Commit b91d3ab1 authored by payno's avatar payno
Browse files

Merge branch 'add_autosumary_and_improve_code_coverage' into 'master'

general improvement

See merge request !76
parents 409f4a0e 92f7f587
Pipeline #56504 passed with stages
in 6 minutes and 12 seconds
[run]
omit = [
nxtomomill/app/*,
*setup.py,
*test_*.py,
nxtomomill/converter/hdf5/acquisition/baseaquisition.py,
]
\ No newline at end of file
......@@ -57,3 +57,5 @@ datasets/
# octave files
octave-workspace
doc/_generated
\ No newline at end of file
nxtomomill API
==============
.. autosummary::
:toctree: _generated
:recursive:
nxtomomill
\ No newline at end of file
......@@ -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",
]
......@@ -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
......
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
nxtomomill.test.utils package
=============================
Submodules
----------
nxtomomill.test.utils.bliss module
----------------------------------