Add documentation to the project

.readthedocs.yaml

@@ -19,4 +19,4 @@ build:
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
+   configuration: doc/conf.py

doc/Makefile

@@ -5,20 +5,20 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
+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 clean Makefile
+.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)
-    
+
 clean:
 	-rm -rf $(BUILDDIR)/*
 

doc/api/generated/west_ic_antenna.antenna.WestIcrhAntenna.rst

@@ -0,0 +1,60 @@
+west\_ic\_antenna.antenna.WestIcrhAntenna
+=========================================
+
+.. currentmodule:: west_ic_antenna.antenna
+
+.. autoclass:: WestIcrhAntenna
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~WestIcrhAntenna.Pr
+      ~WestIcrhAntenna.Rc
+      ~WestIcrhAntenna.Rc_WEST
+      ~WestIcrhAntenna.Z_T
+      ~WestIcrhAntenna.__init__
+      ~WestIcrhAntenna.b
+      ~WestIcrhAntenna.capa
+      ~WestIcrhAntenna.capacitor_predictor
+      ~WestIcrhAntenna.capacitor_velocities
+      ~WestIcrhAntenna.circuit
+      ~WestIcrhAntenna.currents
+      ~WestIcrhAntenna.currents_WEST
+      ~WestIcrhAntenna.error_signals
+      ~WestIcrhAntenna.front_face_Rc
+      ~WestIcrhAntenna.interpolate_front_face
+      ~WestIcrhAntenna.load
+      ~WestIcrhAntenna.match_both_sides
+      ~WestIcrhAntenna.match_both_sides_iterative
+      ~WestIcrhAntenna.match_both_sides_separately
+      ~WestIcrhAntenna.match_one_side
+      ~WestIcrhAntenna.optimum_frequency
+      ~WestIcrhAntenna.optimum_frequency_index
+      ~WestIcrhAntenna.s_act
+      ~WestIcrhAntenna.s_act_db
+      ~WestIcrhAntenna.swit_abcd
+      ~WestIcrhAntenna.voltages
+      ~WestIcrhAntenna.vswr_act
+      ~WestIcrhAntenna.z_T
+      ~WestIcrhAntenna.z_act
+      ~WestIcrhAntenna.z_coupler
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~WestIcrhAntenna.Cs
+      ~WestIcrhAntenna.f
+      ~WestIcrhAntenna.f_scaled
+      ~WestIcrhAntenna.frequency
+
+

doc/api/generated/west_ic_antenna.topica.TopicaResult.rst

@@ -0,0 +1,34 @@
+west\_ic\_antenna.topica.TopicaResult
+=====================================
+
+.. currentmodule:: west_ic_antenna.topica
+
+.. autoclass:: TopicaResult
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~TopicaResult.Rc
+      ~TopicaResult.__init__
+      ~TopicaResult.to_network
+      ~TopicaResult.write_touchstone
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~TopicaResult.raw_data
+      ~TopicaResult.s
+      ~TopicaResult.z
+      ~TopicaResult.z0
+
+

doc/api/index.rst

@@ -0,0 +1,13 @@
+.. _api:
+
+
+API
+=========
+
+.. toctree::
+    :maxdepth: 1
+
+
+    antenna
+    topica
+    digital_twin

doc/api/west_ic_antenna.digital_twin.DigitalTwin.rst

@@ -0,0 +1,78 @@
+west\_ic\_antenna.digital\_twin.DigitalTwin
+===========================================
+
+.. currentmodule:: west_ic_antenna.digital_twin
+
+.. autoclass:: DigitalTwin
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~DigitalTwin.__init__
+      ~DigitalTwin.add_class
+      ~DigitalTwin.add_traits
+      ~DigitalTwin.blur
+      ~DigitalTwin.class_own_trait_events
+      ~DigitalTwin.class_own_traits
+      ~DigitalTwin.class_trait_names
+      ~DigitalTwin.class_traits
+      ~DigitalTwin.close
+      ~DigitalTwin.close_all
+      ~DigitalTwin.focus
+      ~DigitalTwin.get_manager_state
+      ~DigitalTwin.get_state
+      ~DigitalTwin.get_view_spec
+      ~DigitalTwin.handle_comm_opened
+      ~DigitalTwin.handle_control_comm_opened
+      ~DigitalTwin.has_trait
+      ~DigitalTwin.hold_sync
+      ~DigitalTwin.hold_trait_notifications
+      ~DigitalTwin.notify_change
+      ~DigitalTwin.observe
+      ~DigitalTwin.on_msg
+      ~DigitalTwin.on_trait_change
+      ~DigitalTwin.on_widget_constructed
+      ~DigitalTwin.open
+      ~DigitalTwin.remove_class
+      ~DigitalTwin.send
+      ~DigitalTwin.send_state
+      ~DigitalTwin.set_state
+      ~DigitalTwin.set_trait
+      ~DigitalTwin.setup_instance
+      ~DigitalTwin.trait_defaults
+      ~DigitalTwin.trait_events
+      ~DigitalTwin.trait_has_value
+      ~DigitalTwin.trait_metadata
+      ~DigitalTwin.trait_names
+      ~DigitalTwin.trait_values
+      ~DigitalTwin.traits
+      ~DigitalTwin.unobserve
+      ~DigitalTwin.unobserve_all
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~DigitalTwin.box_style
+      ~DigitalTwin.children
+      ~DigitalTwin.comm
+      ~DigitalTwin.cross_validation_lock
+      ~DigitalTwin.keys
+      ~DigitalTwin.layout
+      ~DigitalTwin.log
+      ~DigitalTwin.model_id
+      ~DigitalTwin.tabbable
+      ~DigitalTwin.tooltip
+      ~DigitalTwin.widget_types
+      ~DigitalTwin.widgets
+
+

