viper-in-python 2.0.0__tar.gz → 2.0.2__tar.gz

{viper_in_python-2.0.0/viper_in_python.egg-info → viper_in_python-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: viper-in-python
-Version: 2.0.0
+Version: 2.0.2
 Summary: A package for VIPER-based Protein Activity analysis of transcriptomic data in Python
 Home-page: https://github.com/alevax/pyviper
 Author: Alexander L.E. Wang & Luca Zanella & Zizhao Lin

{viper_in_python-2.0.0 → viper_in_python-2.0.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "viper-in-python"
-version = "2.0.0"
+version = "2.0.2"
 description = "A package for VIPER-based Protein Activity analysis of transcriptomic data in Python"
 readme = "README.md"
 requires-python = ">=3.8"

{viper_in_python-2.0.0 → viper_in_python-2.0.2}/pyviper/__init__.py

@@ -9,4 +9,4 @@ from pyviper.load import *
 from pyviper.pl import *
 from pyviper.tl import *
 
-__version__ = "2.0.0"
+__version__ = "2.0.2"

{viper_in_python-2.0.0 → viper_in_python-2.0.2}/pyviper/_viper.py

@@ -71,7 +71,7 @@ def viper( gex_data,
           store_input_data=True,
           pleiotropy: bool = False
           ):
-         
+
     """
     The VIPER (Virtual Inference of Protein-activity by Enriched Regulon
     analysis) algorithm[1] allows individuals to compute protein activity
@@ -84,9 +84,9 @@ def viper( gex_data,
 
     The Interactome object must not contain any targets that are not in the
     features of gex_data. This can be accomplished by running:
-    
+
         interactome.filter_targets(gex_data.var_names)
-    
+
     It is highly recommend to do this on the unPruned network and then prune to
     ensure the pruned network contains a consistent number of targets per
     regulator, allow of which exist within gex_data.
@@ -161,9 +161,9 @@ def viper( gex_data,
 
     References
     ----------
-    [1] Alvarez, M. J., et al. (2016). Functional characterization of somatic mutations in 
+    [1] Alvarez, M. J., et al. (2016). Functional characterization of somatic mutations in
         cancer using network-based inference of protein activity. Nature Genetics, 48(8), 838–847.
-    [2] Griffin, A. T., et al. (2023). NaRnEA: An Information Theoretic Framework for Gene Set 
+    [2] Griffin, A. T., et al. (2023). NaRnEA: An Information Theoretic Framework for Gene Set
         Analysis. Entropy, 25(3), 542.
     """
 
@@ -320,21 +320,21 @@ def viper( gex_data,
                 op.uns['gex_data'] = gex_data
         # ---- Pleiotropy hook (placeholder) ----
     if pleiotropy and verbose:
-        print("[pleiotropy] hook reached")   
+        print("[pleiotropy] hook reached")
 
  # ---- Pleiotropy post-processing (TableToInteractome → ShadowRegulon_py → areareg) ----
     if pleiotropy:
 
         # progress bar (optional)
         try:
-            from tqdm import tqdm
+            from tqdm import tqdm as tqdm_pleiotropy
             try:
                 # joblib integration
                 from tqdm.contrib import tqdm_joblib
             except Exception:
                 tqdm_joblib = None
         except Exception:
-            def tqdm(x, **kwargs):
+            def tqdm_pleiotropy(x, **kwargs):
                 return x
             tqdm_joblib = None
 
@@ -418,7 +418,7 @@ def viper( gex_data,
         if n_workers > 1:
             try:
                 if verbose and tqdm_joblib is not None:
-                    with tqdm_joblib(tqdm(total=len(samples), desc="[pleiotropy] samples", unit="sample")):
+                    with tqdm_joblib(tqdm_pleiotropy(total=len(samples), desc="[pleiotropy] samples", unit="sample")):
                         results = Parallel(n_jobs=n_workers, backend="loky", prefer="processes")(
                             delayed(_run_one)(s) for s in samples
                         )
@@ -434,7 +434,7 @@ def viper( gex_data,
         if results is None:
             if verbose:
                 results = []
-                for s in tqdm(samples, desc="[pleiotropy] samples", unit="sample"):
+                for s in tqdm_pleiotropy(samples, desc="[pleiotropy] samples", unit="sample"):
                     results.append(_run_one(s))
             else:
                 results = [_run_one(s) for s in samples]

{viper_in_python-2.0.0 → viper_in_python-2.0.2}/pyviper/interactome.py

@@ -34,7 +34,7 @@ class Interactome:
         Either:
         1. A pd.DataFrame containing four columns in this order:
            "regulator", "target", "mor", "likelihood".
-        2. A filepath to this pd.DataFrame stored as .csv, .tsv, .parquet, 
+        2. A filepath to this pd.DataFrame stored as .csv, .tsv, .parquet,
            .parquet.gzip, .pkl, or .loom.
         3. A filepath to an Interactome object stored as a .pkl.
     input_type : str, default: None
@@ -44,9 +44,9 @@ class Interactome:
 
