Merge branch 'main' into feature/202306_support_multipolygons

Author: timtreis

.github/codecov.yml

@@ -1,4 +1,4 @@
-# Based on spatialdata
+# Based on pydata/xarray
 codecov:
     require_ci_to_pass: false
 
@@ -15,3 +15,6 @@ comment:
     layout: "diff, flags, files"
     behavior: once
     require_base: false
+
+fixes:
+    - "/spatialdata-plot/spatialdata-plot/::spatialdata-plot/src/spatialdat_plot/"

.github/workflows/build.yaml

@@ -6,21 +6,15 @@ on:
     pull_request:
         branches: [main]
 
-concurrency:
-    group: ${{ github.workflow }}-${{ github.ref }}
-    cancel-in-progress: true
-
 jobs:
     package:
         runs-on: ubuntu-latest
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v2
             - name: Set up Python 3.10
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v2
               with:
                   python-version: "3.10"
-                  cache: "pip"
-                  cache-dependency-path: "**/pyproject.toml"
             - name: Install build dependencies
               run: python -m pip install --upgrade pip wheel twine build
             - name: Build package

.github/workflows/test_and_deploy.yaml

@@ -8,10 +8,6 @@ on:
     pull_request:
         branches: [main]
 
-concurrency:
-    group: ${{ github.workflow }}-${{ github.ref }}
-    cancel-in-progress: true
-
 jobs:
     test:
         runs-on: ${{ matrix.os }}
@@ -30,9 +26,9 @@ jobs:
             PYTHON: ${{ matrix.python }}
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v3
             - name: Set up Python ${{ matrix.python }}
-              uses: actions/setup-python@v2
+              uses: actions/setup-python@v3
               with:
                   python-version: ${{ matrix.python }}
 
@@ -41,7 +37,7 @@ jobs:
               run: |
                   echo "::set-output name=dir::$(pip cache dir)"
             - name: Restore pip cache
-              uses: actions/cache@v2
+              uses: actions/cache@v3
               with:
                   path: ${{ steps.pip-cache-dir.outputs.dir }}
                   key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}

pyproject.toml

@@ -1,24 +1,19 @@
-[build-system]
-build-backend = "hatchling.build"
-requires = ["hatchling", "hatch-vcs"]
-
-
 [project]
 name = "spatialdata-plot"
-description = "Static plotting for SpatialData."
+description = "Static plotting for spatial data."
 authors = [
     {name = "scverse"},
 ]
 maintainers = [
     {name = "scverse", email = "[email protected]"},
 ]
-urls.Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/"
+urls.Documentation = "https://spatialdata.readthedocs.io/"
 urls.Source = "https://github.com/scverse/spatialdata-plot.git"
 urls.Home-page = "https://github.com/scverse/spatialdata-plot.git"
+requires-python = ">=3.9"
 dynamic= [
   "version" # allow version to be set by git tags
 ]
-requires-python = ">=3.9"
 license = {file = "LICENSE"}
 readme = "README.md"
 dependencies = [
@@ -51,14 +46,9 @@ test = [
     "pytest",
     "pytest-cov",
 ]
-torch = [
-    "torch"
-]
-extra  = [
-]
 
 [tool.coverage.run]
-source = ["spatialdata-plot"]
+source = ["spatialdata_plot"]
 omit = [
     "**/test_*.py",
 ]
@@ -100,9 +90,6 @@ exclude = '''
 [tool.jupytext]
 formats = "ipynb,md"
 
-[tool.hatch.metadata]
-allow-direct-references = true
-
 [tool.hatch.build.targets.wheel]
 packages = ['src/spatialdata_plot']
 
@@ -112,6 +99,9 @@ source = "vcs"
 [tool.hatch.build.hooks.vcs]
 version-file = "_version.py"
 
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [tool.ruff]
 exclude = [
     ".git",
@@ -173,4 +163,4 @@ target-version = "py39"
 convention = "numpy"
 [tool.ruff.pyupgrade]
 # Preserve types, even if a file imports `from __future__ import annotations`.
-keep-runtime-typing = true
+keep-runtime-typing = true

src/spatialdata_plot/pl/basic.py

@@ -139,7 +139,7 @@ def _copy(
 
     def render_shapes(
         self,
-        element: str | None = None,
+        elements: str | list[str] | None = None,
         color: str | None = None,
         groups: str | Sequence[str] | None = None,
         size: float = 1.0,
@@ -161,8 +161,8 @@ def render_shapes(
 
         Parameters
         ----------
-        element
-            The name of the shapes element to render. If `None`, the first
+        elements
+            The name of the shapes element(s) to render. If `None`, all
             shapes element in the `SpatialData` object will be used.
         color
             Key for annotations in :attr:`anndata.AnnData.obs` or variables/genes.
@@ -209,7 +209,7 @@ def render_shapes(
         )
         outline_params = _set_outline(size, outline, outline_width, outline_color)
         sdata.plotting_tree[f"{n_steps+1}_render_shapes"] = ShapesRenderParams(
-            element=element,
+            elements=elements,
             color=color,
             groups=groups,
             outline_params=outline_params,
@@ -219,13 +219,14 @@ def render_shapes(
             palette=palette,
             outline_alpha=outline_alpha,
             fill_alpha=fill_alpha,
+            transfunc=kwargs.get("transfunc", None),
         )
 
         return sdata
 
     def render_points(
         self,
-        element: str | None = None,
+        elements: str | list[str] | None = None,
         color: str | None = None,
         groups: str | Sequence[str] | None = None,
         size: float = 1.0,
@@ -241,8 +242,8 @@ def render_points(
 
