From ebbfd78c9a78c54ecfa012cb6aedcb4fa2aa98f4 Mon Sep 17 00:00:00 2001
From: Raniere Silva <raniere@rgaiacs.com>
Date: Fri, 13 Jan 2017 19:56:51 +0000
Subject: [PATCH 1/2] Proposal for use of Jupyter Notebook

---
 Makefile                                      |  25 +-
 _config.yml                                   |   3 +
 .../{07-maintenance.md => 08-maintenance.md}  |   0
 _episodes/{08-coffee.md => 09-coffee.md}      |   0
 _episodes_ipynb/07-jupyter.ipynb              | 214 ++++++++++++++++++
 _layouts/ipynb2md.tpl                         |  78 +++++++
 6 files changed, 310 insertions(+), 10 deletions(-)
 rename _episodes/{07-maintenance.md => 08-maintenance.md} (100%)
 rename _episodes/{08-coffee.md => 09-coffee.md} (100%)
 create mode 100644 _episodes_ipynb/07-jupyter.ipynb
 create mode 100644 _layouts/ipynb2md.tpl

diff --git a/Makefile b/Makefile
index b5dfe2fa..9300ee0c 100644
--- a/Makefile
+++ b/Makefile
@@ -6,10 +6,10 @@ MAKEFILES=Makefile $(wildcard *.mk)
 JEKYLL=jekyll
 PARSER=bin/markdown_ast.rb
 DST=_site
+JUPYTER=jupyter
 
 # Controls
 .PHONY : commands clean files
-.NOTPARALLEL:
 all : commands
 
 ## commands         : show all commands.
@@ -17,11 +17,11 @@ commands :
 	@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
 
 ## serve            : run a local server.
-serve : lesson-md
+serve : lesson-rmd lesson-jupyter
 	${JEKYLL} serve
 
 ## site             : build files but do not run a server.
-site : lesson-md
+site : lesson-rmd lesson-jupyter
 	${JEKYLL} build
 
 # repo-check        : check repository settings.
@@ -54,12 +54,16 @@ workshop-check :
 ## ----------------------------------------
 ## Commands specific to lesson websites.
 
-.PHONY : lesson-check lesson-md lesson-files lesson-fixme
+.PHONY : lesson-check lesson-rmd lesson-files lesson-fixme
 
 # RMarkdown files
 RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
 RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))
 
+# JUPYTER files
+JUPYTER_SRC = $(wildcard _episodes_ipynb/??-*.ipynb)
+JUPYTER_DST = $(patsubst _episodes_ipynb/%.ipynb,_episodes/%.ipynb,$(JUPYTER_SRC))
+
 # Lesson source files in the order they appear in the navigation menu.
 MARKDOWN_SRC = \
   index.md \
@@ -80,16 +84,17 @@ HTML_DST = \
   $(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \
   ${DST}/license/index.html
 
-## lesson-md        : convert Rmarkdown files to markdown
-lesson-md : ${RMD_DST}
+## lesson-rmd       : convert Rmarkdown files to markdown
+lesson-rmd: $(RMD_SRC)
+	@bin/knit_lessons.sh $(RMD_SRC)
 
-# Use of .NOTPARALLEL makes rule execute only once
-${RMD_DST} : ${RMD_SRC}
-	@bin/knit_lessons.sh ${RMD_SRC}
+## lesson-jupyter   : convert Jupyter Notebook files to markdown
+lesson-jupyter: $(JUPYTER_SRC)
+	${JUPYTER} nbconvert -y --execute --allow-errors --to markdown --output-dir=_episodes --NbConvertApp.output_files_dir="" --template=_layouts/ipynb2md.tpl $(JUPYTER_SRC)
 
 ## lesson-check     : validate lesson Markdown.
 lesson-check :
-	@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
+	@bin/lesson_check.py -s . -p ${PARSER}
 
 ## lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace.
 lesson-check-all :
diff --git a/_config.yml b/_config.yml
index cc650eec..1fb2afaf 100644
--- a/_config.yml
+++ b/_config.yml
@@ -67,3 +67,6 @@ exclude:
 
