add ability to prefix file names

You may want to output something like
"docs/tests/test_{name}.py"
and expect "nest/deep.md" to output
"docs/tests/nest/test_deep.py"

before this commmit nested files would output:
"docs/tests/test_nest/deep.py"

Here pathlib makes for less code

mkcodes.py

@@ -1,4 +1,5 @@
 import os
+from pathlib import Path
 import re
 import glob
 import warnings
@@ -63,29 +64,23 @@ def extendMarkdown(self, md, md_globals):
 
     doctestextension = DoctestExtension()
     markdowner = markdown.Markdown(extensions=[doctestextension])
-    markdowner.convertFile(filepath, output=os.devnull)
+    markdowner.convertFile(str(filepath), output=os.devnull)
     return codeblocks
 
 
-def is_markdown(f):
-    markdown_extensions = ['.markdown', '.mdown', '.mkdn', '.mkd', '.md']
-    return os.path.splitext(f)[1] in markdown_extensions
-
-
-def get_nested_files(directory, depth):
-    for i in glob.iglob(directory + '/*'):
-        if os.path.isdir(i):
-            yield from get_nested_files(i, depth+1)
-        elif is_markdown(i):
-            yield (i, depth)
-
-
 def get_files(inputs):
+    """ Take in an iterable of paths, yield the files and parent dirs in those paths"""
+    markdown_extensions = ['.markdown', '.mdown', '.mkdn', '.mkd', '.md']
     for i in inputs:
-        if os.path.isdir(i):
-            yield from get_nested_files(i, 0)
-        elif is_markdown(i):
-            yield (i, 0)
+        path = Path(i)
+        if path.is_dir():
+            """ let's iterate the directory and yield files """
+            for child in path.rglob('*'):
+                if child.is_file() and child.suffix in markdown_extensions:
+                    yield child, path
+        else:
+            if path.suffix in markdown_extensions:
+                yield path, path.parent
 
 
 def makedirs(directory):
@@ -116,15 +111,23 @@ def makedirs(directory):
               help='Allow code blocks without language hints.')
 def main(inputs, output, github, safe):
     collect_codeblocks = github_codeblocks if github else markdown_codeblocks
+    # to output deep trees with a file pattern
+    # we should break out the directory and the filename pattern
+    outputbasedir = Path(output).parent
+    outputbasename = Path(output).name
 
-    for filepath, depth in get_files(inputs):
+    for filepath, input_path in get_files(inputs):
         codeblocks = collect_codeblocks(filepath, safe)
 
         if codeblocks:
-            filename = os.path.splitext(filepath)[0]
-            outputname = os.sep.join(filename.split(os.sep)[-1-depth:])
-
-            outputfilename = output.format(name=outputname)
+            #we want the path to the file, and the file without an extension
+            fp = Path(filepath)
+            filedir =fp.parent.relative_to(input_path)
+            filename = fp.stem
+
+            # stitch together the OUTPUT base directory, with the input directories
+            # add the file format at the end.
+            outputfilename = outputbasedir / filedir / outputbasename.format(name=filename)
 
             outputdir = os.path.dirname(outputfilename)
             if not os.path.exists(outputdir):

tests/data/nest/more/why.md

@@ -0,0 +1,9 @@
+# why?
+
+We want to make sure that in more complext documentation structures, which may have multiple sub directories, we are still formatting name and paths correctly.
+
+```py
+print("oh that makes sense")
+```
+
+Good.

tests/test.py

@@ -94,6 +94,7 @@ def test_directory_recursive(self):
         self.assertTrue(self._output_path_exists('other.py'))
         self.assertTrue(self._output_path_exists('nest/deep.py'))
         self.assertFalse(self._output_path_exists('not_markdown.py'))
+        self.assertTrue(self._output_path_exists('nest/more/why.py'))
 
     def test_multiple(self):
         self.call(
@@ -121,6 +122,15 @@ def test_unexistant_output_directory(self):
             backticks = range(5, 7)
             """)
 
+    def test_prefixed_deep_blocks(self):
+        self.call(
+            '--output', 'tests/output/test_{name}.py', '--github',
+            'tests/data')
+        self.assertTrue(self._output_path_exists('test_some.py'))
+        self.assertTrue(self._output_path_exists('test_other.py'))
+        self.assertTrue(self._output_path_exists('nest/test_deep.py'))
+        self.assertTrue(self._output_path_exists('nest/more/test_why.py'))
+
     @unittest.skip
     def test_glob(self):
         raise NotImplementedError