     References
     ----------
-    [1] Alvarez, M. J., Shen, Y., Giorgi, F. M., Lachmann, A., Ding, B. B., 
-        Ye, B. H., & Califano, A. (2016). Functional characterization of 
-        somatic mutations in cancer using network-based inference of protein 
+    [1] Alvarez, M. J., Shen, Y., Giorgi, F. M., Lachmann, A., Ding, B. B.,
+        Ye, B. H., & Califano, A. (2016). Functional characterization of
+        somatic mutations in cancer using network-based inference of protein
         activity. Nature Genetics, 48(8), 838-847.
     """
     def __init__(self, name, net_table=None, input_type=None):
@@ -106,7 +106,7 @@ class Interactome:
         if n_duplicates > 1:
             warn(
                 "There are " + str(n_duplicates) + " duplicate regulator" +\
-                "-target pairs in your Interactome" + interactome.name + "." +\
+                "-target pairs in your Interactome" + self.name + "." +\
                 "Use Interactome.remove_duplicate_pairs() to resolve them."
             )
 
@@ -255,12 +255,12 @@ class Interactome:
     def integrate(self, network_list, network_weights = None, normalize_likelihoods = False, verbose=False):
         """
         Integrate this Interactome object with one or more other Interactome
-        objects to create a consensus network. This operation modifies the current 
+        objects to create a consensus network. This operation modifies the current
         Interactome in place; no new object is returned. In general, this should be done
         when interactome objects have the same epigenetics (e.g. due to being
         made from different datasets of same celltype). MetaVIPER should be used
         instead when you have multiple interactomes with different epigenetics
-        (e.g. due to being made of data with different celltypes). 
+        (e.g. due to being made of data with different celltypes).
 
         Parameters
         ----------
@@ -312,13 +312,13 @@ class Interactome:
         # adding empty rows of 0s so they be all lined up together in a stack
         net_array_list = []
 
-        loop = (tqdm(range(0, n_networks), 'Standardizing network') 
+        loop = (tqdm(range(0, n_networks), 'Standardizing network')
                 if verbose else range(0, n_networks))
         for i in loop:
             # Get the missing pairs from a single dataframe
             net_df = network_list[i]
             pairs_in_single_df = net_df[reg_targ]
-            
+
             ## Convert the columns to sets for faster set operations
             # all_pairs_set = set(map(tuple, all_pairs_df[['regulator', 'target']].values)) # We can just use all_pairs_df which was already computed
             # single_pairs_set = set(map(tuple, pairs_in_single_df[['regulator', 'target']].values))  # We can just use drop_duplicates() again
@@ -326,12 +326,12 @@ class Interactome:
             # missing_pairs_set = all_pairs_set - single_pairs_set
             ## Convert the missing pairs back to a DataFrame
             # missing_pairs_df = pd.DataFrame(list(missing_pairs_set), columns=['regulator', 'target'])
-            
+
             # Using pd.merge avoids expensive set conversion operations
             single_pairs_set = pairs_in_single_df[reg_targ].drop_duplicates()
             mrg = all_pairs_df.merge(single_pairs_set, how='left', on=reg_targ, indicator=True)
             missing_pairs_df = mrg[mrg['_merge'] == 'left_only'][reg_targ]
-            
+
             # Check if regulators in missing_pairs_df are in net_df["regulator"]
             in_net_df = missing_pairs_df['regulator'].isin(net_df['regulator'])
             # Create two DataFrames based on the condition
@@ -743,12 +743,12 @@ class Interactome:
         """
         Translate the regulators of the Interactome. The current name format of
         the regulators should be one of the following:
-            
-        - mouse_symbol 
-        - mouse_ensembl 
-        - mouse_entrez 
-        - human_symbol 
-        - human_ensembl 
+
+        - mouse_symbol
+        - mouse_ensembl
+        - mouse_entrez
+        - human_symbol
+        - human_ensembl
         - human_entrez
 
         Parameters

{viper_in_python-2.0.0 → viper_in_python-2.0.2}/setup.py

@@ -11,7 +11,7 @@ long_description = (this_directory / "README.md").read_text()
 
 setuptools.setup(
     name="viper-in-python",
-    version="2.0.0",
+    version="2.0.2",
     author="Alexander L.E. Wang & Luca Zanella & Zizhao Lin",
     author_email="aw3436@cumc.columbia.edu",
     packages=setuptools.find_packages(),

{viper_in_python-2.0.0 → viper_in_python-2.0.2/viper_in_python.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: viper-in-python
-Version: 2.0.0
+Version: 2.0.2
 Summary: A package for VIPER-based Protein Activity analysis of transcriptomic data in Python
 Home-page: https://github.com/alevax/pyviper
 Author: Alexander L.E. Wang & Luca Zanella & Zizhao Lin