Merge branch 'add_autosumary_and_improve_code_coverage' into 'master'

general improvement See merge request !76

Merge branch 'add_autosumary_and_improve_code_coverage' into 'master'
general improvement See merge request !76
b91d3ab1 · payno · 409f4a0e · 92f7f587 · b91d3ab1 · b91d3ab1
Commit b91d3ab1 authored Oct 12, 2021 by payno
--- a/.coveragerc
+++ b/.coveragerc
 [run]
 omit = [
-	nxtomomill/app/*,
 	*setup.py,
+	*test_*.py,
+	nxtomomill/converter/hdf5/acquisition/baseaquisition.py,
 ]
\ No newline at end of file
--- a/.gitignore
+++ b/.gitignore
@@ -57,3 +57,5 @@ datasets/

 # octave files
 octave-workspace
+
+doc/_generated
\ No newline at end of file
--- a/doc/api.rst
+++ b/doc/api.rst
+nxtomomill API
+==============
+
+
+.. autosummary::
+    :toctree: _generated
+    :recursive:
+
+    nxtomomill
\ No newline at end of file
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -37,6 +37,7 @@ extensions = [
    "sphinx.ext.viewcode",
    "sphinx.ext.doctest",
    "sphinx.ext.inheritance_diagram",
+    "sphinx.ext.autosummary",
 ]

 # Add any paths that contain templates here, relative to this directory.
@@ -58,9 +59,13 @@ html_theme = "nature"
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "sphinx"

-# 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_logo = "img/nxtomomill.png"
+
+# autosummary options
+autosummary_generate = True
+
+autodoc_default_flags = [
+    "members",
+    "undoc-members",
+    "show-inheritance",
+]
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -8,18 +8,32 @@
 |foo| Welcome to nxtomomill's documentation!
 ============================================

-nxtomomill provide a set of applications to convert tomography acquisition made from bliss (@ESRF) from their original file format (.edf, .h5) to a Nexus compliant file format (using `NXtomo <https://manual.nexusformat.org/classes/applications/NXtomo.html>`_)
+nxtomomill provide a set of applications to convert tomography acquisition made by `BLISS <https://www.esrf.fr/BLISS>`_ from their original file format (.edf, .h5) to a Nexus compliant file format (using `NXtomo <https://manual.nexusformat.org/classes/applications/NXtomo.html>`_)

+.. include:: install.rst
+
+Tutorials
+=========

 .. toctree::
   :maxdepth: 2

-   install.rst
   tutorials/index.rst
-   modules/nxtomomill.rst
-   plugins.rst
-   settings.rst
-   design/index.rst
+
+API
+===
+
+.. toctree::
+   :maxdepth: 4
+
+   api.rst
+
+
+.. include:: plugins.rst
+
+.. include:: settings.rst
+
+.. include:: design/index.rst


