Modernize setup (#434)

Signed-off-by: Lukas Heumos <[email protected]>

Author: Zethson

.flake8

@@ -11,7 +11,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python 3.12
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.12"
           cache: pip

.github/workflows/release.yaml

@@ -26,9 +26,9 @@ jobs:
       PYTHON: ${{ matrix.python }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
 

.github/workflows/test.yaml

@@ -8,26 +8,19 @@ minimum_pre_commit_version: 2.16.0
 ci:
   skip: []
 repos:
-  - repo: https://github.com/psf/black
-    rev: 25.1.0
-    hooks:
-      - id: black
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.5.1
     hooks:
       - id: prettier
-  - repo: https://github.com/asottile/blacken-docs
-    rev: 1.19.1
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.2
     hooks:
-      - id: blacken-docs
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.15.0
     hooks:
       - id: mypy
         additional_dependencies: [numpy, types-requests]
         exclude: tests/|docs/
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.0
-    hooks:
-      - id: ruff
-        args: [--fix, --exit-non-zero-on-fix]

.pre-commit-config.yaml

@@ -1,16 +1,15 @@
-# https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "3.10"
+    python: "3.12"
+  commands:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv venv
+    - uv pip install .[docs,pre]
+    - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
 sphinx:
   configuration: docs/conf.py
   fail_on_warning: false
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
-        - pre

.readthedocs.yaml

@@ -18,7 +18,10 @@
 
 The `spatialdata-plot` package extends `spatialdata` with a declarative plotting API that enables to quickly visualize `spatialdata` objects and their respective elements (i.e. `images`, `labels`, `points` and `shapes`).
 
-SpatialData’s plotting capabilities allow to quickly visualise all contained modalities. The user can specify which elements should be rendered (images, labels, points, shapes) and specify certain parameters for each layer, such as for example the intent to color shapes by a gene’s expression profile or which color to use for which image channel. When the plot is then eventually displayed, all transformations, alignments and coordinate systems are internally processed to form the final visualisation. In concordance with the general SpatialData philosophy, all modalities of the major spatial technologies are supported out of the box.
+SpatialData’s plotting capabilities allow to quickly visualise all contained modalities.
+The user can specify which elements should be rendered (images, labels, points, shapes) and specify certain parameters for each layer, such as for example the intent to color shapes by a gene’s expression profile or which color to use for which image channel.
+When the plot is then eventually displayed, all transformations, alignments and coordinate systems are internally processed to form the final visualisation.
+In concordance with the general SpatialData philosophy, all modalities of the major spatial technologies are supported out of the box.
 
 <img src='https://raw.githubusercontent.com/scverse/spatialdata-plot/main/docs/spatialdata-plot.png'/>
 
@@ -36,15 +39,13 @@ Python installed, we recommend installing [Mambaforge](https://github.com/conda-
 
 There are several alternative options to install spatialdata-plot:
 
-<!--
-1) Install the latest release of `spatialdata-plot` from `PyPI <https://pypi.org/project/spatialdata-plot/>`_:
+1. Install the latest release of `spatialdata-plot` from `PyPI <https://pypi.org/project/spatialdata-plot/>`\_:
 
 ```bash
 pip install spatialdata-plot
 ```
--->
 
-1. Install the latest development version:
+2. Install the latest development version:
 
 ```bash
 pip install git+https://github.com/scverse/spatialdata-plot.git@main

README.md

@@ -4,7 +4,6 @@
 :maxdepth: 1
 :caption: API
 
-preprocessing.rst
 plotting.rst
 
 ```

docs/_static/.gitkeep

@@ -73,27 +73,6 @@ filterwarnings = [
     #     "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
-[tool.black]
-line-length = 120
-target-version = ['py310']
-include = '\.pyi?$'
-exclude = '''
-(
-  /(
-      \.eggs
-    | \.git
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | buck-out
-    | build
-    | dist
-  )/
-)
-'''
-
 [tool.jupytext]
 formats = "ipynb,md"
 
@@ -110,6 +89,7 @@ version-file = "_version.py"
 allow-direct-references = true
 
 [tool.ruff]
+line-length = 120
 exclude = [
     ".git",
     ".tox",
@@ -119,7 +99,8 @@ exclude = [
     "dist",
     "setup.py",
 ]
-lint.ignore = [
+[tool.ruff.lint]
+ignore = [
     # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
     "E731",
     # allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
@@ -137,8 +118,7 @@ lint.ignore = [
     # Missing docstring in magic method
     "D105",
 ]
-line-length = 120
-lint.select = [
+select = [
     "D", # flake8-docstrings
     "I", # isort
     "E", # pycodestyle
@@ -157,15 +137,16 @@ lint.select = [
     "RET", # flake8-raise
     "PGH", # pygrep-hooks
 ]
-lint.unfixable = ["B", "UP", "C4", "BLE", "T20", "RET"]
-target-version = "py310"
+unfixable = ["B", "UP", "C4", "BLE", "T20", "RET"]
+
 [tool.ruff.lint.per-file-ignores]
     "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"
 
@@ -189,4 +170,3 @@ push = false
     "{version}",
     "{pep440_version}",
 ]
-

docs/_templates/.gitkeep

@@ -214,8 +214,7 @@ def empty_table() -> SpatialData:
 
 @pytest.fixture(
     # params=["labels"]
-    params=["full", "empty"]
-    + ["images", "labels", "points", "table_single_annotation", "table_multiple_annotations"]
+    params=["full", "empty"] + ["images", "labels", "points", "table_single_annotation", "table_multiple_annotations"]
     # + ["empty_" + x for x in ["table"]] # TODO: empty table not supported yet
 )
 def sdata(request) -> SpatialData:

docs/api.md

@@ -98,9 +98,7 @@ def test_plot_can_color_labels_by_categorical_variable(self, sdata_blobs: Spatia
         ],
     )
     def test_plot_can_color_labels_by_categorical_variable_in_other_table(self, sdata_blobs: SpatialData, label: str):
-
         def _make_tablemodel_with_categorical_labels(sdata_blobs, label):
-
             adata = sdata_blobs.tables["table"].copy()
             max_col = adata.to_df().idxmax(axis=1)
             max_col = max_col.str.replace("channel_", "ch").str.replace("_sum", "")
@@ -163,7 +161,6 @@ def test_plot_label_colorbar_uses_alpha_of_less_transparent_infill(
         self,
         sdata_blobs: SpatialData,
     ):
-
         sdata_blobs.pl.render_labels(
             "blobs_labels", color="channel_0_sum", fill_alpha=0.1, outline_alpha=0.7, contour_px=15
         ).pl.show()
@@ -172,7 +169,6 @@ def test_plot_label_colorbar_uses_alpha_of_less_transparent_outline(
         self,
         sdata_blobs: SpatialData,
     ):
-
         sdata_blobs.pl.render_labels("blobs_labels", color="channel_0_sum", fill_alpha=0.7, outline_alpha=0.1).pl.show()
 
     def test_can_plot_with_one_element_color_table(self, sdata_blobs: SpatialData):

docs/conf.py.rej

@@ -86,7 +86,6 @@ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData
     ],
 )
 def test_is_color_like(color_result: tuple[ColorLike, bool]):
-
     color, result = color_result
 
     assert spatialdata_plot.pl.utils._is_color_like(color) == result
@@ -121,7 +120,6 @@ def test_utils_sanitise_na_color(input_output):
     ],
 )
 def test_utils_sanitise_na_color_accepts_valid_inputs(input_output):
-
     func_input, expected_output = input_output
 
     assert _sanitise_na_color(func_input) == expected_output
@@ -141,7 +139,6 @@ def test_utils_sanitise_na_color_fails_when_input_isnt_a_color():
     ],
 )
 def test_utils_get_subplots_produces_correct_axs_layout(input_output):
-
     num_images, ncols, len_axs, axs_visible = input_output
 
     _, axs = _get_subplots(num_images=num_images, ncols=ncols)