Merge branch 'main' into bugfix/issue355-nan-in-categorical-coloring

Author: timtreis

.github/release.yml

@@ -4,6 +4,7 @@ changelog:
       - release-ignore
     authors:
       - pre-commit-ci
+      - pre-commit-ci[bot]
   categories:
     - title: Added
       labels:

.github/workflows/test.yaml

@@ -3,66 +3,69 @@ name: Test
 on:
   push:
     branches: [main]
-    tags:
-      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+    tags: ["v*"] # Push events to matching v*, i.e. v1.0, v20.15.10
   pull_request:
-    branches: "*"
+    branches: ["*"]
 
 jobs:
   test:
-    runs-on: ${{ matrix.os }}
-    defaults:
-      run:
-        shell: bash -e {0} # -e to fail on error
-
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.10", "3.12"]
-        os: [ubuntu-latest]
+        env: ["dev-py311", "dev-py313"]
 
+    # Configure pytest-xdist
     env:
-      OS: ${{ matrix.os }}
-      PYTHON: ${{ matrix.python }}
+      OMP_NUM_THREADS: "1"
+      OPENBLAS_NUM_THREADS: "1"
+      MKL_NUM_THREADS: "1"
+      NUMEXPR_MAX_THREADS: "1"
+      MPLBACKEND: "agg"
+      DISPLAY: ":42"
+      PYTEST_ADDOPTS: "-n auto --dist=load --durations=10"
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python }}
 
-      - name: Get pip cache dir
-        id: pip-cache-dir
-        run: |
-          echo "::set-output name=dir::$(pip cache dir)"
-      - name: Restore pip cache
-        uses: actions/cache@v3
+      # Cache rattler's shared package cache (speeds up downloads)
+      - name: Restore rattler cache
+        uses: actions/cache@v4
         with:
-          path: ${{ steps.pip-cache-dir.outputs.dir }}
-          key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
+          path: ~/.cache/rattler
+          key: rattler-${{ runner.os }}-${{ matrix.env }}-${{ hashFiles('pyproject.toml') }}
           restore-keys: |
-            pip-${{ runner.os }}-${{ env.pythonLocation }}-
-      - name: Install test dependencies
-        run: |
-          python -m pip install --upgrade pip wheel
-          pip install pytest-cov
-      - name: Install dependencies
+            rattler-${{ runner.os }}-${{ matrix.env }}-
+            rattler-${{ runner.os }}-
+
+      # Install pixi and the requested environment
+      - uses: prefix-dev/[email protected]
+        with:
+          environments: ${{ matrix.env }}
+          # We're not comitting the pixi-lock file
+          locked: false
+          cache: false
+          activate-environment: ${{ matrix.env }}
+
+      - name: Show versions
         run: |
-          pip install --pre -e ".[dev,test,pre]"
-      - name: Test
+          python --version
+          pixi --version
+
+      - name: Run tests
         env:
           MPLBACKEND: agg
-          PLATFORM: ${{ matrix.os }}
-          DISPLAY: :42
+          DISPLAY: ":42"
         run: |
           pytest -v --cov --color=yes --cov-report=xml
+
       - name: Archive figures generated during testing
         if: always()
         uses: actions/upload-artifact@v4
         with:
-          name: visual_test_results_${{ matrix.os }}-python${{ matrix.python }}
+          name: visual_test_results_${{ matrix.env }}
           path: /home/runner/work/spatialdata-plot/spatialdata-plot/tests/figures/*
+
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:

.gitignore

@@ -44,3 +44,6 @@ tests/figures/
 # other
 _version.py
 /temp/
+
+# pixi
+pixi.lock

.mypy.ini

@@ -1,6 +1,5 @@
 [mypy]
 python_version = 3.10
-plugins = numpy.typing.mypy_plugin
 
 ignore_errors = False
 warn_redundant_casts = True

.pre-commit-config.yaml

@@ -9,17 +9,17 @@ ci:
   skip: []
 repos:
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.5.3
+    rev: v3.7.4
     hooks:
       - id: prettier
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.6
+    rev: v0.14.8
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.15.0
+    rev: v1.19.0
     hooks:
       - id: mypy
         additional_dependencies: [numpy, types-requests]

docs/conf.py

@@ -21,7 +21,7 @@
 info = metadata("spatialdata-plot")
 project_name = info["Name"]
 author = info["Author"]
-copyright = f"{datetime.now():%Y}, {author}."
+copyright = f"{datetime.now():%Y}, {author}"
 version = info["Version"]
 
 # repository_url = f"https://github.com/scverse/{project_name}"

pyproject.toml

@@ -9,14 +9,14 @@ authors = [
     {name = "scverse"},
 ]
 maintainers = [
-    {name = "scverse", email = "[email protected]"},
+    {name = "Tim Treis", email = "[email protected]"},
 ]
 urls.Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/index.html"
 urls.Source = "https://github.com/scverse/spatialdata-plot.git"
 urls.Home-page = "https://github.com/scverse/spatialdata-plot.git"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dynamic= [
-  "version" # allow version to be set by git tags
+    "version" # allow version to be set by git tags
 ]
 license = {file = "LICENSE"}
 readme = "README.md"
@@ -30,7 +30,16 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-    "bump2version",
+    "jupyterlab",
+    "notebook",
+    "ipykernel",
+    "ipywidgets",
+    "jupytext",
+    "pytest",
+    "pytest-cov",
+    "pooch",
+    "ruff",
+    "pre-commit",
 ]
 docs = [
     "sphinx>=4.5",
@@ -47,12 +56,9 @@ docs = [
 test = [
     "pytest",
     "pytest-cov",
+    "pytest-xdist",
     "pooch", # for scipy.datasets module
 ]
-# this will be used by readthedocs and will make pip also look for pre-releases, generally installing the latest available version
-pre = [
-    "spatialdata>=0.1.0-pre0"
-]
 
