Update proposal for phylib

.github/workflows/ci.yml

@@ -0,0 +1,70 @@
+name: CI
+
+on:
+  push:
+    branches: [ main, master ]
+  pull_request:
+    branches: [ main, master ]
+
+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"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - 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
+
+    - name: Lint with ruff
+      run: uv run ruff check .
+
+    - name: Check formatting with ruff
+      run: uv run ruff format --check .
+
+    - name: Test with pytest
+      run: uv run pytest --cov=phylib --cov-report=xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        fail_ci_if_error: true
+      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/

Makefile

@@ -2,29 +2,61 @@ 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
 
 lint:
-	flake8 phylib
+	uv run ruff check phylib
+
+format:
+	uv run ruff format phylib
+
+format-check:
+	uv run ruff format --check phylib
+
+lint-fix:
+	uv run ruff check --fix phylib
 
-test: lint
-	py.test --cov-report term-missing --cov=phylib phylib
+test: lint format-check
+	uv run pytest --cov-report term-missing --cov=phylib phylib
+
+test-fast:
+	uv run pytest phylib
 
 coverage:
-	coverage --html
+	uv run coverage html
 
 apidoc:
-	python tools/api.py
+	uv run python tools/api.py
 
 build:
-	python setup.py sdist --formats=zip
+	uv build
 
 upload:
-	python setup.py sdist --formats=zip upload
+	uv publish
+
+upload-test:
+	uv publish --publish-url https://test.pypi.org/legacy/
+
+dev: install lint format test
+
+ci: lint format-check test build
+
+.PHONY: clean-build clean-pyc clean-test clean install lint format format-check lint-fix test test-fast coverage apidoc build upload upload-test dev ci

setup.py → deprecated/setup.py

@@ -4,9 +4,9 @@
 """Installation script."""
 
 
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 # Imports
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 
 import os
 import os.path as op
@@ -16,15 +16,18 @@
 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
 
 
@@ -41,7 +44,7 @@ def _package_tree(pkgroot):
 setup(
     name='phylib',
     version=version,
-    license="BSD",
+    license='BSD',
     description='Ephys data analysis for thousands of channels',
     long_description=readme,
     long_description_content_type='text/markdown',
@@ -52,8 +55,17 @@ def _package_tree(pkgroot):
     package_dir={'phylib': 'phylib'},
     package_data={
         'phylib': [
-            '*.vert', '*.frag', '*.glsl', '*.npy', '*.gz', '*.txt',
-            '*.html', '*.css', '*.js', '*.prb'],
+            '*.vert',
+            '*.frag',
+            '*.glsl',
+            '*.npy',
+            '*.gz',
+            '*.txt',
+            '*.html',
+            '*.css',
+            '*.js',
+            '*.prb',
+        ],
     },
     include_package_data=True,
     keywords='phy,data analysis,electrophysiology,neuroscience',
@@ -62,7 +74,7 @@ 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',
     ],

phylib/__init__.py

@@ -4,9 +4,9 @@
 """Utilities for large-scale ephys data analysis."""
 
 
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 # Imports
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 
 import atexit
 import logging
@@ -16,9 +16,9 @@
 from .utils.event import connect, unconnect, emit
 
 
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 # Global variables and functions
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 
 __author__ = 'Cyrille Rossant'
 __email__ = 'cyrille.rossant at gmail.com'
@@ -43,10 +43,10 @@ def format(self, record):
         # Only keep the first character in the level name.
         record.levelname = record.levelname[0]
         filename = op.splitext(op.basename(record.pathname))[0]
-        record.caller = '{:s}:{:d}'.format(filename, record.lineno).ljust(20)
+        record.caller = f'{filename:s}:{record.lineno:d}'.ljust(20)
         message = super(_Formatter, self).format(record)
         color_code = self.color_codes.get(record.levelname, '90')
-        message = '\33[%sm%s\33[0m' % (color_code, message)
+        message = f'\x1b[{color_code}m{message}\x1b[0m'
         return message
 
 
@@ -80,4 +80,5 @@ def on_exit():  # pragma: no cover
 def test():  # pragma: no cover
     """Run the full testing suite of phylib."""
     import pytest
+
     pytest.main()

phylib/conftest.py

@@ -1,27 +1,24 @@
-# -*- coding: utf-8 -*-
-
 """py.test utilities."""
 
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 # Imports
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 
 import logging
 import os
-from pathlib import Path
-import tempfile
 import shutil
+import tempfile
 import warnings
+from pathlib import Path
 
 import numpy as np
 from pytest import fixture
 
 from phylib import add_default_handler
 
-
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 # Common fixtures
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 
 logger = logging.getLogger('phylib')
 logger.setLevel(10)
@@ -30,8 +27,8 @@
 # Fix the random seed in the tests.
 np.random.seed(2015)
 
-warnings.filterwarnings("ignore", message="numpy.dtype size changed")
-warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
+warnings.filterwarnings('ignore', message='numpy.dtype size changed')
+warnings.filterwarnings('ignore', message='numpy.ufunc size changed')
 
 
 @fixture