Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
42 commits
Select commit Hold shift + click to select a range
51a6e21
add conditional and total normalization
chiarasch Apr 25, 2025
a9bdafd
remove prints
chiarasch Apr 25, 2025
52cc04a
hande nan
chiarasch Apr 29, 2025
cafd835
add normalization tests
chiarasch Apr 29, 2025
eeef861
add docstring
chiarasch Apr 29, 2025
7b89081
filter out low cond counts
chiarasch May 6, 2025
26e90bf
add warnings low cond counts
chiarasch May 6, 2025
bb0eeb8
add min_cell_count filter
chiarasch Aug 7, 2025
e7a33ab
add CCR dotplot
chiarasch Aug 7, 2025
02f361d
Merge branch 'main' into cozi_nhood_enrichment
chiarasch Aug 7, 2025
fc8c1b8
add cozi tests
chiarasch Aug 11, 2025
c9956fc
clean script
chiarasch Aug 11, 2025
28a77dc
add cozi parameters in docs
chiarasch Aug 11, 2025
74e77fc
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 12, 2025
23cf1a2
Merge branch 'main' into cozi_nhood_enrichment
chiarasch Aug 18, 2025
02fb792
fix precommit hooks
chiarasch Aug 19, 2025
3cd8c44
set min_cell_count default to 0
chiarasch Aug 19, 2025
785a3ee
add dotplot test image and function
chiarasch Aug 19, 2025
f14f31d
remove matplotlib loading from function
chiarasch Aug 19, 2025
005a57b
fix typo
chiarasch Aug 19, 2025
2d34d99
update code with changes in #1043
chiarasch Oct 6, 2025
b90dbb0
add optional cond_ratio to result class
chiarasch Oct 6, 2025
7ac43a4
adapt plotting to result class changes
chiarasch Oct 6, 2025
a82ddaa
fix optional cond ratio output
chiarasch Oct 6, 2025
7a71607
remove dict plotting changes again
chiarasch Oct 6, 2025
4972f96
adapt tests to new output format
chiarasch Oct 6, 2025
c2c40e7
typo
chiarasch Oct 6, 2025
8fe9a08
Merge branch 'main' into cozi_nhood_enrichment
selmanozleyen May 27, 2026
274a7cf
Merge branch 'main' into cozi_nhood_enrichment
selmanozleyen May 29, 2026
b97eb8c
remove unused imports
selmanozleyen May 29, 2026
434a617
undo PR change
selmanozleyen May 29, 2026
7b2354b
Merge branch 'main' into cozi_nhood_enrichment
selmanozleyen Jun 1, 2026
3c98edf
Merge branch 'main' into cozi_nhood_enrichment
selmanozleyen Jun 19, 2026
acd8a9a
fix doc problem
selmanozleyen Jun 19, 2026
db93810
add tests for correctness before refactoring with numba
selmanozleyen Jun 19, 2026
bd1422e
numbafy nhood_enrichment
selmanozleyen Jun 19, 2026
e1a720e
precommit formatting
selmanozleyen Jun 19, 2026
e6888f8
remove docrep
selmanozleyen Jun 19, 2026
be6e509
progress bar try-out
selmanozleyen Jun 19, 2026
7824c66
undo progress bar changes. Use chunk updates for progress bar
selmanozleyen Jun 19, 2026
71e6808
full numbafication
selmanozleyen Jun 19, 2026
ca32444
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 19, 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
3 changes: 2 additions & 1 deletion pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,7 @@ dependencies = [
"matplotlib-scalebar>=0.8",
"networkx>=2.6",
"numba>=0.56.4",
"numba-progress>=1.1",
"numpy>=1.23",
"omnipath>=1.0.7",
"pandas>=2.1",
Expand All @@ -66,7 +67,7 @@ dependencies = [
"scikit-image>=0.25",
# due to https://github.com/scikit-image/scikit-image/issues/6850 breaks rescale ufunc
"scikit-learn>=0.24",
"spatialdata>=0.7.2", # 0.7.2 dropped xarray-schema (pkg_resources break, #1115)
"spatialdata>=0.7.2", # 0.7.2 dropped xarray-schema (pkg_resources break, #1115)
"spatialdata-plot>=0.3.3",
"statsmodels>=0.12",
# https://github.com/scverse/squidpy/issues/526
Expand Down
2 changes: 1 addition & 1 deletion src/squidpy/datasets/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
ImageDatasets,
SpatialDataDatasets,
VisiumDatasets,
cells,
# AnnData datasets
four_i,
imc,
Expand All @@ -25,7 +26,6 @@
visium_hne_image,
visium_hne_image_crop,
visium_hne_sdata,
cells,
)

__all__ = [
Expand Down
Loading
Loading