updated UtilsLite and DOC

ebertolazzi · Sep 1, 2024 · 6008816 · 6008816
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diff --git a/README.md b/README.md
@@ -1,9 +1,8 @@
-Splines
-=======
+# Splines
 
 [![](https://travis-ci.org/ebertolazzi/Splines.svg?branch=master)](https://travis-ci.org/ebertolazzi/Splines) [![](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://it.mathworks.com/matlabcentral/fileexchange/54481-splines)
 
-``Splines`` is a set of C++ classes (with MATLAB mex interface) which
+`Splines` is a set of `C++` classes (with `MATLAB` mex interface) which
 implements various spline interpolation.
 
 The library contains the following objects:

diff --git a/doc_generate/.gitignore b/doc_generate/.gitignore
@@ -0,0 +1,2 @@
+doxygen2
+doxygen
diff --git a/doc_generate/Doxyfile b/doc_generate/Doxyfile
diff --git a/doc_generate/Doxyfile_custom b/doc_generate/Doxyfile_custom
@@ -0,0 +1,37 @@
+@INCLUDE = Doxyfile
+
+PROJECT_NAME           = "Splines"
+INPUT                  = ../src
+FILE_PATTERNS          = *.c *.cc *.h *.hh *.hxx *.cxx
+INCLUDE_FILE_PATTERNS  =
+RECURSIVE              = YES
+IMAGE_PATH             = images
+USE_MATHJAX            = YES
+MATHJAX_VERSION        = MathJax_3
+SEARCHENGINE           = NO   # deactivate search engine (as sphinx has it's own search)
+SOURCE_BROWSER         = NO
+INLINE_SOURCES         = NO
+REFERENCES_LINK_SOURCE = NO
+NUM_PROC_THREADS       = 0
+
+OUTPUT_DIRECTORY       = doxygen
+GENERATE_TAGFILE       = doxygen/html/tagfile.xml  # generate a tag file
+                              # this could be stored anywhere, however we recommend to put it into the
+                              # documentation output folder which is the value of the OUTPUT_DIRECTORY variable
+                              # + the value of the HTML_OUTPUT variable (your have to expand it for yourself
+                              # because doxygen has no mechanism to reference config settings that were defined
+                              # beforehand.
+                              # The tagfile is also needed for the doxylink extension
+
+PREDEFINED = DOXYGEN_SHOULD_SKIP_THIS
+
+DOT_IMAGE_FORMAT       = svg  # generates nicer svg images
+DOT_TRANSPARENT        = YES  # generate transparent images
+INTERACTIVE_SVG        = YES  # to be able to scroll and zoom into big images
+
+# if you want to use aliases instead of markdown fences for commenting (see syntax guide) you have to add
+# something like this (which doesn't hurt either):
+#ALIASES               = html_image{2}="\htmlonly<div class='image'><img src='\1' \2/></div>\endhtmlonly"
+ALIASES               = html_image{2}="\image html \1' \2"
+HTML_EXTRA_STYLESHEET = doxygen-awesome.css
+HTML_OUTPUT           = html
diff --git a/doc_generate/Doxyfile_custom2 b/doc_generate/Doxyfile_custom2
@@ -0,0 +1,40 @@
+@INCLUDE = Doxyfile
+
+PROJECT_NAME           = "Splines"
+INPUT                  = ../toolbox/lib
+RECURSIVE              = YES
+IMAGE_PATH             = images
+USE_MATHJAX            = YES
+MATHJAX_VERSION        = MathJax_3
+SEARCHENGINE           = NO   # deactivate search engine (as sphinx has it's own search)
+SOURCE_BROWSER         = NO
+INLINE_SOURCES         = NO
+REFERENCES_LINK_SOURCE = NO
+NUM_PROC_THREADS       = 0
+
+EXTENSION_MAPPING      = .m=C++
+FILE_PATTERNS          = *.m
+FILTER_PATTERNS        = *.m=./m2cpp.pl
+INCLUDE_FILE_PATTERNS  =
+
+OUTPUT_DIRECTORY       = doxygen2
+GENERATE_TAGFILE       = doxygen2/html/tagfile.xml  # generate a tag file
+                              # this could be stored anywhere, however we recommend to put it into the
+                              # documentation output folder which is the value of the OUTPUT_DIRECTORY variable
+                              # + the value of the HTML_OUTPUT variable (your have to expand it for yourself
