Skip to content

fix: restore the test suite on Python 3.12 (pandas 3, anndata 0.13) #849

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
selmanozleyen merged 2 commits into from
Aug 25, 2026
Merged

fix: restore the test suite on Python 3.12 (pandas 3, anndata 0.13) #849

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e087a51
fix: restore the test suite on Python 3.12 (pandas 3, anndata 0.13)
Aug 25, 2026
56801ee
Merge branch 'main' into fix/py312-pandas3-anndata013
Marius1311 Aug 25, 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
4 changes: 2 additions & 2 deletions src/moscot/base/problems/_mixins.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -285,7 +285,7 @@ def _annotation_mapping(
key_added=None,
)
v = np.array(tm_batch.argmax(0))
out.extend(source_df[annotation_label][v[i]] for i in range(len(v)))
out.extend(source_df[annotation_label].iloc[v[i]] for i in range(len(v)))

else:
target_df = _get_df_cell_transition(
Expand All @@ -309,7 +309,7 @@ def _annotation_mapping(
key_added=None,
)
v = np.array(tm_batch.argmax(0))
out.extend(target_df[annotation_label][v[i]] for i in range(len(v)))
out.extend(target_df[annotation_label].iloc[v[i]] for i in range(len(v)))
categories = pd.Categorical(out)
return pd.DataFrame(categories, columns=[annotation_label])
raise NotImplementedError(f"Mapping mode `{mapping_mode!r}` is not yet implemented.")
Expand Down
5 changes: 3 additions & 2 deletions tests/problems/base/test_general_problem.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
from ott.geometry.pointcloud import PointCloud
from ott.solvers.linear import solve as sinkhorn

import anndata as ad
import scanpy as sc
from anndata import AnnData

Expand Down Expand Up @@ -205,7 +206,7 @@ def test_set_graph_xy(self, adata_x: AnnData, adata_y: AnnData, ts: Tuple[Option
new_obs_names = [name + "_src" for name in adata_x.obs_names]
adata_x.obs_names = new_obs_names

adata_concat = adata_x.concatenate(adata_y, index_unique=None)
adata_concat = ad.concat([adata_x, adata_y], index_unique=None)
sc.pp.neighbors(adata_concat, n_neighbors=15)
graph_to_set = pd.DataFrame(
index=adata_concat.obs_names,
Expand Down Expand Up @@ -323,7 +324,7 @@ def test_set_graph_xy_test_t(self, adata_x: AnnData, adata_y: AnnData, t: float)
new_obs_names = [name + "_src" for name in adata_x.obs_names]
adata_x.obs_names = new_obs_names

adata_concat = adata_x.concatenate(adata_y, index_unique=None)
adata_concat = ad.concat([adata_x, adata_y], index_unique=None)
sc.pp.neighbors(adata_concat, n_neighbors=5)
graph_to_set = pd.DataFrame(
index=adata_concat.obs_names,
Expand Down
Loading