risk-network 0.0.7b10__py3-none-any.whl → 0.0.7b11__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.7-beta.10"
+__version__ = "0.0.7-beta.11"

risk/annotations/io.py

@@ -219,6 +219,6 @@ def _log_loading(filetype: str, filepath: str = "") -> None:
         filepath (str, optional): The path to the file being loaded.
     """
     log_header("Loading annotations")
-    logger.debug(f"Filetype: {filetype}")
+    logger.info(f"Filetype: {filetype}")
     if filepath:
-        logger.debug(f"Filepath: {filepath}")
+        logger.info(f"Filepath: {filepath}")

risk/log/config.py

@@ -5,17 +5,16 @@ risk/log/config
 
 import logging
 
-# Create a global logger
+# Create and configure the global logger
 logger = logging.getLogger("risk_logger")
-logger.setLevel(logging.DEBUG)  # Start with the highest level; adjust as needed
-# Create a console handler
+logger.setLevel(logging.INFO)
+# Create and configure the console handler
 console_handler = logging.StreamHandler()
-console_handler.setLevel(logging.DEBUG)  # Set the handler level (can be controlled later)
-# Create a formatter and set it for the handler
+console_handler.setLevel(logging.INFO)
+# Set the output format for the logger
 formatter = logging.Formatter("%(message)s")
 console_handler.setFormatter(formatter)
-
-# Add the handler to the logger if it doesn't already exist
+# Add the console handler to the logger if not already attached
 if not logger.hasHandlers():
     logger.addHandler(console_handler)
 
@@ -30,8 +29,8 @@ def set_global_verbosity(verbose):
         None
     """
     if verbose:
-        logger.setLevel(logging.DEBUG)  # Show all messages
-        console_handler.setLevel(logging.DEBUG)
+        logger.setLevel(logging.INFO)  # Show all messages
+        console_handler.setLevel(logging.INFO)
     else:
         logger.setLevel(logging.ERROR)  # Show only error messages
         console_handler.setLevel(logging.ERROR)

risk/neighborhoods/domains.py

@@ -46,10 +46,10 @@ def define_domains(
         )
         # Perform hierarchical clustering
         Z = linkage(m, method=best_linkage, metric=best_metric)
-        logger.debug(
+        logger.info(
             f"Linkage criterion: '{linkage_criterion}'\nLinkage method: '{best_linkage}'\nLinkage metric: '{best_metric}'"
         )
-        logger.debug(f"Optimal linkage threshold: {round(best_threshold, 3)}")
+        logger.info(f"Optimal linkage threshold: {round(best_threshold, 3)}")
         # Calculate the optimal threshold for clustering
         max_d_optimal = np.max(Z[:, 2]) * best_threshold
         # Assign domains to the annotations matrix

risk/neighborhoods/neighborhoods.py

@@ -130,7 +130,7 @@ def process_neighborhoods(
     enrichment_matrix = neighborhoods["enrichment_matrix"]
     binary_enrichment_matrix = neighborhoods["binary_enrichment_matrix"]
     significant_enrichment_matrix = neighborhoods["significant_enrichment_matrix"]
-    logger.debug(f"Imputation depth: {impute_depth}")
+    logger.info(f"Imputation depth: {impute_depth}")
     if impute_depth:
         (
             enrichment_matrix,
@@ -143,7 +143,7 @@ def process_neighborhoods(
             max_depth=impute_depth,
         )
 
-    logger.debug(f"Pruning threshold: {prune_threshold}")
+    logger.info(f"Pruning threshold: {prune_threshold}")
     if prune_threshold:
         (
             enrichment_matrix,

risk/network/io.py

@@ -451,10 +451,10 @@ class NetworkIO:
         # Log the number of nodes and edges before and after cleaning
         num_final_nodes = G.number_of_nodes()
         num_final_edges = G.number_of_edges()
-        logger.debug(f"Initial node count: {num_initial_nodes}")
-        logger.debug(f"Final node count: {num_final_nodes}")
-        logger.debug(f"Initial edge count: {num_initial_edges}")
-        logger.debug(f"Final edge count: {num_final_edges}")
+        logger.info(f"Initial node count: {num_initial_nodes}")
+        logger.info(f"Final node count: {num_final_nodes}")
+        logger.info(f"Initial edge count: {num_initial_edges}")
+        logger.info(f"Final edge count: {num_final_edges}")
 
     def _assign_edge_weights(self, G: nx.Graph) -> None:
         """Assign weights to the edges in the graph.
@@ -472,7 +472,7 @@ class NetworkIO:
             )  # Default to 1.0 if 'weight' not present
 
         if self.include_edge_weight and missing_weights:
-            logger.debug(f"Total edges missing weights: {missing_weights}")
+            logger.info(f"Total edges missing weights: {missing_weights}")
 
     def _validate_nodes(self, G: nx.Graph) -> None:
         """Validate the graph structure and attributes.
@@ -511,13 +511,13 @@ class NetworkIO:
             filepath (str, optional): The path to the file being loaded. Defaults to "".
         """
         log_header("Loading network")
-        logger.debug(f"Filetype: {filetype}")
+        logger.info(f"Filetype: {filetype}")
         if filepath:
-            logger.debug(f"Filepath: {filepath}")
-        logger.debug(f"Edge weight: {'Included' if self.include_edge_weight else 'Excluded'}")
+            logger.info(f"Filepath: {filepath}")
+        logger.info(f"Edge weight: {'Included' if self.include_edge_weight else 'Excluded'}")
         if self.include_edge_weight:
-            logger.debug(f"Weight label: {self.weight_label}")
-        logger.debug(f"Minimum edges per node: {self.min_edges_per_node}")
-        logger.debug(f"Projection: {'Sphere' if self.compute_sphere else 'Plane'}")
+            logger.info(f"Weight label: {self.weight_label}")
+        logger.info(f"Minimum edges per node: {self.min_edges_per_node}")
+        logger.info(f"Projection: {'Sphere' if self.compute_sphere else 'Plane'}")
         if self.compute_sphere:
-            logger.debug(f"Surface depth: {self.surface_depth}")
+            logger.info(f"Surface depth: {self.surface_depth}")

risk/risk.py

@@ -221,10 +221,10 @@ class RISK(NetworkIO, AnnotationsIO):
         )
 
         # Log and display permutation test settings
-        logger.debug(f"Neighborhood scoring metric: '{score_metric}'")
-        logger.debug(f"Null distribution: '{null_distribution}'")
-        logger.debug(f"Number of permutations: {num_permutations}")
-        logger.debug(f"Maximum workers: {max_workers}")
+        logger.info(f"Neighborhood scoring metric: '{score_metric}'")
+        logger.info(f"Null distribution: '{null_distribution}'")
+        logger.info(f"Number of permutations: {num_permutations}")
+        logger.info(f"Maximum workers: {max_workers}")
         # Run permutation test to compute neighborhood significance
         neighborhood_significance = compute_permutation_test(
             neighborhoods=neighborhoods,
@@ -290,9 +290,9 @@ class RISK(NetworkIO, AnnotationsIO):
             max_cluster_size=max_cluster_size,
         )
 
-        logger.debug(f"p-value cutoff: {pval_cutoff}")
-        logger.debug(f"FDR BH cutoff: {fdr_cutoff}")
-        logger.debug(
+        logger.info(f"p-value cutoff: {pval_cutoff}")
+        logger.info(f"FDR BH cutoff: {fdr_cutoff}")
+        logger.info(
             f"Significance tail: '{tail}' ({'enrichment' if tail == 'right' else 'depletion' if tail == 'left' else 'both'})"
         )
         # Calculate significant neighborhoods based on the provided parameters
@@ -314,8 +314,8 @@ class RISK(NetworkIO, AnnotationsIO):
         )
 
         log_header("Finding top annotations")
-        logger.debug(f"Min cluster size: {min_cluster_size}")
-        logger.debug(f"Max cluster size: {max_cluster_size}")
+        logger.info(f"Min cluster size: {min_cluster_size}")
+        logger.info(f"Max cluster size: {max_cluster_size}")
         # Define top annotations based on processed neighborhoods
         top_annotations = self._define_top_annotations(
             network=network,
@@ -414,9 +414,9 @@ class RISK(NetworkIO, AnnotationsIO):
         else:
             for_print_distance_metric = distance_metric
         # Log and display neighborhood settings
-        logger.debug(f"Distance metric: '{for_print_distance_metric}'")
-        logger.debug(f"Edge length threshold: {edge_length_threshold}")
-        logger.debug(f"Random seed: {random_seed}")
+        logger.info(f"Distance metric: '{for_print_distance_metric}'")
+        logger.info(f"Edge length threshold: {edge_length_threshold}")
+        logger.info(f"Random seed: {random_seed}")
 
         # Compute neighborhoods based on the network and distance metric
         neighborhoods = get_network_neighborhoods(

risk/stats/permutation/test_functions.py

@@ -1,6 +1,6 @@
 """
-risk/stats/permutation/test_function
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/stats/permutation/test_functions
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 import numpy as np

{risk_network-0.0.7b10.dist-info → risk_network-0.0.7b11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.7b10
+Version: 0.0.7b11
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.7b10.dist-info → risk_network-0.0.7b11.dist-info}/RECORD

