add many files

.gitignore

+
+# Created by https://www.gitignore.io/api/jupyternotebooks
+# Edit at https://www.gitignore.io/?templates=jupyternotebooks
+
+### JupyterNotebooks ###
+# gitignore template for Jupyter Notebooks
+# website: http://jupyter.org/
+
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+*.so
+*.so.dSYM
+*.so.dSYM/*
+.nfs*
+*__pycache__*
+
+# IPython
+profile_default/
+ipython_config.py
+
+# Remove previous ipynb_checkpoints
+#   git rm -r .ipynb_checkpoints/
+
+# End of https://www.gitignore.io/api/jupyternotebooks
+
+# bocop files (build and exec)
+build/
+bocopApp
+bocopwrapper.py
+!bocop/
+*.sol
+

.gitlab-ci.yml

+image: intelpython/intelpython3_full:latest
+
+pages:
+  stage: deploy
+  before_script:
+    - conda install -c conda-forge pandoc
+  script:
+    - python --version
+    - python -m pip install -r requirements.txt
+    - pip list
+    - conda list
+    - python -m sphinx -b html examples/ public
+  artifacts:
+    paths:
+      - public
+  only:
+    - master
+

README.md

@@ -14,7 +14,7 @@
 * [Introduction to the multiple shooting method](doc/exercices/bsb_turnpike_regularized.ipynb)
 
 
-[FAQ](https://optimalcontrol.zulip.beta.cimpa-lms.info/#narrow/stream/284-geometric_methods1)
+[FAQ](https://optimalcontrol.zulip.beta.cimpa-lms.info/#narrow/stream/285-geometric_methods2)
 
