Change to uv

Author: finsberg

.github/workflows/build_docs.yml

@@ -12,35 +12,26 @@ jobs:
   build_docs:
     runs-on: ubuntu-24.04
     env:
-      PYTHON_VERSION: "3.12"
       PUBLISH_DIR: ./_build/html
 
     steps:
       # checkout the repository
       - uses: actions/checkout@v5
 
       # setup Python
-      - name: Install Python ${{ env.PYTHON_VERSION }}
+      - 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@v4
-        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: |
-            ${{ runner.os }}-pip-${{ hashFiles('requirements-docs.txt') }}
-      - 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 --extras docs
 
       - name: Build docs
-        run: python3 -m jupyter book build .
+        run: uv run jupyter book build .
 
       - name: Upload artifact
         uses: actions/upload-artifact@v5

.github/workflows/pre-commit.yml

@@ -14,6 +14,9 @@ jobs:
       # This action sets the current path to the root of your github repo
       - 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

@@ -24,32 +24,26 @@ jobs:
     steps:
       - uses: actions/checkout@v5
 
-      - name: Setup Python
+    # setup Python
+      - name: Install Python
         uses: actions/setup-python@v6
         with:
-          python-version: "3.12"
+          python-version-file: ".python-version"
 
-      - name: Cache
-        id: cache
-        uses: actions/cache@v4
-        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()

.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",