v0.10.0

.github/workflows/main.yml

@@ -13,13 +13,22 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
+    env:
+      QT_QPA_PLATFORM: offscreen
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.10
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
-        python-version: 3.10.19
+        python-version: ${{ matrix.python-version }}
+    - name: Install Qt system libraries
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libegl1 libgl1 libxkbcommon-x11-0 libdbus-1-3 libxcb-cursor0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-shape0 libxcb-sync1 libxcb-xfixes0 libxcb-xkb1 libxkbcommon0
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -29,9 +38,30 @@ jobs:
         pip install flake8
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        # exit-zero treats all errors as warnings. Line length and E203 match black configuration
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=79 --extend-ignore=E203 --statistics
     - name: Test with pytest
       run: |
         pip install pytest
         pytest
+
+  test-minimum-versions:
+      runs-on: ubuntu-latest
+      env:
+        QT_QPA_PLATFORM: offscreen
+      steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install Qt system libraries
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libegl1 libgl1 libxkbcommon-x11-0 libdbus-1-3 libxcb-cursor0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-shape0 libxcb-sync1 libxcb-xfixes0 libxcb-xkb1 libxkbcommon0
+      - run: |
+          grep -oE '"[A-Za-z0-9_.\-]+>=[^",]+' pyproject.toml | tr -d '"' | sed 's/>=/==/' > constraints-minimum.txt
+          cat constraints-minimum.txt
+          python -m pip install --upgrade pip
+          pip install . --constraint constraints-minimum.txt
+          pip install pytest
+          pytest

.pre-commit-config.yaml

@@ -4,4 +4,13 @@ repos:
     hooks:
       - id: black
         args: [--line-length=79]
-        language_version: python3.10
+        language_version: python3.14
+
+  - repo: local
+    hooks:
+      - id: sync-installer-readmes
+        name: Sync shared sections into installer readmes
+        entry: python3 release/sync_installer_readmes.py
+        language: system
+        files: ^(readme\.rst|release/one_click_(macos|windows)_gui/readme\.rst|release/sync_installer_readmes\.py)$
+        pass_filenames: false

CONTRIBUTING.rst

@@ -2,14 +2,17 @@
 Contributing
 ============
 
-Contributions are welcome, and they are greatly appreciated! Every
-little bit helps, and credit will always be given.
+Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
 
-You can contribute in many ways:
+.. contents:: Table of Contents
+   :local:
+   :depth: 2
 
 Types of Contributions
 ----------------------
 
+You can contribute in many ways:
+
 Report Bugs
 ~~~~~~~~~~~
 
@@ -24,21 +27,17 @@ If you are reporting a bug, please include:
 Fix Bugs
 ~~~~~~~~
 
-Look through the GitHub issues for bugs. Anything tagged with "bug"
-and "help wanted" is open to whoever wants to implement it.
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it.
 
 Implement Features
 ~~~~~~~~~~~~~~~~~~
 
-Look through the GitHub issues for features. Anything tagged with "enhancement"
-and "help wanted" is open to whoever wants to implement it.
+Look through the GitHub issues for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.
 
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-Picasso could always use more documentation, whether as part of the
-official Picasso docs, in docstrings, or even on the web in blog posts,
-articles, and such.
+Picasso could always use more documentation, whether as part of the official Picasso docs, in docstrings, or even on the web in blog posts, articles, and such.
 
 Submit Feedback
 ~~~~~~~~~~~~~~~
@@ -49,53 +48,89 @@ If you are proposing a feature:
 
 * Explain in detail how it would work.
 * Keep the scope as narrow as possible, to make it easier to implement.
-* Remember that this is a volunteer-driven project, and that contributions
-  are welcome :)
+* Remember that this is a volunteer-driven project, and that contributions are welcome :)
 
-Get Started!
-------------
+Contributing Code
+-----------------
 
-Ready to contribute? Here's how to set up `picasso` for local development.
+Development Setup
+~~~~~~~~~~~~~~~~~
 
-1. Fork the `picasso` repo on GitHub.
+Here's how to set up ``picasso`` for local development. If you are new to git and GitHub, you might want to familiarize yourself with the basics of git and GitHub first. The internet is full of great resources on this topic!
+
+1. Fork the ``picasso`` repo on GitHub.
 2. Clone your fork locally::
 