 # References
 

doc/conf.py

+#!/usr/bin/env python3
+
+import os
+import sys
+#import pkg_resources
+
+#sys.path.insert(0, os.path.abspath('../../src'))
+
+# Use sphinx-quickstart to create your own conf.py file!
+# After that, you have to edit a few things.  See below.
+
+# ----------------------------------------------------------------------------------------
+# ----------------------------------------------------------------------------------------
+# Select nbsphinx and, if needed, other Sphinx extensions:
+extensions = [
+    'matplotlib.sphinxext.plot_directive',
+    'sphinx.ext.autodoc',   # for generation of api documentation
+    'sphinx.ext.napoleon',  # numpy docstrings
+    'sphinx.ext.intersphinx', # to reference others projects, as numpy.ndarray
+#    'sphinx.ext.doctest',   # for the presentation of result in api documentation examples
+    'recommonmark',         # for the use of markdown files for the documentation
+    'nbsphinx',
+    'nbsphinx_link', # A sphinx extension for including notebook files from outside the sphinx source root.
+    'sphinx_copybutton',  # for "copy to clipboard" buttons
+    'sphinx.ext.mathjax',  # for math equations
+    'sphinx.ext.viewcode',
+    'sphinxcontrib.bibtex',  # for bibliographic references
+#    'sphinxcontrib.rsvgconverter',  # for SVG->PDF conversion in LaTeX output
+    'sphinx_gallery.load_style',  # load CSS for gallery (needs SG >= 0.6)
+]
+
+## Napoleon settings
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+#napoleon_include_init_with_doc = False
+#napoleon_include_private_with_doc = False
+#napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = True
+napoleon_use_admonition_for_notes = True
+napoleon_use_admonition_for_references = True
+napoleon_use_ivar = True
+napoleon_use_param = False
+napoleon_use_rtype = False
+#napoleon_use_keyword = True
+
+
+# images for the gallery
+#nbsphinx_thumbnails = {
+#    'bacteria/bacteria': 'bacteria/maintenance.png',
+#}
+
+#intersphinx_mapping = {
+#    'python': ('https://docs.python.org/', None),
+#    'numpy': ('http://docs.scipy.org/doc/numpy/', None)
+#}
+intersphinx_mapping = {'python': ('http://docs.python.org/', None),
+                       'numpy': ('http://docs.scipy.org/doc/numpy', None),
+                       'scipy': ('http://docs.scipy.org/doc/scipy/reference', None),
+                       'matplotlib': ('http://matplotlib.sourceforge.net', None)}
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# ----------------------------------------------------------------------------------------
+# ----------------------------------------------------------------------------------------
+# Exclude build directory and Jupyter backup files:
+exclude_patterns = ['_build', '**.ipynb_checkpoints', 'Thumbs.db', '.DS_Store']
+
+# Default language for syntax highlighting in reST and Markdown cells:
+highlight_language = 'none'
+
+# Don't add .txt suffix to source files:
+#html_sourcelink_suffix = ''
+
+# Work-around until https://github.com/sphinx-doc/sphinx/issues/4229 is solved:
+#html_scaled_image_link = False
+
+# List of arguments to be passed to the kernel that executes the notebooks:
+# If you use Matplotlib for plots, this setting is recommended:
+nbsphinx_execute_arguments = [
+    "--InlineBackend.figure_formats={'svg', 'pdf'}",
+    "--InlineBackend.rc={'figure.dpi': 96}",
+]
+
+nbsphinx_execute = 'never'
+
+# To get a prompt similar to the Classic Notebook, use
+nbsphinx_input_prompt = ' In [%s]:'
+nbsphinx_output_prompt = ' Out [%s]:'
+#nbsphinx_prompt_width = '10'
+
+# Use a different kernel than stored in the notebook metadata, e.g.:
+# nbsphinx_kernel_name = 'python3'
+
+# Environment variables to be passed to the kernel:
+#os.environ['MY_DUMMY_VARIABLE'] = 'Hello from conf.py!'
+
+#nbsphinx_thumbnails = {
+#    'gallery/thumbnail-from-conf-py': 'gallery/a-local-file.png',
+#    'gallery/*-rst': '_static/copy-button.svg',
+#}
+
+# --------------------------------------------
+# --------------------------------------------
+# Debut : Cette partie ne fonctionne pas
+# --------------------------------------------
+# --------------------------------------------
+## This is processed by Jinja2 and inserted before each notebook
+#nbsphinx_prolog = """
+#{% set docname = env.doc2path(env.docname, base=None) %}
+#
+#.. only:: html
+#
+#    Mettre ici un lien vers binder, etc. Pour l'instant, je ne sais pas comment faire.
+#    Il faut peut-être que le projet soit public.
+#    On peut comme ici mettre un texte automatique pour tous les notebooks. Voir https://github.com/spatialaudio/nbsphinx/tree/0.6.0.
+#    On peut aussi mettre le lien binder dans le notebook directement.
+#
+#.. only:: latex
+#
+#    The following section was created from :file:`{{ docname }}`.
+#"""
+
+
+# This is processed by Jinja2 and inserted before each notebook
+nbsphinx_prolog = r"""
+{% set docname = 'examples/' + env.doc2path(env.docname, base=None) %}
+
+.. raw:: html
+
+    <div class="admonition note">
+      <p>Notebook source code:
+        <a class="reference external" href="https://gitlab.irit.fr/toc/cimpa/gnmoc/-/blob/master/{{ docname|e }}">{{ docname|e }}</a>
+        <br>Run it yourself on binder
+        <a href="https://mybinder.org/v2/git/https%3A%2F%2Fgitlab.irit.fr%2Ftoc%2F%2Fcimpa%2Fgnmoc.git/master?urlpath=lab/tree/{{ docname|e }}"><img alt="Binder badge" src="https://mybinder.org/badge_logo.svg" style="vertical-align:text-bottom"></a>
+      </p>
+    </div>
+
+.. raw:: latex
+
+    \nbsphinxstartnotebook{\scriptsize\noindent\strut
+    \textcolor{gray}{The following section was generated from
+    \sphinxcode{\sphinxupquote{\strut {{ docname | escape_latex }}}} \dotfill}}
+"""
+
+
+#      <script>
+#        if (document.location.host) {
+#          var p = document.currentScript.previousSibling.previousSibling;
+#          var a = document.createElement('a');
+#          a.innerHTML = 'View in <em>nbviewer</em>';
+#          a.href = `https://nbviewer.jupyter.org/url${
+#            (window.location.protocol == 'https:' ? 's/' : '/') +
+#            window.location.host +
+#            window.location.pathname.slice(0, -4) }ipynb`;
+#          a.classList.add('reference');
+#          a.classList.add('external');
+#          p.appendChild(a);
+#          p.appendChild(document.createTextNode('.'));
+#        }
+#      </script>
+
+#nbsphinx_prolog = """
+#----
+#
+#Generated by nbsphinx_ from a Jupyter_ notebook.
+#
+#.. _nbsphinx: https://nbsphinx.readthedocs.io/
+#.. _Jupyter: https://jupyter.org/
+#"""
+#
+#nbsphinx_prolog = """
+#Go there: https://example.org/notebooks/{{ env.doc2path(env.docname, base=None) }}
+#
+#----
+#"""
+
+
+#
+## This is processed by Jinja2 and inserted after each notebook
+#nbsphinx_epilog = r"""
+#{% set docname = 'doc/' + env.doc2path(env.docname, base=None) %}
+#.. raw:: latex
+#    \nbsphinxstopnotebook{\scriptsize\noindent\strut
+#    \textcolor{gray}{\dotfill\ \sphinxcode{\sphinxupquote{\strut
+#    {{ docname | escape_latex }}}} ends here.}}
+#"""
+# --------------------------------------------
+# --------------------------------------------
+# Fin : Cette partie ne fonctionne pas
+# --------------------------------------------
+# --------------------------------------------
+
+mathjax_config = {
+    'TeX': {'equationNumbers': {'autoNumber': 'AMS', 'useLabelIds': True}},
+}
+
+# Additional files needed for generating LaTeX/PDF output:
+#latex_additional_files = ['references.bib']
+
+# Support for notebook formats other than .ipynb
+#nbsphinx_custom_formats = {
+#    '.pct.py': ['jupytext.reads', {'fmt': 'py:percent'}],
+#}
+
+# ----------------------------------------------------------------------------------------
+# ----------------------------------------------------------------------------------------
+# -- The settings below this line are not specific to nbsphinx ------------
+#
+
+# where we stop the documentation: when coming to fortran files
+#autodoc_mock_imports = ['nutopy.mod_nlesolve',
+#                        'nutopy.mod_ivpsolve',
+#                        'nutopy.mod_pathsolve',
+#                        ]
+
+# Default processing flags for sphinx
+autoclass_content = 'class'
+autodoc_member_order = 'bysource'
+autodoc_default_options = {
+    'members': True,
+    'undoc-members':True,
+    'show-inheritance':True
+}
+
+#autodoc_member_order = 'alphabetical' #'bysource'
+add_module_names = False
+add_function_parentheses = False
+
+# The suffix(es) of source filenames.
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.md': 'markdown'
+}
+
+#---sphinx-themes-----
+html_theme = 'sphinx_rtd_theme'
+
+# options for sphinx_rtd_theme: see https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html#
+html_theme_options = {
+    'canonical_url': '',
+#    'analytics_id': 'UA-XXXXXXX-1',  #  Provided by Google in your dashboard
+    'logo_only': False,
+    'display_version': False,
+    'prev_next_buttons_location': 'bottom',
+    'style_external_links': False,
+ #   'style_nav_header_background': 'white',
+    # Toc options
+    'collapse_navigation': True,
+    'sticky_navigation': True,
+    'navigation_depth': 4,
+    'includehidden': True,
+    'titles_only': False
+}
+
+author      = 'Olivier Cots'
+project     = u'Cimpa course'
+import time
+copyright   =  u'%s, cimpa course project.' % time.strftime('%Y') # a changer
+#version     = '0.2' # a voir comment gerer doc et version
+#release     = '0.2.1'
+html_logo   = 'logo-ct.svg'
+
+master_doc = 'index'
+
+# Grab the setup entry
+#distribution = pkg_resources.require(project)[0]
+
+
+#linkcheck_ignore = [r'http://localhost:\d+/']
+
+# -- Get version information and date from Git ----------------------------
+
+try:
+    from subprocess import check_output
+    release = check_output(['git', 'describe', '--tags', '--always'])
+    release = release.decode().strip()
+    today = check_output(['git', 'show', '-s', '--format=%ad', '--date=short'])
+    today = today.decode().strip()
+except Exception:
+    release = '<unknown>'
+    today = '<unknown date>'
+
+# -- Options for HTML output ----------------------------------------------
+
+html_title = project #+ ' version ' + release
+
+# -- Options for LaTeX output ---------------------------------------------
+
+# See https://www.sphinx-doc.org/en/master/latex.html
+#latex_elements = {
+#    'papersize': 'a4paper',
+#    'printindex': '',
+#    'sphinxsetup': r"""
+#        %verbatimwithframe=false,
+#        %verbatimwrapslines=false,
+#        %verbatimhintsturnover=false,
+#        VerbatimColor={HTML}{F5F5F5},
+#        VerbatimBorderColor={HTML}{E0E0E0},
+#        noteBorderColor={HTML}{E0E0E0},
+#        noteborder=1.5pt,
+#        warningBorderColor={HTML}{E0E0E0},
+#        warningborder=1.5pt,
+#        warningBgColor={HTML}{FBFBFB},
+#    """,
+#    'preamble': r"""
+#\usepackage[sc,osf]{mathpazo}
+#\linespread{1.05}  % see http://www.tug.dk/FontCatalogue/urwpalladio/
+#\renewcommand{\sfdefault}{pplj}  % Palatino instead of sans serif
+#\IfFileExists{zlmtt.sty}{
+#    \usepackage[light,scaled=1.05]{zlmtt}  % light typewriter font from lmodern
+#}{
+#    \renewcommand{\ttdefault}{lmtt}  % typewriter font from lmodern
+#}
+#\usepackage{booktabs}  % for Pandas dataframes
+#""",
+#}
+#
+#latex_documents = [
+#    (master_doc, 'nbsphinx.tex', project, author, 'howto'),
+#]
+#
+#latex_show_urls = 'footnote'
+#latex_show_pagerefs = True
+
+# -- Options for EPUB output ----------------------------------------------
+
+# These are just defined to avoid Sphinx warnings related to EPUB:
+version = release
+#suppress_warnings = ['epub.unknown_project_files']
+
+

