new doc: addition of tuto for scripts

Notes_Upgrades/Communications/SeminaireStras20/2019_LM_SeminaireStras.tex

@@ -987,7 +987,7 @@ \section{What's next}
 \textbf{Meshing and Inversions}:
 \begin{itemize}
 	\item Meshing and Basis functions (local and global) with visualization
-	
+
 	\item Geometry matrix (fast) computation
 \end{itemize}
 
@@ -1070,7 +1070,7 @@ \section{What's next}
 \textbf{Meshing and Inversions}:
 \begin{itemize}
 	\item Meshing and Basis functions (local and global) with visualization
-	
+
 	\item Geometry matrix (fast) computation and introspection plots
 	\item \textcolor{myblue}{Multiple Inversion-Regularization (linear and non-linear) and visualization
 	\item pre- and post-inversion tools}
@@ -1111,7 +1111,7 @@ \section{What's next}
 \textbf{Meshing and Inversions}:
 \begin{itemize}
 	\item Meshing and Basis functions (local and global) with visualization
-	
+
 	\item Geometry matrix (fast) computation and introspection plots
 	\item Multiple Inversion-Regularization (linear and non-linear) and visualization
 	\item post-inversion analysis tools

doc/source/index.rst

@@ -65,6 +65,7 @@ Contents
    A guide to contributing to tofu <contributing.rst>
    A list of all different device configurations available (ITER, WEST, JET, ...) <auto_examples/tutorials/tuto_plot_gallery_fusion_machines.rst>
    Tutorials and examples <auto_examples/index.rst>
+   Using tofu from a bash terminal <tofu_from_bash.rst>
 
 * How to create / handle a diagnostic geometry
    - Visit the basic_ tutorial for getting started: create, plot and save

doc/source/tofu.data.rst

@@ -41,14 +41,6 @@ tofu.data.\_def module
    :undoc-members:
    :show-inheritance:
 
-tofu.data.\_physics module
---------------------------
-
-.. automodule:: tofu.data._physics
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 tofu.data.\_plot module
 -----------------------
 

doc/source/tofu.geom.rst

@@ -9,6 +9,14 @@ tofu.geom package
 Submodules
 ----------
 
+tofu.geom.\_GG.cpython\-36m\-darwin module
+------------------------------------------
+
+.. automodule:: tofu.geom._GG.cpython-36m-darwin
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 tofu.geom.\_GG module
 ---------------------
 
@@ -17,6 +25,14 @@ tofu.geom.\_GG module
    :undoc-members:
    :show-inheritance:
 
+tofu.geom.\_basic\_geom\_tools.cpython\-36m\-darwin module
+----------------------------------------------------------
+
+.. automodule:: tofu.geom._basic_geom_tools.cpython-36m-darwin
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 tofu.geom.\_basic\_geom\_tools module
 -------------------------------------
 
@@ -65,6 +81,14 @@ tofu.geom.\_def module
    :undoc-members:
    :show-inheritance:
 
+tofu.geom.\_distance\_tools.cpython\-36m\-darwin module
+-------------------------------------------------------
+
+.. automodule:: tofu.geom._distance_tools.cpython-36m-darwin
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 tofu.geom.\_distance\_tools module
 ----------------------------------
 
@@ -89,6 +113,14 @@ tofu.geom.\_plot\_optics module
    :undoc-members:
    :show-inheritance:
 
+tofu.geom.\_raytracing\_tools.cpython\-36m\-darwin module
+---------------------------------------------------------
+
+.. automodule:: tofu.geom._raytracing_tools.cpython-36m-darwin
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 tofu.geom.\_raytracing\_tools module
 ------------------------------------
 
@@ -97,6 +129,14 @@ tofu.geom.\_raytracing\_tools module
    :undoc-members:
    :show-inheritance:
 
+tofu.geom.\_sampling\_tools.cpython\-36m\-darwin module
+-------------------------------------------------------
+
+.. automodule:: tofu.geom._sampling_tools.cpython-36m-darwin
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 tofu.geom.\_sampling\_tools module
 ----------------------------------
 
@@ -105,6 +145,14 @@ tofu.geom.\_sampling\_tools module
    :undoc-members:
    :show-inheritance:
 
+tofu.geom.\_vignetting\_tools.cpython\-36m\-darwin module
+---------------------------------------------------------
+
+.. automodule:: tofu.geom._vignetting_tools.cpython-36m-darwin
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 tofu.geom.\_vignetting\_tools module
 ------------------------------------
 

doc/source/tofu.rst

@@ -15,10 +15,20 @@ Subpackages
    tofu.dumpro
    tofu.dust
    tofu.geom
+   tofu.scripts
+   tofu.tests
 
 Submodules
 ----------
 
+tofu.\_physics module
+---------------------
+
+.. automodule:: tofu._physics
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 tofu.\_plot module
 ------------------
 

doc/source/tofu.scripts.rst

@@ -0,0 +1,35 @@
+tofu.scripts package
+====================
+
+.. automodule:: tofu.scripts
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+tofu.scripts.tofucalc module
+----------------------------
+
+.. automodule:: tofu.scripts.tofucalc
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tofu.scripts.tofucustom module
+------------------------------
+
+.. automodule:: tofu.scripts.tofucustom
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tofu.scripts.tofuplot module
+----------------------------
+
+.. automodule:: tofu.scripts.tofuplot
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

doc/source/tofu.tests.rst

@@ -0,0 +1,17 @@
+tofu.tests package
+==================
+
+.. automodule:: tofu.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+   tofu.tests.tests00_root
+   tofu.tests.tests01_geom
+   tofu.tests.tests02_data
+   tofu.tests.tests09_tutorials

doc/source/tofu.tests.tests00_root.rst

@@ -0,0 +1,19 @@
+tofu.tests.tests00\_root package
+================================
+
+.. automodule:: tofu.tests.tests00_root
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+tofu.tests.tests00\_root.tests03\_plot module
+---------------------------------------------
+
+.. automodule:: tofu.tests.tests00_root.tests03_plot
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

doc/source/tofu.tests.tests01_geom.rst

@@ -0,0 +1,50 @@
+tofu.tests.tests01\_geom package
+================================
+
+.. automodule:: tofu.tests.tests01_geom
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+   tofu.tests.tests01_geom.tests03_core_data
+
+Submodules
+----------
+
+tofu.tests.tests01\_geom.test\_get\_sample module
+-------------------------------------------------
+
+.. automodule:: tofu.tests.tests01_geom.test_get_sample
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tofu.tests.tests01\_geom.tests01\_GG module
+-------------------------------------------
+
+.. automodule:: tofu.tests.tests01_geom.tests01_GG
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tofu.tests.tests01\_geom.tests02\_compute module
+------------------------------------------------
+
+.. automodule:: tofu.tests.tests01_geom.tests02_compute
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tofu.tests.tests01\_geom.tests03\_core module
+---------------------------------------------
+
+.. automodule:: tofu.tests.tests01_geom.tests03_core
+   :members:
+   :undoc-members:
+   :show-inheritance:
+