python 3.12 does not have imp module

cgat/cgat.py

@@ -27,19 +27,18 @@
 
     cgat <tool> --help
 '''
-
 import os
 import sys
 import re
 import glob
-import imp
+import importlib.util
 import collections
 import cgatcore.iotools as iotools
 import cgat
 
 
 def mapKeyword2Script(path):
-    '''collect keywords from scripts.'''
+    '''Collect keywords from scripts.'''
 
     map_keyword2script = collections.defaultdict(list)
 
@@ -57,79 +56,110 @@ def mapKeyword2Script(path):
 
 
 def printListInColumns(l, ncolumns):
-    '''output list *l* in *ncolumns*.'''
+    '''Output list *l* in *ncolumns*.'''
     ll = len(l)
 
     if ll == 0:
         return
 
     max_width = max([len(x) for x in l]) + 3
     n = ll // ncolumns
-    if ll % 3 != 0:
+    if ll % ncolumns != 0:
         n += 1
 
-    # build columns
+    # Build columns
     columns = [l[x * n:x * n + n] for x in range(ncolumns)]
 
-    # add empty fields for missing columns in last row
+    # Add empty fields for missing columns in last row
     for x in range(ncolumns - (len(l) % ncolumns)):
         columns[-(x + 1)].append('')
 
-    # convert to rows
+    # Convert to rows
     rows = list(zip(*columns))
 
-    # build pattern for a row
+    # Build pattern for a row
     p = '%-' + str(max_width) + 's'
-    pattern = ' '.join([p for x in range(ncolumns)])
+    pattern = ' '.join([p for _ in range(ncolumns)])
 
-    # put it all together
+    # Put it all together
     return '\n'.join([pattern % row for row in rows])
 
 
 def main(argv=None):
-
     argv = sys.argv
 
     path = os.path.join(os.path.abspath(os.path.dirname(cgat.__file__)),
                         "tools")
 
-    if len(argv) == 1 or argv[1] == "--help" or argv[1] == "-h":
-        print((globals()["__doc__"]))
+    if len(argv) == 1 or argv[1] in ("--help", "-h"):
+        print(globals().get("__doc__", "No documentation available."))
 
         map_keyword2script = mapKeyword2Script(path)
 
         if len(argv) <= 2:
-
             print('cgat tools are grouped by keywords. The following keywords')
             print('are defined:\n')
-            print(("%s\n" % printListInColumns(list(map_keyword2script.keys()),
-                                               3)))
+            print("%s\n" % printListInColumns(list(map_keyword2script.keys()), 3))
 
         if 'all' in argv[2:]:
             print("The list of all available commands is:\n")
-            print(("%s\n" % printListInColumns(
+            print("%s\n" % printListInColumns(
                 sorted([os.path.basename(x)[:-3]
                         for x in glob.glob(os.path.join(path, "*.py"))]),
-                3)))
-
+                3))
         else:
             for arg in argv[2:]:
                 if arg in map_keyword2script:
-                    print(("Tools matching the keyword '%s':\n" % arg))
-                    print(('%s\n' % printListInColumns(
+                    print("Tools matching the keyword '%s':\n" % arg)
+                    print('%s\n' % printListInColumns(
                         sorted(map_keyword2script[arg]),
-                        3)))
+                        3))
         return
 
+    if len(argv) < 2:
+        print("Error: No command provided.\nUse --help for more information.", file=sys.stderr)
+        sys.exit(1)
+
     command = argv[1]
 
+    # Replace hyphens with underscores to match Python module naming conventions
     command = re.sub("-", "_", command)
-
-    (file, pathname, description) = imp.find_module(command, [path, ])
-    module = imp.load_module(command, file, pathname, description)
-    # remove 'cgat' from sys.argv
-    del sys.argv[0]
-    module.main(sys.argv)
+
+    # Dynamically load the specified module using importlib
+    module_path = os.path.join(path, f"{command}.py")
+
+    if not os.path.isfile(module_path):
+        print(f"Error: Module '{command}' not found in path '{path}'.", file=sys.stderr)
+        sys.exit(1)
+
+    spec = importlib.util.spec_from_file_location(command, module_path)
+    if spec is None:
+        print(f"Error: Cannot create a module spec for '{command}'.", file=sys.stderr)
+        sys.exit(1)
+
+    module = importlib.util.module_from_spec(spec)
+    try:
+        spec.loader.exec_module(module)
+    except Exception as e:
+        print(f"Error: Failed to load module '{command}': {e}", file=sys.stderr)
+        sys.exit(1)
+
+    # Remove 'cgat' from sys.argv to pass the remaining arguments to the module's main function
+    if len(sys.argv) > 0:
+        del sys.argv[0]
+
+    # Ensure the module has a 'main' function
+    if not hasattr(module, 'main'):
+        print(f"Error: The module '{command}' does not have a 'main' function.", file=sys.stderr)
+        sys.exit(1)
+
+    # Call the module's main function with the remaining arguments
+    try:
+        module.main(sys.argv)
+    except Exception as e:
+        print(f"Error: An exception occurred while executing the 'main' function of '{command}': {e}", file=sys.stderr)
+        sys.exit(1)
+
 
 if __name__ == "__main__":
     sys.exit(main())