         Parameters
         ----------
-        element
-            The name of the points element to render. If `None`, the first
+        elements
+            The name of the points element(s) to render. If `None`, all
             shapes element in the `SpatialData` object will be used.
         color
             Key for annotations in :attr:`anndata.AnnData.obs` or variables/genes.
@@ -278,19 +279,21 @@ def render_points(
             **kwargs,
         )
         sdata.plotting_tree[f"{n_steps+1}_render_points"] = PointsRenderParams(
-            element=element,
+            elements=elements,
             color=color,
             groups=groups,
             cmap_params=cmap_params,
             palette=palette,
             alpha=alpha,
+            transfunc=kwargs.get("transfunc", None),
+            size=size,
         )
 
         return sdata
 
     def render_images(
         self,
-        element: str | None = None,
+        elements: str | list[str] | None = None,
         channel: list[str] | list[int] | int | str | None = None,
         cmap: Colormap | str | None = None,
         norm: Optional[Normalize] = None,
@@ -304,9 +307,9 @@ def render_images(
 
         Parameters
         ----------
-        element
-            The name of the image element to render. If `None`, the first
-            shapes element in the `SpatialData` object will be used.
+        elements
+            The name of the image element(s) to render. If `None`, all
+            shapes elements in the `SpatialData` object will be used.
         channel
             To select which channel to plot (all by default).
         cmap
@@ -335,7 +338,7 @@ def render_images(
             **kwargs,
         )
         sdata.plotting_tree[f"{n_steps+1}_render_images"] = ImageRenderParams(
-            element=element,
+            elements=elements,
             channel=channel,
             cmap_params=cmap_params,
             palette=palette,
@@ -346,7 +349,7 @@ def render_images(
 
     def render_labels(
         self,
-        element: str | None = None,
+        elements: str | list[str] | None = None,
         color: str | None = None,
         groups: str | Sequence[str] | None = None,
         contour_px: int = 3,
@@ -366,9 +369,9 @@ def render_labels(
 
         Parameters
         ----------
-        element
-            The name of the labels element to render. If `None`, the first
-            labels element in the `SpatialData` object will be used.
+        elements
+            The name of the labels element(s) to render. If `None`, all
+            labels elements in the `SpatialData` object will be used.
         color
             Key for annotations in :attr:`anndata.AnnData.obs` or variables/genes.
         groups
@@ -417,7 +420,7 @@ def render_labels(
             **kwargs,
         )
         sdata.plotting_tree[f"{n_steps+1}_render_labels"] = LabelsRenderParams(
-            element=element,
+            elements=elements,
             color=color,
             groups=groups,
             contour_px=contour_px,
@@ -428,6 +431,7 @@ def render_labels(
             palette=palette,
             outline_alpha=outline_alpha,
             fill_alpha=fill_alpha,
+            transfunc=kwargs.get("transfunc", None),
         )
 
         return sdata
@@ -519,6 +523,15 @@ def show(
         # Simplicstic solution: If the images are multiscale, just use the first
         sdata = _multiscale_to_image(sdata)
 
+        # handle coordinate system
+        coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
+        if isinstance(coordinate_systems, str):
+            coordinate_systems = [coordinate_systems]
+
+        for cs in coordinate_systems:
+            if cs not in sdata.coordinate_systems:
+                raise ValueError(f"Unknown coordinate system '{cs}', valid choices are: {sdata.coordinate_systems}")
+
         extent = _get_extent(
             sdata=sdata,
             has_images="render_images" in render_cmds,
@@ -528,11 +541,6 @@ def show(
             coordinate_systems=coordinate_systems,
         )
 
-        # handle coordinate system
-        coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
-        if isinstance(coordinate_systems, str):
-            coordinate_systems = [coordinate_systems]
-
         # Use extent to filter out coordinate system without the relevant elements
         valid_cs = []
         for cs in coordinate_systems:
@@ -542,13 +550,18 @@ def show(
                 logg.info(f"Dropping coordinate system '{cs}' since it doesn't have relevant elements.")
         coordinate_systems = valid_cs
 
+        # print(coordinate_systems)
+        # cs_mapping = _get_coordinate_system_mapping(sdata)
+        # print(cs_mapping)
+
         # check that coordinate system and elements to be rendered match
-        for cmd, params in render_cmds.items():
-            if params.element is not None and len([params.element]) != len(coordinate_systems):
-                raise ValueError(
-                    f"Number of coordinate systems ({len(coordinate_systems)}) does not match number of elements "
-                    f"({len(params.element)}) in command {cmd}."
-                )
+        # for cmd, params in render_cmds.items():
+        #     if params.elements is not None and len([params.elements]) != len(coordinate_systems):
+        #         print(params.elements)
+        #         raise ValueError(
+        #             f"Number of coordinate systems ({len(coordinate_systems)}) does not match number of elements "
+        #             f"({len(params.elements)}) in command {cmd}."
+        #         )
 
         # set up canvas
         fig_params, scalebar_params = _prepare_params_plot(
@@ -679,8 +692,15 @@ def show(
                     cs_contents.query(f"cs == '{cs}'")["has_shapes"][0],
                 ]
             ):
-                ax.set_xlim(extent[cs][0], extent[cs][1])
-                ax.set_ylim(extent[cs][3], extent[cs][2])  # (0, 0) is top-left
+                # If the axis already has limits, only expand them but not overwrite
+                x_min, x_max = ax.get_xlim()
+                y_min, y_max = ax.get_ylim()
+                x_min = min(x_min, extent[cs][0])
+                x_max = max(x_max, extent[cs][1])
+                y_min = min(y_min, extent[cs][2])
+                y_max = max(y_max, extent[cs][3])
+                ax.set_xlim(x_min, x_max)
+                ax.set_ylim(y_max, y_min)  # (0, 0) is top-left
 
         if fig_params.fig is not None and save is not None:
             save_fig(fig_params.fig, path=save)