+                              # because doxygen has no mechanism to reference config settings that were defined
+                              # beforehand.
+                              # The tagfile is also needed for the doxylink extension
+
+PREDEFINED = DOXYGEN_SHOULD_SKIP_THIS
+
+#DOT_IMAGE_FORMAT       = svg  # generates nicer svg images
+#DOT_TRANSPARENT        = YES  # generate transparent images
+#INTERACTIVE_SVG        = YES  # to be able to scroll and zoom into big images
+
+# if you want to use aliases instead of markdown fences for commenting (see syntax guide) you have to add
+# something like this (which doesn't hurt either):
+#ALIASES               = html_image{2}="\htmlonly<div class='image'><img src='\1' \2/></div>\endhtmlonly"
+ALIASES               = html_image{2}="\image html \1' \2"
+HTML_EXTRA_STYLESHEET = doxygen-awesome.css
+HTML_OUTPUT           = html
diff --git a/doc_generate/LICENSE.md b/doc_generate/LICENSE.md
@@ -0,0 +1,5 @@
+```{title} License
+```
+
+```{include} ../license.txt
+```
diff --git a/doc_generate/Makefile b/doc_generate/Makefile
@@ -0,0 +1,42 @@
+# You can set these variables from the command line.
+SPHINX_OPTS     =
+BUILD_DIR       = build
+DOCS_SOURCE_DIR = .
+DOXYFILE        = Doxyfile_custom
+DOXYFILE2       = Doxyfile_custom2
+
+.PHONY: help clean html doxygen doxysphinx sphinx
+
+help:
+	@echo "Please use make <target> where <target> is one of"
+	@echo "  sphinx      to run sphinx."
+	@echo "  doxygen     to run doxygen."
+	@echo "  doxysphinx  to run doxysphinx."
+	@echo "  html        to run everything in correct order to generate the documentation."
+	@echo "  clean       to clean up everything"
+
+clean:
+	doxysphinx --verbosity=DEBUG clean $(DOCS_SOURCE_DIR) $(BUILD_DIR)/html $(DOXYFILE)
+	doxysphinx --verbosity=DEBUG clean $(DOCS_SOURCE_DIR) $(BUILD_DIR)/html $(DOXYFILE2)
+# cannot use rm here because it's not portable (win/linux)
+	@rm -rf doxygen/*
+	@rm -rf doxygen2/*
+	@rm -rf build/*
+
+# sphinx
+sphinx:
+	sphinx-build -M html "$(DOCS_SOURCE_DIR)" "$(BUILD_DIR)" '--keep-going' '-j' 'auto' $(SPHINX_OPTS)
+
+# some aliases
+doxygen:
+	@doxygen $(DOXYFILE)
+	@doxygen $(DOXYFILE2)
+	@ruby filter.rb
+
+doxysphinx:
+	doxysphinx --verbosity=DEBUG build $(DOCS_SOURCE_DIR) $(BUILD_DIR)/html $(DOXYFILE)
+	doxysphinx --verbosity=DEBUG build $(DOCS_SOURCE_DIR) $(BUILD_DIR)/html $(DOXYFILE2)
+
+html: doxygen doxysphinx sphinx
+	@echo ""
+	@echo "Build finished. The Documentation is in $(BUILD_DIR)/html."
diff --git a/doc_generate/README-DOC.md b/doc_generate/README-DOC.md
@@ -0,0 +1,52 @@
+# README
+
+## Setup the code and environment
+
+Install *miniconda* or a similar tool (e.g. *Anaconda*) and create a conda
+environment for the book::
+
+```{bash}
+conda env create -f doxygen-doc-env.yml
+```
+
+- [miniconda](https://docs.conda.io/en/latest/miniconda.html)
+- [Anaconda](https://www.anaconda.com/products/individual)
+
+Activate the conda environment::
+
+```{bash}
+conda activate doxygen-doc
+```
+
+```
+doxysphinx build . out html
+sphinx-build -b html . ../out
+```
+
+
+## Build and view the website
+
+To build the website run::
+
+```{bash}
+make html
+```
+
+When complete, the website is then viewable in your browser::
+
+```
+<yourbrowser> _build/html/index.html
+```
+
+You can also run sphinx-autobuild (updates while while you edit) with::
+
+```
+make autobuild
+```
+
+## remove conda env
+
+```{bash}
+conda deactivate
+conda remove --name doxygen-doc --all
+```
diff --git a/docs/_static/Spline_interpolation.svg → doc_generate/Spline_interpolation.svg b/docs/_static/Spline_interpolation.svg → doc_generate/Spline_interpolation.svg
diff --git a/doc_generate/_static/custom.css b/doc_generate/_static/custom.css
@@ -0,0 +1,11 @@
+/*
+html {
