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1 .. _htmlnotebook:
1 .. _htmlnotebook:
2
2
3 The IPython Notebook
3 The IPython Notebook
4 ====================
4 ====================
5
5
6 .. seealso::
6 .. seealso::
7
7
8 :ref:`Installation requirements <installnotebook>` for the Notebook.
8 :ref:`Installation requirements <installnotebook>` for the Notebook.
9
9
10 The IPython Notebook combines two components:
10 The IPython Notebook combines two components:
11
11
12 * A web application, called the *IPython Notebook web app*, for interactive authoring of literate computations, in which explanatory text, mathematics, computations and rich media output may be combined. Input and output are stored in persistent cells that may be edited in-place.
12 * A web application, called the *IPython Notebook web app*, for interactive authoring of literate computations, in which explanatory text, mathematics, computations and rich media output may be combined. Input and output are stored in persistent cells that may be edited in-place.
13
13
14 * Plain text documents, called *notebook documents*, or *notebooks*, for recording and distributing the results of the rich computations.
14 * Plain text documents, called *notebook documents*, or *notebooks*, for recording and distributing the results of the rich computations.
15
15
16 In the documentation, the distinction between the *N*otebook app and *n*otebook documents is made by capitalization.
16 In the documentation, the distinction between the *N*otebook app and *n*otebook documents is made by capitalization.
17
17
18 The Notebook app automatically saves the current state of the computation in the web browser to the corresponding notebook document.
18 The Notebook app automatically saves the current state of the computation in the web browser to the corresponding notebook document.
19
19
20 It is also common to refer to the current state of the computation, as represented by the sequence of input cells in the Notebook app, as a
20 It is also common to refer to the current state of the computation, as represented by the sequence of input cells in the Notebook app, as a
21 *notebook*. There is no problem with confounding these two concepts, since
21 *notebook*. There is no problem with confounding these two concepts, since
22 there is actually a one-to-one correspondence between what you see on the
22 there is actually a one-to-one correspondence between what you see on the
23 screen inside the app, and what is stored in the corresponding ``.ipynb`` notebook document.
23 screen inside the app, and what is stored in the corresponding ``.ipynb`` notebook document.
24
24
25
25
26
26
27 Features of the IPython Notebook web app
27 Features of the IPython Notebook web app
28 ----------------------------------------
28 ----------------------------------------
29
29
30 Some of the main
30 Some of the main
31 features of the IPython Notebook app include:
31 features of the IPython Notebook app include:
32
32
33 * Display rich data representations (e.g. HTML / LaTeX / SVG) in the browser as a result of computations.
33 * Display rich data representations (e.g. HTML / LaTeX / SVG) in the browser as a result of computations.
34 * Compose text cells using Markdown and HTML.
34 * Compose text cells using Markdown and HTML.
35 * Include mathematical equations, rendered directly in the browser by MathJax.
35 * Include mathematical equations, rendered directly in the browser by MathJax.
36 * Import standard Python scripts
36 * Import standard Python scripts
37 * In-browser editing, syntax highlighting, tab completion and autoindentation.
37 * In-browser editing, syntax highlighting, tab completion and autoindentation.
38 * Inline figures rendered by the ``matplotlib`` library with publication quality, in a range of formats (SVG / PDF / PNG).
38 * Inline figures rendered by the ``matplotlib`` library with publication quality, in a range of formats (SVG / PDF / PNG).
39
39
40 If you have ever used the Mathematica or SAGE notebooks (the latter is also
40 If you have ever used the Mathematica or SAGE notebooks (the latter is also
41 web-based__) you should feel right at home. If you have not, you will be
41 web-based__) you should feel right at home. If you have not, you will be
42 able to learn how to use the IPython Notebook in just a few minutes.
42 able to learn how to use the IPython Notebook in just a few minutes.
43
43
44 .. __: http://sagenb.org
44 .. __: http://sagenb.org
45
45
46
46
47 Notebook documents
47 Notebook documents
48 ------------------
48 ------------------
49
49
50 Notebook document files are just standard text files with the extension
50 Notebook document files are just standard text files with the extension
51 ``.ipynb``, stored in the working directory on your computer. This file can be easily put under version control and shared with colleagues.
51 ``.ipynb``, stored in the working directory on your computer. This file can be easily put under version control and shared with colleagues.
52
52
53 Despite the fact that the notebook documents are plain text files, they use
53 Despite the fact that the notebook documents are plain text files, they use
54 the JSON format in order to store a *complete*, *reproducible* copy of the
54 the JSON format in order to store a *complete*, *reproducible* copy of the
55 state of the computation as it is inside the Notebook app.
55 state of the computation as it is inside the Notebook app.
56 That is, they record all computations carried out and the results obtained in a literate way; inputs and outputs of computations can be freely mixed with descriptive text, mathematics, and HTML 5 objects.
56 That is, they record all computations carried out and the results obtained in a literate way; inputs and outputs of computations can be freely mixed with descriptive text, mathematics, and HTML 5 objects.
57
57
58 Notebooks may easily be exported to a range of static formats, including HTML (for example, for blog posts), PDF and slide shows.
58 Notebooks may easily be exported to a range of static formats, including HTML (for example, for blog posts), PDF and slide shows.
59 Furthermore, any publicly
59 Furthermore, any publicly
60 available notebook may be shared via the `IPython Notebook Viewer
60 available notebook may be shared via the `IPython Notebook Viewer
61 <http://nbviewer.ipython.org>`_ service, which will provide it as a static web
61 <http://nbviewer.ipython.org>`_ service, which will provide it as a static web
62 page. The results may thus be shared without having to install anything.
62 page. The results may thus be shared without having to install anything.
63
63
64
64
65 See :ref:`our installation documentation <install_index>` for directions on
65 See :ref:`our installation documentation <install_index>` for directions on
66 how to install the notebook and its dependencies.
66 how to install the notebook and its dependencies.
67
67
68 .. note::
68 .. note::
69
69
70 You can start more than one notebook server at the same time, if you want to
70 You can start more than one notebook server at the same time, if you want to
71 work on notebooks in different directories. By default the first notebook
71 work on notebooks in different directories. By default the first notebook
72 server starts on port 8888, and later notebook servers search for ports near
72 server starts on port 8888, and later notebook servers search for ports near
73 that one. You can also manually specify the port with the ``--port``
73 that one. You can also manually specify the port with the ``--port``
74 option.
