Update website to version 4.9.0

conf.py

@@ -13,7 +13,7 @@
 # extensions = ['sphinxcontrib.youtube']
 
 project = u'Neper'
-version = u'4.8.2'
+version = u'4.9.0'
 release = version
 author = u'Romain Quey'
 copyright = u'Romain Quey'

doc/neper_t.rst

@@ -282,7 +282,7 @@ These options can be used to set the cell morphology.
 
   - :data:`<ori_definition>` can be:
 
-    - :data:`file(<file_name>[,des=<descriptor>])`: discrete orientations to be read from a :ref:`data_file` written using a specific descriptor (see :ref:`rotations_and_orientations`, default :data:`rodrigues`).
+    - :data:`file(<file_name>[,des=<descriptor>])`: discrete orientations to be read from a :ref:`data_file` written using a specific descriptor (see :ref:`rotations_and_orientations`, default :data:`rodrigues`).  :option:`-ori` :data:`from_morpho` must also be used.
 
   - :data:`<id_definition>` can be:
 
@@ -491,6 +491,10 @@ Crystal Orientation Options
 
   - :data:`parent[:<distribution>]`: orientations inherited from the ones of the parent cells, with an optional continuous distribution about the nominal orientations (see below);
 
+  - :data:`ks[:<distribution>]`: orientations inherited from the ones of the parent cells using the Kurdjumov-Sachs (KS) orientation relationship (austenite--ferrite transformation), with an optional continuous distribution about the nominal orientations (see below);
+
+  - :data:`ti_beta2alpha[:<distribution>]`: orientations inherited from the ones of the parent cells using the :math:`\beta\rightarrow\alpha` transformation orientation relationship in titanium, with an optional continuous distribution about the nominal orientations (see below);
+
   - :data:`file(<file_name>[,des=<descriptor>])`: discrete orientations to be read from a :ref:`data_file` written using a specific descriptor (see :ref:`rotations_and_orientations`, default :data:`rodrigues`).
 
   - :data:`from_morpho`: discrete orientations read from :option:`-morphooptiini`:data:`ori`.

doc/neper_v.rst

@@ -124,7 +124,8 @@ When a simulation directory is loaded as input, it is possible to specify the si
 
   Specify the simulation step(s), which can be:
 
-  - :data:`0`: initial state;
+  - :data:`0`: the initial state;
+  - :data:`final`: the final step;
   - any step number;
   - :data:`all`: all steps;
   - a list of steps combined with :data:`,`; a range of values can also be specified using :data:`-`.  An example is :data:`0-10,20` (for steps 0 to 10, and 20).
@@ -424,6 +425,18 @@ The following options enable the definition of the properties (color, size, etc.
 
   **Default value**: :data:`palette` for integer values, :data:`viridis` for real values, and :data:`rodrigues` for crystal orientations.
 
+.. index::
+   single: -dataelt2dtrs
+   single: -dataelset2dtrs
+
+.. option:: -data{elt2d,elset2d}trs <transparency>
+
+  Specify the transparencies (values from 0 to 1), which can be:
+
+  - a real value;
+  - an expression based on the variables described in :ref:`mesh_keys`, such as :data:`x` or :data:`area`;
+  - :data:`file(<file_name>)`: individual values to load from a :ref:`data_file`.
+
 .. option:: -data{elt,elset,node,elt{0-3}d,elset{0-3}d}scale <scale>
 
   Specify the scale relative to the :data:`-data...col real` data, which can be:
@@ -664,9 +677,11 @@ The following options apply to the full tessellations, mesh, etc.
    single: -showcsys
    single: -showscale
 
-.. option:: -show{tess,tesr,mesh,meshslice,csys,scale} <logical>
+.. option:: -show{tess,tesr,mesh,meshslice,meshsliceelt1d,csys,scale} <logical>
 
-  Show or hide a full tessellation, mesh, etc.
+  Show or hide a full tessellation or mesh, the mesh slices, the 1D elements of the mesh slices, the coordinate system, or the scale, respectively.
+
+  .. note:: The 1D elements of the mesh slices are printed as specified by options :option:`-dataelt1d*`.
 
   **Default value**: :data:`1` for the more informative data (mesh slice :math:`>` mesh :math:`>` tessellation) and :data:`0` for others.
 

docs/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c3f5171eb78a70830e7d01cb1571c82e
+config: 847b9e03a60865cb25b9b3c864dcbebc
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_sources/doc/neper_t.rst.txt

@@ -282,7 +282,7 @@ These options can be used to set the cell morphology.
 
