Fix docstring indentation

docs/_writing_argparse.rst

@@ -25,6 +25,4 @@ since in most cases ``argparse`` does not distinguish between input and output
 files all file parameters will be rendered as input parameters of the tool.
 
 Please open an issue if you have ideas on how to improve the generated tools:
-https://github.com/galaxyproject/planemo/issues
-
-
+https://github.com/galaxyproject/planemo/issues

planemo/autopygen/argument_parser_conversion.py

@@ -1,7 +1,7 @@
 """
 Functions used to extract initialized ArgumentParser from target source code,
 and to transform it into easily usable ParamInfo class containing
- all the necessary info for 'inputs' element initialization
+all the necessary info for 'inputs' element initialization
 """
 import ast
 import logging
@@ -57,7 +57,7 @@ def obtain_and_convert_parser(path: str) -> Optional[DecoyParser]:
     Parameters
     ----------
     path : str
-     path to the source file containing argument parser init
+      path to the source file containing argument parser init
 
     Returns
     -------
@@ -80,7 +80,7 @@ def obtain_and_convert_parser_from_str(text: str) -> Optional[ArgumentParser]:
     Parameters
     ----------
     text : str
-     variable containing target source code
+      variable containing target source code
 
     Returns
     -------

planemo/autopygen/commands/command_utils.py

@@ -3,6 +3,7 @@
 are parts of template, separated from the rest by comments
 with specific structure
 Example of the comments:
+
     ## foo definition
     ... block itself ...
     ## end foo definition
@@ -42,8 +43,8 @@ def create_flag(
     comment : str
         wrapping comment
     depth : int
-     integer, used to set the depth of the current element.
-     This value is used to indent the block properly
+      integer, used to set the depth of the current element.
+      This value is used to indent the block properly
     indent : int
       default value for size of the block indent
     add_comment : bool
@@ -73,18 +74,18 @@ def create_element_with_body(
     Parameters
     ----------
     kind : str
-     string defining what kind of element is created, for example if or for
-     (loop)
+      string defining what kind of element is created, for example if or for
+      (loop)
     head : str
-     body of block header, for example predicate of condition, or the
-     body of loop
+      body of block header, for example predicate of condition, or the
+      body of loop
     body : str
-     body of the block, can be another element
+      body of the block, can be another element
     comment : str
-     comment, used to set the start and end of the block
+      comment, used to set the start and end of the block
     depth : int
-     integer, used to set the depth of the current element.
-     This value is used to indent the block properly
+      integer, used to set the depth of the current element.
+      This value is used to indent the block properly
     indent : int
       default value for size of the block indent
     body_indented : bool

planemo/autopygen/source_file_parsing/local_module_parsing.py

@@ -23,9 +23,10 @@ class UnknownNamesRemoval(ast.NodeVisitor):
 
     Attributes
     ---
+
     unknown: Set[str]
-     set of names that represent variables used in parser initialization,
-     that have not been resolved yet
+      set of names that represent variables used in parser initialization,
+      that have not been resolved yet
 
     """
 
@@ -104,10 +105,10 @@ def handle_local_module_names(actions: List[ast.AST], unknown_names: Set[str]) -
 
     Parameters
     ----------
-    actions : List[ast.AST]
-     list of actions extracted so far
-    unknown_names :
-     set of unknown names that have to be extracted
+    actions: List[ast.AST]
+      list of actions extracted so far
+    unknown_names:
+      set of unknown names that have to be extracted
 
     Returns
     -------

planemo/autopygen/source_file_parsing/parser_discovery_and_init.py

@@ -90,7 +90,7 @@ class SimpleParserDiscoveryAndReplacement(Discovery):
     """
     Class responsible for discovery of ArgumentParser creation
     and assignment, and replacement of the class definition
-     by the one supplied through constructor
+    by the one supplied through constructor
     """
 
     def __init__(
@@ -230,7 +230,7 @@ def get_parser_init_and_actions(source: ast.Module) -> Tuple[List[ast.AST], str,
     Parameters
     ----------
     source : ast.Module
-     source file parsed into ATT
+      source file parsed into ATT
 
     Returns
     -------