v2023.7.18

Fixed issue with `SampleSpecificPerturbationNetwork` not being able to handle `X.index` with a `.name` that was not `NoneType`.  Created a hack to allow `pd.MultiIndex` support (converts to strings and warns). Made `include_reference_for_samplespecific=True` the new default which creates a clone of the reference and uses that as the background network.  Added `is_square` to `Symmetric` object.

devel.txt → CHANGELOG.md

@@ -1,12 +1,8 @@
-Pending: 
-========
-* Create a PerturbationNetwork and make SampleSpecificPerturbationNetwork dependent on the more general PerturbationNetwork.  Adapt this so there can be more than one sample as the query.  
-* Should convert_network actually be convert_symmetric? 
-* Since iGraph is a dependency, just make code cleaner without the workarounds for not having it as a dependency
 
-Completed:
-==========
-* 2022.02.09 - Added support for iGraph and non-fully connected networks. Also added UMAP fuzzy_simplical_set graph
+
+#### Completed:
+* 2023.07.18 - Fixed issue with `SampleSpecificPerturbationNetwork` not being able to handle `X.index` with a `.name` that was not `NoneType`.  Created a hack to allow `pd.MultiIndex` support (converts to strings and warns). Made `include_reference_for_samplespecific=True` the new default which creates a clone of the reference and uses that as the background network.  Added `is_square` to `Symmetric` object.
+* 2022.02.09 - Added support for iGraph and non-fully connected networks. Also added UMAP `fuzzy_simplical_set` graph
 * 2021.06.24 - Added `get_weights_from_graph` function
 * 2021.06.09 - Fixed `condensed_to_dense` ability to handle self interactions
 * 2021.04.21 - Fixed `idx_nodes = pd.Index(sorted(set(groups[lambda x: x == group].index) & set(df_dense.index)))` in `connectivity` function to prepare for pandas deprecation.
@@ -15,3 +11,8 @@ Completed:
 * 2020.07.24 - Added `DifferentialEnsembleAssociationNetwork`
 * 2020.07.21 - `SampleSpecificPerturbationNetwork` fit method returns self
 
+
+#### Pending:  
+* Rename `Symmetric` object to something more generalizable to similarity and dissimilarity matrices that do not have to be symmetric or completely connected.
+* Should `convert_network` actually be `convert_symmetric`? 
+* Since iGraph is a dependency, just make code cleaner without the workarounds for not having it as a dependency

LICENSE.txt → LICENSE

@@ -1,17 +1,3 @@
-# ==============
-# Ensemble NetworkX
-# ==============
-# Ensemble network methods in Python
-# ------------------------------------
-# GitHub: https://github.com/jolespin/ensemble_networkx
-# PyPI: https://pypi.org/project/ensemble_networkx
-# ------------------------------------
-# =======
-# Contact
-# =======
-# Producer: Josh L. Espinoza
-# Contact: [email protected], [email protected]
-# Google Scholar: https://scholar.google.com/citations?user=r9y1tTQAAAAJ&hl
 # =======
 # License BSD-3
 # =======

README.md

@@ -22,9 +22,10 @@ Compatible for Python 3.
 
 #### Install:
 ```
-# "Stable" release (still developmental)
+# Stable release (Preferred)
 pip install ensemble_networkx
-# Current release
+
+# Current developmental release
 pip install git+https://github.com/jolespin/ensemble_networkx
 ```
 
@@ -45,7 +46,7 @@ import ensemble_networkx as enx
 ```python
 # Load in data
 import soothsayer_utils as syu
-X = syu.get_iris_data(["X"])
+X,y = syu.get_iris_data(["X", "y"])
 
 # Create ensemble network
 ens = enx.EnsembleAssociationNetwork(name="Iris", node_type="leaf measurement", edge_type="association", observation_type="specimen")

ensemble_networkx/__init__.py

@@ -33,7 +33,7 @@
 # =======
 # Version
 # =======
-__version__= "2022.2.9"
+__version__= "2023.7.18"
 __author__ = "Josh L. Espinoza"
 __email__ = "[email protected], [email protected]"
 __url__ = "https://github.com/jolespin/ensemble_networkx"
@@ -48,7 +48,6 @@
     "umap_fuzzy_simplical_set_graph",
 ] + [
     "signed",
-    "get_weights_from_graph",
     "get_symmetric_category",
     "dense_to_condensed",
     "condensed_to_dense",