   - :data:`<ori_definition>` can be:
 
-    - :data:`file(<file_name>[,des=<descriptor>])`: discrete orientations to be read from a :ref:`data_file` written using a specific descriptor (see :ref:`rotations_and_orientations`, default :data:`rodrigues`).
+    - :data:`file(<file_name>[,des=<descriptor>])`: discrete orientations to be read from a :ref:`data_file` written using a specific descriptor (see :ref:`rotations_and_orientations`, default :data:`rodrigues`).  :option:`-ori` :data:`from_morpho` must also be used.
 
   - :data:`<id_definition>` can be:
 
@@ -491,6 +491,10 @@ Crystal Orientation Options
 
   - :data:`parent[:<distribution>]`: orientations inherited from the ones of the parent cells, with an optional continuous distribution about the nominal orientations (see below);
 
+  - :data:`ks[:<distribution>]`: orientations inherited from the ones of the parent cells using the Kurdjumov-Sachs (KS) orientation relationship (austenite--ferrite transformation), with an optional continuous distribution about the nominal orientations (see below);
+
+  - :data:`ti_beta2alpha[:<distribution>]`: orientations inherited from the ones of the parent cells using the :math:`\beta\rightarrow\alpha` transformation orientation relationship in titanium, with an optional continuous distribution about the nominal orientations (see below);
+
   - :data:`file(<file_name>[,des=<descriptor>])`: discrete orientations to be read from a :ref:`data_file` written using a specific descriptor (see :ref:`rotations_and_orientations`, default :data:`rodrigues`).
 
   - :data:`from_morpho`: discrete orientations read from :option:`-morphooptiini`:data:`ori`.

docs/_sources/doc/neper_v.rst.txt

@@ -124,7 +124,8 @@ When a simulation directory is loaded as input, it is possible to specify the si
 
   Specify the simulation step(s), which can be:
 
-  - :data:`0`: initial state;
+  - :data:`0`: the initial state;
+  - :data:`final`: the final step;
   - any step number;
   - :data:`all`: all steps;
   - a list of steps combined with :data:`,`; a range of values can also be specified using :data:`-`.  An example is :data:`0-10,20` (for steps 0 to 10, and 20).
@@ -424,6 +425,18 @@ The following options enable the definition of the properties (color, size, etc.
 
   **Default value**: :data:`palette` for integer values, :data:`viridis` for real values, and :data:`rodrigues` for crystal orientations.
 
+.. index::
+   single: -dataelt2dtrs
+   single: -dataelset2dtrs
+
+.. option:: -data{elt2d,elset2d}trs <transparency>
+
+  Specify the transparencies (values from 0 to 1), which can be:
+
+  - a real value;
+  - an expression based on the variables described in :ref:`mesh_keys`, such as :data:`x` or :data:`area`;
+  - :data:`file(<file_name>)`: individual values to load from a :ref:`data_file`.
+
 .. option:: -data{elt,elset,node,elt{0-3}d,elset{0-3}d}scale <scale>
 
   Specify the scale relative to the :data:`-data...col real` data, which can be:
@@ -664,9 +677,11 @@ The following options apply to the full tessellations, mesh, etc.
    single: -showcsys
    single: -showscale
 
-.. option:: -show{tess,tesr,mesh,meshslice,csys,scale} <logical>
+.. option:: -show{tess,tesr,mesh,meshslice,meshsliceelt1d,csys,scale} <logical>
 
-  Show or hide a full tessellation, mesh, etc.
+  Show or hide a full tessellation or mesh, the mesh slices, the 1D elements of the mesh slices, the coordinate system, or the scale, respectively.
+
+  .. note:: The 1D elements of the mesh slices are printed as specified by options :option:`-dataelt1d*`.
 
