chore: Add UV support (#99)

This PR includes all changes to
[`pasteur-python-template`](https://github.com/pasteurlabs/pasteur-python-template)
from v0.5.1 to v0.6.0.

**Conflicting files are automatically overwritten with the template
version**. Repo maintainers, please review and cherry-pick changes /
restore original files as appropriate before merging.

---------

Co-authored-by: Alessandro Angioi <[email protected]>

Author: dionhaefner

.github/dependabot.yml

@@ -1,32 +1,15 @@
 version: 2
 
 updates:
-- package-ecosystem: pip
-  directory: "/"
-  schedule:
-    interval: "weekly"
-    timezone: "America/New_York"
-  open-pull-requests-limit: 10
-
-  groups:
-    deps:
-      patterns:
-          - "*"
-
-  commit-message:
-    prefix: chore
-
 - package-ecosystem: github-actions
   directory: "/"
   schedule:
     interval: "weekly"
+    day: "monday"
     timezone: "America/New_York"
   open-pull-requests-limit: 10
 
   groups:
     actions:
       patterns:
       - "*"
-
-  commit-message:
-    prefix: ci

.github/workflows/build_docs.yml

@@ -1,35 +1,41 @@
 name: Build documentation
 
 on:
+  # run on PRs for validation
   pull_request:
-    branches:
-      - main
 
 jobs:
   test-docs:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Checkout
+      - name: Set up Git repository
         uses: actions/checkout@v4
 
       - name: Install system requirements
         run: |
           sudo apt-get update
           sudo apt-get install -y pandoc
 
-      - name: Setup Python environment
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version-file: "pyproject.toml"
+
+      - name: Restore UV environment
+        run: cp production.uv.lock uv.lock
 
       - name: Install doc requirements
         run: |
-          pip install .[dev] -r requirements.txt
-          pip install -r docs/requirements.txt
+          uv sync --extra docs --frozen
 
       - name: Build docs
+        working-directory: docs
         run: |
-          cd docs
           export SPHINXOPTS="-W"  # treat warnings as errors
-          make html
+          uv run --no-sync make html

.github/workflows/bump_lockfile.yml

@@ -0,0 +1,59 @@
+name: Bump UV lockfile
+
+on:
+  workflow_dispatch:  # Allows manual trigger
+
+  schedule:
+    - cron:  '0 0 * * 1'  # 12AM only on Mondays
+
+jobs:
+  bump-lockfile:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Set up Git repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Update lockfile
+        run: |
+          mv production.uv.lock uv.lock
+          uv lock --upgrade
+          mv uv.lock production.uv.lock
+
+      - name: Generate new requirements.txt
+        run : |
+          pip install pre-commit
+          pre-commit run update-requirements --all-files || true
+
+      - name: Detect if changes were made
+        id: git-diff
+        run: |
+          changes=false
+          git diff --exit-code || changes=true
+          echo "update_done=$changes" >> $GITHUB_OUTPUT
+
+      - name: Create Pull Request
+        if: steps.git-diff.outputs.update_done == 'true'
+        uses: peter-evans/create-pull-request@v7
+        with:
+            token: ${{ secrets.GITHUB_TOKEN }}
+            commit-message: Update dependencies
+            title: 📦 Update dependencies
+            branch: _bot/update-deps
+            draft: false
+            base: main
+            body: |
+              This PR updates the lockfile to the latest versions of the dependencies.
+              Please review the changes and merge when ready.
+
+              To trigger CI checks, please close and reopen this PR.

.github/workflows/get_coverage.yml

@@ -2,6 +2,7 @@ name: Auto update pre-commit hooks
 
 on:
   workflow_dispatch:  # Allows manual trigger
+
   schedule:
     - cron:  '0 0 * * 1'  # 12AM only on Mondays
 
@@ -14,8 +15,7 @@ jobs:
 
     - uses: actions/setup-python@v5
       with:
-          python-version: '3.12'
-          cache: 'pip'
+          python-version-file: "pyproject.toml"
 
     - name: Install pre-commit
       run: pip install pre-commit
@@ -62,7 +62,7 @@ jobs:
       with:
           token: ${{ secrets.GITHUB_TOKEN }}
           commit-message: Update pre-commit hooks
-          title: "chore: update pre-commit hooks"
+          title: "chore: ✅ Update pre-commit hooks"
           branch: _bot/update-precommit
           draft: false
           body: |
@@ -74,7 +74,7 @@ jobs:
       with:
           token: ${{ secrets.GITHUB_TOKEN }}
           commit-message: Update pre-commit hooks
-          title: "chore: update pre-commit hooks [review required]"
+          title: "chore: ⚠️ Update pre-commit hooks [review required]"
           branch: _bot/update-precommit
           draft: true
           body: |

.github/workflows/pre-commit-cron-updater.yml

@@ -15,5 +15,5 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-          python-version: '3.12'
+          python-version-file: "pyproject.toml"
     - uses: pre-commit/[email protected]

.github/workflows/pre_commit.yml

@@ -1,7 +1,7 @@
 name: Publish
 
 on:
-  workflow_dispatch:
+  workflow_dispatch:  # Allows manual trigger
 
   release:
     types:
@@ -13,10 +13,15 @@ jobs:
     runs-on: '${{ matrix.os }}'
     strategy:
       matrix:
+        # TODO: Comment in additional platforms if using C extensions / platform-specific wheels
         os:
           - ubuntu-latest
+          # - macos-latest
         python-version:
-          - "3.12"
+          # - "3.10"
+          # - "3.11"
+          # - "3.12"
+          - "3.13"
 
     steps:
       - name: Checkout
@@ -27,16 +32,22 @@ jobs:
         run: |
           git fetch --prune --unshallow --tags
 
-      - name: Setup Python
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install Build
-        run: pip install build
+      - name: Restore UV environment
+        run: cp production.uv.lock uv.lock
 
       - name: Build Package
-        run: python -m build
+        run: |
+          uv build
 
       - name: Store the distribution packages
         uses: actions/upload-artifact@v4