[doc] move to autosumary and improve doc

.gitignore

@@ -64,3 +64,6 @@ pushworkflow
 # Visual Studio Code files
 .vscode/
 .empty/
+
+# sphinx files
+_generated

doc/api.rst

+est API
+=======
+
+
+.. autosummary::
+    :toctree: _generated
+    :recursive:
+
+    est

doc/conf.py

@@ -34,11 +34,13 @@ sys.path.append(os.path.join(os.path.dirname(os.path.abspath(__file__)), "ext"))
 # ones.
 extensions = [
     "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
     "nbsphinx",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ["templates"]
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
@@ -283,3 +285,11 @@ texinfo_documents = [
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 # texinfo_no_detailmenu = False
+
+autosummary_generate = True
+
+autodoc_default_flags = [
+    "members",
+    "undoc-members",
+    "show-inheritance",
+]

doc/index.rst

@@ -18,7 +18,7 @@ An `Orange3 <https://github.com/biolab/orange3>`_ add-on is also provided by the
 
    tutorials/index.rst
    install.rst
-   modules/index.rst
+   api.rst
    larch_pymca.rst
    app/index.rst
 
@@ -29,7 +29,7 @@ An `Orange3 <https://github.com/biolab/orange3>`_ add-on is also provided by the
 :doc:`app/index`
     Applications
 
-:doc:`modules/index`
+:doc:`api`
     API
 
 :doc:`tutorials/index`

doc/modules/core/index.rst

-est.core package
-================
-
-Subpackages
------------
-
-.. toctree::
-
-   utils/index.rst
-   process/index.rst
-
-est.core.io module
-------------------
-
-.. automodule:: est.core.io
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.reprocessing module
-----------------------------
-
-.. automodule:: est.core.reprocessing
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.types module
----------------------
-
-.. automodule:: est.core.types
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: est.core
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-.. toctree::
-   :maxdepth: 4
-
-   utils/index.rst

doc/modules/core/process/index.rst

-est.core.process package
-========================
-
-Subpackages
------------
-
-.. toctree::
-
-   est.core.process.larch
-   est.core.process.pymca
-
-est.core.process.process module
--------------------------------
-
-.. automodule:: est.core.process.process
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.process.progress module
---------------------------------
-
-.. automodule:: est.core.process.progress
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.process.roi module
----------------------------
-
-.. automodule:: est.core.process.roi
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.process.setup module
------------------------------
-
-.. automodule:: est.core.process.setup
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: est.core.process
-   :members:
-   :undoc-members:
-   :show-inheritance:

doc/modules/core/process/xas.core.process.larch.rst

-est.core.process.larch package
-==============================
-
-est.core.process.larch.autobk module
-------------------------------------
-
-.. automodule:: est.core.process.larch.autobk
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.process.larch.mback module
------------------------------------
-
-.. automodule:: est.core.process.larch.mback
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.process.larch.mback\_norm module
------------------------------------------
-
-.. automodule:: est.core.process.larch.mback_norm
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.process.larch.pre\_edge module
----------------------------------------
-
-.. automodule:: est.core.process.larch.pre_edge
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.process.larch.xftf module
-----------------------------------
-
-.. automodule:: est.core.process.larch.xftf
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: est.core.process.larch
-   :members:
-   :undoc-members:
-   :show-inheritance:

doc/modules/core/process/xas.core.process.pymca.rst

-est.core.process.pymca package
-==============================
-
-est.core.process.pymca.exafs module
------------------------------------
-
-.. automodule:: est.core.process.pymca.exafs
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.process.pymca.ft module
---------------------------------
-
-.. automodule:: est.core.process.pymca.ft
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.process.pymca.k\_weight module
----------------------------------------
-
-.. automodule:: est.core.process.pymca.k_weight
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.process.pymca.normalization module
--------------------------------------------
-
-.. automodule:: est.core.process.pymca.normalization
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.process.pymca.setup module
------------------------------------
-
-.. automodule:: est.core.process.pymca.setup
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: est.core.process.pymca
-   :members:
-   :undoc-members:
-   :show-inheritance:

