Fc matplotlib

CHANGELOG.md

@@ -4,14 +4,16 @@
 ## [latest]
 
 ### added
-
+- added documentation on ingesting custom h5ad/h5mu objects
 
 ### fixed
 
-- matplotlib 3.9 issue with get_cmap ([API](https://matplotlib.org/stable/api/cm_api.html#:~:text=The%20colormap%20name%20can%20then%20be%20used%20as%20a%20string%20argument%20to%20any%20cmap%20parameter%20in%20Matplotlib.%20It%20is%20also%20available%20in%20pyplot.get_cmap.))
 
 ### dependencies
 
+- pinned matplotlib 3.8 as temporary fix 
+ next release will unpin and fix get_cmap ([API](https://matplotlib.org/stable/api/cm_api.html#:~:text=The%20colormap%20name%20can%20then%20be%20used%20as%20a%20string%20argument%20to%20any%20cmap%20parameter%20in%20Matplotlib.%20It%20is%20also%20available%20in%20pyplot.get_cmap.)) and legendHandles ([API](https://matplotlib.org/stable/api/prev_api_changes/api_changes_3.9.0.html))
+
 
 ## v0.5.0
 

docs/release_notes.md

@@ -4,14 +4,16 @@
 ## [latest]
 
 ### added
-
+- added documentation on ingesting custom h5ad/h5mu objects
 
 ### fixed
 
-- matplotlib 3.9 issue with get_cmap ([API](https://matplotlib.org/stable/api/cm_api.html#:~:text=The%20colormap%20name%20can%20then%20be%20used%20as%20a%20string%20argument%20to%20any%20cmap%20parameter%20in%20Matplotlib.%20It%20is%20also%20available%20in%20pyplot.get_cmap.))
 
 ### dependencies
 
+- pinned matplotlib 3.8 as temporary fix 
+ next release will unpin and fix get_cmap ([API](https://matplotlib.org/stable/api/cm_api.html#:~:text=The%20colormap%20name%20can%20then%20be%20used%20as%20a%20string%20argument%20to%20any%20cmap%20parameter%20in%20Matplotlib.%20It%20is%20also%20available%20in%20pyplot.get_cmap.)) and legendHandles ([API](https://matplotlib.org/stable/api/prev_api_changes/api_changes_3.9.0.html))
+
 
 ## v0.5.0
 

docs/usage/different_entry_points.md

@@ -1,7 +1,7 @@
 # Running pipeline modules from different entry points.
 
 For circumstances where you already have a quality controlled Mudata object, you can run any of the other pipelines. In order to do so, you need to follow some specific file naming conventions.
-You must always have a column called sample_id within each modality in the MuData object, as well as in the top `mdata.obs`.
+You must always have a column called `sample_id` within the `.obs` of each modality in the MuData object, as well as in the top `mdata.obs`. Please note that the `anndata`/`MuData` object must have the gene/feature name as the index of the `.var` dataframe to be ingested in panpipes. 
 
 ## Preprocess
 

panpipes/funcs/plotting.py

@@ -3,7 +3,7 @@
 import matplotlib.pyplot as plt
 import seaborn as sns
 from scanpy.get import obs_df
-from matplotlib.pyplot import get_cmap
+from matplotlib.cm import get_cmap
 import itertools
 import logging
 from matplotlib import use

panpipes/python_scripts/plot_umaps_batch_correct.py

@@ -6,7 +6,7 @@
 import muon as mu
 import os
 import re
-from matplotlib.pyplot import get_cmap
+from matplotlib.cm import get_cmap
 from matplotlib.colors import ListedColormap
 import yaml 
 from panpipes.funcs.io import read_yaml

pyproject.toml

@@ -30,13 +30,15 @@ dependencies = [
     "harmonypy",
     "mofapy2",
     "muon",
+    "matplotlib<=3.8",
     "openpyxl",
     "paramiko",
     "pysam",
     "pyyaml",
     "ruffus",
     "scanorama",
     "scanpy",
+    "seaborn",
     "leidenalg",
     "louvain",
     "scib",