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

CODE_OF_CONDUCT.md

@@ -0,0 +1,116 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances
+  of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Project maintainers are responsible for clarifying and enforcing our standards
+of acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Project maintainers have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all project spaces, and also applies when an
+individual is officially representing the project in public spaces. Examples of
+representing the project include using an official email address, posting via an
+official social media account, or acting as an appointed representative at an
+online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the project maintainers responsible for enforcement at
+cyrille.rossant@gmail.com. All complaints will be reviewed and investigated
+promptly and fairly.
+
+All project maintainers are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Project maintainers will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+Community Impact: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+Consequence: A private, written warning from project maintainers, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+Community Impact: A violation through a single incident or series of actions.
+
+Consequence: A warning with consequences for continued behavior. No interaction
+with the people involved, including unsolicited interaction with those enforcing
+the Code of Conduct, for a specified period of time. Violating these terms may
+lead to a temporary or permanent ban.
+
+### 3. Temporary Ban
+
+Community Impact: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+Consequence: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. Violating
+these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+Community Impact: Demonstrating a pattern of violation of community standards,
+including sustained inappropriate behavior, harassment of an individual, or
+aggression toward or disparagement of classes of individuals.
+
+Consequence: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the Contributor Covenant, version 2.1,
+available at <https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by Mozilla's code of conduct
+enforcement ladder.

CONTRIBUTE.md

@@ -1,5 +1,7 @@
 ## Contribute
 
+Participation in phy is governed by the project [Code of Conduct](CODE_OF_CONDUCT.md).
+
 ### Setup
 
 On your development computer:

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]