doc/conf.py

@@ -0,0 +1,63 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'WEST IC Antenna'
+copyright = '2024, Julien Hillairet'
+author = 'Julien Hillairet'
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+sys.setrecursionlimit(1500)
+
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "nbsphinx",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosectionlabel",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', '**.ipynb_checkpoints', 'Thumbs.db', '.DS_Store']
+# exclude some notebooks not yet ready to be converted into html
+exclude_files = [
+    #'chart_strap_reactance.ipynb',
+    #'chart_manual_matching.ipynb',
+    'coupling_to_ideal_load.ipynb',
+    'coupling_to_plasma_from_COMSOL.ipynb',
+    'coupling_to_plasma_from_TOPICA.ipynb',
+    'coupling_to_water_tank.ipynb',
+    'digital_twin.ipynb',
+    #'introduction.ipynb',
+    'phase_scan.ipynb',
+    'Plasma Startup.ipynb',
+    #'tutorial_matching_automatic.ipynb',
+    #'tutorial_matching_manual.ipynb'
+]
+for file in exclude_files:
+    exclude_patterns.append(file)
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ['_static']
+
+nbsphinx_allow_errors = True

doc/index.rst

@@ -0,0 +1,17 @@
+.. WEST IC Antenna documentation master file
+
+WEST IC Antenna documentation
+=============================
+
+Welcome to the documentation pages of the WEST IC Antenna RF model.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents
+
+   introduction.ipynb
+   tutorial_matching_manual.ipynb
+   tutorial_matching_automatic.ipynb
+   chart_strap_reactance.ipynb
+   chart_manual_matching.ipynb
+   api/index.rst

doc/introduction.ipynb

@@ -2,9 +2,11 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "jp-MarkdownHeadingCollapsed": true
+   },
    "source": [
-    "# WEST ICRH Antenna RF Model\n",
+    "# Introduction\n",
     "## The WEST ICRH antennas \n",
     "Three identical ELM-resilient and CW power ICRH antennas have been designed for WEST. The ELM resilience property is obtained through an internal conjugate-T electrical scheme with series capacitors. An antenna has 4 straps (2 toroidal x 2 poloidal) and is fed by 2 generators (left side and right side). Each antenna is equipped with four internal COMET® tuneable vacuum capacitors, with capacitances ranging from 15 pF to 150 pF and specifically upgraded for CW operation. A two-stage quarter-wavelength and water cooled impedance transformer is connected from the T-junction to the vacuum feedthrough.\n",
     "\n",

doc/make.bat

@@ -7,11 +7,9 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
-set SOURCEDIR=source
+set SOURCEDIR=./
 set BUILDDIR=build
 
-if "%1" == "" goto help
-
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (
 	echo.
@@ -21,10 +19,12 @@ if errorlevel 9009 (
 	echo.may add the Sphinx directory to PATH.
 	echo.
 	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
+	echo.https://www.sphinx-doc.org/
 	exit /b 1
 )
 
+if "%1" == "" goto help
+
 %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
 goto end
 

doc/tutorial_matching_automatic.ipynb

@@ -896,7 +896,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

pyproject.toml

@@ -8,8 +8,8 @@ license = {text="LICENSE"}
 dependencies = [
     "ipywidgets>=8.1.5",
     "matplotlib>=3.9.2",
+    "networkx>=3.4.2",
     "numpy>=2.1.3",
-    "pytest>=8.3.3",
     "scikit-rf>=1.4.1",
     "tqdm>=4.67.0",
 ]
@@ -18,4 +18,16 @@ dependencies = [
 license-files = ["LICENSE"]
 
 [tool.setuptools.dynamic]
-version = {attr = "west_ic_antenna.__version__"}
+version = {attr = "west_ic_antenna.__version__"}
+
+[dependency-groups]
+test = [
+    "pytest>=8.3.3",
+]
+doc = [
+    "ipykernel>=6.29.5",
+    "nbsphinx>=0.9.5",
+    "sphinx-rtd-theme>=3.0.2",
+    "sphinx>=8.1.3",
+]
+