Renamed the tool

bin/cmi → bin/crgem

@@ -4,41 +4,43 @@ import logging
 import sys
 import os
 
-from cmi.stages.functional_analysis import functional_analysis
-from cmi.stages.mechanistic_insights import mechanistic_insights
-from cmi.stages.grn_inference import grn_inference
-from cmi.stages.trrust_analysis import trrust_analysis
-from cmi.stages.create_network import create_network
-from cmi.stages.generate_hypothesis import generate_hypothesis
+from crgem.stages.functional_analysis import functional_analysis
+from crgem.stages.mechanistic_insights import mechanistic_insights
+from crgem.stages.grn_inference import grn_inference
+from crgem.stages.trrust_analysis import trrust_analysis
+from crgem.stages.create_network import create_network
+from crgem.stages.generate_hypothesis import generate_hypothesis
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
 file_handler = logging.FileHandler('logs.log')
-formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+formatter = logging.Formatter(
+    '%(asctime)s - %(name)s - %(levelname)s - %(message)s')
 file_handler.setFormatter(formatter)
 logger.addHandler(file_handler)
 
- 
+
 abs_path = os.path.dirname(__file__)
 DEPS_PATH = f"{abs_path}/dependencies"
 
+
 def run_all(artefacts_path, *args):
     TERDATA = args[5]
     TRRUST_DB_FILE = args[6] or "./data/trrust_rawdata_human.tsv"
 
-
     mechanistic_insights(artefacts_path, *args)
     grn_inference(artefacts_path=artefacts_path, ter_data=TERDATA)
     trrust_analysis(TRRUST_DB_FILE, artefacts_path)
-    create_network(artefacts_path, artefacts_path + "/Trrust_Analysis/trrust_analysis.csv")
-    functional_analysis(artefacts_path,"/Trrust_Analysis/transsynw_genes.csv","/Trrust_Analysis/signet_genes.csv")
-
+    create_network(artefacts_path, artefacts_path +
+                   "/Trrust_Analysis/trrust_analysis.csv")
+    functional_analysis(artefacts_path, "/Trrust_Analysis/transsynw_genes.csv",
+                        "/Trrust_Analysis/signet_genes.csv")
+
 
-
 def main():
     stage_name = sys.argv[2]
     artefacts_path = os.path.abspath(sys.argv[4])
-    
+
     if stage_name == "generate_hypothesis":
         params = sys.argv[6:]
         generate_hypothesis(artefacts_path, *params)
@@ -47,7 +49,8 @@ def main():
         mechanistic_insights(artefacts_path, *params)
     elif stage_name == "grn_inference":
         TERDATA = sys.argv[6]
-        grn_inference(deps_root=DEPS_PATH, artefacts_path=artefacts_path, ter_data=TERDATA)
+        grn_inference(deps_root=DEPS_PATH,
+                      artefacts_path=artefacts_path, ter_data=TERDATA)
     elif stage_name == "trrust_analysis":
         trrust_db_file = sys.argv[6]
         trrust_analysis(trrust_db_file, artefacts_path)
@@ -57,13 +60,17 @@ def main():
     elif stage_name == "functional_analysis":
         transsynw_genes_file = sys.argv[5]
         signet_genes_file = sys.argv[6]
-        functional_analysis(artefacts_path, transsynw_genes_file, signet_genes_file)
-
+        functional_analysis(
+            artefacts_path, transsynw_genes_file, signet_genes_file)
+
     elif stage_name == "all":
         run_all(artefacts_path, *sys.argv[6:])
     else:
-        logger.warning("usage: run stage-name --artefacts <artefacts_path> --params [...params]")
-        logger.warning("available stages: transsynw, mechanistic_insights, grn_inference, trrust_analysis, generate_network, functional_analysis")
+        logger.warning(
+            "usage: run stage-name --artefacts <artefacts_path> --params [...params]")
+        logger.warning(
+            "available stages: transsynw, mechanistic_insights, grn_inference, trrust_analysis, generate_network, functional_analysis")
         sys.exit(1)
 
-main()
+
+main()