Merge branch 'main' into feature/outline_refactoring

Author: Sonja-Stockhaus

.github/workflows/test.yaml

@@ -3,67 +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 numpy
-          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:

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/pl/render.py

@@ -19,7 +19,7 @@
 from scanpy._settings import settings as sc_settings
 from spatialdata import get_extent, get_values, join_spatialelement_table
 from spatialdata.models import PointsModel, ShapesModel, get_table_keys
-from spatialdata.transformations import get_transformation, set_transformation
+from spatialdata.transformations import set_transformation
 from spatialdata.transformations.transformations import Identity
 from xarray import DataTree
 
@@ -46,7 +46,6 @@
     _get_colors_for_categorical_obs,
     _get_extent_and_range_for_datashader_canvas,
     _get_linear_colormap,
-    _get_transformation_matrix_for_datashader,
     _hex_no_alpha,
     _is_coercable_to_float,
     _map_color_seg,
@@ -190,10 +189,9 @@ def _render_shapes(
             sdata_filt.shapes[element].loc[is_point, "geometry"] = _geometry[is_point].buffer(scale.to_numpy())
 
         # apply transformations to the individual points
-        element_trans = get_transformation(sdata_filt.shapes[element], to_coordinate_system=coordinate_system)
-        tm = _get_transformation_matrix_for_datashader(element_trans)
+        tm = trans.get_matrix()
         transformed_element = sdata_filt.shapes[element].transform(
-            lambda x: (np.hstack([x, np.ones((x.shape[0], 1))]) @ tm)[:, :2]
+            lambda x: (np.hstack([x, np.ones((x.shape[0], 1))]) @ tm.T)[:, :2]
         )
         transformed_element = ShapesModel.parse(
             gpd.GeoDataFrame(

src/spatialdata_plot/pl/utils.py

@@ -65,11 +65,8 @@
 from spatialdata._core.query.relational_query import _locate_value
 from spatialdata._types import ArrayLike
 from spatialdata.models import Image2DModel, Labels2DModel, SpatialElement
-
-# from spatialdata.transformations.transformations import Scale
-from spatialdata.transformations import Affine, Identity, MapAxis, Scale, Translation
-from spatialdata.transformations import Sequence as SDSequence
 from spatialdata.transformations.operations import get_transformation
+from spatialdata.transformations.transformations import Scale
 from xarray import DataArray, DataTree
 
 from spatialdata_plot._logging import logger
@@ -2490,39 +2487,6 @@ def _prepare_transformation(
     return trans, trans_data
 
 
-def _get_datashader_trans_matrix_of_single_element(
-    trans: Identity | Scale | Affine | MapAxis | Translation,
-) -> ArrayLike:
-    flip_matrix = np.array([[1, 0, 0], [0, -1, 0], [0, 0, 1]])
-    tm: ArrayLike = trans.to_affine_matrix(("x", "y"), ("x", "y"))
-
-    if isinstance(trans, Identity):
-        return np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
-    if isinstance(trans, (Scale | Affine)):
-        # idea: "flip the y-axis", apply transformation, flip back
-        flip_and_transform: ArrayLike = flip_matrix @ tm @ flip_matrix
-        return flip_and_transform
-    if isinstance(trans, MapAxis):
-        # no flipping needed
-        return tm
-    # for a Translation, we need the transposed transformation matrix
-    tm_T = tm.T
-    assert isinstance(tm_T, np.ndarray)
-    return tm_T
-
-
-def _get_transformation_matrix_for_datashader(
-    trans: Scale | Identity | Affine | MapAxis | Translation | SDSequence,
-) -> ArrayLike:
-    """Get the affine matrix needed to transform shapes for rendering with datashader."""
-    if isinstance(trans, SDSequence):
-        tm = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
-        for x in trans.transformations:
-            tm = tm @ _get_datashader_trans_matrix_of_single_element(x)
-        return tm
-    return _get_datashader_trans_matrix_of_single_element(trans)
-
-
 def _datashader_map_aggregate_to_color(
     agg: DataArray,
     cmap: str | list[str] | ListedColormap,