 Indices and tables

--- a/doc/modules/nxtomomill.app.rst
+++ b/doc/modules/nxtomomill.app.rst
-nxtomomill.app package
-======================
-
-Submodules
----------
-
-nxtomomill.app.edf2nx module
----------------------------
-
-.. automodule:: nxtomomill.app.edf2nx
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.app.h52nx module
---------------------------
-
-.. automodule:: nxtomomill.app.h52nx
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.app.h5\_3dxrd2nx module
----------------------------------
-
-.. automodule:: nxtomomill.app.h5_3dxrd2nx
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.app.h5quickstart module
----------------------------------
-
-.. automodule:: nxtomomill.app.h5quickstart
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.app.patch\_nx module
-------------------------------
-
-.. automodule:: nxtomomill.app.patch_nx
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
---------------
-
-.. automodule:: nxtomomill.app
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/doc/modules/nxtomomill.converter.dxfile.rst
+++ b/doc/modules/nxtomomill.converter.dxfile.rst
-nxtomomill.converter.dxfile package
-===================================
-
-Submodules
----------
-
-nxtomomill.converter.dxfile.dxfileconverter module
--------------------------------------------------
-
-.. automodule:: nxtomomill.converter.dxfile.dxfileconverter
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.converter.dxfile.test\_dxfile module
-----------------------------------------------
-
-.. automodule:: nxtomomill.converter.dxfile.test_dxfile
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
---------------
-
-.. automodule:: nxtomomill.converter.dxfile
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/doc/modules/nxtomomill.converter.edf.rst
+++ b/doc/modules/nxtomomill.converter.edf.rst
-nxtomomill.converter.edf package
-================================
-
-Submodules
----------
-
-nxtomomill.converter.edf.edfconverter module
--------------------------------------------
-
-.. automodule:: nxtomomill.converter.edf.edfconverter
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
---------------
-
-.. automodule:: nxtomomill.converter.edf
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/doc/modules/nxtomomill.converter.hdf5.acquisition.rst
+++ b/doc/modules/nxtomomill.converter.hdf5.acquisition.rst
-nxtomomill.converter.hdf5.acquisition package
-=============================================
-
-Submodules
----------
-
-nxtomomill.converter.hdf5.acquisition.baseacquisition module
------------------------------------------------------------
-
-.. automodule:: nxtomomill.converter.hdf5.acquisition.baseacquisition
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.converter.hdf5.acquisition.baseaquisition module
-----------------------------------------------------------
-
-.. automodule:: nxtomomill.converter.hdf5.acquisition.baseaquisition
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.converter.hdf5.acquisition.standardacquisition module
----------------------------------------------------------------
-
-.. automodule:: nxtomomill.converter.hdf5.acquisition.standardacquisition
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.converter.hdf5.acquisition.utils module
--------------------------------------------------
-
-.. automodule:: nxtomomill.converter.hdf5.acquisition.utils
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.converter.hdf5.acquisition.xrd3dacquisition module
-------------------------------------------------------------
-
-.. automodule:: nxtomomill.converter.hdf5.acquisition.xrd3dacquisition
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.converter.hdf5.acquisition.xrdctacquisition module
-------------------------------------------------------------
-
-.. automodule:: nxtomomill.converter.hdf5.acquisition.xrdctacquisition
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.converter.hdf5.acquisition.zseriesacquisition module
---------------------------------------------------------------
-
-.. automodule:: nxtomomill.converter.hdf5.acquisition.zseriesacquisition
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
---------------
-
-.. automodule:: nxtomomill.converter.hdf5.acquisition
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/doc/modules/nxtomomill.converter.hdf5.acquisition.test.rst
+++ b/doc/modules/nxtomomill.converter.hdf5.acquisition.test.rst
-nxtomomill.converter.hdf5.acquisition.test package
-==================================================
-
-Submodules
----------
-
-nxtomomill.converter.hdf5.acquisition.test.test\_acquisition module
-------------------------------------------------------------------
-
-.. automodule:: nxtomomill.converter.hdf5.acquisition.test.test_acquisition
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
---------------
-
-.. automodule:: nxtomomill.converter.hdf5.acquisition.test
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/doc/modules/nxtomomill.converter.hdf5.rst
+++ b/doc/modules/nxtomomill.converter.hdf5.rst
-nxtomomill.converter.hdf5 package
-=================================
-
-Subpackages
-----------
-
-.. toctree::
-
-   nxtomomill.converter.hdf5.acquisition
-
-Submodules
----------
-
-nxtomomill.converter.hdf5.hdf5converter module
----------------------------------------------
-
-.. automodule:: nxtomomill.converter.hdf5.hdf5converter
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.converter.hdf5.setup module
--------------------------------------
-
-.. automodule:: nxtomomill.converter.hdf5.setup
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.converter.hdf5.utils module
--------------------------------------