@@ -1,20 +1,20 @@
-risk/__init__.py,sha256=cMQ9biQEb8gYBZtC-NebxpomJpoEQOMHT0jhH6N5dJc,113
+risk/__init__.py,sha256=LDYtIaVSfLSXLCFAOtMfMWteX-C8tpOnI8OPnqr90bY,113
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
-risk/risk.py,sha256=JlKkNrdM3LwMl1Wqs3KZDOhnOwGm9EzsquoJ1GBsU0g,21339
+risk/risk.py,sha256=TYuZbEiEZugwZgR0Kr8kSXiH2GWE-6BxanSEZeSVpFU,21327
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
 risk/annotations/annotations.py,sha256=3FFyJE9Gp5oRN72_8iVAUnecsmTtx2G2fp5AlCY1oUk,11405
-risk/annotations/io.py,sha256=om_3e26PQmrICY25UJnXuuZ20oXENNlr1QCBmOxYlMI,9475
+risk/annotations/io.py,sha256=ZcONDioLZjLQAbXhhoNHQRsY9nq-aTpyPtHGUSW7ka0,9473
 risk/log/__init__.py,sha256=aDUz5LMFQsz0UlsQI2EdXtiBKRLfml1UMeZKC7QQIGU,134
-risk/log/config.py,sha256=tYFQ75yyVUYB5WA040037dtOL1SDoDwyGVpkP2P1dZc,1439
+risk/log/config.py,sha256=hXUewhm35wgc7UYQWmwy9YHDdmDwHP-bAUvi8edlFGM,1360
 risk/log/params.py,sha256=DUmsqPo9hi3rQHFgLTunP14I-vVoyQSFZbx5aSYmVts,6363
 risk/neighborhoods/__init__.py,sha256=tKKEg4lsbqFukpgYlUGxU_v_9FOqK7V0uvM9T2QzoL0,206
 risk/neighborhoods/community.py,sha256=stYYBXeZlGLMV-k8ckQeIqThT6v9y-S3hETobAo9590,6817
-risk/neighborhoods/domains.py,sha256=X-qmnhb7K_CHCrRDBtpBizt8BmyJjKCzKZdh-NSUf_c,10736
-risk/neighborhoods/neighborhoods.py,sha256=M-wL4xB_BUTlSZg90swygO5NdrZ6hFUFqs6jsiZaqHk,18260
+risk/neighborhoods/domains.py,sha256=_N4E4EJoMNa7M7-6eHRJKzPYREd24kPPKdYQ3jTByxo,10734
+risk/neighborhoods/neighborhoods.py,sha256=0hxi1jFoXQQX7eg94LfX6qrK_S7E4NGe5fIlOsAOg0Y,18258
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=H1yGVVqgbfpzBzJwEheDLfvGLSA284jGQQTn612L4Vc,6759
 risk/network/graph.py,sha256=_LEoom4EEowGALuJKSXcev9RAAHu2FqIeq3u7mkifW0,16479
-risk/network/io.py,sha256=ASoKG4vkCC_aHwxlF4502W_SyaaCrRnHsTmRwL00spI,21266
+risk/network/io.py,sha256=LmjivifAZURzSaPs-dx3KkNDGmVnfUFJdj5WY0BZJI8,21254
 risk/network/plot.py,sha256=3OucCoKJwx9M9H4lqAvcQdM9YiCSyIxz21jyqDbpffc,62286
 risk/stats/__init__.py,sha256=WcgoETQ-hS0LQqKRsAMIPtP15xZ-4eul6VUBuUx4Wzc,220
 risk/stats/hypergeom.py,sha256=o6Qnj31gCAKxr2uQirXrbv7XvdDJGEq69MFW-ubx_hA,2272
@@ -22,9 +22,9 @@ risk/stats/poisson.py,sha256=8x9hB4DCukq4gNIlIKO-c_jYG1-BTwTX53oLauFyfj8,1793
 risk/stats/stats.py,sha256=kvShov-94W6ffgDUTb522vB9hDJQSyTsYif_UIaFfSM,7059
 risk/stats/permutation/__init__.py,sha256=neJp7FENC-zg_CGOXqv-iIvz1r5XUKI9Ruxhmq7kDOI,105
 risk/stats/permutation/permutation.py,sha256=kmSZ7bQ-AD0TFiQDgIwfxTeqHa4pjp7fIcOzAqyhUNY,9714
-risk/stats/permutation/test_functions.py,sha256=HuDIM-V1jkkfE1rlaIqrWWBSKZt3dQ1f-YEDjWpnLSE,2343
-risk_network-0.0.7b10.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.7b10.dist-info/METADATA,sha256=H_rRPorQwnrzeJ26vQph8anQHm0GPMjA_N3xro13oxs,43143
-risk_network-0.0.7b10.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-risk_network-0.0.7b10.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.7b10.dist-info/RECORD,,
+risk/stats/permutation/test_functions.py,sha256=lftOude6hee0pyR80HlBD32522JkDoN5hrKQ9VEbuoY,2345
+risk_network-0.0.7b11.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.7b11.dist-info/METADATA,sha256=x4uCZ5QCWk-nyaVLFGSsZX1eJs21dbLSo1FpDbyQ83Y,43143
+risk_network-0.0.7b11.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+risk_network-0.0.7b11.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.7b11.dist-info/RECORD,,