+    --font-family: -apple-system, BlinkMacSystemFont, Segoe UI, Roboto, Oxygen, Ubuntu, Cantarell, Fira Sans, Droid Sans, Helvetica Neue, sans-serif;
+    --font-family-monospace: ui-monospace, SFMono-Regular, SF Mono, Menlo, Consolas, Liberation Mono, monospace;
+}
+*/
+
+.headertitle {
+  color:#204a87;
+  font-size: 16px !important;
+}
diff --git a/doc_generate/_templates/layout.html b/doc_generate/_templates/layout.html
@@ -0,0 +1,106 @@
+{#
+    agogo/layout.html
+    ~~~~~~~~~~~~~~~~~
+
+    Sphinx layout template for the agogo theme, originally written
+    by Andi Albrecht.
+
+    :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+    :license: BSD, see LICENSE for details.
+#}
+{%- extends "basic/layout.html" %}
+
+{% block header %}
+    <div class="header-wrapper" role="banner">
+      <div class="header">
+        {%- if logo_url %}
+          <p class="logo"><a href="{{ pathto(root_doc)|e }}">
+            <img class="logo" src="{{ logo_url|e }}" alt="{{ logo_alt|e }}"/>
+          </a></p>
+        {%- endif %}
+        {%- block headertitle %}
+        <div class="headertitle"><a
+          href="{{ pathto(root_doc)|e }}">{{ shorttitle|e }}</a></div>
+        {%- endblock %}
+<!--
+        <div class="rel" role="navigation" aria-label="Related">
+          {%- for rellink in rellinks|reverse %}
+          <a href="{{ pathto(rellink[0])|e }}" title="{{ rellink[1]|striptags|e }}"
+             {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a>
+          {%- if not loop.last %}{{ reldelim2 }}{% endif %}
+          {%- endfor %}
+        </div>
+-->
+       </div>
+    </div>
+{% endblock %}
+
+{%- macro agogo_sidebar() %}
+          {%- block sidebartoc %}
+          <h3>{{ _('Table of Contents') }}</h3>
+          {{ toctree(includehidden=True) }}
+          {%- endblock %}
+          {%- block sidebarsearch %}
+          <search role="search">
+            <h3 style="margin-top: 1.5em;">{{ _('Search') }}</h3>
+            <form class="search" action="{{ pathto('search') }}" method="get">
+                <input type="text" name="q" />
+                <input type="submit" value="{{ _('Go') }}" />
+            </form>
+          </search>
+          {%- endblock %}
+{% endmacro %}
+
+{% block content %}
+    <div class="content-wrapper">
+      <div class="content">
+        {%- if not theme_rightsidebar|tobool %}
+        <div class="sidebar">
+          {{ agogo_sidebar() }}
+        </div>
+        {%- endif %}
+        <div class="document">
+          {%- block document %}
+            {{ super() }}
+          {%- endblock %}
+        </div>
+        {%- if theme_rightsidebar|tobool %}
+        <div class="sidebar">
+          {{ agogo_sidebar() }}
+        </div>
+        {%- endif %}
+        <div class="clearer"></div>
+      </div>
+    </div>
+{% endblock %}
+
+{% block footer %}
+    <div class="footer-wrapper">
+      <div class="footer">
+<!--
+        <div class="left">
+          <div role="navigation" aria-label="Related">
+            {%- for rellink in rellinks|reverse %}
+            <a href="{{ pathto(rellink[0])|e }}" title="{{ rellink[1]|striptags|e }}"
+              {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a>
+            {%- if not loop.last %}{{ reldelim2 }}{% endif %}
+            {%- endfor %}
+          </div>
+          <div role="note" aria-label="source link">
+            {%- if show_source and has_source and sourcename %}
+              <br/>
+              <a href="{{ pathto('_sources/' + sourcename, true)|e }}"
+                rel="nofollow">{{ _('Show Source') }}</a>
+            {%- endif %}
+          </div>
+        </div>
+-->
+        <div class="right">
+          {{ super() }}
+        </div>
+        <div class="clearer"></div>
+      </div>
+    </div>
+{% endblock %}
+{% block relbar1 %}{% endblock %}
+{% block relbar2 %}{% endblock %}