Merge pull request #47 from nrv-framework/doc-api

Doc api
nrv-framework · Sep 2, 2024 · ac0c065 · ac0c065
2 parents df5b533 + 44a006f
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diff --git a/.gitignore b/.gitignore
@@ -207,3 +207,5 @@ tests/log_NRV_test.txt
 .vscode/settings.json
 tests/log_NRV_test.txt
 .vscode/*
+docs/_nrv/*
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,20 @@
 
 All notable changes to NRV are sumed up in this file.
 
+## [1.1.2] - 2024-09-??
+
+### Added
+- 'ui', a subpackage for user interface to separate from utils which are ment to stay internal.
+- Help restructuration to have a API description more user firendly.
+
+### Fixed
+
+### Removed
+- methods such as load_any_axon, load_any_electrode... (load_any_ + somthing) are deprecated, though not removed for backward compatibility. Please only use load_any function.
+
+
+
+
 ## [1.1.1] - 2024-08-05
 
 ### Added

diff --git a/TODO.md b/TODO.md
@@ -0,0 +1,16 @@
+LIST OF POINTS TO ADDRESS BEFORE NEXT VERSION
+---------------------------------------------
+THIS NEEDS TO BE DONE FOR BIOCAS AND EASE DEMOS!!! 
+
+* in backend/_NRV_Simulable, twice the same function (is_NRV_simulable and simulable), suppress the second
+
+* suppress maximum of * in the primary __init__.py
+
+* add top level docstring (cf. scipy init.py), and subprocess init files
+
+* add missing docstring functions (see utils...)
+
+* CL_simulation rename
+
+* test to deploy on binder -> build an environnement.yaml file with the requirements... to do in emergency !!!
+  * Almost done (technically working, need polish and truly demo file )
diff --git a/docs/_templates/autosummary/base.rst b/docs/_templates/autosummary/base.rst
@@ -0,0 +1,5 @@
+{{ objname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. auto{{ objtype }}:: {{ objname }}
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
@@ -0,0 +1,30 @@
+{{ objname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+{% block attributes %}
+{% if attributes %}
+Attributes
+----------
+.. autosummary::
+    :toctree: {{ name }}
+{% for item in attributes %}
+    {{ name }}.{{ item }}
+{% endfor %}
+{% endif %}
+{% endblock %}
+
+{% block methods %}
+{% if methods %}
+Methods
+-------
+.. autosummary::
+    :toctree: {{ name }}
+
+{% for item in methods %}
+    {{ name }}.{{ item }}
+{% endfor %}
+{% endif %}
+{% endblock %}
diff --git a/docs/_templates/autosummary/module.rst b/docs/_templates/autosummary/module.rst
@@ -0,0 +1,41 @@
+{{ fullname | escape | underline }}
+
+Description
+-----------
+.. automodule:: {{ fullname }}
+.. currentmodule:: {{ fullname }}
+
+
+{% if modules %}
+Subpackages
+-----------
+.. autosummary::
+    :toctree: {{ name }}
+    :recursive:
+    {% for module in modules %}
+    {{ module }}
+    {% endfor %}
+{% endif %}
+
+
+
+{% if classes %}
+Classes
+-------
+.. autosummary::
+    :toctree: {{ name }}
+    {% for class in classes %}
+    {{ class }}
+    {% endfor %}
+{% endif %}
+
+{% if functions %}
+Functions
+---------
+
+.. autosummary:: 
+    :toctree: {{ name }}
+    {% for function in functions %}
+    {{ function }}
+    {% endfor %}
+{% endif %}
diff --git a/docs/conf.py b/docs/conf.py
@@ -119,3 +119,5 @@
 autodoc_member_order = 'bysource' # keep the order of class and function source files
 #                                   (thus don't use alphabetical order)
 autosummary_generate = True
+
+autosummary_ignore_module_all = False
diff --git a/docs/modules.rst b/docs/modules.rst
@@ -1,9 +1,29 @@
 .. _modules:
 