-
-.. automodule:: nxtomomill.converter.hdf5.utils
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
---------------
-
-.. automodule:: nxtomomill.converter.hdf5
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/doc/modules/nxtomomill.converter.hdf5.test.rst
+++ b/doc/modules/nxtomomill.converter.hdf5.test.rst
-nxtomomill.converter.hdf5.test package
-======================================
-
-Submodules
----------
-
-nxtomomill.converter.hdf5.test.test\_h52nx module
-------------------------------------------------
-
-.. automodule:: nxtomomill.converter.hdf5.test.test_h52nx
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
---------------
-
-.. automodule:: nxtomomill.converter.hdf5.test
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/doc/modules/nxtomomill.converter.rst
+++ b/doc/modules/nxtomomill.converter.rst
-nxtomomill.converter package
-============================
-
-Subpackages
-----------
-
-.. toctree::
-
-   nxtomomill.converter.dxfile
-   nxtomomill.converter.edf
-   nxtomomill.converter.hdf5
-
-Submodules
----------
-
-nxtomomill.converter.baseconverter module
-----------------------------------------
-
-.. automodule:: nxtomomill.converter.baseconverter
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.converter.setup module
---------------------------------
-
-.. automodule:: nxtomomill.converter.setup
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.converter.version module
-----------------------------------
-
-.. automodule:: nxtomomill.converter.version
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
---------------
-
-.. automodule:: nxtomomill.converter
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/doc/modules/nxtomomill.io.rst
+++ b/doc/modules/nxtomomill.io.rst
-nxtomomill.io package
-=====================
-
-Subpackages
-----------
-
-.. toctree::
-
-   nxtomomill.io.test
-
-Submodules
----------
-
-nxtomomill.io.acquisitionstep module
------------------------------------
-
-.. automodule:: nxtomomill.io.acquisitionstep
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.io.config module
---------------------------
-
-.. automodule:: nxtomomill.io.config
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.io.confighandler module
----------------------------------
-
-.. automodule:: nxtomomill.io.confighandler
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.io.framegroup module
-------------------------------
-
-.. automodule:: nxtomomill.io.framegroup
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.io.setup module
--------------------------
-
-.. automodule:: nxtomomill.io.setup
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.io.utils module
--------------------------
-
-.. automodule:: nxtomomill.io.utils
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
---------------
-
-.. automodule:: nxtomomill.io
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/doc/modules/nxtomomill.io.test.rst
+++ b/doc/modules/nxtomomill.io.test.rst
-nxtomomill.io.test package
-==========================
-
-Submodules
----------
-
-nxtomomill.io.test.test\_config module
--------------------------------------
-
-.. automodule:: nxtomomill.io.test.test_config
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.io.test.test\_confighandler module
---------------------------------------------
-
-.. automodule:: nxtomomill.io.test.test_confighandler
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.io.test.test\_frame\_group module
--------------------------------------------
-
-.. automodule:: nxtomomill.io.test.test_frame_group
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.io.test.test\_utils module
-------------------------------------
-
-.. automodule:: nxtomomill.io.test.test_utils
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
---------------
-
-.. automodule:: nxtomomill.io.test
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/doc/modules/nxtomomill.rst
+++ b/doc/modules/nxtomomill.rst
-nxtomomill package
-==================
-
-Subpackages
-----------
-
-.. toctree::
-
-   nxtomomill.app
-   nxtomomill.converter
-   nxtomomill.io
-   nxtomomill.test
-
-Submodules
----------
-
-nxtomomill.plugins module
-------------------------
-
-.. automodule:: nxtomomill.plugins
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.settings module
--------------------------
-
-.. automodule:: nxtomomill.settings
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.setup module
-----------------------
-
-.. automodule:: nxtomomill.setup
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.utils module
-----------------------
-
-.. automodule:: nxtomomill.utils
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nxtomomill.version module
-------------------------
-
-.. automodule:: nxtomomill.version
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
---------------
-
-.. automodule:: nxtomomill
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/doc/modules/nxtomomill.test.rst
+++ b/doc/modules/nxtomomill.test.rst
-nxtomomill.test package
-=======================
-
-Subpackages
-----------
-
-.. toctree::
-
-   nxtomomill.test.utils
-
-Submodules
----------
-
-nxtomomill.test.test\_utils module
----------------------------------
-
-.. automodule:: nxtomomill.test.test_utils
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
---------------
-
-.. automodule:: nxtomomill.test
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/doc/modules/nxtomomill.test.utils.rst
+++ b/doc/modules/nxtomomill.test.utils.rst
-nxtomomill.test.utils package
-=============================
-
-Submodules
----------
-
-nxtomomill.test.utils.bliss module
----------------------------------