Finish merge

scanpy/_settings.py

@@ -27,9 +27,9 @@
 
 # Collected from the print_* functions in matplotlib.backends
 _Format = Union[
-    Literal['png', 'jpg', 'tif', 'tiff'],
-    Literal['pdf', 'ps', 'eps', 'svg', 'svgz', 'pgf'],
-    Literal['raw', 'rgba'],
+    Literal["png", "jpg", "tif", "tiff"],
+    Literal["pdf", "ps", "eps", "svg", "svgz", "pgf"],
+    Literal["raw", "rgba"],
 ]
 
 

scanpy/external/pl.py

@@ -20,7 +20,7 @@
 from .tl._wishbone import _anndata_to_wishbone
 
 
-@doctest_needs('phate')
+@doctest_needs("phate")
 @_wraps_plot_scatter
 @_doc_params(
     adata_color_etc=doc_adata_color_etc,

scanpy/external/pp/_harmony_integrate.py

@@ -8,7 +8,7 @@
 from ...testing._doctests import doctest_needs
 
 
-@doctest_needs('harmonypy')
+@doctest_needs("harmonypy")
 def harmony_integrate(
     adata: AnnData,
     key: str,

scanpy/external/pp/_hashsolo.py

@@ -257,7 +257,7 @@ def _calculate_bayes_rule(data, priors, number_of_noise_barcodes):
     }
 
 
-@doctest_skip('Illustrative but not runnable doctest code')
+@doctest_skip("Illustrative but not runnable doctest code")
 def hashsolo(
     adata: anndata.AnnData,
     cell_hashing_columns: list,

scanpy/external/pp/_magic.py

@@ -15,7 +15,7 @@
 MIN_VERSION = "2.0"
 
 
-@doctest_needs('magic')
+@doctest_needs("magic")
 def magic(
     adata: AnnData,
     name_list: Union[Literal["all_genes", "pca_only"], Sequence[str], None] = None,

scanpy/external/pp/_scanorama_integrate.py

@@ -9,7 +9,7 @@
 from ...testing._doctests import doctest_needs
 
 
-@doctest_needs('scanorama')
+@doctest_needs("scanorama")
 def scanorama_integrate(
     adata: AnnData,
     key: str,

scanpy/external/tl/_harmony_timeseries.py

@@ -13,7 +13,7 @@
 from ...testing._doctests import doctest_needs
 
 
-@doctest_needs('harmony')
+@doctest_needs("harmony")
 def harmony_timeseries(
     adata: AnnData,
     tp: str,

scanpy/external/tl/_palantir.py

@@ -10,7 +10,7 @@
 from ...testing._doctests import doctest_needs
 
 
-@doctest_needs('palantir')
+@doctest_needs("palantir")
 def palantir(
     adata: AnnData,
     n_components: int = 10,

scanpy/external/tl/_phate.py

@@ -11,7 +11,7 @@
 from ...testing._doctests import doctest_needs
 
 
-@doctest_needs('phate')
+@doctest_needs("phate")
 def phate(
     adata: AnnData,
     n_components: int = 2,

scanpy/external/tl/_phenograph.py

@@ -13,7 +13,7 @@
 from ...testing._doctests import doctest_needs
 
 
-@doctest_needs('phenograph')
+@doctest_needs("phenograph")
 def phenograph(
     adata: Union[AnnData, np.ndarray, spmatrix],
     clustering_algo: Optional[Literal["louvain", "leiden"]] = "louvain",

scanpy/external/tl/_pypairs.py

@@ -14,7 +14,7 @@
 Genes = Collection[Union[str, int, bool]]
 
 
-@doctest_needs('pypairs')
+@doctest_needs("pypairs")
 def sandbag(
     adata: AnnData,
     annotation: Optional[Mapping[str, Genes]] = None,

scanpy/external/tl/_sam.py

@@ -15,7 +15,7 @@
 from ...testing._doctests import doctest_needs
 
 
-@doctest_needs('samalg')
+@doctest_needs("samalg")
 def sam(
     adata: AnnData,
     max_iter: int = 10,

scanpy/external/tl/_trimap.py

@@ -11,7 +11,7 @@
 from ...testing._doctests import doctest_needs
 
 
-@doctest_needs('trimap')
+@doctest_needs("trimap")
 def trimap(
     adata: AnnData,
     n_components: int = 2,

scanpy/external/tl/_wishbone.py

@@ -9,7 +9,7 @@
 from ...testing._doctests import doctest_needs
 
 
-@doctest_needs('wishbone')
+@doctest_needs("wishbone")
 def wishbone(
     adata: AnnData,
     start_cell: str,

scanpy/queries/_queries.py

@@ -72,7 +72,7 @@ def simple_query(
     return res
 
 
-@doctest_needs('pybiomart')
+@doctest_needs("pybiomart")
 @_doc_params(doc_org=_doc_org, doc_host=_doc_host, doc_use_cache=_doc_use_cache)
 def biomart_annotations(
     org: str,
@@ -110,7 +110,7 @@ def biomart_annotations(
     return simple_query(org=org, attrs=attrs, host=host, use_cache=use_cache)
 
