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Add SpatialLeiden as clustering method #1019

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Add SpatialLeiden as clustering method #1019

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0aefdec
add spatialleiden
melocery Jul 16, 2025
65edf84
support updated spatialleiden API + resolution list
melocery Jul 18, 2025
cb6faed
update type signatures for resolutions
melocery Jul 28, 2025
1eed4dd
optional dependency
melocery Jul 31, 2025
fb1d740
try fix test
melocery Jul 31, 2025
39f7ea8
Merge branch 'main' into add-spatialleiden
selmanozleyen Sep 1, 2025
30c1c99
Merge branch 'main' into add-spatialleiden
timtreis Nov 26, 2025
653fc68
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 26, 2025
a88e234
updated import
timtreis Nov 26, 2025
eb2ef68
updated import
timtreis Nov 26, 2025
d091d48
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 26, 2025
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12 changes: 7 additions & 5 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,10 @@ optional-dependencies.docs = [
"sphinxcontrib-bibtex>=2.3",
"sphinxcontrib-spelling>=7.6.2",
]
optional-dependencies.leiden = [
"leidenalg",
"spatialleiden>=0.3",
]
optional-dependencies.test = [
"coverage[toml]>=7",
"pytest>=7",
Expand All @@ -109,12 +113,10 @@ optional-dependencies.test = [
"pytest-xdist>=3",
"scanpy[leiden]",
]

urls."Bug Tracker" = "https://github.com/scverse/squidpy/issues"

urls.Documentation = "https://squidpy.readthedocs.io"
urls.Home-page = "https://github.com/scverse/squidpy"
urls.Source = "https://github.com/scverse/squidpy"
urls."Documentation" = "https://squidpy.readthedocs.io"
urls."Home-page" = "https://github.com/scverse/squidpy"
urls."Source" = "https://github.com/scverse/squidpy"

[tool.setuptools]
package-dir = { "" = "src" }
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1 change: 1 addition & 0 deletions src/squidpy/_constants/_constants.py
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Expand Up @@ -130,5 +130,6 @@ class NicheDefinitions(ModeEnum):
NEIGHBORHOOD = "neighborhood"
UTAG = "utag"
CELLCHARTER = "cellcharter"
SPATIALLEIDEN = "spatialleiden"
SPOT = "spot"
BANKSY = "banksy"
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