -m pip install -r requirements-docs.txt
 
       - name: Build docs
-        run: jupyter book build docs
+        run: jupyter book build .
 
-      - name: Copy requirements.txt into gh-pages
-        run: cp requirements.txt ${PUBLISH_DIR}/
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v2
+        with:
+          path: ${{ env.PUBLISH_DIR }}
 
-      - name: Copy code and data into gh-pages
-        run: |
-          cp -r code ${PUBLISH_DIR}/
-          cp -r data ${PUBLISH_DIR}/
-          cp runtime.txt ${PUBLISH_DIR}/
+  # 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 }}
 
-      - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ${{ env.PUBLISH_DIR }}
+    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/build_docs.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@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: .
           push: true

.github/workflows/docker-image.yml

@@ -0,0 +1,17 @@
+name: Pre-commit
+
+on: [push]
+
+
+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/pre-commit.yml

@@ -1,3 +1,4 @@
+_build
 code/results
 data/data.txt
 code/figures

.gitignore

@@ -1,41 +1,34 @@
 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
-    hooks:
-      - id: pyupgrade
-        args: [--py38-plus]

.pre-commit-config.yaml

@@ -2,9 +2,10 @@
 # Learn more at https://jupyterbook.org/customize/config.html
 
 title: Example paper
-author: Henrik Finsberg
-logo: "logo.png"
-copyright: "2022"
+author: Henrik Finsberg and Jørgen Dokken
+logo: "docs/logo.png"
+copyright: "2023"
+only_build_toc_files: true
 
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
@@ -31,12 +32,24 @@ parse:
     - dollarmath
     - linkify
 
+
 sphinx:
   config:
-    bibtex_bibfiles: ["refs.bib"]
+    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/*"]

docs/_config.yml renamed to _config.yml

@@ -0,0 +1,8 @@
+format: jb-book
+root: README
+
+chapters:
+  - file: docs/abstract
+  - file: docs/reproducing
+  - file: code/demo
+  - file: docs/citation

_toc.yml

@@ -0,0 +1,55 @@
+# ---
+# jupyter:
+#   jupytext:
+#     text_representation:
+#       extension: .py
+#       format_name: light
+#       format_version: '1.5'
+#       jupytext_version: 1.15.2
+#   kernelspec:
+#     display_name: Python 3.10.6 64-bit ('3.10.6')
+#     language: python
+#     name: python3
+# ---
+# # Demo
+#
+# This notebook contains a simple demo on how to work with the code.
+import sys
+
+sys.path.insert(0, "../code")
+
+# +
+import numpy as np
+from scipy.integrate import solve_ivp
+import ap_features as apf
+
+from run_simulation import fitzhugh_nagumo
+
+# +
+a = -0.22
+b = 1.17
+time = np.arange(0, 1000.0, 1.0)
+
+res = solve_ivp(
+    fitzhugh_nagumo,
+    [0, 1000.0],
+    [0, 0],
+    args=(a, b),
+    t_eval=time,
+)
+
+v_all = apf.Beats(y=res.y[0, :], t=time)
+w_all = apf.Beats(y=res.y[1, :], t=time)
+# -
+
+v_all.plot()
+
+w_all.plot()
+
+v = v_all.average_beat()
+print(v.apd(50))
+v.plot()
+
+w = w_all.average_beat()
+print(w.apd(50))
+w.plot()