Merge pull request #9 from AllenNeuralDynamics/cdci-add-uv-support

Add support for uv package manager

.github/workflows/ci.yml

@@ -11,36 +11,42 @@ on:
 jobs:
   linters:
     runs-on: windows-latest
+    name: Lint ${{ matrix.python-version }}
+    strategy:
+      fail-fast: false
+      matrix:
+        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 . --config .\pyproject.toml
       - name: Run ruff check
-        run: ruff check .
+        run: uv run ruff check . --config .\pyproject.toml
       - name: Run codespell
-        run : codespell .
+        run : uv run codespell .
+
 
   tests:
     runs-on: windows-latest
     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
+        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
-      - name: Check for uncommitted changes
-        run: |
-          git config --global core.safecrlf false
-          git diff --exit-code || (echo "Untracked changes found" && exit 1)
+        run: uv run -m unittest

.github/workflows/tag_and_publish.yml

@@ -0,0 +1,63 @@
+name: Tag and Publish
+
+on:
+    workflow_dispatch: {}
+
+jobs:
+  tag:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.11
+    - uses: actions/checkout@v3
+    - 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

@@ -1,7 +1,10 @@
 # aind-behavior-core-analysis
 
+![CI](https://github.com/AllenNeuralDynamics/Aind.Behavior.CoreAnalysis/actions/workflows/ci.yml/badge.svg)
+[![PyPI - Version](https://img.shields.io/pypi/v/aind-behavior-services)](https://pypi.org/project/aind-behavior-core-analysis/)
 [![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
-[![CodeStyle](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![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)
 
 A repository with core primitives for analysis shared across all `Aind.Behavior` tasks
 

pyproject.toml

@@ -5,25 +5,38 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "aind-behavior-core-analysis"
 description = "A library with core primitives for analysis shared across all `Aind.Behavior` tasks"
+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",
 ]
+
 dynamic = ["version", "readme"]
 
 dependencies = [
     'harp-python',
-    'numpy<2.0.0', # numpy 2.0.0 is not supported by harp
     'aind_behavior_services>=0.8.0',
     'pyyaml',
     'requests',
 ]
 
+[project.urls]
+Documentation = "https://allenneuraldynamics.github.io/Aind.Behavior.CoreAnalysis/"
+Repository = "https://github.com/AllenNeuralDynamics/Aind.Behavior.CoreAnalysis/"
+Issues = "https://github.com/AllenNeuralDynamics/Aind.Behavior.CoreAnalysis/issues"
+Changelog = "https://github.com/AllenNeuralDynamics/Aind.Behavior.CoreAnalysis/releases"
+
+
 [project.optional-dependencies]
 
 
-linters = [
+dev = [
     'ruff',
     'codespell'
 ]
@@ -53,5 +66,5 @@ mccabe = { max-complexity = 14 }
 pydocstyle = { convention = 'google' }
 
 [tool.codespell]
-skip = '.git,*.pdf,*.svg,./bonsai,*.bonsai,./docs/_build,./build'
+skip = '.git,*.pdf,*.svg,./bonsai,*.bonsai,./docs/_build,uv.lock'
 ignore-words-list = 'nd'