     $ git clone git@github.com:your_name_here/picasso.git
 
-3. Follow the installation instructions in the readme to install a picasso environment.
+3. Follow the installation instructions for developers here: https://github.com/jungmannlab/picasso?tab=readme-ov-file#for-developers-local-editable-installation.
+
+4. Set up ``pre-commit`` hooks. This ensures your code is automatically formatted with ``black`` before each commit::
 
-4. (Optionally) Build the docs (Note that you need to install sphinx and the rtd-theme)::
+    $ pre-commit install
+
+5. (Optionally) Build the docs (Note that you need to install sphinx and the rtd-theme)::
 
     $ cd docs/
-    $ make html  # docs will found in _build/html/. Open `index.html` to view the docs; macOS users can do `open _build/html/index.html` to open the docs in your default browser.
+    $ make html  # docs will be found in _build/html/. Open `index.html` to view the docs; macOS users can do `open _build/html/index.html` to open the docs in your default browser.
+
+Development Workflow
+~~~~~~~~~~~~~~~~~~~~
 
-4. Create a branch for local development::
+1. Create a branch for local development. Use a descriptive name prefixed with the type of change, e.g. ``fix/broken-rendering``, ``feat/new-filter``, ``docs/update-readme``::
 
-    $ git checkout -b name-of-your-bugfix-or-feature
+    $ git checkout -b fix/broken-rendering
 
    Now you can make your changes locally.
 
-5. When you're done making changes, check that your changes pass pycodestyle and the tests::
+2. Keep your fork in sync with the upstream repository to avoid merge conflicts::
+
+    $ git remote add upstream https://github.com/jungmannlab/picasso.git
+    $ git fetch upstream
+    $ git rebase upstream/main
+
+   You only need to run the ``git remote add`` command once.
 
-    $ py.test
-    $ cd picasso
-    $ pycodestyle .
+Code Style
+^^^^^^^^^^
 
-   To get flake8 and tox, just pip install them into your virtualenv.
+This project uses `black <https://github.com/psf/black>`_ for code formatting with a line length of 79 characters. The ``pre-commit`` hook (set up above) will automatically format your code on each commit. You can also run it manually::
 
-6. Commit your changes and push your branch to GitHub::
+    $ black --line-length=79 .
+
+Testing
+^^^^^^^
+
+3. When you're done making changes, run the tests from the repository root::
+
+    $ pytest
+
+   To run a specific test file for faster iteration::
+
+    $ pytest tests/test_render.py
+
+Committing & Pushing
+^^^^^^^^^^^^^^^^^^^^^
+
+4. Commit your changes using the imperative mood (e.g. "Fix bug" not "Fixed bug" or "Fixes bug"). Reference related issues in the commit message (#123 in the example below)::
 
     $ git add .
-    $ git commit -m "Your detailed description of your changes."
-    $ git push origin name-of-your-bugfix-or-feature
+    $ git commit -m "Fix rendering crash for large datasets (#123)"
+    $ git push origin fix/broken-rendering
+
+5. Update the changelog (``changelog.md``) with a brief summary of your changes under the appropriate section.
 
-7. Submit a pull request through the GitHub website.
+6. Submit a pull request through the GitHub website. See below for guidelines!
 
 Pull Request Guidelines
 -----------------------
 
 Before you submit a pull request, check that it meets these guidelines:
 
 1. The pull request should include tests.
-2. If the pull request adds functionality, the docs should be updated. 
-3. The pull request should work for Python 3.10.
+2. If the pull request adds functionality, the docs should be updated.
+3. The pull request should work for all Python versions specified in ``pyproject.toml`` (currently 3.10–3.14).
+4. Keep pull requests small and focused to make them easier to review. Make one pull request per issue/feature. If your pull request addresses multiple issues, consider splitting it into multiple pull requests.
+5. Reference the related issue (if any was raised) in the pull request description (e.g. "Closes #123").
+6. All CI checks must pass before the pull request can be merged. If your pull request fails CI checks, don't worry! The maintainers will work with you to resolve any issues. If you're not sure how to fix a CI failure, feel free to ask for help in the pull request comments.
+7. Many thanks for contributing! We will review your pull request as soon as we can.

LICENSE.txt

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2016 Jungmann Lab jungmannlab.org
+Copyright (c) 2016-2026 Jungmann Lab, MPI of Biochemistry (jungmannlab.org)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal