[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.14
+    rev: v0.2.0
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

.vscode/settings.json

@@ -3,12 +3,11 @@
         "editor.formatOnSave": true,
         "editor.defaultFormatter": "charliermarsh.ruff",
         "editor.codeActionsOnSave": {
-            "source.fixAll.ruff": true,
-            "source.organizeImports.ruff": true,
+            "source.fixAll.ruff": "always",
+            "source.organizeImports.ruff": "always",
         },
     },
-    "python.testing.pytestArgs": [],
-    "python.testing.unittestEnabled": false,
     "python.testing.pytestEnabled": true,
+    "python.testing.pytestArgs": ["--color=yes", "-vv"],
     "python.terminal.activateEnvironment": false,
 }

pyproject.toml

@@ -66,6 +66,7 @@ addopts = [
 
 [tool.ruff]
 line-length = 120
+[tool.ruff.lint]
 select = ['ALL']
 ignore = [
     'Q', # handled by formatter
@@ -79,7 +80,7 @@ ignore = [
     'S101', # asserts are fine
 ]
 allowed-confusables = ['’', '×']
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 'src/**/*.py' = ['PT']  # No Pytest checks
 'docs/**/*.py' = ['INP001']  # No __init__.py in docs
 'tests/**/*.py' = [
@@ -89,7 +90,7 @@ allowed-confusables = ['’', '×']
     'PD901', # “df” is a fine var name in tests
     'PLR2004', # magic numbers are fine in tests
 ]
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 known-first-party = ['anndata2ri']
 lines-after-imports = 2
 [tool.ruff.format]

src/anndata2ri/_py2r.py

@@ -26,8 +26,8 @@ class NotConvertedWarning(Warning):
 
 dict_converter = conversion.Converter('Converter handling dicts')
 dict_converter.py2rpy.register(np.bool_, lambda x: conversion.py2rpy(bool(x)))
-dict_converter.py2rpy.register(np.int_, lambda x: conversion.py2rpy(int(x)))
-dict_converter.py2rpy.register(np.float_, lambda x: conversion.py2rpy(float(x)))
+dict_converter.py2rpy.register(np.integer, lambda x: conversion.py2rpy(int(x)))
+dict_converter.py2rpy.register(np.floating, lambda x: conversion.py2rpy(float(x)))
 dict_converter.py2rpy.register(np.bytes_, lambda x: conversion.py2rpy(bytes(x)))
 dict_converter.py2rpy.register(np.str_, lambda x: conversion.py2rpy(str(x)))
 

src/anndata2ri/scipy2ri/_r2py.py

@@ -59,7 +59,7 @@ def rmat_to_spmat(rmat: SexpS4) -> sparse.spmatrix:
                 if supported_r_matrix_classes(types='n') & r_classes
                 else slots['x']
             )
-            dtype = np.bool_ if supported_r_matrix_classes(types=('n', 'l')) & r_classes else np.float_
+            dtype = np.bool_ if supported_r_matrix_classes(types=('n', 'l')) & r_classes else np.float64
             return mat_cls((data, *coord_spec), shape=shape, dtype=dtype)
 
         msg = 'Should have hit one of the branches'

tests/test_py2rpy.py

@@ -57,7 +57,13 @@ def test_py2rpy(
     dataset: Callable[[], AnnData],
 ) -> None:
     if dataset is sc.datasets.krumsiek11:
-        with pytest.warns(UserWarning, match=r'Duplicated obs_names'):
+        with (
+            pytest.warns(UserWarning, match=r'Duplicated obs_names'),
+            pytest.warns(UserWarning, match=r'Observation names are not unique'),
+            # TODO(flying-sheep): Adapt to rpy2 changes instead
+            # https://github.com/theislab/anndata2ri/issues/109
+            pytest.warns(DeprecationWarning, match=r'rpy2\.robjects\.conversion is deprecated'),
+        ):
             ex = py2r(anndata2ri, dataset())
     else:
         ex = py2r(anndata2ri, dataset())

tests/test_scipy_rpy2py.py

@@ -49,10 +49,10 @@
 coo_b2 = [[0, 0, 1], [0, 1, 0], [0, 0, 0]]
 
 mats = [
-    pytest.param((0, 0), sparse.csc_matrix, np.float_, csc_empty, dgc_empty, id='dgC_empty'),
-    pytest.param((3, 2), sparse.csc_matrix, np.float_, csc_f, dgc, id='dgC'),
-    pytest.param((2, 3), sparse.csr_matrix, np.float_, csr_f, dgr, id='dgR'),
-    pytest.param((2, 3), sparse.coo_matrix, np.float_, coo_f, dgt, id='dgT'),
+    pytest.param((0, 0), sparse.csc_matrix, np.float64, csc_empty, dgc_empty, id='dgC_empty'),
+    pytest.param((3, 2), sparse.csc_matrix, np.float64, csc_f, dgc, id='dgC'),
+    pytest.param((2, 3), sparse.csr_matrix, np.float64, csr_f, dgr, id='dgR'),
+    pytest.param((2, 3), sparse.coo_matrix, np.float64, coo_f, dgt, id='dgT'),
     pytest.param((2, 3), sparse.csc_matrix, np.bool_, csc_b1, lgc, id='lgC'),
     pytest.param((3, 3), sparse.csr_matrix, np.bool_, csr_b1, lgr, id='lgR'),
     # pytest.param((?, ?), sparse.coo_matrix, np.bool_, coo_b1, lgt, id="lgT"),