-API documentation
-=================
+API Reference
+=============
 
-.. toctree::
-   :maxdepth: 5
 
-   nrv/nrv
+Module contents
+---------------
+
+.. automodule:: nrv
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :exclude-members: DummyClass
+
+Subpackages
+-----------
+
+.. autosummary::
+   :toctree: _nrv
+   :recursive:
+
+   nmod
+   fmod
+   optim
+   eit
+   utils
+   ui
+   backend
diff --git a/docs/nrv/backend/mod_10_compileMods.rst b/docs/nrv/backend/mod_10_compileMods.rst
diff --git a/docs/nrv/backend/mod_11_wrappers.rst b/docs/nrv/backend/mod_11_wrappers.rst
diff --git a/docs/nrv/backend/mod_1_NRV_Class.rst b/docs/nrv/backend/mod_1_NRV_Class.rst
diff --git a/docs/nrv/backend/mod_2_NRV_Simulable.rst b/docs/nrv/backend/mod_2_NRV_Simulable.rst
diff --git a/docs/nrv/backend/mod_3_NRV_Results.rst b/docs/nrv/backend/mod_3_NRV_Results.rst
diff --git a/docs/nrv/backend/mod_4_NRV_Singleton.rst b/docs/nrv/backend/mod_4_NRV_Singleton.rst
diff --git a/docs/nrv/backend/mod_5_parameters.rst b/docs/nrv/backend/mod_5_parameters.rst
diff --git a/docs/nrv/backend/mod_6_log_interface.rst b/docs/nrv/backend/mod_6_log_interface.rst
diff --git a/docs/nrv/backend/mod_7_MCore.rst b/docs/nrv/backend/mod_7_MCore.rst
diff --git a/docs/nrv/backend/mod_8_file_handler.rst b/docs/nrv/backend/mod_8_file_handler.rst
diff --git a/docs/nrv/backend/mod_9_inouts.rst b/docs/nrv/backend/mod_9_inouts.rst
diff --git a/docs/nrv/backend/nrv.backend.rst b/docs/nrv/backend/nrv.backend.rst
diff --git a/docs/nrv/fmod/FEM/fenics_utils/mod_1_FEMParameters.rst b/docs/nrv/fmod/FEM/fenics_utils/mod_1_FEMParameters.rst
diff --git a/docs/nrv/fmod/FEM/fenics_utils/mod_2_FEMSimulation.rst b/docs/nrv/fmod/FEM/fenics_utils/mod_2_FEMSimulation.rst
diff --git a/docs/nrv/fmod/FEM/fenics_utils/mod_3_FEMResults.rst b/docs/nrv/fmod/FEM/fenics_utils/mod_3_FEMResults.rst
diff --git a/docs/nrv/fmod/FEM/fenics_utils/mod_4_f_materials.rst b/docs/nrv/fmod/FEM/fenics_utils/mod_4_f_materials.rst
diff --git a/docs/nrv/fmod/FEM/fenics_utils/mod_5_fenics_materials.rst b/docs/nrv/fmod/FEM/fenics_utils/mod_5_fenics_materials.rst
diff --git a/docs/nrv/fmod/FEM/fenics_utils/mod_6_layered_materials.rst b/docs/nrv/fmod/FEM/fenics_utils/mod_6_layered_materials.rst
diff --git a/docs/nrv/fmod/FEM/fenics_utils/nrv.fmod.FEM.fenics_utils.rst b/docs/nrv/fmod/FEM/fenics_utils/nrv.fmod.FEM.fenics_utils.rst
diff --git a/docs/nrv/fmod/FEM/mesh_creator/mod_1_MshCreator.rst b/docs/nrv/fmod/FEM/mesh_creator/mod_1_MshCreator.rst
diff --git a/docs/nrv/fmod/FEM/mesh_creator/mod_2_NerveMshCreator.rst b/docs/nrv/fmod/FEM/mesh_creator/mod_2_NerveMshCreator.rst
diff --git a/docs/nrv/fmod/FEM/mesh_creator/mod_3_NRV_Msh.rst b/docs/nrv/fmod/FEM/mesh_creator/mod_3_NRV_Msh.rst