Merge pull request #831 from scverse/niche_definitions

Add function for calculating niches

Author: LLehner

.github/workflows/test.yml

@@ -90,9 +90,9 @@ jobs:
                   DISPLAY: :42
               run: |
                   tox -vv
-
-            - name: List figures for potential debugging
-                  ls -alh /home/runner/work/squidpy/squidpy/tests/figures
+            # check if this can be deprecated
+            #- name: List figures for potential debugging
+            #      ls -alh /home/runner/work/squidpy/squidpy/tests/figures
 
             - name: Archive figures generated during testing
               if: always()

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 fail_fast: false
 default_stages:
-    - pre-commit
-    - pre-push
+    - commit
+    - push
 minimum_pre_commit_version: 2.9.3
 repos:
     - repo: https://github.com/astral-sh/ruff-pre-commit

src/squidpy/_constants/_constants.py

@@ -123,3 +123,12 @@ class TenxVersions(str, ModeEnum):
     V1 = "1.1.0"
     V2 = "1.2.0"
     V3 = "1.3.0"
+
+
+@unique
+class NicheDefinitions(ModeEnum):
+    NEIGHBORHOOD = "neighborhood"
+    UTAG = "utag"
+    CELLCHARTER = "cellcharter"
+    SPOT = "spot"
+    BANKSY = "banksy"

src/squidpy/gr/__init__.py

@@ -5,6 +5,7 @@
 from squidpy.gr._build import mask_graph, spatial_neighbors
 from squidpy.gr._ligrec import ligrec
 from squidpy.gr._nhood import centrality_scores, interaction_matrix, nhood_enrichment
+from squidpy.gr._niche import calculate_niche
 from squidpy.gr._ppatterns import co_occurrence, spatial_autocorr
 from squidpy.gr._ripley import ripley
 from squidpy.gr._sepal import sepal