74 option.
75
75
76
76
77 Starting up the IPython Notebook web app
77 Starting up the IPython Notebook web app
78 ----------------------------------------
78 ----------------------------------------
79
79
80 The Notebook web app is started with the command::
80 The Notebook web app is started with the command::
81
81
82 $ ipython notebook
82 $ ipython notebook
83
83
84 The landing page of the notebook server application, the *dashboard*, shows the notebooks currently available in the *working directory* (the directory from which the notebook was started).
84 The landing page of the notebook server application, the *dashboard*, shows the notebooks currently available in the *working directory* (the directory from which the notebook was started).
85 You can create new notebooks from the dashboard with the ``New Notebook``
85 You can create new notebooks from the dashboard with the ``New Notebook``
86 button, or open existing ones by clicking on their name.
86 button, or open existing ones by clicking on their name.
87 You can also drag and drop ``.ipynb`` notebooks and standard ``.py`` Python source code files into the notebook list area.
87 You can also drag and drop ``.ipynb`` notebooks and standard ``.py`` Python source code files into the notebook list area.
88
88
89 ``.py`` files will be imported into the IPython Notebook as a notebook with the same name, but an ``.ipynb`` extension, located in the working directory. The notebook will consist of a single cell containing all the
89 ``.py`` files will be imported into the IPython Notebook as a notebook with the same name, but an ``.ipynb`` extension, located in the working directory. The notebook will consist of a single cell containing all the
90 code in the ``.py`` file, which you can later manually partition into individual cells.
90 code in the ``.py`` file, which you can later manually partition into individual cells.
91
91
92 .. Alternatively, prior to importing the ``.py``, you can manually add ``# <nbformat>2</nbformat>`` at the start of the file, and then add separators for text and code cells, to get a cleaner import with the file already broken into individual cells.
92 .. Alternatively, prior to importing the ``.py``, you can manually add ``# <nbformat>2</nbformat>`` at the start of the file, and then add separators for text and code cells, to get a cleaner import with the file already broken into individual cells.
93
93
94
94
95 The IPython Notebook web app is based on a server-client structure.
95 The IPython Notebook web app is based on a server-client structure.
96 This server uses a two-process kernel architecture based on ZeroMQ, as well as Tornado for serving HTTP requests. Other clients may connect to the same underlying IPython kernel.
96 This server uses a two-process kernel architecture based on ZeroMQ, as well as Tornado for serving HTTP requests. Other clients may connect to the same underlying IPython kernel.
97
97
98
98
99 When you open or create a new notebook, your browser tab will reflect the name of that notebook, prefixed with "IPy".
99 When you open or create a new notebook, your browser tab will reflect the name of that notebook, prefixed with "IPy".
100 The URL is currently not meant to be human-readable and is not persistent across invocations of the notebook server; however, this will change in a future version of IPython.
100 The URL is currently not meant to be human-readable and is not persistent across invocations of the notebook server; however, this will change in a future version of IPython.
101
101
102
102
103 Notebook user interface
103 Notebook user interface
104 -----------------------
104 -----------------------
105
105
106 When you finally start editing a notebook document in the Notebook, you will be presented with the title of the notebook, a *menu bar*, a *toolbar* and an empty *input cell*.
106 When you finally start editing a notebook document in the Notebook, you will be presented with the title of the notebook, a *menu bar*, a *toolbar* and an empty *input cell*.
107
107
108 Notebook title
108 Notebook title
109 ~~~~~~~~~~~~~~
109 ~~~~~~~~~~~~~~
110 The title of the notebook document that is currently being edited is displayed at the top of the page, next to the ``IP[y]: Notebook`` logo. This title may be edited directly by clicking on it. The title is reflected in the name of the ``.ipynb`` notebook document file that is saved.
110 The title of the notebook document that is currently being edited is displayed at the top of the page, next to the ``IP[y]: Notebook`` logo. This title may be edited directly by clicking on it. The title is reflected in the name of the ``.ipynb`` notebook document file that is saved.
111
111
112 Menu bar
112 Menu bar
113 ~~~~~~~~
113 ~~~~~~~~
114 The menu bar presents different options that may be used to manipulate the way the Notebook functions.
114 The menu bar presents different options that may be used to manipulate the way the Notebook functions.
115
115
116 Toolbar
116 Toolbar
117 ~~~~~~~
117 ~~~~~~~
118 The tool bar gives handy icons for the most-used operations within the Notebook.
118 The tool bar gives handy icons for the most-used operations within the Notebook.
119
119
120
120
121 Input cells
121 Input cells
122 -----------
122 -----------
123 Input cells are the core of the functionality of the IPython Notebook.
123 Input cells are the core of the functionality of the IPython Notebook.
124 They are regions in the document where you can enter different types of text and commands. These regions are then executed using :kbd:`Shift-Enter`, at which point the Notebook executes the current input cell, displays the resulting output beneath it, and adds a new input cell below.
124 They are regions in the document where you can enter different types of text and commands. These regions are then executed using :kbd:`Shift-Enter`, at which point the Notebook executes the current input cell, displays the resulting output beneath it, and adds a new input cell below.
125
125
126 The notebook consists of a sequence of input cells,
126 The notebook consists of a sequence of input cells,
127 providing the means to direct the computational process.
127 providing the means to direct the computational process.
