SC_39 fix docs (#76)

setup.cfg

@@ -34,7 +34,6 @@ packages = find:
 install_requires =
     spatialdata>=0.2.0
     ome-zarr>=0.9.0
-    squidpy>=1.5.0
     scanpy>=1.9.1
     voronoi-diagram-for-polygons>=0.1.6
     rasterio>=1.3.2
@@ -70,14 +69,15 @@ plugin =
     hydra-core>=1.2.0
     hydra-colorlog>=1.2.0
     napari-spatialdata>=0.2.6
-
+    squidpy>=1.5.0
     cellpose>=2.2.3
     pytest-qt
 
 testing =
     hydra-core>=1.2.0
     hydra-colorlog>=1.2.0
     cellpose>=2.2.3
+    squidpy>=1.5.0
     datasets
     jax>=0.4.6
     jaxlib>=0.4.6
@@ -108,7 +108,7 @@ docs =
 
 clustering =
     scikit-learn>=1.3.1
-    flowsom
+    #flowsom @ git+https://[email protected]/saeyslab/FlowSOM_Python # wait for release. Pypi does not support git+ dependencies
     datasets
     textalloc
     joypy

src/harpy/image/_tiling.py

@@ -2,7 +2,6 @@
 
 import dask.array as da
 import numpy as np
-import squidpy as sq
 from spatialdata import SpatialData
 from spatialdata.models.models import ScaleFactors_t
 from spatialdata.transformations import Translation, get_transformation
@@ -30,6 +29,11 @@
 except ImportError:
     log.warning("'OpenCV (cv2)' not installed, to use 'harpy.im.tiling_correction' please install this library.")
 
+try:
+    import squidpy as sq
+except ImportError:
+    log.warning("'squidpy' not installed, to use 'harpy.im.tiling_correction' please install this library.")
+
 
 def tiling_correction(
     sdata: SpatialData,

src/harpy/image/pixel_clustering/_clustering.py

@@ -23,7 +23,9 @@
 
     from harpy.utils._flowsom import _flowsom
 except ImportError:
-    log.warning("'flowsom' not installed, to use 'harpy.im.flowsom', please install this library.")
+    log.warning(
+        "'flowsom' not installed, to use 'harpy.im.flowsom', please install this library (https://[email protected]/saeyslab/FlowSOM_Python)."
+    )
 
 
 def flowsom(

src/harpy/plot/_enrichment.py

@@ -2,10 +2,17 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-import squidpy as sq
 from spatialdata import SpatialData
 
 from harpy.utils._keys import _ANNOTATION_KEY
+from harpy.utils.pylogger import get_pylogger
+
+log = get_pylogger(__name__)
+
+try:
+    import squidpy as sq
+except ImportError:
+    log.warning("'squidpy' not installed, to use 'harpy.pl.nhood_enrichment' please install this library.")
 
 
 def nhood_enrichment(

src/harpy/table/_enrichment.py

@@ -1,8 +1,15 @@
-import squidpy as sq
 from spatialdata import SpatialData
 
 from harpy.table._table import ProcessTable, add_table_layer
 from harpy.utils._keys import _ANNOTATION_KEY
+from harpy.utils.pylogger import get_pylogger
+
+log = get_pylogger(__name__)
+
+try:
+    import squidpy as sq
+except ImportError:
+    log.warning("'squidpy' not installed, to use 'harpy.tb.nhood_enrichment' please install this library.")
 
 
 def nhood_enrichment(

src/harpy/table/cell_clustering/_clustering.py

@@ -21,7 +21,9 @@
     from harpy.utils._flowsom import _flowsom
 
 except ImportError:
-    log.warning("'flowsom' not installed, to use 'harpy.tb.flowsom', please install this library.")
+    log.warning(
+        "'flowsom' not installed, to use 'harpy.tb.flowsom', please install this library (https://[email protected]/saeyslab/FlowSOM_Python)."
+    )
 
 
 def flowsom(