fix apps for imp

docs/apps/docapps.py

@@ -1,16 +1,18 @@
 #!/usr/bin/python
 
 import os
-from prody.utilities.misctools import importImp
-imp = importImp()
+import sys
 import importlib
 from subprocess import Popen, PIPE
 
-path = [importlib.util.find_spec("prody").submodule_search_locations[0]]
-apps = imp.load_module('prody.apps',
-                           *imp.find_module('apps', path))
+from prody.utilities.misctools import impLoadModule
 
-for cmd, subcmds in [('prody', apps.PRODY_APPS), ('evol', apps.EVOL_APPS)]:
+path_apps = importlib.util.find_spec("prody.apps").submodule_search_locations[0]
+
+prody_apps = impLoadModule('prody.apps.prody_apps', path_apps + '/prody_apps/', '__init__')
+evol_apps = impLoadModule('prody.apps.evol_apps', path_apps + '/evol_apps/', '__init__')
+
+for cmd, subcmds in [('prody', prody_apps.PRODY_APPS), ('evol', evol_apps.EVOL_APPS)]:
 
     pipe = Popen([cmd, '-h'], stdout=PIPE, stderr=PIPE)
     with open(os.path.join(cmd, cmd + '.txt'), 'w') as rst:

prody/apps/evol_apps/__init__.py

@@ -1,23 +1,31 @@
 """This module defines some sequence evolution applications."""
 
-from prody.utilities.misctools import importImp
-imp = importImp()
 import importlib
+import importlib.machinery
+import importlib.resources
 import sys
 
 try:
     import argparse
 except ImportError:
     from .. import argparse
 
-from ..apptools import *
+from prody.apps.apptools import *
+from prody.utilities.misctools import impLoadModule
 
 if sys.version_info[0] == 2:
+    import imp
     path_prody = imp.find_module('prody')[1]
 else:
     path_prody = importlib.util.find_spec("prody").submodule_search_locations[0]
-path_apps = imp.find_module('apps', [path_prody])[1]
-path_apps = imp.find_module('evol_apps', [path_apps])[1]
+
+try:
+    import imp
+    path_apps = imp.find_module('apps', [path_prody])[1]
+    path_apps = imp.find_module('evol_apps', [path_apps])[1]
+except ModuleNotFoundError:
+    path_apps = importlib.util.find_spec("prody.apps").submodule_search_locations[0]
+    path_apps += '/evol_apps/'
 
 EVOL_APPS = ['search', 'fetch', 'filter', 'refine', 'merge', 'occupancy',
              'conserv', 'coevol', 'rankorder']
@@ -82,8 +90,7 @@
 
 for cmd in EVOL_APPS:
     cmd = 'evol_' + cmd
-    mod = imp.load_module('prody.apps.evol_apps.' + cmd,
-                          *imp.find_module(cmd, [path_apps]))
+    mod = impLoadModule('prody.apps.evol_apps.', cmd, path_apps)
     mod.APP.addApplication(evol_commands)
 
 

prody/apps/prody_apps/__init__.py

@@ -1,7 +1,5 @@
 """This module defines structure and dynamics analysis applications."""
 
-from prody.utilities.misctools import importImp
-imp = importImp()
 import importlib
 import sys
 
@@ -10,14 +8,22 @@
 except ImportError:
     from .. import argparse
 
-from ..apptools import *
+from prody.apps.apptools import *
+from prody.utilities.misctools import impLoadModule
 
 if sys.version_info[0] == 2:
+    import imp
     path_prody = imp.find_module('prody')[1]
 else:
     path_prody = importlib.util.find_spec("prody").submodule_search_locations[0]
-path_apps = imp.find_module('apps', [path_prody])[1]
-path_apps = imp.find_module('prody_apps', [path_apps])[1]
+
+try:
+    import imp
+    path_apps = imp.find_module('apps', [path_prody])[1]
+    path_apps = imp.find_module('prody_apps', [path_apps])[1]
+except ModuleNotFoundError:
+    path_apps = importlib.util.find_spec("prody.apps").submodule_search_locations[0]
+    path_apps += '/prody_apps/'
 
 PRODY_APPS = ['anm', 'gnm', 'pca', 'eda', 'align', 'blast', 'biomol',
                   'catdcd', 'contacts', 'fetch', 'select', 'energy', 
@@ -49,7 +55,6 @@
                           *imp.find_module(cmd, [path_apps]))
     mod.addCommand(prody_commands)
 
-
 def prody_main():
 
     if len(sys.argv) == 1:

prody/utilities/misctools.py

@@ -22,7 +22,7 @@
            'getValue', 'indentElement', 'isPDB', 'isURL', 'isListLike', 'isSymmetric', 'makeSymmetric',
            'getDistance', 'fastin', 'createStringIO', 'div0', 'wmean', 'bin2dec', 'wrapModes', 
            'fixArraySize', 'decToHybrid36', 'hybrid36ToDec', 'DTYPE', 'checkIdentifiers', 'split', 'mad',
-           'importDec']
+           'importDec', 'impLoadModule']
 
 DTYPE = array(['a']).dtype.char  # 'S' for PY2K and 'U' for PY3K
 CURSORS = []
@@ -803,11 +803,22 @@ def importDec():
 
     return dec
 
-def importImp():
+
+def impLoadModule(name, cmd, path):
     """Returns an  an imported module equivalent to imp."""
+
+    if not name.endswith('.'):
+        name += '.'
+
     try:
         import imp
-    except ModuleNotFoundError:
-        from importlib import import_module as imp
+        mod = imp.load_module(name + cmd,
+                              *imp.find_module(cmd, [path]))
+    except ImportError:
+        import importlib
+        loader = importlib.machinery.SourceFileLoader(name + cmd,
+                                                      path + cmd + '.py')
+        mod = importlib.util.types.ModuleType(loader.name)
+        loader.exec_module(mod)
 
-    return imp
+    return mod