128
128
129
129
130 Basic workflow
130 Basic workflow
131 --------------
131 --------------
132 The normal workflow in a notebook is, then, quite similar to a standard IPython session, with the difference that you can edit cells in-place multiple
132 The normal workflow in a notebook is, then, quite similar to a standard IPython session, with the difference that you can edit cells in-place multiple
133 times until you obtain the desired results, rather than having to
133 times until you obtain the desired results, rather than having to
134 rerun separate scripts with the ``%run`` magic command. (Magic commands do, however, also work in the notebook; see below). Typically, you'll work on a problem in pieces,
134 rerun separate scripts with the ``%run`` magic command. (Magic commands do, however, also work in the notebook; see below). Typically, you'll work on a problem in pieces,
135 organizing related pieces into cells and moving forward as previous
135 organizing related pieces into cells and moving forward as previous
136 parts work correctly. This is much more convenient for interactive exploration than breaking up a computation into scripts that must be
136 parts work correctly. This is much more convenient for interactive exploration than breaking up a computation into scripts that must be
137 executed together, especially if parts of them take a long time to run
137 executed together, especially if parts of them take a long time to run
138
138
139 The only significant limitation that the notebook currently has, compared to the Qt console, is that it cannot run any code that
139 The only significant limitation that the notebook currently has, compared to the Qt console, is that it cannot run any code that
140 expects input from the kernel (such as scripts that call
140 expects input from the kernel (such as scripts that call
141 :func:`raw_input`). Very importantly, this means that the ``%debug``
141 :func:`raw_input`). Very importantly, this means that the ``%debug``
142 magic does *not* currently work in the notebook! This limitation will
142 magic does *not* currently work in the notebook! This limitation will
143 be overcome in the future, but in the meantime, there is a way to debug problems in the notebook: you can attach a Qt console to your existing notebook kernel, and run ``%debug`` from the Qt console.
143 be overcome in the future, but in the meantime, there is a way to debug problems in the notebook: you can attach a Qt console to your existing notebook kernel, and run ``%debug`` from the Qt console.
144 If your notebook is running on a local
144 If your notebook is running on a local
145 computer (i.e. if you are accessing it via your localhost address at ``127.0.0.1``), you can just type ``%qtconsole`` in the notebook and a Qt console will open up, connected to that same kernel.
145 computer (i.e. if you are accessing it via your localhost address at ``127.0.0.1``), you can just type ``%qtconsole`` in the notebook and a Qt console will open up, connected to that same kernel.
146
146
147 At certain moments, it may be necessary to interrupt a particularly long calculation, or even to kill the entire computational process. This may be achieved by interrupting or restarting the kernel, respectively.
147 At certain moments, it may be necessary to interrupt a particularly long calculation, or even to kill the entire computational process. This may be achieved by interrupting or restarting the kernel, respectively.
148 After a restart, all relevant cells must be re-evaluated
148 After a restart, all relevant cells must be re-evaluated
149
149
150
150
151 A notebook may be downloaded in either ``.ipynb`` or raw ``.py`` form from the menu option ``File -> Download as``
151 A notebook may be downloaded in either ``.ipynb`` or raw ``.py`` form from the menu option ``File -> Download as``
152 Choosing the ``.py`` option removes all output and saves the text cells
152 Choosing the ``.py`` option removes all output and saves the text cells
153 in comment areas. See ref:`below <notebook_format>` for more details on the
153 in comment areas. See ref:`below <notebook_format>` for more details on the
154 notebook format.
154 notebook format.
155
155
156
156
157 .. warning::
157 .. warning::
158
158
159 While in simple cases you can "roundtrip" a notebook to Python, edit the
159 While in simple cases you can "roundtrip" a notebook to Python, edit the
160 Python file, and then import it back without loss of main content, this is in general *not guaranteed to work*. First, there is extra metadata
160 Python file, and then import it back without loss of main content, this is in general *not guaranteed to work*. First, there is extra metadata
161 saved in the notebook that may not be saved to the ``.py`` format. And as
161 saved in the notebook that may not be saved to the ``.py`` format. And as
162 the notebook format evolves in complexity, there will be attributes of the
162 the notebook format evolves in complexity, there will be attributes of the
163 notebook that will not survive a roundtrip through the Python form. You
163 notebook that will not survive a roundtrip through the Python form. You
164 should think of the Python format as a way to output a script version of a
164 should think of the Python format as a way to output a script version of a
165 notebook and the import capabilities as a way to load existing code to get a
165 notebook and the import capabilities as a way to load existing code to get a
166 notebook started. But the Python version is *not* an alternate notebook
166 notebook started. But the Python version is *not* an alternate notebook
167 format.
167 format.
168
168
169
169
170 Keyboard shortcuts
170 Keyboard shortcuts
171 ------------------
171 ------------------
172 All actions in the notebook can be achieved with the mouse, but we have also
172 All actions in the notebook can be achieved with the mouse, but we have also
173 added keyboard shortcuts for the most common ones, so that productive use of
173 added keyboard shortcuts for the most common ones, so that productive use of
174 the notebook can be achieved with minimal mouse intervention. The main
174 the notebook can be achieved with minimal mouse intervention. The main
175 key bindings you need to remember are:
175 key bindings you need to remember are:
176
176
177 * :kbd:`Shift-Enter`:
177 * :kbd:`Shift-Enter`:
178 execute the current cell, show output (if any), and jump
178 execute the current cell, show output (if any), and jump
179 to the next cell below. If :kbd:`Shift-Enter`
179 to the next cell below. If :kbd:`Shift-Enter`
180 was invoked on the last input line, a new code cell will also be created. Note that in the notebook, simply using :kbd:`Enter` *never* forces execution, it simply inserts a new line in the current cell. Therefore, in the notebook you must always use :kbd:`Shift-Enter` to get execution (or use the mouse and click on the ``Run Selected`` button).
180 was invoked on the last input line, a new code cell will also be created. Note that in the notebook, simply using :kbd:`Enter` *never* forces execution, it simply inserts a new line in the current cell. Therefore, in the notebook you must always use :kbd:`Shift-Enter` to get execution (or use the mouse and click on the ``Run Selected`` button).
181
181
182 * :kbd:`Alt-Enter`:
182 * :kbd:`Alt-Enter`:
183 this combination is similar to the previous one, with the
183 this combination is similar to the previous one, with the
184 exception that, if the next cell below is not empty, a new code cell will be
184 exception that, if the next cell below is not empty, a new code cell will be
185 added to the notebook, even if the cell execution happens not in the last cell. :kbd:`Alt-Enter`: is a shortcut for the sequence :kbd:`Shift-Enter`, :kbd:`Ctrl-m a`.
185 added to the notebook, even if the cell execution happens not in the last cell. :kbd:`Alt-Enter`: is a shortcut for the sequence :kbd:`Shift-Enter`, :kbd:`Ctrl-m a`.
186
186
187 * :kbd:`Ctrl-Enter`:
187 * :kbd:`Ctrl-Enter`:
188 execute the current cell in "terminal mode", where any
188 execute the current cell in "terminal mode", where any
189 output is shown, but the cursor remains in the current cell. This is convenient to do quick in-place experiments, or query things like filesystem content, without creating additional cells that you may not want saved in your notebook.
189 output is shown, but the cursor remains in the current cell. This is convenient to do quick in-place experiments, or query things like filesystem content, without creating additional cells that you may not want saved in your notebook.
190
190
191 * :kbd:`Ctrl-m`:
191 * :kbd:`Ctrl-m`:
192 this is the prefix for all other keybindings, which consist of an additional single letter or character. Type :kbd:`Ctrl-m h` (that is, the sole letter
192 this is the prefix for all other keybindings, which consist of an additional single letter or character. Type :kbd:`Ctrl-m h` (that is, the sole letter
193 :kbd:`h` after :kbd:`Ctrl-m`) and IPython will show you the remaining available keybindings.
193 :kbd:`h` after :kbd:`Ctrl-m`) and IPython will show you the remaining available keybindings.
194
194
195
195
196
196
197
197
198
198
199 Cell types
199 Cell types
200 ----------
200 ----------
201 Each IPython input cell has a *cell type*.
201 Each IPython input cell has a *cell type*.
202 There is a restricted number of possible cell types, which may be set by using the cell type dropdown on the toolbar, or via the following keyboard shortcuts:
202 There is a restricted number of possible cell types, which may be set by using the cell type dropdown on the toolbar, or via the following keyboard shortcuts:
203
203
204 * **code**: :kbd:`Ctrl-m y`
204 * **code**: :kbd:`Ctrl-m y`
205 * **markdown**: :kbd:`Ctrl-m m`
205 * **markdown**: :kbd:`Ctrl-m m`
206 * **raw**: :kbd:`Ctrl-m t`
206 * **raw**: :kbd:`Ctrl-m t`
207 * **heading**: :kbd:`Ctrl-m 1` - :kbd:`Ctrl-m 6`
207 * **heading**: :kbd:`Ctrl-m 1` - :kbd:`Ctrl-m 6`
208
208
209
209
210 Code cells
210 Code cells
211 ~~~~~~~~~~
211 ~~~~~~~~~~
212 Code cells contain code written in some computer language, which is Python by default. When the cell is executed with :kbd:`Shift-Enter`, this code is executed, and the result returned by Python (or the corresponding language) after running the code will be displayed as its output.
212 Code cells contain code written in some computer language, which is Python by default. When the cell is executed with :kbd:`Shift-Enter`, this code is executed, and the result returned by Python (or the corresponding language) after running the code will be displayed as its output.
213
213
214 Code may be edited inline in the cell, with full syntax highlighting.
214 Code may be edited inline in the cell, with full syntax highlighting.
215
215
216
216
217 Rich text using Markdown
217 Rich text using Markdown
218 ~~~~~~~~~~~~~~~~~~~~~~~~
218 ~~~~~~~~~~~~~~~~~~~~~~~~
219 The computational process may be documented in a literate way using rich text.
219 The computational process may be documented in a literate way using rich text.
220 For this purpose, the Notebook provides markdown cells. Text is entered using Markdown_ syntax, allowing for italics, bold, ordered and unordered lists, etc. This is rendered using Markdown syntax to a rich HTML representation when the cell is executed. In this case, the output *replaces* the input cell.
220 For this purpose, the Notebook provides markdown cells. Text is entered using Markdown_ syntax, allowing for italics, bold, ordered and unordered lists, etc. This is rendered using Markdown syntax to a rich HTML representation when the cell is executed. In this case, the output *replaces* the input cell.
221
221
222 Within markdown cells, mathematics can be included in a straightforward manner using LaTeX notation: ``$...$`` for inline math and ``$$...$$`` for displayed math. Standard LaTeX environments, such as ``\begin{equation}...\end{equation}``, also work. New commands may be defined using standard LaTeX commands, placed anywhere in a markdown cell.
222 Within markdown cells, mathematics can be included in a straightforward manner using LaTeX notation: ``$...$`` for inline math and ``$$...$$`` for displayed math. Standard LaTeX environments, such as ``\begin{equation}...\end{equation}``, also work. New commands may be defined using standard LaTeX commands, placed anywhere in a markdown cell.
223
223
224 Raw cells
224 Raw cells
225 ~~~~~~~~~
225 ~~~~~~~~~
226 Raw cells provide a place to put additional information which is not evaluated by the Notebook. This can be used, for example, for extra information to be used when the notebook is exported to a certain format.
226 Raw cells provide a place to put additional information which is not evaluated by the Notebook. This can be used, for example, for extra information to be used when the notebook is exported to a certain format.
227
227
228
228
229 Magic commands
229 Magic commands
230 --------------
230 --------------
231 Magic commands, or *magics*, are one-word commands beginning with the symbol ``%``, which send commands to IPython itself (as opposed to standard Python commands which are exported to be run in a Python interpreter).
231 Magic commands, or *magics*, are one-word commands beginning with the symbol ``%``, which send commands to IPython itself (as opposed to standard Python commands which are exported to be run in a Python interpreter).
232
232
233 Magics control different elements of the way that the IPython notebook operates. They are entered into standard code cells and executed as usual with :kbd:`Shift-Enter`.
233 Magics control different elements of the way that the IPython notebook operates. They are entered into standard code cells and executed as usual with :kbd:`Shift-Enter`.
234
234
235 There are two types of magics: *line magics*, which begin with a single ``%`` and operate on a single line of the code cell; and *cell magics*, which begin with ``%%`` and operate on the entire contents of the cell.
235 There are two types of magics: *line magics*, which begin with a single ``%`` and operate on a single line of the code cell; and *cell magics*, which begin with ``%%`` and operate on the entire contents of the cell.
