Test auto update

.azure-pipelines.yml

@@ -16,8 +16,8 @@ jobs:
         Python3.11:
           python.version: "3.11"
           RUN_COVERAGE: yes
-        Python3.8:
-          python.version: "3.8"
+        Python3.9:
+          python.version: "3.9"
         PreRelease:
           python.version: "3.11"
           PRERELEASE_DEPENDENCIES: yes

anndata/__init__.py

@@ -10,7 +10,7 @@
     except ModuleNotFoundError:
         raise RuntimeError(
             "anndata is not correctly installed. Please install it, e.g. with pip."
-        )
+        ) from None
 
 # Allowing notes to be added to exceptions. See: https://github.com/scverse/anndata/issues/868
 import sys
@@ -39,7 +39,9 @@
     ImplicitModificationWarning,
     ExperimentalFeatureWarning,
 )
-from . import experimental
+
+if True:  # Bypass isort, this needs to come last
+    from . import experimental
 
 
 def read(*args, **kwargs):

anndata/_core/aligned_mapping.py

@@ -1,9 +1,9 @@
 from abc import ABC, abstractmethod
 from collections import abc as cabc
 from copy import copy
-from typing import Union, Optional, Type, ClassVar, TypeVar  # Special types
-from typing import Iterator, Mapping, Sequence  # ABCs
-from typing import Tuple, List, Dict  # Generic base types
+from typing import Union, Optional, Type, ClassVar, TypeVar
+from typing import Iterator, Mapping, Sequence
+from typing import Tuple, List, Dict
 import warnings
 
 import numpy as np

anndata/_io/utils.py

@@ -204,7 +204,7 @@ def func_wrapper(*args, **kwargs):
                 break
         try:
             return func(*args, **kwargs)
-        except Exception as e:
+        except Exception as e:  # noqa: BLE001
             re_raise_error(e, elem, elem.name, "read")
 
     return func_wrapper
@@ -237,7 +237,7 @@ def func_wrapper(*args, **kwargs):
                 break
         try:
             return func(*args, **kwargs)
-        except Exception as e:
+        except Exception as e:  # noqa: BLE001
             re_raise_error(e, elem, key, "writ")
 
     return func_wrapper

anndata/_io/write.py

@@ -54,7 +54,7 @@ def write_csvs(
                 value = value[None]
             try:
                 df = pd.DataFrame(value)
-            except Exception as e:
+            except Exception as e:  # noqa: BLE001
                 warnings.warn(
                     f"Omitting to write {key!r} of type {type(e)}.",
                     WriteWarning,

anndata/experimental/merge.py

@@ -108,7 +108,7 @@ def as_group(store, *args, **kwargs) -> Union[ZarrGroup, H5Group]:
     raise NotImplementedError("This is not yet implemented.")
 
 
-@as_group.register
+@as_group.register(os.PathLike)
 def _(store: os.PathLike, *args, **kwargs) -> Union[ZarrGroup, H5Group]:
     if store.suffix == ".h5ad":
         import h5py
@@ -119,7 +119,7 @@ def _(store: os.PathLike, *args, **kwargs) -> Union[ZarrGroup, H5Group]:
     return zarr.open_group(store, *args, **kwargs)
 
 
-@as_group.register
+@as_group.register(str)
 def _(store: str, *args, **kwargs) -> Union[ZarrGroup, H5Group]:
     return as_group(Path(store), *args, **kwargs)
 

anndata/tests/test_base.py

@@ -1,3 +1,4 @@
+from functools import partial
 from itertools import product
 import warnings
 
@@ -9,6 +10,7 @@
 from scipy.sparse import csr_matrix, issparse
 
 from anndata import AnnData
+from anndata._core.raw import Raw
 from anndata.tests.helpers import assert_equal, gen_adata
 
