Feat/pydantic

.docker/Dockerfile

@@ -32,5 +32,3 @@ RUN conda run -p /env python -m pip install --no-deps /pkg
 SHELL ["conda", "run", "-p", "/env", "/bin/bash", "-c" ]
 RUN python -m ipykernel install --name cell2mol --display-name "cell2mol env"
 USER ${NB_USER}
-
-

.gitattributes

@@ -0,0 +1 @@
+tests/fixtures/*.cell filter=lfs diff=lfs merge=lfs -text

.github/actions/setup/action.yml

@@ -0,0 +1,23 @@
+name: "Setup dev environment"
+description: "Setup Python development environment with uv"
+
+inputs:
+  uv-version:
+    description: "Version of uv to install"
+    required: false
+    default: "0.8.17"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6.7.0
+      with:
+        version: ${{ inputs.uv-version }}
+        enable-cache: true
+        cache-dependency-glob: uv.lock
+
+    - name: Set up Python
+      uses: actions/setup-python@v5.4.0
+      with:
+        python-version-file: pyproject.toml

.github/workflows/code-quality.yml

@@ -0,0 +1,36 @@
+name: Code quality checks
+
+on:
+  push:
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  ci:
+    name: Lint & Test
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          lfs: true
+
+      - name: Setup environment
+        uses: ./.github/actions/setup
+
+      # TODO: add ruff check
+      # - name: Ruff check
+      #   run: uv run --dev ruff check cell2mol --output-format=github
+
+      - name: Ruff format
+        run: uv run --dev ruff format --check
+
+      - name: Pre-commit hooks
+        if: ${{ !cancelled() }}
+        run: SKIP=ruff-format uv run --dev pre-commit run --all-files
+
+      - name: Run unit tests
+        if: ${{ !cancelled() }}
+        run: uv run --group test pytest

.gitignore

@@ -1,10 +1,13 @@
+*.out
+
 __pycache__/
 *.pyc
 .coverage
 .mypy_cache
 .pytest_cache
 .ipynb_checkpoints/*
 .ipynb_checkpoints/
+playground/*
 
 # Distribution/packaging
 build/

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+default_stages: [pre-commit, commit-msg]
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-case-conflict
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-toml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.13.1
+    hooks:
+      # - id: ruff-check
+      #   args: [--fix]
+      - id: ruff-format

.python-version

@@ -0,0 +1 @@
+3.13

.vscode/extensions.json

@@ -0,0 +1,5 @@
+{
+    "recommendations": [
+        "charliermarsh.ruff"
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,6 @@
+{
+    "editor.formatOnSave": true,
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff"
+    }
+}