Removed $ESGEMME_PATH dependency for default.conf.

esgemme/esgemme.py

@@ -27,8 +27,8 @@ import biotite.structure.io as strucio
 import biotite.application.dssp as dssp
 import biotite.structure.io.pdb as pdb
 
-#from gemmeAnal import *
-
+import importlib.resources
+from importlib.resources import files, as_file
 import pandas as pd
 
 def selectMaxFastaSequences(inputMSAfile, outputMSAfile, maxNumSeqs=40001):
@@ -202,12 +202,15 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
     """
 
     chainID = chains[0]
-	
-	#TODO: Remove Bash dependency here. Make the copying process in Python
-	#subprocess.call("cp $ESGEMME_PATH/default.conf .",shell=True)
-    esgemme_path = os.path.expandvars ('$ESGEMME_PATH')
 
-    shutil.copy2(os.path.join(esgemme_path, "default.conf"), os.getcwd())
+    # esgemme_path = os.path.expandvars ('$ESGEMME_PATH')
+    # shutil.copy2(os.path.join(esgemme_path, "default.conf"), os.getcwd())
+#    esgemme_default_conf_path = importlib.resources.path('esgemme', 'default.conf')
+#    print(esgemme_default_conf_path)
+    source = files('esgemme').joinpath('default.conf')
+    with as_file(source) as esgemme_default_conf_path:
+        #third_party_api_requiring_file_system_path(eml)
+        shutil.copy2(esgemme_default_conf_path, os.getcwd())
     
 
     if retMet=="input":
@@ -360,8 +363,8 @@ def cleanTheMess(prot,bFile,fFile, chainID, verbosity=False):
     if os.path.isfile("caracTest.dat"):
         os.remove("caracTest.dat")
 
-    if os.path.isfile("default.conf"):
-        os.remove("default.conf")
+   if os.path.isfile("default.conf"):
+       os.remove("default.conf")
 
     if verbosity == False:
         if os.path.isfile(prot+"_normPred_evolInd.txt"):

setup.py

@@ -63,5 +63,7 @@ setup(name='esgemme',
           'console_scripts': [
               'esgemme=esgemme.esgemme:main'
           ]
-      }
+      },
+      include_package_data=True,
+      package_data={'esgemme':['default.conf']},
       )