 
@@ -422,15 +424,15 @@ def test_equality_comparisons():
     adata1 = AnnData(np.array([[1, 2], [3, 4], [5, 6]]))
     adata2 = AnnData(np.array([[1, 2], [3, 4], [5, 6]]))
     with pytest.raises(NotImplementedError):
-        adata1 == adata1
+        adata1 == adata1  # noqa: B015
     with pytest.raises(NotImplementedError):
-        adata1 == adata2
+        adata1 == adata2  # noqa: B015
     with pytest.raises(NotImplementedError):
-        adata1 != adata2
+        adata1 != adata2  # noqa: B015
     with pytest.raises(NotImplementedError):
-        adata1 == 1
+        adata1 == 1  # noqa: B015
     with pytest.raises(NotImplementedError):
-        adata1 != 1
+        adata1 != 1  # noqa: B015
 
 
 def test_rename_categories():
@@ -494,19 +496,19 @@ def assert_same_op_result(a1, a2, op):
 
     for obs_k, layer in product(["a", "b", "c", "anno1"], [None, "x2"]):
         assert_same_op_result(
-            adata, adata_dense, lambda x: x.obs_vector(obs_k, layer=layer)
+            adata, adata_dense, partial(AnnData.obs_vector, k=obs_k, layer=layer)
         )
 
     for obs_k in ["a", "b", "c"]:
-        assert_same_op_result(adata, adata_dense, lambda x: x.raw.obs_vector(obs_k))
+        assert_same_op_result(adata.raw, adata_dense.raw, partial(Raw.obs_vector, k=obs_k))
 
     for var_k, layer in product(["s1", "s2", "anno2"], [None, "x2"]):
         assert_same_op_result(
-            adata, adata_dense, lambda x: x.var_vector(var_k, layer=layer)
+            adata, adata_dense, partial(AnnData.var_vector, k=var_k, layer=layer)
         )
 
     for var_k in ["s1", "s2", "anno2"]:
-        assert_same_op_result(adata, adata_dense, lambda x: x.raw.var_vector(var_k))
+        assert_same_op_result(adata.raw, adata_dense.raw, partial(Raw.var_vector, k=var_k))
 
 
 def test_1d_slice_dtypes():

anndata/tests/test_concatenate.py

@@ -1347,8 +1347,8 @@ def test_concatenate_size_0_dim():
     b = gen_adata((5, 0))
 
     # Mostly testing that this doesn't error
-    a.concatenate([b]).shape == (10, 0)
-    b.concatenate([a]).shape == (10, 0)
+    assert a.concatenate([b]).shape == (10, 0)
+    assert b.concatenate([a]).shape == (10, 0)
 
 
 def test_concat_null_X():

anndata/tests/test_dask.py

@@ -82,7 +82,7 @@ def test_dask_write(adata, tmp_path, diskfmt):
     write(orig, pth)
     curr = read(pth)
 
-    with pytest.raises(Exception):
+    with pytest.raises(AssertionError):
         assert_equal(curr.obsm["a"], curr.obsm["b"])
 
     assert_equal(curr.varm["a"], orig.varm["a"])
@@ -120,7 +120,7 @@ def test_dask_distributed_write(adata, tmp_path, diskfmt):
             write_elem(g, "", orig)
             curr = read_elem(g)
 
-    with pytest.raises(Exception):
+    with pytest.raises(AssertionError):
         assert_equal(curr.obsm["a"], curr.obsm["b"])
 
     assert_equal(curr.varm["a"], orig.varm["a"])
@@ -157,7 +157,7 @@ def test_dask_to_memory_check_array_types(adata, tmp_path, diskfmt):
 
     mem = orig.to_memory()
 
-    with pytest.raises(Exception):
+    with pytest.raises(AssertionError):
         assert_equal(curr.obsm["a"], curr.obsm["b"])
 
     assert_equal(curr.varm["a"], orig.varm["a"])
@@ -195,7 +195,7 @@ def test_dask_to_memory_copy_check_array_types(adata, tmp_path, diskfmt):
 
     mem = orig.to_memory(copy=True)
 