doc/modules/core/utils/index.rst

-est.core.utils package
-======================
-
-est.core.utils.designpattern module
------------------------------------
-
-.. automodule:: est.core.utils.designpattern
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.core.utils.spectra module
------------------------------
-
-.. automodule:: est.core.utils.spectra
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: est.core.utils
-   :members:
-   :undoc-members:
-   :show-inheritance:

doc/modules/gui/index.rst

-est.gui package
-===============
-
-Subpackages
------------
-
-est.gui.XasObjectViewer module
-------------------------------
-
-.. automodule:: est.gui.XasObjectViewer
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.gui.icons module
---------------------
-
-.. automodule:: est.gui.icons
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.gui.qtapplicationmanager module
------------------------------------
-
-.. automodule:: est.gui.qtapplicationmanager
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.gui.roiselector module
---------------------------
-
-.. automodule:: est.gui.roiselector
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.gui.xas\_object\_definition module
---------------------------------------
-
-.. automodule:: est.gui.xas_object_definition
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: est.gui
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-.. toctree::
-   :maxdepth: 4
-
-   larch/est.gui.larch.rst

doc/modules/gui/larch/xas.gui.larch.rst

-est.gui.larch package
-=====================
-
-est.gui.larch.autobk module
----------------------------
-
-.. automodule:: est.gui.larch.autobk
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.gui.larch.mback module
---------------------------
-
-.. automodule:: est.gui.larch.mback
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.gui.larch.pre\_edge module
-------------------------------
-
-.. automodule:: est.gui.larch.pre_edge
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.gui.larch.utils module
---------------------------
-
-.. automodule:: est.gui.larch.utils
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.gui.larch.xftf module
--------------------------
-
-.. automodule:: est.gui.larch.xftf
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: est.gui.larch
-   :members:
-   :undoc-members:
-   :show-inheritance:

doc/modules/index.rst

-API
-===
-
-.. toctree::
-   :maxdepth: 4
-
-   core/index.rst
-   gui/index.rst
-   io/index.rst
-   pushworkflow/index.rst

doc/modules/io/est.io.utils.rst

-est.io.utils package
-====================
-
-est.io.utils.larch module
--------------------------
-
-.. automodule:: est.io.utils.larch
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-est.io.utils.pymca module
--------------------------
-
-.. automodule:: est.io.utils.pymca
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: est.io.utils
-   :members:
-   :undoc-members:
-   :show-inheritance:

doc/modules/io/index.rst

-est.io package
-==============
-
-Subpackages
------------
-
-.. toctree::
-
-   est.io.utils
-
-est.io.io module
-----------------
-
-.. automodule:: est.io.io
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: est.io
-   :members:
-   :undoc-members:
-   :show-inheritance:

est/__init__.py

@@ -22,6 +22,7 @@
 # THE SOFTWARE.
 #
 # ###########################################################################*/
+"""est package provides a way to create processing workflows for spectroscopy from pymca and larch libraries"""
 
 from __future__ import absolute_import, print_function, division
 

est/app/__init__.py

+"""est applications"""

est/core/__init__.py

+"""est core module. Contains core features. It must stay Qt free"""

est/core/io.py

@@ -22,7 +22,7 @@
 # THE SOFTWARE.
 #
 # ###########################################################################*/
-"""simple helper function to link io module and XASObject"""
+"""simple helper functions to insure a simple link with the `io` module (and XASObject)"""
 
 __authors__ = ["H. Payno"]
 __license__ = "MIT"

est/core/process/__init__.py

+"""est core processing module"""

est/core/process/energyroi.py

@@ -22,6 +22,7 @@
 # THE SOFTWARE.
 #
 # ###########################################################################*/
+"""contains `energy roi` related functions / classes"""
 
 __authors__ = ["H. Payno"]
 __license__ = "MIT"