   **Default value**: :data:`1` for the more informative data (mesh slice :math:`>` mesh :math:`>` tessellation) and :data:`0` for others.
 

docs/_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '4.8.2',
+    VERSION: '4.9.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/applications.html

@@ -4,15 +4,15 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Applications &mdash; Neper 4.8.2 documentation</title>
+  <title>Applications &mdash; Neper 4.9.0 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/my_theme.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="_static/documentation_options.js?v=98cca9dd"></script>
+        <script src="_static/documentation_options.js?v=7a99edf7"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
@@ -30,7 +30,7 @@
             <a href="index.html" class="icon icon-home"> Neper
           </a>
               <div class="version">
-                4.8.2
+                4.9.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">

docs/community.html

@@ -4,15 +4,15 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Community &mdash; Neper 4.8.2 documentation</title>
+  <title>Community &mdash; Neper 4.9.0 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/my_theme.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="_static/documentation_options.js?v=98cca9dd"></script>
+        <script src="_static/documentation_options.js?v=7a99edf7"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
@@ -30,7 +30,7 @@
             <a href="index.html" class="icon icon-home"> Neper
           </a>
               <div class="version">
-                4.8.2
+                4.9.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">

docs/doc/copying.html

@@ -4,15 +4,15 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Conditions of Use &mdash; Neper 4.8.2 documentation</title>
+  <title>Conditions of Use &mdash; Neper 4.9.0 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/my_theme.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="../_static/documentation_options.js?v=98cca9dd"></script>
+        <script src="../_static/documentation_options.js?v=7a99edf7"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
@@ -30,7 +30,7 @@
             <a href="../index.html" class="icon icon-home"> Neper
           </a>
               <div class="version">
-                4.8.2
+                4.9.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">

docs/doc/exprskeys.html

@@ -4,15 +4,15 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Expressions and Keys &mdash; Neper 4.8.2 documentation</title>
+  <title>Expressions and Keys &mdash; Neper 4.9.0 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/my_theme.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="../_static/documentation_options.js?v=98cca9dd"></script>
+        <script src="../_static/documentation_options.js?v=7a99edf7"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
@@ -31,7 +31,7 @@
             <a href="../index.html" class="icon icon-home"> Neper
           </a>
               <div class="version">
-                4.8.2
+                4.9.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">

docs/doc/fdl.html

@@ -4,15 +4,15 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>GNU Free Documentation License &mdash; Neper 4.8.2 documentation</title>
+  <title>GNU Free Documentation License &mdash; Neper 4.9.0 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/my_theme.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="../_static/documentation_options.js?v=98cca9dd"></script>
+        <script src="../_static/documentation_options.js?v=7a99edf7"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
@@ -30,7 +30,7 @@
             <a href="../index.html" class="icon icon-home"> Neper
           </a>
               <div class="version">
-                4.8.2
+                4.9.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">

docs/doc/fileformat.html

@@ -4,15 +4,15 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>File and Directory Formats &mdash; Neper 4.8.2 documentation</title>
+  <title>File and Directory Formats &mdash; Neper 4.9.0 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/my_theme.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="../_static/documentation_options.js?v=98cca9dd"></script>
+        <script src="../_static/documentation_options.js?v=7a99edf7"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
@@ -31,7 +31,7 @@
             <a href="../index.html" class="icon icon-home"> Neper
           </a>
               <div class="version">
-                4.8.2
+                4.9.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">

docs/doc/gpl.html

@@ -4,15 +4,15 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>GNU General Public License &mdash; Neper 4.8.2 documentation</title>
+  <title>GNU General Public License &mdash; Neper 4.9.0 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/my_theme.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="../_static/documentation_options.js?v=98cca9dd"></script>
+        <script src="../_static/documentation_options.js?v=7a99edf7"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
@@ -30,7 +30,7 @@
             <a href="../index.html" class="icon icon-home"> Neper
           </a>
               <div class="version">
-                4.8.2
+                4.9.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">

docs/doc/index.html

@@ -4,15 +4,15 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Documentation &mdash; Neper 4.8.2 documentation</title>
+  <title>Documentation &mdash; Neper 4.9.0 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/my_theme.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="../_static/documentation_options.js?v=98cca9dd"></script>
+        <script src="../_static/documentation_options.js?v=7a99edf7"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
@@ -30,7 +30,7 @@
             <a href="../index.html" class="icon icon-home"> Neper
           </a>
               <div class="version">
-                4.8.2
+                4.9.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">

docs/doc/introduction.html

@@ -4,15 +4,15 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Introduction &mdash; Neper 4.8.2 documentation</title>
+  <title>Introduction &mdash; Neper 4.9.0 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/my_theme.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="../_static/documentation_options.js?v=98cca9dd"></script>
+        <script src="../_static/documentation_options.js?v=7a99edf7"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
@@ -30,7 +30,7 @@
             <a href="../index.html" class="icon icon-home"> Neper
           </a>
               <div class="version">
-                4.8.2
+                4.9.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">