initial release.

02c40e51 · Emmanuel Bruno · 7a3081c5 · 02c40e51 · 02c40e51 · 02c40e51
Commit 02c40e51 authored Mar 27, 2023 by Emmanuel Bruno
--- a/.gitignore
+++ b/.gitignore
+.ipynb_checkpoints
+_config.yml
+_build           
+_toc.yml
--- a/Dockerfile
+++ b/Dockerfile
+FROM  brunoe/jupyter-base:develop
+COPY . ${HOME}/work
+USER root
+RUN chown -R ${NB_UID} ${HOME}
+USER ${NB_USER}
--- a/latex/.gitignore
+++ b/latex/.gitignore
+## Core latex/pdflatex auxiliary files:
+*.aux
+*.lof
+*.log
+*.lot
+*.fls
+*.out
+*.toc
+*.fmt
+*.fot
+*.cb
+*.cb2
+.*.lb
+
+## Intermediate documents:
+*.dvi
+*.xdv
+*-converted-to.*
+# these rules might exclude image files for figures etc.
+# *.ps
+# *.eps
+# *.pdf
+
+## Generated if empty string is given at "Please type another file name for output:"
+.pdf
+
+## Bibliography auxiliary files (bibtex/biblatex/biber):
+*.bbl
+*.bcf
+*.blg
+*-blx.aux
+*-blx.bib
+*.run.xml
+
+## Build tool auxiliary files:
+*.fdb_latexmk
+*.synctex
+*.synctex(busy)
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+
+## Build tool directories for auxiliary files
+# latexrun
+latex.out/
+
+## Auxiliary and intermediate files from other packages:
+# algorithms
+*.alg
+*.loa
+
+# achemso
+acs-*.bib
+
+# amsthm
+*.thm
+
+# beamer
+*.nav
+*.pre
+*.snm
+*.vrb
+
+# changes
+*.soc
+
+# comment
+*.cut
+
+# cprotect
+*.cpt
+
+# elsarticle (documentclass of Elsevier journals)
+*.spl
+
+# endnotes
+*.ent
+
+# fixme
+*.lox
+
+# feynmf/feynmp
+*.mf
+*.mp
+*.t[1-9]
+*.t[1-9][0-9]
+*.tfm
+
+#(r)(e)ledmac/(r)(e)ledpar
+*.end
+*.?end
+*.[1-9]
+*.[1-9][0-9]
+*.[1-9][0-9][0-9]
+*.[1-9]R
+*.[1-9][0-9]R
+*.[1-9][0-9][0-9]R
+*.eledsec[1-9]
+*.eledsec[1-9]R
+*.eledsec[1-9][0-9]
+*.eledsec[1-9][0-9]R
+*.eledsec[1-9][0-9][0-9]
+*.eledsec[1-9][0-9][0-9]R
+
+# glossaries
+*.acn
+*.acr
+*.glg
+*.glo
+*.gls
+*.glsdefs
+*.lzo
+*.lzs
+*.slg
+*.slo
+*.sls
+
+# uncomment this for glossaries-extra (will ignore makeindex's style files!)
+# *.ist
+
+# gnuplot
+*.gnuplot
+*.table
+
+# gnuplottex
+*-gnuplottex-*
+
+# gregoriotex
+*.gaux
+*.glog
+*.gtex
+
+# htlatex
+*.4ct
+*.4tc
+*.idv
+*.lg
+*.trc
+*.xref
+
+# hyperref
+*.brf
+
+# knitr
+*-concordance.tex
+# TODO Uncomment the next line if you use knitr and want to ignore its generated tikz files
+# *.tikz
+*-tikzDictionary
+
+# listings
+*.lol
+
+# luatexja-ruby
+*.ltjruby
+
+# makeidx
+*.idx
+*.ilg
+*.ind
+
+# minitoc
+*.maf
+*.mlf
+*.mlt
+*.mtc[0-9]*
+*.slf[0-9]*
+*.slt[0-9]*
+*.stc[0-9]*
+
+# minted
+_minted*
+*.pyg
+
+# morewrites
+*.mw
+
+# newpax
+*.newpax
+
+# nomencl
+*.nlg
+*.nlo
+*.nls
+
+# pax
+*.pax
+
+# pdfpcnotes
+*.pdfpc
+
+# sagetex
+*.sagetex.sage
+*.sagetex.py
+*.sagetex.scmd
+
+# scrwfile
+*.wrt
+
+# svg
+svg-inkscape/
+
+# sympy
+*.sout
+*.sympy
+sympy-plots-for-*.tex/
+
+# pdfcomment
+*.upa
+*.upb
+
+# pythontex
+*.pytxcode
+pythontex-files-*/
+
+# tcolorbox
+*.listing
+
+# thmtools
+*.loe
+
+# TikZ & PGF
+*.dpth
+*.md5
+*.auxlock
+
+# titletoc
+*.ptc
+
+# todonotes
+*.tdo
+
+# vhistory
+*.hst
+*.ver
+
+# easy-todo
+*.lod
+
+# xcolor
+*.xcp
+
+# xmpincl
+*.xmpi
+
+# xindy
+*.xdy
+
+# xypic precompiled matrices and outlines
+*.xyc
+*.xyd
+
+# endfloat
+*.ttt
+*.fff
+
+# Latexian
+TSWLatexianTemp*
+
+## Editors:
+# WinEdt
+*.bak
+*.sav
+
+# Texpad
+.texpadtmp
+
