Merge pull request #26 from HBPMedical/docs/add-html-documentation

docs: add html documentation

.gitignore

@@ -15,3 +15,10 @@ build
 
 # Ignore QT Designer files
 *.ui
+
+# Ignore build documentation
+docs/api
+docs/build
+
+# Ignore Mac OS X system files
+.DS_Store

README.md

@@ -104,7 +104,7 @@ optional arguments:
 
 If you are using the MIP Dataset Mapper (`mip_dmp`) in your work, please acknowledge this software with the following entry:
 
-  > Tourbier, Sebastien, Schaffhauser, Birgit, & Ryvlin, Philippe. (2023). HBPMedical/mip-dmp: v0.0.3 (0.0.3). Zenodo. https://doi.org/10.5281/zenodo.8056371
+  > Tourbier, Sebastien, Schaffhauser, Birgit, & Ryvlin, Philippe. (2023). HBPMedical/mip-dmp: v0.0.6 (0.0.6). Zenodo. https://doi.org/10.5281/zenodo.8056371
 
 ## Funding
 

docs/LICENSE.rst

@@ -0,0 +1,7 @@
+.. _LICENSE:
+
+*******
+License
+*******
+
+.. include:: ../LICENSE

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?= -vP
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/api_cli_subpackage.rst

@@ -0,0 +1,16 @@
+.. _apidoc_cli:
+
+******************
+``mip_dmp.cli``
+******************
+
+The ``mip_dmp.cli`` subpackage contains the `mip_dataset_mapper_cli` script that defines the command line interface (CLI) for the ``mip_dmp`` package.
+
+`datahipy.cli.run`
+======================
+
+.. automodule:: mip_dmp.cli.mip_dataset_mapper_cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:

docs/api_gui_subpackage.rst

@@ -0,0 +1,16 @@
+.. _apidoc_ui:
+
+*******************
+``mip_dmp.ui``
+*******************
+
+The ``mip_dmp.ui`` subpackage stores the script that launches the MIP Dataset Mapper with graphical user interface (GUI).
+
+`mip_dmp.ui.mip_dataset_mapper_ui`
+===================================
+
+.. automodule:: mip_dmp.ui.mip_dataset_mapper_ui
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:

docs/api_plot_subpackage.rst

@@ -0,0 +1,25 @@
+.. _apidoc_plot:
+
+**********************
+``mip_dmp.plot``
+**********************
+
+The ``mip_dmp.plot`` subpackage contains modules that define classes and functions that handle the reading and writing of BIDS data. The classes are also designed to be used with the ``datahipy`` command line interface.
+
+`mip_dmp.plot.embedding`
+================================
+
+.. automodule:: mip_dmp.plot.embedding
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:
+
+`mip_dmp.plot.matching`
+====================================
+
+.. automodule:: mip_dmp.plot.matching
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:

docs/api_process_subpackage.rst

@@ -0,0 +1,43 @@
+.. _apidoc_process:
+
+*******************
+``mip_dmp.process``
+*******************
+
+The ``mip_dmp.process`` subpackage contains modules that provide processing functions for the MIP Dataset Mapper.
+
+`mip_dmp.process.embedding`
+===========================
+
+.. automodule:: mip_dmp.process.embedding
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:
+
+`mip_dmp.process.mapping`
+===========================
+
+.. automodule:: mip_dmp.process.mapping
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:
+
+`mip_dmp.process.matching`
+===============================
+
+.. automodule:: mip_dmp.process.matching
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:
+
+`mip_dmp.process.utils`
+==============================
+
+.. automodule:: mip_dmp.process.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:

docs/api_qt5_subpackage.rst

@@ -0,0 +1,50 @@
+.. _apidoc_qt5:
+
+**********************
+``mip_dmp.qt5``
+**********************
+
+The ``mip_dmp.qt5`` subpackage contains sub-packages and modules for PySide2 UI components of the MIP Dataset Mapper.
+
+`mip_dmp.qt5.components` sub-package
+====================================
+
+`mip_dmp.qt5.components.dataset_mapper_window`
+----------------------------------------------
+
+.. automodule:: mip_dmp.qt5.components.dataset_mapper_window
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:
+   :member-order: bysource
+
+`mip_dmp.qt5.components.embedding_visualization_widget`
+--------------------------------------------------------
+
+.. automodule:: mip_dmp.qt5.components.embedding_visualization_widget
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:
+
+`mip_dmp.qt5.components.matching_visualization_widget`
+-------------------------------------------------------
+
+.. automodule:: mip_dmp.qt5.components.matching_visualization_widget
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:
+
+`mip_dmp.qt5.model` sub-package
+===============================
+
+`mip_dmp.qt5.model.table_model`
+-------------------------------
+
+.. automodule:: mip_dmp.qt5.model.table_model
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:

docs/api_utils_subpackage.rst

@@ -0,0 +1,34 @@
+.. _apidoc_utils:
+
+******************
+``mip_dmp.utils``
+******************
+
+The ``mip_dmp.utils`` package contains modules with utility functions for i/o, logging, and script argument parsing.
+
+`mip_dmp.utils.io`
+==================
+
+.. automodule:: mip_dmp.utils.io
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:
+
+`mip_dmp.utils.logger`
+======================
+
+.. automodule:: mip_dmp.utils.logger
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:
+
+`mip_dmp.utils.parser`
+======================
+
+.. automodule:: mip_dmp.utils.parser
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :noindex:

docs/citing.rst

@@ -0,0 +1,9 @@
+.. _citing:
+
+************
+How to cite?
+************
+
+If you use this software in a scientific publication, please cite it with the following entry:
+
+    1. Tourbier, Sebastien, Schaffhauser, Birgit, & Ryvlin, Philippe. (2023). HBPMedical/mip-dmp: v0.0.6 (0.0.6). Zenodo. https://doi.org/10.5281/zenodo.8056371

docs/cmd_usage.rst

@@ -0,0 +1,14 @@
+.. _cmdusage:
+
+***********************
+Commandline Usage
+***********************
+
+Commandline Arguments
+=============================
+
+The command to run the MIP Dataset Mapper commandline interface is as follows.
+
+.. argparse::
+		:ref: mip_dmp.utils.parser.create_parser
+		:prog: mip_dataset_mapper