 # Turn off built-in syntax highlighting.
 highlighter: false
+
+kramdown:
+  parse_block_html: true
diff --git a/_episodes/07-maintenance.md b/_episodes/08-maintenance.md
similarity index 100%
rename from _episodes/07-maintenance.md
rename to _episodes/08-maintenance.md
diff --git a/_episodes/08-coffee.md b/_episodes/09-coffee.md
similarity index 100%
rename from _episodes/08-coffee.md
rename to _episodes/09-coffee.md
diff --git a/_episodes_ipynb/07-jupyter.ipynb b/_episodes_ipynb/07-jupyter.ipynb
new file mode 100644
index 00000000..b91d31a1
--- /dev/null
+++ b/_episodes_ipynb/07-jupyter.ipynb
@@ -0,0 +1,214 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "title: Using Jupyter Notebook \n",
+    "teaching: 10\n",
+    "exercises: 1\n",
+    "questions:\n",
+    "- \"How to write a lesson using Jupyter Notebook?\"\n",
+    "objectives:\n",
+    "- \"Explain how to use Jupyter Notebook with the new lesson template.\"\n",
+    "- \"Demonstrate how to include pieces of code, figures, and challenges.\"\n",
+    "keypoints:\n",
+    "- \"It shouldn't be difficult\"\n",
+    "---\n",
+    "\n",
+    "The lesson should be written with a mix of code cells and Markdown cells,\n",
+    "just like you'd normally do."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1.15000000000000"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "1 + 1"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Output with error message:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "ename": "TypeError",
+     "evalue": "'sage.symbolic.expression.Expression' object does not support indexing",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-2-084faa554d6d>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mx\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mInteger\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m: 'sage.symbolic.expression.Expression' object does not support indexing"
+     ]
+    }
+   ],
+   "source": [
+    "x[10]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Output generating figures:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "% matplotlib inline"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[<matplotlib.lines.Line2D at 0x7fb48a03f080>]"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    },
+    {
+     "data": {
+      "image/png": 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IODNmCOfnFIqOJ+fnbCLij5LOSnp05KGpz8+6FvmiD099RZKKPjyFGyYez/x+nO2HtP62\n2PcXNbEOek7SxYh4ZsLjnJ/T2fR4cn6WZ/tjtrdm1z8q6YuSLo0Mm/r8rHy7hg9PVavoeErab/s/\nJf1F0p8lPdHUXNvO9iOSnpT0ZrbvGZK+IelucX5OrczxFOfnND4h6b9t36b1AD+VnY8HNcf5yYeh\nACBhrfk3XgEA1WORB4CEscgDQMJY5AEgYSzyAJAwFnkASBiLPAAkjEUeABL2Nyd8jIN/neVAAAAA\nAElFTkSuQmCC\n",
+      "text/plain": [
+       "<matplotlib.figure.Figure at 0x7fb48c0b8128>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "import matplotlib.pyplot\n",
+    "\n",
+    "matplotlib.pyplot.plot([1,2,3], [1,2,3])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "For the challenges you need to pay attention\n",
+    "to include `<blockquote class=\"challenge\">` before it\n",
+    "and `<\\blockquote>` after it.\n",
+    "And for the solutions you need to pay attention\n",
+    "to include `<blockquote class=\"solution\">` before it\n",
+    "and `<\\blockquote>` after it.\n",
+    "**This hacks is necessary for allow include Jupyter cells on challenges and solutions.**"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "collapsed": true
+   },
+   "source": [
+    "<blockquote class=\"challenge\">\n",
+    "## Challenge: Can you do it?\n",
+    "\n",
+    "What is the output of this command?\n",
+    "\n",
+    "~~~\n",
+    "\"a\" + \"b\"\n",
+    "~~~\n",
+    "{: .source}\n",
+    "\n",
+    "<blockquote class=\"solution\">\n",
+    "## Solution"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'ab'"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "\"a\" + \"b\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "</blockquote>\n",
+    "</blockquote>"
+   ]
+  }
+ ],
+ "metadata": {
+  "anaconda-cloud": {},
+  "kernelspec": {
+   "display_name": "Python [default]",
+   "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": "3.5.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}
diff --git a/_layouts/ipynb2md.tpl b/_layouts/ipynb2md.tpl
new file mode 100644
index 00000000..805dc2b3
--- /dev/null
+++ b/_layouts/ipynb2md.tpl
@@ -0,0 +1,78 @@
+{% extends 'display_priority.tpl' %}
+
+
+{% block in_prompt %}
+{% endblock in_prompt %}
+
+{% block output_prompt %}
+{%- endblock output_prompt %}
+
+{% block input %}
+~~~
+{{ cell.source}}
+~~~
+{: .source {% if nb.metadata.language_info %}.{{ nb.metadata.language_info.name }}{% endif %}}
+{% endblock input %}
+
+{% block error %}
+~~~
+{{- super()|replace("\n\n", "\n")|replace("    ", "") -}}
+~~~
+{: .error}
+{% endblock error %}
+
+{% block traceback_line %}
+{{ line | indent | strip_ansi }}
+{% endblock traceback_line %}
+
+{% block execute_result %}
+{% block data_priority scoped %}
+{{ super() }}
+{% endblock %}
+{% endblock execute_result %}
+
+{% block stream %}
+~~~
+{{ output.text }}
+~~~
+{: .output}
+{% endblock stream %}
+
+{% block data_svg %}
+![svg](../{{ output.metadata.filenames['image/svg+xml'] | path2url }})
+{% endblock data_svg %}
+
+{% block data_png %}
+![png](../{{ output.metadata.filenames['image/png'] | path2url }})
+{% endblock data_png %}
+
+{% block data_jpg %}
+![jpeg](../{{ output.metadata.filenames['image/jpeg'] | path2url }})
+{% endblock data_jpg %}
+
+{% block data_latex %}
+{{ output.data['text/latex'] }}
+{% endblock data_latex %}
+
+{% block data_html scoped %}
+{{ output.data['text/html'] }}
+{% endblock data_html %}
+
+{% block data_markdown scoped %}
+{{ output.data['text/markdown'] }}
+{% endblock data_markdown %}
+
+{% block data_text scoped %}
+~~~
+{{ output.data['text/plain'] }}
+~~~
+{: .output}
+{% endblock data_text %}
+
+{%- block markdowncell scoped -%}
+{{ cell.source }}
+{% endblock markdowncell %}
+
+{% block unknowncell scoped %}
+unknown type  {{ cell.type }}
+{% endblock unknowncell %}

