Update Proposal

.github/workflows/ci.yml

@@ -0,0 +1,115 @@
+name: CI
+
+on:
+  push:
+    branches: [ main, master, dev ]
+  pull_request:
+    branches: [ main, master, dev ]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        qt-version: ["qt5", "qt6"]
+        exclude:
+          # PyQt6 might have issues on some older Python versions
+          - python-version: "3.9"
+            qt-version: "qt6"
+
+    steps:
+    - uses: actions/checkout@v4
+
+    # Set up display for GUI testing on Linux
+    - name: Set up display (Linux)
+      if: runner.os == 'Linux'
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y xvfb herbstluftwm
+        export DISPLAY=:99.0
+        Xvfb :99 -screen 0 1400x900x24 -ac +extension GLX +render &
+        sleep 3
+        herbstluftwm &
+        sleep 1
+      env:
+        DISPLAY: :99.0
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+      with:
+        version: "latest"
+
+    - name: Set up Python ${{ matrix.python-version }}
+      run: uv python install ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: uv sync --dev --extra ${{ matrix.qt-version }}
+
+    - name: Install phylib from branch
+      run: |
+        if [ "${{ github.ref_name }}" = "master" ]; then
+          uv add "git+https://github.com/cortex-lab/phylib.git@master"
+        elif [ "${{ github.ref_name }}" = "dev" ]; then  
+          uv add "git+https://github.com/cortex-lab/phylib.git@dev"
+        else
+          uv add "git+https://github.com/cortex-lab/phylib.git@${{ github.ref_name }}"
+        fi
+      shell: bash
+
+    - name: Install additional test dependencies
+      run: |
+        uv add "git+https://github.com/kwikteam/klusta.git"
+        uv add "git+https://github.com/kwikteam/klustakwik2.git"
+
+    - name: Lint with ruff
+      run: uv run ruff check phy
+
+    - name: Check formatting with ruff
+      run: uv run ruff format --check phy
+
+    - name: Test with pytest (Linux)
+      if: runner.os == 'Linux'
+      run: uv run make test-full
+      env:
+        DISPLAY: :99.0
+        QT_QPA_PLATFORM: offscreen
+
+    - name: Test with pytest (Windows/macOS)
+      if: runner.os != 'Linux'
+      run: uv run pytest --cov=phy --cov-report=xml phy
+      env:
+        QT_QPA_PLATFORM: offscreen
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        fail_ci_if_error: false
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  build:
+    runs-on: ubuntu-latest
+    needs: test
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+      with:
+        version: "latest"
+
+    - name: Set up Python
+      run: uv python install 3.9
+
+    - name: Build package
+      run: uv build
+
+    - name: Upload build artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: dist
+        path: dist/

.gitignore

@@ -1,3 +1,4 @@
+local_tests
 contrib
 data
 doc

Makefile

@@ -2,36 +2,74 @@ clean-build:
 	rm -fr build/
 	rm -fr dist/
 	rm -fr *.egg-info
+	rm -fr .eggs/
 
 clean-pyc:
 	find . -name '*.pyc' -exec rm -f {} +
 	find . -name '*.pyo' -exec rm -f {} +
 	find . -name '*~' -exec rm -f {} +
 	find . -name '__pycache__' -exec rm -fr {} +
 
-clean: clean-build clean-pyc
+clean-test:
+	rm -fr .tox/
+	rm -f .coverage
+	rm -fr htmlcov/
+	rm -fr .pytest_cache/
+	rm -fr .ruff_cache/
+
+clean: clean-build clean-pyc clean-test
+
+install:
+	uv sync --dev --extra qt5
+
+install-qt6:
+	uv sync --dev --extra qt6
 
 lint:
-	flake8 phy
+	uv run ruff check phy
+
+format:
+	uv run ruff format phy
+
+format-check:
+	uv run ruff format --check phy
+
+lint-fix:
+	uv run ruff check --fix phy
 
-# Test everything except apps.
-test: lint
-	py.test -xvv --cov-report= --cov=phy phy --ignore=phy/apps/ --cov-append
-	coverage report --omit */phy/apps/*,*/phy/plot/gloo/*
+# Test everything except apps
+test: lint format-check
+	uv run pytest -xvv --cov-report= --cov=phy phy --ignore=phy/apps/ --cov-append
+	uv run coverage report --omit "*/phy/apps/*,*/phy/plot/gloo/*"
 
-# Test just the apps.
+# Test just the apps
 test-apps: lint
-	py.test --cov-report term-missing --cov=phy.apps phy/apps/ --cov-append
+	uv run pytest --cov-report term-missing --cov=phy.apps phy/apps/ --cov-append
 
-# Test everything.
+# Test everything
 test-full: test test-apps
-	coverage report --omit */phy/plot/gloo/*
+	uv run coverage report --omit "*/phy/plot/gloo/*"
+
+test-fast:
+	uv run pytest phy
 
 doc:
-	python3 tools/api.py && python tools/extract_shortcuts.py && python tools/plugins_doc.py
+	uv run python tools/api.py && uv run python tools/extract_shortcuts.py && uv run python tools/plugins_doc.py
 
 build:
-	python3 setup.py sdist --formats=zip
+	uv build
 
 upload:
-	twine upload dist/*
+	uv publish
+
+upload-test:
+	uv publish --publish-url https://test.pypi.org/legacy/
+
+coverage:
+	uv run coverage html
+
+dev: install lint format test
+
+ci: lint format-check test-full build
+
+.PHONY: clean-build clean-pyc clean-test clean install install-qt6 lint format format-check lint-fix test test-apps test-full test-fast doc build upload upload-test coverage dev ci

setup.py → deprecated/setup.py

@@ -4,9 +4,9 @@
 """Installation script."""
 
 
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 # Imports
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 
 import os
 import os.path as op
@@ -15,15 +15,18 @@
 from setuptools import setup
 
 
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 # Setup
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
+
 
 def _package_tree(pkgroot):
     path = op.dirname(__file__)
-    subdirs = [op.relpath(i[0], path).replace(op.sep, '.')
-               for i in os.walk(op.join(path, pkgroot))
-               if '__init__.py' in i[2]]
+    subdirs = [
+        op.relpath(i[0], path).replace(op.sep, '.')
+        for i in os.walk(op.join(path, pkgroot))
+        if '__init__.py' in i[2]
+    ]
     return subdirs
 
 
@@ -52,23 +55,34 @@ def _package_tree(pkgroot):
 setup(
     name='phy',
     version=version,
-    license="BSD",
+    license='BSD',
     description='Interactive visualization and manual spike sorting of large-scale ephys data',
     long_description=readme,
-    long_description_content_type="text/markdown",
+    long_description_content_type='text/markdown',
     author='Cyrille Rossant (cortex-lab/UCL/IBL)',
     author_email='cyrille.rossant+pypi@gmail.com',
     url='https://phy.cortexlab.net',
     packages=_package_tree('phy'),
     package_dir={'phy': 'phy'},
     package_data={
-        'phy': ['*.vert', '*.frag', '*.glsl', '*.npy', '*.gz', '*.txt', '*.json',
-                '*.html', '*.css', '*.js', '*.prb', '*.ttf', '*.png'],
+        'phy': [
+            '*.vert',
+            '*.frag',
+            '*.glsl',
+            '*.npy',
+            '*.gz',
+            '*.txt',
+            '*.json',
+            '*.html',
+            '*.css',
+            '*.js',
+            '*.prb',
+            '*.ttf',
+            '*.png',
+        ],
     },
     entry_points={
-        'console_scripts': [
-            'phy = phy.apps:phycli'
-        ],
+        'console_scripts': ['phy = phy.apps:phycli'],
     },
     install_requires=require,
     include_package_data=True,
@@ -78,7 +92,7 @@ def _package_tree(pkgroot):
         'Intended Audience :: Developers',
         'License :: OSI Approved :: BSD License',
         'Natural Language :: English',
-        "Framework :: IPython",
+        'Framework :: IPython',
         'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.7',
     ],

phy/__init__.py

@@ -1,12 +1,11 @@
-# -*- coding: utf-8 -*-
 # flake8: noqa
 
 """phy: interactive visualization and manual spike sorting of large-scale ephys data."""
 
 
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 # Imports
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 
 import atexit
 import logging
@@ -22,9 +21,9 @@
 from .utils.plugin import IPlugin, get_plugin, discover_plugins
 
 
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 # Global variables and functions
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 
 __author__ = 'Cyrille Rossant'
 __email__ = 'cyrille.rossant at gmail.com'
@@ -50,4 +49,5 @@ def on_exit():  # pragma: no cover
 def test():  # pragma: no cover
     """Run the full testing suite of phy."""
     import pytest
+
     pytest.main()