236
236
237 Line magics
237 Line magics
238 ˜˜˜˜˜˜˜˜˜˜˜
238 ˜˜˜˜˜˜˜˜˜˜˜
239 Some of the available line magics are the following:
239 Some of the available line magics are the following:
240
240
241 * ``%load``:
241 * ``%load``:
242 Loads a file and places its content into a new code cell.
242 Loads a file and places its content into a new code cell.
243
243
244 * ``%timeit``:
244 * ``%timeit``:
245 A simple way to time how long a single line of code takes to run
245 A simple way to time how long a single line of code takes to run
246
246
247 * ``%config``:
247 * ``%config``:
248 Configuration of the IPython Notebook
248 Configuration of the IPython Notebook
249
249
250 * ``%lsmagic``:
250 * ``%lsmagic``:
251 Provides a list of all available magic commands
251 Provides a list of all available magic commands
252
252
253 Cell magics
253 Cell magics
254 ˜˜˜˜˜˜˜˜˜˜˜
254 ˜˜˜˜˜˜˜˜˜˜˜
255
255
256 * ``%%bash``:
256 * ``%%bash``:
257 Send the contents of the code cell to be executed by ``bash``
257 Send the contents of the code cell to be executed by ``bash``
258
258
259 * ``%%file``:
259 * ``%%file``:
260 Writes a file with with contents of the cell. *Caution*: The file is ovewritten without asking.
260 Writes a file with with contents of the cell. *Caution*: The file is ovewritten without asking.
261
261
262 * ``%%R``:
262 * ``%%R``:
263 Execute the contents of the cell using the R language.
263 Execute the contents of the cell using the R language.
264
264
265 * ``%%cython``:
265 * ``%%cython``:
266 Execute the contents of the cell using ``Cython``.
266 Execute the contents of the cell using ``Cython``.
267
267
268
268
269
269
270 Plotting
270 Plotting
271 --------
271 --------
272 One major feature of the Notebook is the ability to capture the result of plots as inline output. IPython is designed to work seamlessly together with
272 One major feature of the Notebook is the ability to capture the result of plots as inline output. IPython is designed to work seamlessly together with
273 the ``%matplotlib`` plotting library. In order to set this up, the
273 the ``%matplotlib`` plotting library. In order to set this up, the
274 ``%matplotlib`` magic command must be run before any plotting takes place.
274 ``%matplotlib`` magic command must be run before any plotting takes place.
275
275
276 Note that ``%matplotlib`` only sets up IPython to work correctly with ``matplotlib``; it does not actually execute any ``import`` commands and does not add anything to the namespace.
276 Note that ``%matplotlib`` only sets up IPython to work correctly with ``matplotlib``; it does not actually execute any ``import`` commands and does not add anything to the namespace.
277
277
278 There is an alternative magic, ``%pylab``, which, in addition, also executes a sequence of standard ``import`` statements required for working with the
278 There is an alternative magic, ``%pylab``, which, in addition, also executes a sequence of standard ``import`` statements required for working with the
279 ``%matplotlib`` library. In particular, it automatically imports all names in the ``numpy`` and ``matplotlib`` packages to the namespace. A less invasive solution is ``%pylab --no-import-all``, which imports just the standard names
279 ``%matplotlib`` library. In particular, it automatically imports all names in the ``numpy`` and ``matplotlib`` packages to the namespace. A less invasive solution is ``%pylab --no-import-all``, which imports just the standard names
280 ``np`` for the ``numpy`` module and ``plt`` for the ``matplotlib.pyplot`` module.
280 ``np`` for the ``numpy`` module and ``plt`` for the ``matplotlib.pyplot`` module.
281
281
282 When the default ``%matplotlib`` or ``%pylab`` magics are used, the output of a plotting command is captured in a *separate* window. An alternative is to use::
282 When the default ``%matplotlib`` or ``%pylab`` magics are used, the output of a plotting command is captured in a *separate* window. An alternative is to use::
283 ``%matplotlib inline``
283 ``%matplotlib inline``
284 which captures the output inline within the notebook format. This has the benefit that the resulting plots will be stored in the notebook document.
284 which captures the output inline within the notebook format. This has the benefit that the resulting plots will be stored in the notebook document.
285
285
286
286
287 Converting notebooks to other formats
287 Converting notebooks to other formats
288 -------------------------------------
288 -------------------------------------
289 Newly added in the 1.0 release of IPython is the ``nbconvert`` tool to convert a notebook document into another static format. This is a command line tool; at present, this functionality is not available to export directly from within the Notebook app. The syntax is::
289 Newly added in the 1.0 release of IPython is the ``nbconvert`` tool to convert a notebook document into another static format. This is a command line tool; at present, this functionality is not available to export directly from within the Notebook app. The syntax is::
290
290
291 ``$ ipython nbconvert notebook.ipynb``
291 $ ipython nbconvert notebook.ipynb
292
292
293 for standard HTML output, or::
293 for standard HTML output, or::
294
294
295 ``$ ipython nbconvert --format=FORMAT notebook.ipynb``
295 $ ipython nbconvert --format=FORMAT notebook.ipynb
296
296
297 where ``FORMAT`` is the desired export format. Options for this format include:
297 where ``FORMAT`` is the desired export format. Options for this format include:
298
298
299 * ``full_html``:
299 * ``full_html``:
300 Standard HTML
300 Standard HTML
301
301
302 * ``simple_html``:
302 * ``simple_html``:
303 A simplified version of HTML
303 A simplified version of HTML
304
304
305 * ``reveal``:
305 * ``reveal``:
306 A format to be used with the ``reveal.js`` package for slideshow presentations.
306 A format to be used with the ``reveal.js`` package for slideshow presentations.
307
307
308 * ``sphinx_howto``:
308 * ``sphinx_howto``:
309 A standard documentation format.
309 A standard documentation format.
310
310
311 * ``latex``:
311 * ``latex``:
312 Produces LaTeX output which may be compiled with ``pdflatex`` to PDF.
312 Produces LaTeX output which may be compiled with ``pdflatex`` to PDF.
313
313
314
314
315 Configuration
315 Configuration
316 -------------
316 -------------
317 The IPython Notebook can be run with a variety of command line arguments.
317 The IPython Notebook can be run with a variety of command line arguments.
318 To see a list of available options enter::
318 To see a list of available options enter::
319
319
320 $ ipython notebook --help
320 $ ipython notebook --help
321
321
322 Defaults for these options can also be set by creating a file named
322 Defaults for these options can also be set by creating a file named
323 ``ipython_notebook_config.py`` in your IPython *profile folder*. The profile folder is a subfolder of your IPython directory; ``ipython locate`` will show you where it is located.
323 ``ipython_notebook_config.py`` in your IPython *profile folder*. The profile folder is a subfolder of your IPython directory; ``ipython locate`` will show you where it is located.
324
324
325 To create a new set of default configuration files, with lots of information on available options, use::
325 To create a new set of default configuration files, with lots of information on available options, use::
326
326
327 $ ipython profile create
327 $ ipython profile create
328
328
329 .. seealso:
329 .. seealso:
330
330
331 :ref:`config_overview`, in particular :ref:`Profiles`.
331 :ref:`config_overview`, in particular :ref:`Profiles`.
332
332
333
333
334
334 Extracting standard Python files from notebooks
335 Importing or executing a notebook as a normal Python file
335 -----------------------------------------------
336 ---------------------------------------------------------
337
336
338 The native format of the notebook, a file with a ``.ipynb`` `extension, is a
337 The native format of the notebook, a file with a ``.ipynb`` `extension, is a
339 JSON container of all the input and output of the notebook, and therefore not
338 JSON container of all the input and output of the notebook, and therefore not
340 valid Python by itself. This means that by default, you cannot directly
339 valid Python by itself. This means that by default, you cannot directly
341 import a notebook from Python, nor execute it as a normal python script.
340 import a notebook from Python, nor execute it as a normal python script.
342
341
343 But if you want to be able to use notebooks also as regular Python files, you can start the notebook server with::
342 But if you want to be able to use notebooks also as regular Python files, you can start the notebook server with::
344
343
345 ipython notebook --script
344 ipython notebook --script
346
345
347 or you can set this option permanently in your configuration file with::
346 or you can set this option permanently in your configuration file with::
348
347
349 c.NotebookManager.save_script=True
348 c.NotebookManager.save_script=True
350
349
351 This will instruct the notebook server to save the ``.py`` export of each
350 This will instruct the notebook server to save the ``.py`` export of each
352 notebook, in addition to the ``.ipynb``, at every save. These are standard
351 notebook, in addition to the ``.ipynb``, at every save. These are standard
353 ``.py`` files, and so they can be ``%run``, imported from regular IPython
352 ``.py`` files, and so they can be ``%run``, imported from regular IPython
354 sessions or other notebooks, or executed at the command line. Since we export
353 sessions or other notebooks, or executed at the command line. Since we export
355 the raw code you have typed, for these files to be importable from other code,
354 the raw code you have typed, for these files to be importable from other code,
356 you will have to avoid using syntax such as ``%magic``s and other IPython-specific extensions to the language.
355 you will have to avoid using syntax such as ``%magic``s and other IPython-specific extensions to the language.
357
356
358 In regular practice, the standard way to differentiate importable code from the
357 In regular practice, the standard way to differentiate importable code from the
359 'executable' part of a script is to put at the bottom::
358 'executable' part of a script is to put at the bottom::
360
359
361 if __name__ == '__main__':
360 if __name__ == '__main__':
362 # rest of the code...
361 # rest of the code...
363
362
364 Since all cells in the notebook are run as top-level code, you will need to
363 Since all cells in the notebook are run as top-level code, you will need to
365 similarly protect *all* cells that you do not want executed when other scripts
364 similarly protect *all* cells that you do not want executed when other scripts
366 try to import your notebook. A convenient shortand for this is to define early
365 try to import your notebook. A convenient shortand for this is to define early
367 on::
366 on::
368
367
369 script = __name__ == '__main__'
368 script = __name__ == '__main__'
370
369
371 and then on any cell that you need to protect, use::
370 and then on any cell that you need to protect, use::
372
371
373 if script:
372 if script:
374 # rest of the cell...
373 # rest of the cell...
375
374
376
375
377 .. _notebook_security:
376 .. _notebook_security:
378
377
379 Security
378 Security
380 ========
379 --------
381
380
382 You can protect your notebook server with a simple single-password by
381 You can protect your Notebook server with a simple singlepassword by
383 setting the :attr:`NotebookApp.password` configurable. You can prepare a
382 setting the :attr:`NotebookApp.password` configurable. You can prepare a
384 hashed password using the function :func:`IPython.lib.security.passwd`:
383 hashed password using the function :func:`IPython.lib.security.passwd`:
385
384
386 .. sourcecode:: ipython
385 .. sourcecode:: ipython
387
386
388 In [1]: from IPython.lib import passwd
387 In [1]: from IPython.lib import passwd
389 In [2]: passwd()
388 In [2]: passwd()
390 Enter password:
389 Enter password:
391 Verify password:
390 Verify password:
392 Out[2]: 'sha1:67c9e60bb8b6:9ffede0825894254b2e042ea597d771089e11aed'
391 Out[2]: 'sha1:67c9e60bb8b6:9ffede0825894254b2e042ea597d771089e11aed'
393
392
394 .. note::
393 .. note::
395
394
396 :func:`~IPython.lib.security.passwd` can also take the password as a string
395 :func:`~IPython.lib.security.passwd` can also take the password as a string
397 argument. **Do not** pass it as an argument inside an IPython session, as it
396 argument. **Do not** pass it as an argument inside an IPython session, as it
398 will be saved in your input history.
397 will be saved in your input history.
