Skip to content

fix use raw & docs build #906

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Zethson merged 7 commits into from
Jan 27, 2026
Merged

fix use raw & docs build #906

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
28a062c
fix use raw
Zethson Jan 26, 2026
777e185
pin sphinx
Zethson Jan 26, 2026
8e3325f
pin sphinx
Zethson Jan 26, 2026
21519aa
fix mudata ref
Zethson Jan 27, 2026
d68e48c
overrides
Zethson Jan 27, 2026
f869918
overrides scanpydoc
Zethson Jan 27, 2026
bf40c77
qualnames series
Zethson Jan 27, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 5 additions & 1 deletion docs/conf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
"sphinx.ext.mathjax",
"sphinx.ext.napoleon",
"sphinx_autodoc_typehints", # needs to be after napoleon
"scanpydoc.elegant_typehints",
"sphinx.ext.autosummary",
"sphinx_copybutton",
"sphinx_gallery.load_style",
Expand Down Expand Up @@ -111,7 +112,7 @@
autodoc_mock_imports = ["ete4"]
intersphinx_mapping = {
"anndata": ("https://anndata.readthedocs.io/en/stable/", None),
"mudata": ("https://mudata.readthedocs.io/en/stable/", None),
"mudata": ("https://mudata.readthedocs.io/stable/", None),
"scvi-tools": ("https://docs.scvi-tools.org/en/stable/", None),
"ipython": ("https://ipython.readthedocs.io/en/stable/", None),
"matplotlib": ("https://matplotlib.org/stable/", None),
Expand Down Expand Up @@ -142,6 +143,9 @@
("py:class", "pertpy.tools.lazy_import.<locals>.Placeholder"),
("py:data", "typing.Union"),
]
qualname_overrides = {
"pandas.core.series.Series": "pandas.Series",
}

sphinx_gallery_conf = {"nested_sections=": False}
nbsphinx_thumbnails = {
Expand Down
4 changes: 2 additions & 2 deletions pertpy/tools/_mixscape.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
from fast_array_utils.stats import mean, mean_var
from pandas.errors import PerformanceWarning
from scanpy import get
from scanpy._utils import _check_use_raw, sanitize_anndata
from scanpy._utils import check_use_raw, sanitize_anndata
from scanpy.plotting import _utils
from scanpy.tools._utils import _choose_representation
from scipy.sparse import csr_matrix, issparse, spmatrix
Expand Down Expand Up @@ -980,7 +980,7 @@ def plot_violin( # pragma: no cover # noqa: D417
adata = adata[mixscape_class_mask]

sanitize_anndata(adata)
use_raw = _check_use_raw(adata, use_raw)
use_raw = check_use_raw(adata, use_raw)
if isinstance(keys, str):
keys = [keys]
keys = list(OrderedDict.fromkeys(keys)) # remove duplicates, preserving the order
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,7 @@ dev = [
]
doc = [
"docutils>=0.8",
"sphinx>=8.1",
"sphinx>=8.1,<9.0", # https://github.com/vidartf/nbsphinx-link/pull/26
"scanpydoc",
"sphinx-book-theme",
"myst-nb",
Expand Down
Loading