+# LyX
+*.lyx~
+
+# Kile
+*.backup
+
+# gummi
+.*.swp
+
+# KBibTeX
+*~[0-9]*
+
+# TeXnicCenter
+*.tps
+
+# auto folder when using emacs and auctex
+./auto/*
+*.el
+
+# expex forward references with \gathertags
+*-tags.tex
+
+# standalone packages
+*.sta
+
+# Makeindex log files
+*.lpz
+
+# xwatermark package
+*.xwm
+
+# REVTeX puts footnotes in the bibliography by default, unless the nofootinbib
+# option is specified. Footnotes are the stored in a file with suffix Notes.bib.
+# Uncomment the next line to have this generated file ignored.
+#*Notes.bib
--- a/latex/test.pdf
+++ b/latex/test.pdf
--- a/latex/test.tex
+++ b/latex/test.tex
+\documentclass{article}
+
+\title{My first document}
+\date{2023-03-24}
+\author{John Doe}
+
+\begin{document}
+  \maketitle 
+  
+  \section{Introduction}
+  Hello World!
+
+  \section{Conclusion}
+  It's cool.
+  
+\end{document}
\ No newline at end of file
--- a/makeBook.ipynb
+++ b/makeBook.ipynb
--- a/python/hello.py
+++ b/python/hello.py
+print("hello python in jupyer vscode.")
\ No newline at end of file
--- a/quickstart.ipynb
+++ b/quickstart.ipynb
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "baeb31ec-ca39-49d1-9d43-cad4808c53be",
+   "metadata": {
+    "tags": [],
+    "user_expressions": []
+   },
+   "source": [
+    "# Quickstart for Jupyter base notebook"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "33102a08-870e-41de-89f3-261229b0cf8b",
+   "metadata": {
+    "user_expressions": []
+   },
+   "source": [
+    "## Python"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "69f6863b-6547-4e0e-9c8c-62664db684c0",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Hello\n"
+     ]
+    }
+   ],
+   "source": [
+    "text=\"Hello\"\n",
+    "print(text)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "642a4b7b-42f8-48da-8f17-f6920e45a9ec",
+   "metadata": {
+    "user_expressions": []
+   },
+   "source": [
+    "## Bash"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "b9832d2a-df8d-484f-a783-126e57e9353a",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Linux b891c201ed3e 5.15.49-linuxkit #1 SMP PREEMPT Tue Sep 13 07:51:32 UTC 2022 aarch64 aarch64 aarch64 GNU/Linux\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%bash\n",
+    "uname -a"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f54bc696-6f58-416f-971e-6e7f7b9daa28",
+   "metadata": {
+    "user_expressions": []
+   },
+   "source": [
+    "## Git"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "7f996bc4-5ad6-4b29-884f-2fa243275467",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "git version 2.34.1\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%bash \n",
+    "git --version"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5e04c9ae-3445-455e-99ed-071d1b57abb5",
+   "metadata": {
+    "user_expressions": []
+   },
+   "source": [
+    "## UML"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "f6847b3c-b14e-4176-bd4f-db400e82b691",
+   "metadata": {
+    "tags": [
+     "remove-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "import iplantuml"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "ed7da4ef-1e2a-444f-9622-a037dcb720b4",
+   "metadata": {
+    "tags": [
+     "remove-input"
+    ]
+   },
+   "outputs": [
+    {
+     "data": {
