docs/conf.py

@@ -33,11 +33,11 @@ author = 'Jan Caron'
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.viewcode',
-    'numpydoc'
-]
+extensions = ['sphinx.ext.autodoc',
+              'sphinx.ext.viewcode',
+              'numpydoc',
+              'nbsphinx',
+              'nbsphinx_link']
 
 numpydoc_show_class_members = False
 add_module_names = False
@@ -60,7 +60,7 @@ html_theme = 'sphinx_rtd_theme'
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# html_static_path = ['_static']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
@@ -76,3 +76,7 @@ html_logo = 'EMPyRe Logo.png'
 # the doc.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
 html_favicon = 'icon.ico'
+
+# cannot cache unpickable configuration value: 'nbsphinx_custom_formats
+# See https://github.com/sphinx-doc/sphinx/issues/12300
+suppress_warnings = ["config.cache"]

docs/demos.rst

+Demos
+-----
+
+.. toctree::
+    demos/demo1
+    demos/demo2
+    demos/demo3

docs/demos/demo1.nblink

+{
+    "path": "../../demos/demo1_first_steps.ipynb"
+}
\ No newline at end of file

docs/demos/demo2.nblink

+{
+    "path": "../../demos/demo2_handling_3d_fields.ipynb"
+}
\ No newline at end of file

docs/demos/demo3.nblink

+{
+    "path": "../../demos/demo3_io_and_field_manipulation.ipynb"
+}
\ No newline at end of file

docs/fields.rst

@@ -3,6 +3,8 @@ The Field container class
 
 General empyre.fields docu here!
 
+All functions implemented in the subpackages can be accessed directly in the ``empyre.fields`` namespace.
+
 
 The field module
 ----------------

docs/index.rst

@@ -14,6 +14,8 @@ EMPyRe - Electron Microscopy Reconstruction
 
    fields
    vis
+   io
+   demos
 
 
 Indices and tables

docs/io.rst

+The io visualization submodule
+===============================
+
+General empyre.io docu here!
+
+
+The io_field module
+-------------------
+
+.. automodule:: empyre.io.io_field
+   :members:
+   :show-inheritance:
+
+
+The field_plugins module
+------------------------
+
+.. automodule:: empyre.io.field_plugins
+   :members:
+   :show-inheritance: