Maintenance release v2.1

.github/workflows/ci.yml

@@ -0,0 +1,108 @@
+name: CI
+
+on:
+  workflow_dispatch:
+
+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"]
+
+    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/

.github/workflows/codespell.yml

@@ -3,10 +3,7 @@
 name: Codespell
 
 on:
-  push:
-    branches: [master]
-  pull_request:
-    branches: [master]
+  workflow_dispatch:
 
 permissions:
   contents: read

.github/workflows/python-test.yml

@@ -1,9 +1,6 @@
 name: Install and Test with Pip
 
 on:
-  pull_request:
-  push:
-    branches: [ "main", "master" ]
   workflow_dispatch:
 
 

.gitignore

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

.release-smoke/latest-testpypi-version.txt

@@ -0,0 +1 @@
+2.1.0rc1.dev3

MANIFEST.in

@@ -1,15 +1,9 @@
-include LICENSE
+include LICENSE.md
 include README.md
-include requirements.txt
-include requirements-dev.txt
 
-recursive-include tests *
-recursive-include phy/electrode/probes *.prb
 recursive-include phy/plot/glsl *.vert *.frag *.glsl
-recursive-include phy/plot/static *.npy *.gz *.txt
-recursive-include phy/cluster/static *.html *.css
+recursive-include phy/plot/static *.gz
 recursive-include phy/gui/static *.html *.css *.js *.ttf *.png
-recursive-include phy/gui/static/icons *.html *.css *.js *.ttf *.png
 recursive-include phy/apps/*/static *.json
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

Makefile

@@ -2,36 +2,122 @@ 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/
+	rm -fr .release-smoke/
+
+clean: clean-build clean-pyc clean-test
+
+install:
+	uv sync --dev
 
 lint:
-	flake8 phy
+	uv run ruff check phy
+
+format:
+	uv run ruff format 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/*
+format-check:
+	uv run ruff format --check phy
 
-# Test just the apps.
+lint-fix:
+	uv run ruff check --fix phy
+
+# 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-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/
+
+publish-test:
+	python3 scripts/release_publish.py publish-testpypi-dev
+
+version-test:
+	python3 scripts/release_publish.py print-latest-testpypi-version
+
+publish-pypi:
+	python3 scripts/release_publish.py publish-pypi
+
+coverage:
+	uv run coverage html
+
+dev: install lint format test
+
+ci: lint format-check test-full build
+
+RELEASE_SMOKE_DATASET ?= $(CURDIR)/../phy-data/template
+PYPROJECT_VERSION := $(shell python3 scripts/release_publish.py print-current-version)
+SMOKE_VERSION ?=
+PYPI_SMOKE_VERSION = $(or $(SMOKE_VERSION),$(PYPROJECT_VERSION))
+TEST_SMOKE_VERSION = $(or $(SMOKE_VERSION),$(shell python3 scripts/release_publish.py print-latest-testpypi-version))
+RELEASE_SMOKE_INDEX_URL ?=
+RELEASE_SMOKE_EXTRA_INDEX_URL ?=
+
+define run_smoke
+	RELEASE_SMOKE_DATASET="$(RELEASE_SMOKE_DATASET)" \
+	RELEASE_SMOKE_ENV="$(1)" \
+	RELEASE_SMOKE_VERSION="$(2)" \
+	RELEASE_SMOKE_INDEX_URL="$(3)" \
+	RELEASE_SMOKE_EXTRA_INDEX_URL="$(4)" \
+	bash scripts/release_smoke_test.sh $(5)
+endef
+
+define run_open
+	RELEASE_SMOKE_DATASET="$(RELEASE_SMOKE_DATASET)" \
+	RELEASE_SMOKE_ENV="$(1)" \
+	bash scripts/release_smoke_test.sh open
+endef
+
+smoke-local: build
+	$(call run_smoke,$(CURDIR)/.release-smoke/local,,,,local)
+
+open-local:
+	$(call run_open,$(CURDIR)/.release-smoke/local)
+
+smoke-pypi:
+	$(call run_smoke,$(CURDIR)/.release-smoke/pypi-$(PYPI_SMOKE_VERSION),$(PYPI_SMOKE_VERSION),$(RELEASE_SMOKE_INDEX_URL),$(RELEASE_SMOKE_EXTRA_INDEX_URL),pypi)
+
+open-pypi:
+	$(call run_open,$(CURDIR)/.release-smoke/pypi-$(PYPI_SMOKE_VERSION))
+
+smoke-test:
+	$(call run_smoke,$(CURDIR)/.release-smoke/testpypi-$(TEST_SMOKE_VERSION),$(TEST_SMOKE_VERSION),https://test.pypi.org/simple/,https://pypi.org/simple/,pypi)
+
+open-test:
+	$(call run_open,$(CURDIR)/.release-smoke/testpypi-$(TEST_SMOKE_VERSION))
+
+.PHONY: clean-build clean-pyc clean-test clean install lint format format-check lint-fix test test-apps test-full test-fast doc build upload upload-test publish-test version-test publish-pypi coverage dev ci smoke-local open-local smoke-pypi open-pypi smoke-test open-test