 [tool.coverage.run]
 source = ["spatialdata_plot"]
@@ -143,30 +149,45 @@ unfixable = ["B", "UP", "C4", "BLE", "T20", "RET"]
     "tests/*" = ["D", "PT", "B024"]
     "*/__init__.py" = ["F401", "D104", "D107", "E402"]
     "docs/*" = ["D","B","E","A"]
-    # "src/spatialdata/transformations/transformations.py" = ["D101","D102", "D106", "B024", "T201", "RET504"]
     "tests/conftest.py"= ["E402", "RET504"]
     "src/spatialdata_plot/pl/utils.py"= ["PGH003"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.bumpver]
-current_version = "0.0.2"
-version_pattern = "MAJOR.MINOR.PATCH"
-commit_message = "bump version {old_version} -> {new_version}"
-tag_message = "{new_version}"
-tag_scope = "default"
-pre_commit_hook = ""
-post_commit_hook = ""
-commit = true
-tag = true
-push = false
-
-[tool.bumpver.file_patterns]
-"pyproject.toml" = [
-    'current_version = "{version}"',
-]
-"README.md" = [
-    "{version}",
-    "{pep440_version}",
-]
+[tool.pixi.workspace]
+channels = ["conda-forge"]
+platforms = ["osx-arm64", "linux-64"]
+
+[tool.pixi.dependencies]
+python = ">=3.11"
+
+[tool.pixi.pypi-dependencies]
+spatialdata-plot = { path = ".", editable = true }
+
+# for gh-actions
+[tool.pixi.feature.py311.dependencies]
+python = "3.11.*"
+
+[tool.pixi.feature.py313.dependencies]
+python = "3.13.*"
+
+[tool.pixi.environments]
+# 3.11 lane (for gh-actions)
+dev-py311  = { features = ["dev", "test", "py311"], solve-group = "py311" }
+docs-py311 = { features = ["docs", "py311"],        solve-group = "py311" }
+
+# 3.13 lane
+default    = { features = ["py313"],                 solve-group = "py313" }
+dev-py313  = { features = ["dev", "test", "py313"],  solve-group = "py313" }
+docs-py313 = { features = ["docs", "py313"],         solve-group = "py313" }
+test-py313 = { features = ["test", "py313"],         solve-group = "py313" }
+
+[tool.pixi.tasks]
+lab = "jupyter lab"
+kernel-install = "python -m ipykernel install --user --name pixi-dev --display-name \"sdata-plot (dev)\""
+test = "pytest -v --color=yes --tb=short --durations=10"
+lint = "ruff check ."
+format = "ruff format ."
+pre-commit-install = "pre-commit install"
+pre-commit-run = "pre-commit run --all-files"

src/spatialdata_plot/_logging.py

@@ -1,6 +1,13 @@
 # from https://github.com/scverse/spatialdata/blob/main/src/spatialdata/_logging.py
 
 import logging
+import re
+from collections.abc import Iterator
+from contextlib import contextmanager
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:  # pragma: no cover
+    from _pytest.logging import LogCaptureFixture
 
 
 def _setup_logger() -> "logging.Logger":
@@ -21,3 +28,44 @@ def _setup_logger() -> "logging.Logger":
 
 
 logger = _setup_logger()
+
+
+@contextmanager
+def logger_warns(
+    caplog: "LogCaptureFixture",
+    logger: logging.Logger,
+    match: str | None = None,
+    level: int = logging.WARNING,
+) -> Iterator[None]:
+    """
+    Context manager similar to pytest.warns, but for logging.Logger.
+
+    Usage:
+        with logger_warns(caplog, logger, match="Found 1 NaN"):
+            call_code_that_logs()
+    """
+    # Store initial record count to only check new records
+    initial_record_count = len(caplog.records)
+
+    # Add caplog's handler directly to the logger to capture logs even if propagate=False
+    handler = caplog.handler
+    logger.addHandler(handler)
+    original_level = logger.level
+    logger.setLevel(level)
+
+    # Use caplog.at_level to ensure proper capture setup
+    with caplog.at_level(level, logger=logger.name):
+        try:
+            yield
+        finally:
+            logger.removeHandler(handler)
+            logger.setLevel(original_level)
+
+    # Only check records that were added during this context
+    records = [r for r in caplog.records[initial_record_count:] if r.levelno >= level]
+
+    if match is not None:
+        pattern = re.compile(match)
+        if not any(pattern.search(r.getMessage()) for r in records):
+            msgs = [r.getMessage() for r in records]
+            raise AssertionError(f"Did not find log matching {match!r} in records: {msgs!r}")