Merge pull request #4 from AllenNeuralDynamics/cdci-add-uv-support

Add support of uv package manager

.github/workflows/ci.yml

@@ -1,29 +1,38 @@
 name: CI
 
 on:
-  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
 
 jobs:
   linters:
     runs-on: windows-latest
+    name: Lint ${{ matrix.python-version }}
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ["3.11"]
+        python-version: ['3.11', '3.12', '3.13']
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v3
         with:
-          python-version: "3.11"
+          enable-cache: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
       - name: Install dependencies
-        run: |
-          python -m pip install -e .[linters] --no-cache-dir
+        run: uv sync --extra dev
       - name: Run ruff format
-        run: ruff format .
+        run: uv run ruff format .
       - name: Run ruff check
-        run: ruff check .
+        run: uv run ruff check .
       - name: Run codespell
-        run : codespell .
+        run : uv run codespell .
 
   tests:
     runs-on: windows-latest
@@ -33,26 +42,28 @@ jobs:
       - name: Setup .NET Core SDK
         uses: actions/[email protected]
         with:
-          dotnet-version: 7.x
+          dotnet-version: 8.x
       - name: Restore dotnet tools
         run: dotnet tool restore
       - name: Setup Bonsai
         working-directory: bonsai
         run: .\Setup.ps1
 
-      - name: Set up Python
-        uses: actions/setup-python@v3
+      - uses: astral-sh/setup-uv@v3
         with:
-          python-version: '3.11'
+          enable-cache: true
+
+      - name: Set up Python
+        run: uv python install
+
 
       - name: Install dependencies
-        run: |
-          python -m pip install -e . --no-cache-dir
+        run: uv sync --extra dev
       - name: Run tests
-        run: python -m unittest
+        run: uv run -m unittest
       - name: Regenerate schemas
-        run: regenerate
+        run: uv run regenerate
       - name: Check for uncommitted changes
         run: |
           git config --global core.safecrlf false
-          git diff --exit-code || (echo "Untracked changes found" && exit 1)
+          git diff --exit-code || (echo "Untracked changes found" && exit 1)

.github/workflows/docs.yml

@@ -2,8 +2,8 @@ name: Deploy Sphinx documentation to Pages
 
 on:
   workflow_dispatch:
-  #push:
-  #  branches: [main] # branch to trigger deployment
+  push:
+    branches: main
 
 jobs:
   pages:

.github/workflows/tag_and_publish.yml

@@ -0,0 +1,67 @@
+name: Tag and Publish
+
+on:
+    workflow_dispatch: {}
+
+jobs:
+  tag:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Pull latest changes
+      run: git pull origin ${{ env.DEFAULT_BRANCH }}
+    - uses: astral-sh/setup-uv@v3
+      with:
+        enable-cache: true
+    - name: Set up Python
+      run: uv python install
+
+    - name: Extract version from __init__.py and package name from pyproject.toml
+      id: get_version_and_name
+      run: |
+        package_name=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['name'])")
+        package_name=${package_name//-/_}
+        version=$(python -c "import re; 
+        with open(f'./src/${package_name}/__init__.py', 'r') as f: 
+          content = f.read(); 
+          match = re.search(r'__version__\s*=\s*[\'\"]([^\'\"]+)[\'\"]', content); 
+          print(match.group(1)) if match else exit(1)")
+        echo "PACKAGE_NAME=$package_name" >> $GITHUB_ENV
+        echo "PACKAGE_VERSION=$version" >> $GITHUB_ENV
+      shell: bash
+
+    - name: Create Git tag
+      run: |
+        git config --global user.name "github-actions[bot]"
+        git config --global user.email "github-actions[bot]@users.noreply.github.com"
+        git tag -a v${{ env.PACKAGE_VERSION }} -m "v${{ env.PACKAGE_VERSION }}"
+        git push origin v${{ env.PACKAGE_VERSION }}
+
+    - name: Create GitHub Release
+      uses: softprops/action-gh-release@v2
+      with:
+        token: ${{ secrets.SERVICE_TOKEN }}
+        tag_name: v${{ env.PACKAGE_VERSION }}
+        name: Release v${{ env.PACKAGE_VERSION }}
+        generate_release_notes: true
+
+  publish:
+    needs: tag
+    if: always()  # Enable publishing
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Pull latest changes
+        run: git pull origin ${{ env.DEFAULT_BRANCH }}
+      - uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        run: uv python install
+
+      - name: Build
+        run: uv build
+
+      - name: Publish
+        run: uv publish --token ${{ secrets.AIND_PYPI_TOKEN }}

.python-versions

@@ -0,0 +1,3 @@
+3.11
+3.12
+3.13

README.md

@@ -1,5 +1,11 @@
 # aind-behavior-telekinesis
 
+![CI](https://github.com/AllenNeuralDynamics/Aind.Behavior.VrForaging/actions/workflows/ci.yml/badge.svg)
+[![PyPI - Version](https://img.shields.io/pypi/v/aind-behavior-telekinesis)](https://pypi.org/project/aind-behavior-telekinesis/)
+[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
+[![ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
+
 Task implementation of brain-computer interface experiments.
 
 ## General instructions

pyproject.toml

@@ -5,10 +5,13 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "aind-behavior-telekinesis"
 description = "A library that defines AIND data schema for the brain-computer interface experiments."
+authors = [ {name = "Bruno Cruz", email = "[email protected]"}]
 license = {text = "MIT"}
 requires-python = ">=3.11"
 classifiers = [
-    "Programming Language :: Python :: 3"
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: Microsoft :: Windows",
 ]
 readme = "README.md"
 dynamic = ["version"]
@@ -17,15 +20,22 @@ dependencies = [
   "aind_behavior_services>=0.8, <0.9",
 ]
 
-[project.optional-dependencies]
+[project.urls]
+Documentation = "https://allenneuraldynamics.github.io/Aind.Behavior.Telekinesis/"
+Repository = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Telekinesis/"
+Issues = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Telekinesis/issues"
+Changelog = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Telekinesis/releases"
 
-linters = [
-    'ruff',
-    'codespell'
-]
+[project.optional-dependencies]
 
 launcher = ["aind_behavior_experiment_launcher[aind-services]>=0.2"]
 
+dev = [
+     "aind_behavior_telekinesis[launcher]",
+     "ruff",
+     "codespell",
+]
+
 docs = [
     'Sphinx<7.3',
     'furo',
@@ -57,5 +67,5 @@ mccabe = { max-complexity = 14 }
 pydocstyle = { convention = 'google' }
 
 [tool.codespell]
-skip = '.git,*.pdf,*.svg,./bonsai,*.bonsai,./docs/_build'
+skip = '.git,*.pdf,*.svg,./bonsai,*.bonsai,./docs/_build,uv.lock'
 ignore-words-list = 'nd'