+      "image/svg+xml": [
+       "<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" contentScriptType=\"application/ecmascript\" contentStyleType=\"text/css\" height=\"215px\" preserveAspectRatio=\"none\" style=\"width:300px;height:215px;\" version=\"1.1\" viewBox=\"0 0 300 215\" width=\"300px\" zoomAndPan=\"magnify\"><defs><filter height=\"300%\" id=\"fn3yvorrca0j1\" width=\"300%\" x=\"-1\" y=\"-1\"><feGaussianBlur result=\"blurOut\" stdDeviation=\"2.0\"/><feColorMatrix in=\"blurOut\" result=\"blurOut2\" type=\"matrix\" values=\"0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 .4 0\"/><feOffset dx=\"4.0\" dy=\"4.0\" in=\"blurOut2\" result=\"blurOut3\"/><feBlend in=\"SourceGraphic\" in2=\"blurOut3\" mode=\"normal\"/></filter></defs><g><line style=\"stroke: #A80036; stroke-width: 1.0; stroke-dasharray: 5.0,5.0;\" x1=\"33\" x2=\"33\" y1=\"38.2969\" y2=\"174.8281\"/><line style=\"stroke: #A80036; stroke-width: 1.0; stroke-dasharray: 5.0,5.0;\" x1=\"270\" x2=\"270\" y1=\"38.2969\" y2=\"174.8281\"/><rect fill=\"#FEFECE\" filter=\"url(#fn3yvorrca0j1)\" height=\"30.2969\" style=\"stroke: #A80036; stroke-width: 1.5;\" width=\"46\" x=\"8\" y=\"3\"/><text fill=\"#000000\" font-family=\"sans-serif\" font-size=\"14\" lengthAdjust=\"spacingAndGlyphs\" textLength=\"32\" x=\"15\" y=\"22.9951\">Alice</text><rect fill=\"#FEFECE\" filter=\"url(#fn3yvorrca0j1)\" height=\"30.2969\" style=\"stroke: #A80036; stroke-width: 1.5;\" width=\"46\" x=\"8\" y=\"173.8281\"/><text fill=\"#000000\" font-family=\"sans-serif\" font-size=\"14\" lengthAdjust=\"spacingAndGlyphs\" textLength=\"32\" x=\"15\" y=\"193.8232\">Alice</text><rect fill=\"#FEFECE\" filter=\"url(#fn3yvorrca0j1)\" height=\"30.2969\" style=\"stroke: #A80036; stroke-width: 1.5;\" width=\"42\" x=\"247\" y=\"3\"/><text fill=\"#000000\" font-family=\"sans-serif\" font-size=\"14\" lengthAdjust=\"spacingAndGlyphs\" textLength=\"28\" x=\"254\" y=\"22.9951\">Bob</text><rect fill=\"#FEFECE\" filter=\"url(#fn3yvorrca0j1)\" height=\"30.2969\" style=\"stroke: #A80036; stroke-width: 1.5;\" width=\"42\" x=\"247\" y=\"173.8281\"/><text fill=\"#000000\" font-family=\"sans-serif\" font-size=\"14\" lengthAdjust=\"spacingAndGlyphs\" textLength=\"28\" x=\"254\" y=\"193.8232\">Bob</text><polygon fill=\"#A80036\" points=\"258,65.4297,268,69.4297,258,73.4297,262,69.4297\" style=\"stroke: #A80036; stroke-width: 1.0;\"/><line style=\"stroke: #A80036; stroke-width: 1.0;\" x1=\"33\" x2=\"264\" y1=\"69.4297\" y2=\"69.4297\"/><text fill=\"#000000\" font-family=\"sans-serif\" font-size=\"13\" lengthAdjust=\"spacingAndGlyphs\" textLength=\"149\" x=\"40\" y=\"64.3638\">Authentication Request</text><polygon fill=\"#A80036\" points=\"44,94.5625,34,98.5625,44,102.5625,40,98.5625\" style=\"stroke: #A80036; stroke-width: 1.0;\"/><line style=\"stroke: #A80036; stroke-width: 1.0; stroke-dasharray: 2.0,2.0;\" x1=\"38\" x2=\"269\" y1=\"98.5625\" y2=\"98.5625\"/><text fill=\"#000000\" font-family=\"sans-serif\" font-size=\"13\" lengthAdjust=\"spacingAndGlyphs\" textLength=\"159\" x=\"50\" y=\"93.4966\">Authentication Response</text><polygon fill=\"#A80036\" points=\"258,123.6953,268,127.6953,258,131.6953,262,127.6953\" style=\"stroke: #A80036; stroke-width: 1.0;\"/><line style=\"stroke: #A80036; stroke-width: 