Revert "DOC Sphinx commit extra local files - removed for test"

This reverts commit f571228.

.gitignore

@@ -18,6 +18,6 @@ paper
 _build
 _static
 _templates
-docs/bruker2nifti.parsers.rst
-docs/bruker2nifti.rst
-docs/modules.rst
+#docs/bruker2nifti.parsers.rst
+#docs/bruker2nifti.rst
+#docs/modules.rst

docs/bruker2nifti.parsers.rst

@@ -0,0 +1,30 @@
+bruker2nifti.parsers package
+============================
+
+Submodules
+----------
+
+bruker2nifti.parsers.bruker2nii module
+--------------------------------------
+
+.. automodule:: bruker2nifti.parsers.bruker2nii
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+bruker2nifti.parsers.bruker2nii_scan module
+-------------------------------------------
+
+.. automodule:: bruker2nifti.parsers.bruker2nii_scan
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: bruker2nifti.parsers
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/bruker2nifti.rst

@@ -0,0 +1,37 @@
+bruker2nifti package
+====================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    bruker2nifti.parsers
+
+Submodules
+----------
+
+bruker2nifti.converter module
+-----------------------------
+
+.. automodule:: bruker2nifti.converter
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+bruker2nifti.open_GUI module
+----------------------------
+
+.. automodule:: bruker2nifti.open_GUI
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: bruker2nifti
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/conf.py

@@ -152,23 +152,5 @@
      'Miscellaneous'),
 ]
 
-# Added after https://github.com/rtfd/readthedocs.org/issues/1139
 
 
-import subprocess
-
-
-def run_apidoc(_):
-    modules = ['bruker2nifti', 'bruker2nifti/parsers']
-    for module in modules:
-        cur_dir = os.path.abspath(os.path.dirname(__file__))
-        output_path = os.path.join(cur_dir, module, 'doc')
-        cmd_path = 'sphinx-apidoc'
-        if hasattr(sys, 'real_prefix'):  # Check to see if we are in a virtualenv
-            # If we are, assemble the path manually
-            cmd_path = os.path.abspath(os.path.join(sys.prefix, 'bin', 'sphinx-apidoc'))
-        subprocess.check_call([cmd_path, '-e', '-o', output_path, module, '--force'])
-
-
-def setup(app):
-    app.connect('builder-inited', run_apidoc)

docs/modules.rst

@@ -0,0 +1,7 @@
+bruker2nifti
+============
+
+.. toctree::
+   :maxdepth: 4
+
+   bruker2nifti