 
-@doctest_needs('pybiomart')
+@doctest_needs("pybiomart")
 @_doc_params(doc_org=_doc_org, doc_host=_doc_host, doc_use_cache=_doc_use_cache)
 def gene_coordinates(
     org: str,
@@ -156,7 +156,7 @@ def gene_coordinates(
     return res[~res["chromosome_name"].isin(chr_exclude)]
 
 
-@doctest_needs('pybiomart')
+@doctest_needs("pybiomart")
 @_doc_params(doc_org=_doc_org, doc_host=_doc_host, doc_use_cache=_doc_use_cache)
 def mitochondrial_genes(
     org: str,
@@ -201,7 +201,7 @@ def mitochondrial_genes(
     )
 
 
-@doctest_needs('gprofiler')
+@doctest_needs("gprofiler")
 @singledispatch
 @_doc_params(doc_org=_doc_org)
 def enrich(

scanpy/testing/_doctests.py

@@ -5,7 +5,7 @@
 from collections.abc import Callable
 
 
-F = TypeVar('F', bound=FunctionType)
+F = TypeVar("F", bound=FunctionType)
 
 
 def doctest_needs(mod: str) -> Callable[[F], F]:

scanpy/testing/_pytest/__init__.py

@@ -10,7 +10,7 @@
 from .fixtures import *  # noqa: F403
 
 
-doctest_env_marker = pytest.mark.usefixtures('doctest_env')
+doctest_env_marker = pytest.mark.usefixtures("doctest_env")
 
 
 # Defining it here because it’s autouse.
@@ -20,14 +20,14 @@ def global_test_context() -> Generator[None, None, None]:
     from matplotlib import pyplot
     from scanpy import settings
 
-    pyplot.switch_backend('agg')
+    pyplot.switch_backend("agg")
     settings.logfile = sys.stderr
-    settings.verbosity = 'hint'
+    settings.verbosity = "hint"
     settings.autoshow = True
 
     yield
 
-    pyplot.close('all')
+    pyplot.close("all")
 
 
 def pytest_addoption(parser: pytest.Parser) -> None:
@@ -65,25 +65,25 @@ def pytest_itemcollected(item: pytest.Item) -> None:
     item.add_marker(doctest_env_marker)
 
     func = _import_name(item.name)
-    if marker := getattr(func, '_doctest_mark', None):
+    if marker := getattr(func, "_doctest_mark", None):
         item.add_marker(marker)
-    if skip_reason := getattr(func, '_doctest_skip_reason', False):
+    if skip_reason := getattr(func, "_doctest_skip_reason", False):
         item.add_marker(pytest.mark.skip(reason=skip_reason))
 
 
 def _import_name(name: str) -> Any:
     from importlib import import_module
 
-    parts = name.split('.')
+    parts = name.split(".")
     obj = import_module(parts[0])
     for i, name in enumerate(parts[1:]):
         try:
-            obj = import_module(f'{obj.__name__}.{name}')
+            obj = import_module(f"{obj.__name__}.{name}")
         except ModuleNotFoundError:
             break
     for name in parts[i + 1 :]:
         try:
             obj = getattr(obj, name)
         except AttributeError:
-            raise RuntimeError(f'{parts[:i]}, {parts[i+1:]}, {obj} {name}')
+            raise RuntimeError(f"{parts[:i]}, {parts[i+1:]}, {obj} {name}")
     return obj

scanpy/tools/_ingest.py

@@ -22,7 +22,7 @@
 ANNDATA_MIN_VERSION = version.parse("0.7rc1")
 
 
-@doctest_skip('illustrative short example but not runnable')
+@doctest_skip("illustrative short example but not runnable")
 def ingest(
     adata: AnnData,
     adata_ref: AnnData,

scanpy/tools/_marker_gene_overlap.py

@@ -71,7 +71,7 @@ def _calc_jaccard(markers1: dict, markers2: dict):
 _Method = Literal["overlap_count", "overlap_coef", "jaccard"]
 
 
-@doctest_needs('leidenalg')
+@doctest_needs("leidenalg")
 def marker_gene_overlap(
     adata: AnnData,
     reference_markers: Union[Dict[str, set], Dict[str, list]],