Merge pull request #71 from biocommons/70-adopt-cookiecutter-uv

Closes #70: Adopt cookiecutter-uv as foundation

Author: reece

.devcontainer/devcontainer.json

@@ -0,0 +1,29 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+    "name": "python-package",
+    // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+    "image": "mcr.microsoft.com/devcontainers/python:1-3.11-bullseye",
+    "runArgs": [
+        // avoid UID/GID remapping under rootless Podman
+        "--userns=keep-id"
+      ],
+    "features": {},
+
+    // Use 'postCreateCommand' to run commands after the container is created.
+    "postCreateCommand": "./.devcontainer/postCreateCommand.sh",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        "vscode": {
+            "extensions": ["ms-python.python", "editorconfig.editorconfig"],
+            "settings": {
+                "python.testing.pytestArgs": ["tests"],
+                "python.testing.unittestEnabled": false,
+                "python.testing.pytestEnabled": true,
+                "python.defaultInterpreterPath": "/workspaces/python-package/.venv/bin/python",
+                "python.testing.pytestPath": "/workspaces/python-package/.venv/bin/pytest"
+            }
+        }
+    }
+}

.devcontainer/postCreateCommand.sh

@@ -0,0 +1,10 @@
+#! /usr/bin/env bash
+
+# Install uv
+curl -LsSf https://astral.sh/uv/install.sh | sh
+
+# Install Dependencies
+uv sync
+
+# Install pre-commit hooks
+uv run pre-commit install --install-hooks

.github/actions/setup-python-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/workflows/labels.yml

@@ -26,4 +26,4 @@ jobs:
             https://raw.githubusercontent.com/biocommons/.github/main/etc/labels.yml
             .github/labels.yml
 
-          delete-other-labels: false
+          delete-other-labels: false

.github/workflows/python-ci-cd.yml

@@ -0,0 +1,22 @@
+name: Python CI/CD
+permissions:
+  contents: write
+  id-token: write
+
+on:
+  pull_request:
+    branches: [ "main" ]
+  push:
+    tags:
+      - "[0-9]+.[0-9]+.[0-9]+"
+
+jobs:
+  python-ci-cd:
+    name: python-ci-cd
+    permissions:
+      contents: write
+      id-token: write
+    uses: biocommons/.github/.github/workflows/python-ci-cd.yml@main
+    with:
+      run-deploy: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') }}
+    secrets: inherit

.github/workflows/python-package.yml

@@ -1,5 +1,3 @@
-# https://github.com/actions/stale
-
 name: 'Close stale issues and PRs'
 on:
   workflow_dispatch:

.github/workflows/stale.yml

@@ -0,0 +1,17 @@
+name: validate-codecov-config
+
+on:
+  pull_request:
+    paths: [codecov.yaml]
+  push:
+    branches: [main]
+
+jobs:
+  validate-codecov-config:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@v4
+      - name: Validate codecov configuration
+        run: curl -sSL --fail-with-body --data-binary @codecov.yaml https://codecov.io/validate