-    with pytest.raises(Exception):
+    with pytest.raises(AssertionError):
         assert_equal(curr.obsm["a"], curr.obsm["b"])
 
     assert_equal(curr.varm["a"], orig.varm["a"])
@@ -225,7 +225,7 @@ def test_dask_copy_check_array_types(adata):
     orig = adata
     curr = adata.copy()
 
-    with pytest.raises(Exception):
+    with pytest.raises(AssertionError):
         assert_equal(curr.obsm["a"], curr.obsm["b"])
 
     assert_equal(curr.varm["a"], orig.varm["a"])

anndata/tests/test_io_utils.py

@@ -1,4 +1,4 @@
-from contextlib import suppress
+from contextlib import nullcontext
 
 import pytest
 import zarr
@@ -33,7 +33,7 @@ def read_attr(_):
         raise NotImplementedError()
 
     group = group_fn(tmp_path)
-    with group if hasattr(group, "__enter__") else suppress():
+    with group if hasattr(group, "__enter__") else nullcontext():
         group["X"] = [1, 2, 3]
         group.create_group("group")
 

anndata/utils.py

@@ -273,11 +273,11 @@ def convert_dictionary_to_structured_array(source: Mapping[str, Sequence[Any]]):
             else np.asarray(col).astype("U")
             for col in source.values()
         ]
-    except UnicodeEncodeError:
+    except UnicodeEncodeError as e:
         raise ValueError(
             "Currently only support ascii strings. "
             "Don’t use “ö” etc. for sample annotation."
-        )
+        ) from e
 
     # if old_index_key not in source:
     #     names.append(new_index_key)

docs/release-notes/0.10.0.md

@@ -24,6 +24,8 @@
 ```{rubric} Other updates
 ```
 
+- Bump minimum python version to 3.9 {pr}`820` {user}`flying-sheep`
+
 ```{rubric} Deprecations
 ```
 

pyproject.toml

@@ -5,7 +5,7 @@ requires = ["hatchling", "hatch-vcs"]
 [project]
 name = "anndata"
 description = "Annotated data."
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = "BSD-3-Clause"
 authors = [
     {name = "Philipp Angerer"},
@@ -29,7 +29,6 @@ classifiers = [
     "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
@@ -128,21 +127,37 @@ markers = ["gpu: mark test to run on GPU"]
 
 [tool.ruff]
 ignore = [
+    # TODO: add `stacklevel` arg to all `warn` calls
+    "B028",
+    # dict() calls are prettier for kwargs dicts
+    "C408",
     # line too long -> we accept long comment lines; black gets rid of long code lines
     "E501",
-    # Do not assign a lambda expression, use a def -> Scanpy allows lambda expression assignments,
+    # Do not assign a lambda expression, use a def -> AnnData allows lambda expression assignments
     "E731",
     # allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
     "E741",
 ]
 select = [
-    "E",
-    "F",
-    "W",
+    "F",      # Errors detected by Pyflakes
+    "E",      # Error detected by Pycodestyle
+    "W",      # Warning detected by Pycodestyle
+    "I",      # isort
+    "B",      # flake8-bugbear
+    "C4",     # flake8-comprehensions
+    "BLE",    # flake8-blind-except
+    "UP",     # pyupgrade
+    "TCH",    # manage type checking blocks
+    "RUF100", # Report unused noqa directives
 ]
 [tool.ruff.per-file-ignores]
 # E721 comparing types, but we specifically are checking that we aren't getting subtypes (views)
 "anndata/tests/test_readwrite.py" = ["E721"]
+[tool.ruff.isort]
+known-first-party = ["anndata"]
+required-imports = ["from __future__ import annotations"]
+[tool.ruff.flake8-bugbear]
+extend-immutable-calls = ["slice"]
 
 [tool.codespell]
 skip = ".git,*.pdf,*.svg"