1.0;\" x1=\"33\" x2=\"264\" y1=\"127.6953\" y2=\"127.6953\"/><text fill=\"#000000\" font-family=\"sans-serif\" font-size=\"13\" lengthAdjust=\"spacingAndGlyphs\" textLength=\"203\" x=\"40\" y=\"122.6294\">Another authentication Request</text><polygon fill=\"#A80036\" points=\"44,152.8281,34,156.8281,44,160.8281,40,156.8281\" style=\"stroke: #A80036; stroke-width: 1.0;\"/><line style=\"stroke: #A80036; stroke-width: 1.0; stroke-dasharray: 2.0,2.0;\" x1=\"38\" x2=\"269\" y1=\"156.8281\" y2=\"156.8281\"/><text fill=\"#000000\" font-family=\"sans-serif\" font-size=\"13\" lengthAdjust=\"spacingAndGlyphs\" textLength=\"213\" x=\"50\" y=\"151.7622\">Another authentication Response</text><!--MD5=[1d6f20096108edb94adca4cbf5ef001d]\n",
+       "@startuml\n",
+       "Alice -> Bob: Authentication Request\n",
+       "Bob - -> Alice: Authentication Response\n",
+       "\n",
+       "Alice -> Bob: Another authentication Request\n",
+       "Alice <- - Bob: Another authentication Response\n",
+       "@enduml\n",
+       "\n",
+       "PlantUML version 1.2020.02(Sun Mar 01 10:22:07 UTC 2020)\n",
+       "(GPL source distribution)\n",
+       "Java Runtime: OpenJDK Runtime Environment\n",
+       "JVM: OpenJDK 64-Bit Server VM\n",
+       "Java Version: 11.0.18+10-post-Ubuntu-0ubuntu122.04\n",
+       "Operating System: Linux\n",
+       "Default Encoding: UTF-8\n",
+       "Language: en\n",
+       "Country: US\n",
+       "--></g></svg>"
+      ],
+      "text/plain": [
+       "<IPython.core.display.SVG object>"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "%%plantuml --jar\n",
+    "\n",
+    "@startuml\n",
+    "Alice -> Bob: Authentication Request\n",
+    "Bob --> Alice: Authentication Response\n",
+    "\n",
+    "Alice -> Bob: Another authentication Request\n",
+    "Alice <-- Bob: Another authentication Response\n",
+    "@enduml"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "800287e2-b904-40be-b20f-f6d572395b7f",
+   "metadata": {
+    "user_expressions": []
+   },
+   "source": [
+    "## Extended markdown"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "35b7e483-e14e-4e54-a25b-38dced0f380f",
+   "metadata": {
+    "user_expressions": []
+   },
+   "source": [
+    "<https://jupyterbook.org/en/stable/reference/cheatsheet.html>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f0fe93fd-92dd-4590-be09-279adbb3fbae",
+   "metadata": {
+    "tags": [],
+    "user_expressions": []
+   },
+   "source": [
+    "```{note}\n",
+    "Here is a note\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b4c65d37-2a33-4983-b0f5-984da15f2f9f",
+   "metadata": {
+    "user_expressions": []
+   },
+   "source": [
+    "```{warning} This is my warning\n",
+    "bla\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c6b8bdb8-e501-4557-be51-bc2130dcba23",
+   "metadata": {
+    "user_expressions": []
+   },
+   "source": [
+    "$$\n",
+    "a^2 + b^2 = c^2\n",
+    "$$(eqn:pyth)\n",
+    "\n",
+    "Pythagore cf. {eq}`eqn:pyth`"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c60ddcfe-cbcc-4eec-a355-7621885e7ca9",
+   "metadata": {
+    "user_expressions": []
+   },
+   "source": [
+    "\\begin{align}\n",
+    "a_{11}& =b_{11}&\n",
+    "  a_{12}& =b_{12}\\\\\n",
+    "a_{21}& =b_{21}&\n",
+    "  a_{22}& =b_{22}+c_{22}\n",
