Merge pull request #18 from biosimulations/uv

switch from poetry to uv

Author: jcschaff

.github/actions/setup-poetry-env/action.yml

@@ -0,0 +1,30 @@
+name: "Setup Python Environment"
+description: "Set up Python environment for the given Python version"
+
+inputs:
+  python-version:
+    description: "Python version to use"
+    required: true
+    default: "3.12"
+  uv-version:
+    description: "uv version to use"
+    required: true
+    default: "0.6.14"
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        version: ${{ inputs.uv-version }}
+        enable-cache: "true"
+        cache-suffix: ${{ matrix.python-version }}
+
+    - name: Install Python dependencies
+      run: uv sync --frozen
+      shell: bash

.github/actions/setup-python-env/action.yml

@@ -20,7 +20,7 @@ jobs:
           key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
 
       - name: Set up the environment
-        uses: ./.github/actions/setup-poetry-env
+        uses: ./.github/actions/setup-python-env
 
       - name: Run checks
         run: make check
@@ -29,7 +29,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
       fail-fast: false
     defaults:
       run:
@@ -39,19 +39,21 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up the environment
-        uses: ./.github/actions/setup-poetry-env
+        uses: ./.github/actions/setup-python-env
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Run tests
-        run: poetry run pytest tests --cov --cov-config=pyproject.toml --cov-report=xml
+        run: uv run python -m pytest tests --cov --cov-config=pyproject.toml --cov-report=xml
 
       - name: Check typing
-        run: poetry run mypy
+        run: uv run mypy
 
       - name: Upload coverage reports to Codecov with GitHub Action on Python 3.11
         uses: codecov/codecov-action@v4
         if: ${{ matrix.python-version == '3.11' }}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   check-docs:
     runs-on: ubuntu-latest
@@ -60,7 +62,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up the environment
-        uses: ./.github/actions/setup-poetry-env
+        uses: ./.github/actions/setup-python-env
 
       - name: Check if documentation can be built
-        run: poetry run mkdocs build -s
+        run: uv run mkdocs build -s

.github/workflows/main.yml

@@ -3,7 +3,6 @@ name: release-main
 on:
   release:
     types: [published]
-    branches: [main]
 
 jobs:
   deploy-docs:
@@ -13,7 +12,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up the environment
-        uses: ./.github/actions/setup-poetry-env
+        uses: ./.github/actions/setup-python-env
 
       - name: Deploy documentation
-        run: poetry run mkdocs gh-deploy --force
+        run: uv run mkdocs gh-deploy --force

.github/workflows/on-release-main.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   validate-codecov-config:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - name: Validate codecov configuration

.github/workflows/validate-codecov-config.yml

@@ -4,7 +4,7 @@ docs/source
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
-*.py[cod]
+*.py[codz]
 *$py.class
 
 # C extensions
@@ -50,7 +50,7 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *.cover
-*.py,cover
+*.py.cover
 .hypothesis/
 .pytest_cache/
 cover/
@@ -98,20 +98,35 @@ ipython_config.py
 #   install all needed dependencies.
 #Pipfile.lock
 
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
 # poetry
 #   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
 #   This is especially recommended for binary packages to ensure reproducibility, and is more
 #   commonly ignored for libraries.
 #   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
 #poetry.lock
+#poetry.toml
 
 # pdm
 #   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
 #pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/#use-with-ide
-.pdm.toml
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
 
 # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
@@ -125,6 +140,7 @@ celerybeat.pid
 
 # Environments
 .env
+.envrc
 .venv
 env/
 venv/
@@ -156,6 +172,44 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
 # Vscode config files
 .vscode/
 

.gitignore

@@ -1,23 +1,21 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.4.0"
+    rev: "v5.0.0"
     hooks:
       - id: check-case-conflict
       - id: check-merge-conflict
       - id: check-toml
       - id: check-yaml
         exclude: ^kustomize/
+      - id: check-json
+      - id: pretty-format-json
+        args: [--autofix, --no-sort-keys]
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.5.2"
+    rev: "v0.11.5"
     hooks:
       - id: ruff
         args: [--exit-non-zero-on-fix]
       - id: ruff-format
-
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.0.3"
-    hooks:
-      - id: prettier

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ Anything tagged with "enhancement" and "help wanted" is open to whoever wants to
 
 ## Write Documentation
 
-Cookiecutter PyPackage could always use more documentation, whether as part of the official docs, in docstrings, or even on the web in blog posts, articles, and such.
+compose-api could always use more documentation, whether as part of the official docs, in docstrings, or even on the web in blog posts, articles, and such.
 
 ## Submit Feedback
 
@@ -45,7 +45,7 @@ If you are proposing a new feature:
 # Get Started!
 
 Ready to contribute? Here's how to set up `compose-api` for local development.
-Please note this documentation assumes you already have `poetry` and `Git` installed and ready to go.
+Please note this documentation assumes you already have `uv` and `Git` installed and ready to go.
 
 1. Fork the `compose-api` repo on GitHub.
 
@@ -62,23 +62,16 @@ git clone git@github.com:YOUR_NAME/compose-api.git
 cd compose-api
 ```
 
-If you are using `pyenv`, select a version to use locally. (See installed versions with `pyenv versions`)
-
-```bash
-pyenv local <x.y.z>
-```
-
 Then, install and activate the environment with:
 
 ```bash
-poetry install
-poetry shell
+uv sync
 ```
 
 4. Install pre-commit to run linters/formatters at commit time:
 
 ```bash
-poetry run pre-commit install
+uv run pre-commit install
 ```
 
 5. Create a branch for local development:

CONTRIBUTING.md

@@ -7,26 +7,26 @@ RUN apt-get update && \
     rm -rf /var/lib/apt/lists/*
 
 # Set environment variables
-ENV POETRY_VERSION=2.1.3 \
-    POETRY_VIRTUALENVS_CREATE=false \
-    PYTHONUNBUFFERED=1
+ENV PYTHONUNBUFFERED=1
 
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv
 
-# Install Poetry
-RUN pip install "poetry==$POETRY_VERSION"
-
-# Set the working directory
+# Change the working directory to the `app` directory
 WORKDIR /app
 
-# Copy only the necessary files
-COPY pyproject.toml poetry.lock /app/
+# Copy the lockfile and `pyproject.toml` into the image
+COPY uv.lock /app/uv.lock
+COPY pyproject.toml /app/pyproject.toml
 
 # Install dependencies
-RUN poetry install --no-root --only main
+RUN uv sync --frozen --no-install-project
 
-# Copy the rest of the application code
+# Copy the project into the image
 COPY . /app
 
+# Sync the project
+RUN uv sync --frozen
+
 # Declare the volume for local cache storage
 VOLUME ["/app/scratch"]