From 7c87782ac886139ed40af558e576e8bc8f8994e3 Mon Sep 17 00:00:00 2001
From: Raniere Silva <raniere@rgaiacs.com>
Date: Thu, 19 Jan 2017 00:35:15 +0000
Subject: [PATCH 2/2] Add compiled files from Jupyter Notebook

---
 _episodes/07-jupyter.md      | 111 +++++++++++++++++++++++++++++++++++
 _episodes/07-jupyter_6_1.png | Bin 0 -> 10337 bytes
 2 files changed, 111 insertions(+)
 create mode 100644 _episodes/07-jupyter.md
 create mode 100644 _episodes/07-jupyter_6_1.png

diff --git a/_episodes/07-jupyter.md b/_episodes/07-jupyter.md
new file mode 100644
index 00000000..b801914d
--- /dev/null
+++ b/_episodes/07-jupyter.md
@@ -0,0 +1,111 @@
+---
+title: Using Jupyter Notebook 
+teaching: 10
+exercises: 1
+questions:
+- "How to write a lesson using Jupyter Notebook?"
+objectives:
+- "Explain how to use Jupyter Notebook with the new lesson template."
+- "Demonstrate how to include pieces of code, figures, and challenges."
+keypoints:
+- "It shouldn't be difficult"
+---
+
+The lesson should be written with a mix of code cells and Markdown cells,
+just like you'd normally do.
+
+
+~~~
+1 + 1
+~~~
+{: .source .python}
+
+
+
+~~~
+2
+~~~
+{: .output}
+
+
+Output with error message:
+
+
+~~~
+x[10]
+~~~
+{: .source .python}
+
+~~~
+---------------------------------------------------------------------------
+NameError Traceback (most recent call last)
+<ipython-input-2-7644c71c757c> in <module>()
+----> 1 x[10]
+
+NameError: name 'x' is not defined
+~~~
+{: .error}
+Output generating figures:
+
+
+~~~
+% matplotlib inline
+~~~
+{: .source .python}
+
+
+~~~
+import matplotlib.pyplot
+
+matplotlib.pyplot.plot([1,2,3], [1,2,3])
+~~~
+{: .source .python}
+
+
+
+~~~
+[<matplotlib.lines.Line2D at 0x7f542455f208>]
+~~~
+{: .output}
+
+
+
+
+![png](../07-jupyter_6_1.png)
+
+For the challenges you need to pay attention
+to include `<blockquote class="challenge">` before it
+and `<\blockquote>` after it.
+And for the solutions you need to pay attention
+to include `<blockquote class="solution">` before it
+and `<\blockquote>` after it.
+**This hacks is necessary for allow include Jupyter cells on challenges and solutions.**
+<blockquote class="challenge">
+## Challenge: Can you do it?
+
+What is the output of this command?
+
+~~~
+"a" + "b"
+~~~
+{: .source}
+
+<blockquote class="solution">
+## Solution
+
+
+~~~
+"a" + "b"
+~~~
+{: .source .python}
+
+
+
+~~~
+'ab'
+~~~
+{: .output}
+
+
+</blockquote>
+</blockquote>
diff --git a/_episodes/07-jupyter_6_1.png b/_episodes/07-jupyter_6_1.png
new file mode 100644
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