399
398
400 You can then add this to your :file:`ipython_notebook_config.py`, e.g.::
399 You can then add this to your :file:`ipython_notebook_config.py`, e.g.::
401
400
402 # Password to use for web authentication
401 # Password to use for web authentication
403 c.NotebookApp.password = u'sha1:67c9e60bb8b6:9ffede0825894254b2e042ea597d771089e11aed'
402 c.NotebookApp.password = u'sha1:67c9e60bb8b6:9ffede0825894254b2e042ea597d771089e11aed'
404
403
405 When using a password, it is a good idea to also use SSL, so that your password
404 When using a password, it is a good idea to also use SSL, so that your password
406 is not sent unencrypted by your browser. You can start the notebook to
405 is not sent unencrypted by your browser. You can start the notebook to
407 communicate via a secure protocol mode using a self-signed certificate by
406 communicate via a secure protocol mode using a self-signed certificate with the command::
408 typing::
409
407
410 $ ipython notebook --certfile=mycert.pem
408 $ ipython notebook --certfile=mycert.pem
411
409
412 .. note::
410 .. note::
413
411
414 A self-signed certificate can be generated with openssl. For example, the
412 A self-signed certificate can be generated with ``openssl``. For example, the following command will create a certificate valid for 365 days with both the key and certificate data written to the same file::
415 following command will create a certificate valid for 365 days with both
416 the key and certificate data written to the same file::
417
413
418 $ openssl req -x509 -nodes -days 365 -newkey rsa:1024 -keyout mycert.pem -out mycert.pem
414 $ openssl req -x509 -nodes -days 365 -newkey rsa:1024 -keyout mycert.pem -out mycert.pem
419
415
420 Your browser will warn you of a dangerous certificate because it is
416 Your browser will warn you of a dangerous certificate because it is
421 self-signed. If you want to have a fully compliant certificate that will not
417 self-signed. If you want to have a fully compliant certificate that will not
422 raise warnings, it is possible (but rather involved) to obtain one for free,
418 raise warnings, it is possible (but rather involved) to obtain one for free,
423 `as explained in detailed in this tutorial`__.
419 `as explained in detailed in this tutorial`__.
424
420
425 .. __: http://arstechnica.com/security/news/2009/12/how-to-get-set-with-a-secure-sertificate-for-free.ars
421 .. __: http://arstechnica.com/security/news/2009/12/how-to-get-set-with-a-secure-sertificate-for-free.ars
426
422
427 Keep in mind that when you enable SSL support, you'll need to access the
423 Keep in mind that when you enable SSL support, you'll need to access the
428 notebook server over ``https://``, not over plain ``http://``. The startup
424 notebook server over ``https://``, not over plain ``http://``. The startup
429 message from the server prints this, but it's easy to overlook and think the
425 message from the server prints this, but it's easy to overlook and think the
430 server is for some reason non-responsive.
426 server is for some reason non-responsive.
431
427
432 Quick how to's
433 ==============
434
428
435 Connecting to an existing kernel
429 Connecting to an existing kernel
436 ---------------------------------
430 ---------------------------------
437
431
438 The notebook server always prints to the terminal the full details of
432 The notebook server always prints to the terminal the full details of
439 how to connect to each kernel, with lines like::
433 how to connect to each kernel, with lines like::
440
434
441 [IPKernelApp] To connect another client to this kernel, use:
435 [IPKernelApp] To connect another client to this kernel, use:
442 [IPKernelApp] --existing kernel-3bb93edd-6b5a-455c-99c8-3b658f45dde5.json
436 [IPKernelApp] --existing kernel-3bb93edd-6b5a-455c-99c8-3b658f45dde5.json
443
437
444 This is the name of a JSON file that contains all the port and
438 This is the name of a JSON file that contains all the port and
445 validation information necessary to connect to the kernel. You can
439 validation information necessary to connect to the kernel. You can
446 manually start a Qt console with::
440 manually start a Qt console with::
447
441
448 ipython qtconsole --existing kernel-3bb93edd-6b5a-455c-99c8-3b658f45dde5.json
442 ipython qtconsole --existing kernel-3bb93edd-6b5a-455c-99c8-3b658f45dde5.json
449
443
450 and if you only have a single kernel running, simply typing::
444 and if you only have a single kernel running, simply typing::
451
445
452 ipython qtconsole --existing
446 ipython qtconsole --existing
453
447
454 will automatically find it (it will always find the most recently
448 will automatically find it (it will always find the most recently
455 started kernel if there is more than one). You can also request this
449 started kernel if there is more than one). You can also request this
456 connection data by typing ``%connect_info``; this will print the same
450 connection data by typing ``%connect_info``; this will print the same
457 file information as well as the content of the JSON data structure it contains.
451 file information as well as the content of the JSON data structure it contains.
458
452
459
453
460 Running a public notebook server
454 Running a public notebook server
461 --------------------------------
455 --------------------------------
462
456
463 If you want to access your notebook server remotely with just a web browser,
457 If you want to access your notebook server remotely with just a web browser,
464 here is a quick set of instructions. Start by creating a certificate file and
458 here is a quick set of instructions. Start by creating a certificate file and
465 a hashed password as explained above. Then, create a custom profile for the
459 a hashed password as explained above. Then, create a custom profile for the
466 notebook. At the command line, type::
460 notebook. At the command line, type::
467
461
468 ipython profile create nbserver
462 ipython profile create nbserver
469
463
470 In the profile directory, edit the file ``ipython_notebook_config.py``. By
464 In the profile directory, edit the file ``ipython_notebook_config.py``. By
471 default the file has all fields commented, the minimum set you need to
465 default the file has all fields commented, the minimum set you need to
472 uncomment and edit is here::
466 uncomment and edit is here::
473
467
474 c = get_config()
468 c = get_config()
475
469
476 # Kernel config
470 # Kernel config
477 c.IPKernelApp.pylab = 'inline' # if you want plotting support always
471 c.IPKernelApp.pylab = 'inline' # if you want plotting support always
478
472
479 # Notebook config
473 # Notebook config
480 c.NotebookApp.certfile = u'/absolute/path/to/your/certificate/mycert.pem'
474 c.NotebookApp.certfile = u'/absolute/path/to/your/certificate/mycert.pem'
481 c.NotebookApp.ip = '*'
475 c.NotebookApp.ip = '*'
482 c.NotebookApp.open_browser = False
476 c.NotebookApp.open_browser = False
483 c.NotebookApp.password = u'sha1:bcd259ccf...your hashed password here'
477 c.NotebookApp.password = u'sha1:bcd259ccf...your hashed password here'
484 # It's a good idea to put it on a known, fixed port
478 # It's a good idea to put it on a known, fixed port
485 c.NotebookApp.port = 9999
479 c.NotebookApp.port = 9999
486
480
487 You can then start the notebook and access it later by pointing your browser to
481 You can then start the notebook and access it later by pointing your browser to
488 ``https://your.host.com:9999`` with ``ipython notebook --profile=nbserver``.