doc/index.rst

+.. include:: ../README.rst

doc/logo-ct.svg

+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   inkscape:version="1.0 (4035a4f, 2020-05-01)"
+   sodipodi:docname="ct.svg"
+   xml:space="preserve"
+   enable-background="new 0 0 134 140"
+   viewBox="0 0 134 140"
+   height="140px"
+   width="134px"
+   y="0px"
+   x="0px"
+   id="Calque_1"
+   version="1.1"><metadata
+   id="metadata19"><rdf:RDF><cc:Work
+       rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
+         rdf:resource="http://purl.org/dc/dcmitype/StillImage" /></cc:Work></rdf:RDF></metadata><defs
+   id="defs17" /><sodipodi:namedview
+   inkscape:current-layer="Calque_1"
+   inkscape:window-maximized="0"
+   inkscape:window-y="23"
+   inkscape:window-x="0"
+   inkscape:cy="70"
+   inkscape:cx="67"
+   inkscape:zoom="6.3642857"
+   showgrid="false"
+   id="namedview15"
+   inkscape:window-height="973"
+   inkscape:window-width="1007"
+   inkscape:pageshadow="2"
+   inkscape:pageopacity="0"
+   guidetolerance="10"
+   gridtolerance="10"
+   objecttolerance="10"
+   borderopacity="1"
+   bordercolor="#666666"
+   pagecolor="#ffffff" />
+<g
+   id="g12">
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+   id="path10"
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environment.yml

+name: ct-gallery
+channels:
+  - control-toolbox
+  - conda-forge
+  - dtk-forge
+dependencies:
+  - cmake
+  - gfortran_linux-64
+  - kernda
+  - scipy
+  - matplotlib
+  - numba
+  - numpy
+  - bocop
+  - nutopy
+  - nodejs
+  - ipywidgets
+  - jupyterlab
+  - swig
+  - pip
+  - pip:
+    - jupyter_contrib_nbextensions

mykernel.sh

+#! /bin/bash
+
+CONDA_HOME=`which conda`
+CONDA_HOME=`dirname ${CONDA_HOME}`
+CONDA_HOME=`dirname ${CONDA_HOME}`
+<<<<<<< HEAD
+CONDA_HOME2=${HOME}/.conda
+JUPYTER_DIR=`jupyter --data-dir`
+
+if [ -d ${CONDA_HOME2}/envs/$1 ]
+then
+   source ${CONDA_HOME}/bin/activate ${CONDA_HOME2}/envs/$1
+=======
+CONDA_ENVS=${HOME}/.conda/envs
+JUPYTER_DIR=`jupyter --data-dir`
+
+if [ -d ${CONDA_ENVS}/$1 ]
+then
+   source ${CONDA_HOME}/bin/activate ${CONDA_ENVS}/$1
+>>>>>>> develop
+   python -m ipykernel install --user --name $1
+   conda deactivate
+   kernda ${JUPYTER_DIR}/kernels/$1/kernel.json -o > /dev/null
+else
+   echo "Unknown conda environment"
+fi

pkg/env/cimpa-linux.yaml

+name: cimpa
+
+channels:
+  - control-toolbox
+  - conda-forge
+  - dtk-forge
+
+dependencies:
+  - scipy
+  - matplotlib
+  - nutopy
+  - bocop
+  - cmake
+  - gfortran_linux-64
+  - jupyterlab
+  - numba
+  - ipympl

pkg/env/cimpa-mac.yaml

+name: cimpa
+
+channels:
+  - control-toolbox
+  - conda-forge
+  - dtk-forge
+
+dependencies:
+  - scipy
+  - matplotlib
+  - nutopy
+  - bocop
+  - cmake
+  - gfortran_osx-64
+  - jupyterlab
+  - numba
+  - ipympl

pkg/env/cimpa-windows.yaml

+name: cimpa
+
+channels:
+  - control-toolbox
+  - conda-forge
+  - dtk-forge
+
+dependencies:
+  - bocop>3.0.0
+  - jupyterlab
+  - m2w64-gcc-fortran
+  - matplotlib=3.1.*
+  - numba
+  - nutopy=0.3.*
+  - scipy

postBuild

+jupyter contrib nbextension install --user
+jupyter nbextension enable --py widgetsnbextension
+jupyter labextension install @jupyter-widgets/jupyterlab-manager --minimize=False

requirements.txt

+pandas
+ipywidgets
+sphinx
+sphinx_rtd_theme
+recommonmark
+nbsphinx
+sphinxcontrib-bibtex<2.0.0
+sphinx_copybutton
+sphinx-gallery
+nbsphinx_link
+ipython