Add dependabot

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/build_docs.yml

@@ -10,40 +10,31 @@ on:
 
 jobs:
   build_docs:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     env:
-      PYTHON_VERSION: "3.10"
       PUBLISH_DIR: ./_build/html
 
     steps:
       # checkout the repository
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       # setup Python
-      - name: Install Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@v4
+      - name: Install Python
+        uses: actions/setup-python@v6
         with:
-          python-version: ${{ env.PYTHON_VERSION }}
+          python-version-file: ".python-version"
 
-      # preserve pip cache to speed up installation
-      - name: Cache pip
-        uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          # Look to see if there is a cache hit for the corresponding requirements file
-          key: ${{ runner.os }}-pip-${{ hashFiles('*requirements-docs.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-      - name: Install Python dependencies
-        run: |
-          python3 -m pip install --upgrade pip
-          python3 -m pip install -r requirements-docs.txt
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Install the project
+        run: uv sync --extra docs
 
       - name: Build docs
-        run: python3 -m jupyter book build .
+        run: uv run jupyter book build .
 
       - name: Upload artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v5
         with:
           name: documentation
           path: ${{ env.PUBLISH_DIR }}

.github/workflows/deploy_docs.yml

@@ -1,51 +1,41 @@
-name: Github Pages
+name: Publish documentation
 
 on:
   push:
-    branches: [main]  # Only run on push to main
+    branches: [main]
+  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-docs:
+
+  build:
     uses: ./.github/workflows/build_docs.yml
 
   deploy:
-    needs: [build-docs]
-
+    needs: build
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
 
     runs-on: ubuntu-latest
-    steps:
-      - name: Download docs artifact
-        # docs artifact is uploaded by build-docs job
-        uses: actions/download-artifact@v3
-        with:
-          name: documentation
-          path: "./public"
-
-      - name: Upload artifact
-        uses: actions/upload-pages-artifact@v2
-        with:
-          path: "./public"
 
+    steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup Pages
-        uses: actions/configure-pages@v3
+        uses: actions/configure-pages@v5
+
 
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v4

.github/workflows/pre-commit.yml

@@ -9,10 +9,13 @@ on:
 
 jobs:
   check-code:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
       # This action sets the current path to the root of your github repo
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
+
+      - name: Install Python
+        uses: actions/setup-python@v6
 
       - name: Install pre-commit
         run: python3 -m pip install pre-commit

.github/workflows/reproduce_results.yml

@@ -22,38 +22,32 @@ jobs:
       RESULTDIR: ./artifacts/results
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
-      - name: Setup Python
-        uses: actions/setup-python@v4
+    # setup Python
+      - name: Install Python
+        uses: actions/setup-python@v6
         with:
-          python-version: "3.10"
+          python-version-file: ".python-version"
 
-      - name: Cache
-        id: cache
-        uses: actions/cache@v3
-        with:
-          path: |
-            ~/.cache/pip
-          key: cache_v1
-          restore-keys: |
-            cache_v1
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
 
-      - name: Install dependencies
-        run: python3 -m pip install -r requirements.txt
+      - name: Install the project
+        run: uv sync
 
       - name: Run pre-processing
-        run: python3 code/pre_processing.py --datapath=${{ env.DATAPATH }}
+        run: uv run python3 code/pre_processing.py --datapath=${{ env.DATAPATH }}
 
       - name: Run simulation
-        run: python3 code/run_all.py --resultdir=${{ env.RESULTDIR }}
+        run: uv run python3 code/run_all.py --resultdir=${{ env.RESULTDIR }}
 
       - name: Postprocess
-        run: python3 code/postprocess.py --resultdir=${{ env.RESULTDIR }} --datapath=${{ env.DATAPATH }} --figdir=${{ env.FIGDIR }}
+        run: uv run python3 code/postprocess.py --resultdir=${{ env.RESULTDIR }} --datapath=${{ env.DATAPATH }} --figdir=${{ env.FIGDIR }}
 
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v5
         with:
           path: ./artifacts
           if-no-files-found: error

.python-version

@@ -0,0 +1 @@
+3.12

README.md

@@ -11,7 +11,19 @@ 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 to ensure that you have [docker installed](https://docs.docker.com/get-docker/).
+First install `uv`
+```bash
+curl -LsSf https://astral.sh/uv/install.sh | sh
+```
+Then create a virtual environment and install dependencies
+
+```bash
+uv venv
+source .venv/bin/activate
+uv sync --locked --all-extras --dev
+```
+
+We also 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

@@ -51,4 +51,4 @@ sphinx:
   - "sphinxcontrib.bibtex"
 
 
-exclude_patterns: [".pytest_cache/*", ".github/*"]
+exclude_patterns: [".pytest_cache/*", ".github/*", "venv/*", ".venv/*"]

cspell.json

@@ -12,7 +12,8 @@
         "nagumo",
         "postprocess",
         "scientificcomputing",
-        "zenodo"
+        "zenodo",
+        "venv"
     ],
     "ignoreWords": [],
     "import": []

pyproject.toml

@@ -5,6 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "my-paper"
 version = "1.2.0"
+requires-python = ">=3.10"
 dependencies = [
     "ap_features",
     "matplotlib",