+    "\\end{align}"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e388047e-b8a6-4854-a7c3-f63824b5a81d",
+   "metadata": {
+    "user_expressions": []
+   },
+   "source": [
+    "```{list-table} Table title\n",
+    ":header-rows: 1\n",
+    ":name: label-to-reference\n",
+    "\n",
+    "* - Col1\n",
+    "  - Col2\n",
+    "* - Row1 under Col1\n",
+    "  - Row1 under Col2\n",
+    "* - Row2 under Col1\n",
+    "  - Row2 under Col2\n",
+    "```"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
+%% Cell type:markdown id:baeb31ec-ca39-49d1-9d43-cad4808c53be tags:
+
+# Quickstart for Jupyter base notebook
+
+%% Cell type:markdown id:33102a08-870e-41de-89f3-261229b0cf8b tags:
+
+## Python
+
+%% Cell type:code id:69f6863b-6547-4e0e-9c8c-62664db684c0 tags:
+
+``` python
+text="Hello"
+print(text)
+```
+
+%% Output
+
+    Hello
+
+%% Cell type:markdown id:642a4b7b-42f8-48da-8f17-f6920e45a9ec tags:
+
+## Bash
+
+%% Cell type:code id:b9832d2a-df8d-484f-a783-126e57e9353a tags:
+
+``` python
+%%bash
+uname -a
+```
+
+%% Output
+
+    Linux b891c201ed3e 5.15.49-linuxkit #1 SMP PREEMPT Tue Sep 13 07:51:32 UTC 2022 aarch64 aarch64 aarch64 GNU/Linux
+
+%% Cell type:markdown id:f54bc696-6f58-416f-971e-6e7f7b9daa28 tags:
+
+## Git
+
+%% Cell type:code id:7f996bc4-5ad6-4b29-884f-2fa243275467 tags:
+
+``` python
+%%bash
+git --version
+```
+
+%% Output
+
+    git version 2.34.1
+
+%% Cell type:markdown id:5e04c9ae-3445-455e-99ed-071d1b57abb5 tags:
+
+## UML
+
+%% Cell type:code id:f6847b3c-b14e-4176-bd4f-db400e82b691 tags:remove-cell
+
+``` python
+import iplantuml
+```
+
+%% Cell type:code id:ed7da4ef-1e2a-444f-9622-a037dcb720b4 tags:remove-input
+
+``` python
+%%plantuml --jar
+
+@startuml
+Alice -> Bob: Authentication Request
+Bob --> Alice: Authentication Response
+
+Alice -> Bob: Another authentication Request
+Alice <-- Bob: Another authentication Response
+@enduml
+```
+
+%% Output
+
+
+    <IPython.core.display.SVG object>
+
+%% Cell type:markdown id:800287e2-b904-40be-b20f-f6d572395b7f tags:
+
+## Extended markdown
+
+%% Cell type:markdown id:35b7e483-e14e-4e54-a25b-38dced0f380f tags:
+
+<https://jupyterbook.org/en/stable/reference/cheatsheet.html>
+
+%% Cell type:markdown id:f0fe93fd-92dd-4590-be09-279adbb3fbae tags:
+
+```{note}
+Here is a note
+```
+
+%% Cell type:markdown id:b4c65d37-2a33-4983-b0f5-984da15f2f9f tags:
+
+```{warning} This is my warning
+bla
+```
+
+%% Cell type:markdown id:c6b8bdb8-e501-4557-be51-bc2130dcba23 tags:
+
+$$
+a^2 + b^2 = c^2
+$$(eqn:pyth)
+
+Pythagore cf. {eq}`eqn:pyth`
+
+%% Cell type:markdown id:c60ddcfe-cbcc-4eec-a355-7621885e7ca9 tags:
+
+\begin{align}
+a_{11}& =b_{11}&
+  a_{12}& =b_{12}\\
+a_{21}& =b_{21}&
+  a_{22}& =b_{22}+c_{22}
+\end{align}
+
+%% Cell type:markdown id:e388047e-b8a6-4854-a7c3-f63824b5a81d tags:
+
+```{list-table} Table title
+:header-rows: 1
+:name: label-to-reference
+
+* - Col1
+  - Col2
+* - Row1 under Col1
+  - Row1 under Col2
+* - Row2 under Col1
+  - Row2 under Col2
+```
--- a/uml/demo.puml
+++ b/uml/demo.puml
+@startuml
+Alice -> Bob: Authentication Request
+Bob --> Alice: Authentication Response
+
+Alice -> Bob: Another authentication Request
+Alice <-- Bob: Another authentication Response
+@enduml
\ No newline at end of file