482 ``https://your.host.com:9999`` with ``ipython notebook --profile=nbserver``.
489
483
490 Running with a different URL prefix
484 Running with a different URL prefix
491 -----------------------------------
485 -----------------------------------
492
486
493 The notebook dashboard (i.e. the default landing page with an overview
487 The notebook dashboard (i.e. the default landing page with an overview
494 of all your notebooks) typically lives at a URL path of
488 of all your notebooks) typically lives at a URL path of
495 "http://localhost:8888/". If you want to have it, and the rest of the
489 "http://localhost:8888/". If you want to have it, and the rest of the
496 notebook, live under a sub-directory,
490 notebook, live under a sub-directory,
497 e.g. "http://localhost:8888/ipython/", you can do so with
491 e.g. "http://localhost:8888/ipython/", you can do so with
498 configuration options like these (see above for instructions about
492 configuration options like these (see above for instructions about
499 modifying ``ipython_notebook_config.py``)::
493 modifying ``ipython_notebook_config.py``)::
500
494
501 c.NotebookApp.base_project_url = '/ipython/'
495 c.NotebookApp.base_project_url = '/ipython/'
502 c.NotebookApp.base_kernel_url = '/ipython/'
496 c.NotebookApp.base_kernel_url = '/ipython/'
503 c.NotebookApp.webapp_settings = {'static_url_prefix':'/ipython/static/'}
497 c.NotebookApp.webapp_settings = {'static_url_prefix':'/ipython/static/'}
504
498
505 Using a different notebook store
499 Using a different notebook store
506 --------------------------------
500 --------------------------------
507
501
508 By default the notebook server stores notebooks as files in the working
502 By default the notebook server stores notebooks as files in the working
509 directory of the notebook server, also known as the ``notebook_dir``. This
503 directory of the notebook server, also known as the ``notebook_dir``. This
510 logic is implemented in the :class:`FileNotebookManager` class. However, the
504 logic is implemented in the :class:`FileNotebookManager` class. However, the
511 server can be configured to use a different notebook manager class, which can
505 server can be configured to use a different notebook manager class, which can
512 store the notebooks in a different format. Currently, we ship a
506 store the notebooks in a different format. Currently, we ship a
513 :class:`AzureNotebookManager` class that stores notebooks in Azure blob
507 :class:`AzureNotebookManager` class that stores notebooks in Azure blob
514 storage. This can be used by adding the following lines to your
508 storage. This can be used by adding the following lines to your
515 ``ipython_notebook_config.py`` file::
509 ``ipython_notebook_config.py`` file::
516
510
517 c.NotebookApp.notebook_manager_class = 'IPython.html.services.notebooks.azurenbmanager.AzureNotebookManager'
511 c.NotebookApp.notebook_manager_class = 'IPython.html.services.notebooks.azurenbmanager.AzureNotebookManager'
518 c.AzureNotebookManager.account_name = u'paste_your_account_name_here'
512 c.AzureNotebookManager.account_name = u'paste_your_account_name_here'
519 c.AzureNotebookManager.account_key = u'paste_your_account_key_here'
513 c.AzureNotebookManager.account_key = u'paste_your_account_key_here'
520 c.AzureNotebookManager.container = u'notebooks'
514 c.AzureNotebookManager.container = u'notebooks'
521
515
522 In addition to providing your Azure Blob Storage account name and key, you will
516 In addition to providing your Azure Blob Storage account name and key, you will
523 have to provide a container name; you can use multiple containers to organize
517 have to provide a container name; you can use multiple containers to organize
524 your Notebooks.
518 your Notebooks.
525
519
526 .. _notebook_format:
520 .. _notebook_format:
527
521
528 The notebook format
522 Notebook JSON format
529 ===================
523 ====================
530
524
531 The notebooks themselves are JSON files with an ``ipynb`` extension, formatted
525 Notebooks are JSON files with an ``.ipynb`` extension, formatted
532 as legibly as possible with minimal extra indentation and cell content broken
526 as legibly as possible with minimal extra indentation and cell content broken
533 across lines to make them reasonably friendly to use in version-control
527 across lines to make them reasonably friendly to use in version-control
534 workflows. You should be very careful if you ever edit manually this JSON
528 workflows. You should be very careful if you ever manually edit this JSON
535 data, as it is extremely easy to corrupt its internal structure and make the
529 data, as it is extremely easy to corrupt its internal structure and make the
536 file impossible to load. In general, you should consider the notebook as a
530 file impossible to load. In general, you should consider the notebook as a
537 file meant only to be edited by IPython itself, not for hand-editing.
531 file meant only to be edited by the IPython Notebook app itself, not for hand-editing.
538
532
539 .. note::
533 .. note::
540
534
541 Binary data such as figures are directly saved in the JSON file. This
535 Binary data such as figures are directly saved in the JSON file. This
542 provides convenient single-file portability but means the files can be
536 provides convenient single-file portability, but means that the files can
543 large and diffs of binary data aren't very meaningful. Since the binary
537 be large; ``diff``s of binary data also are not very meaningful. Since the
544 blobs are encoded in a single line they only affect one line of the diff
538 binary blobs are encoded in a single line, they affect only one line of
545 output, but they are typically very long lines. You can use the
539 the ``diff`` output, but they are typically very long lines. You can use the ``Cell -> All Output -> Clear`` menu option to remove all output from a notebook prior to committing it to version control, if this is a concern.
546 'ClearAll' button to remove all output from a notebook prior to
540
547 committing it to version control, if this is a concern.
541 The notebook server can also generate a pure Python version of your notebook,
548
542 using the ``File -> Download as`` menu option. The resulting ``.py`` file will
549 The notebook server can also generate a pure-python version of your notebook,
543 contain all the code cells from your notebook verbatim, and all text cells
550 by clicking on the 'Download' button and selecting ``py`` as the format. This
544 prepended with a comment marker. The separation between code and text
551 file will contain all the code cells from your notebook verbatim, and all text
552 cells prepended with a comment marker. The separation between code and text
553 cells is indicated with special comments and there is a header indicating the
545 cells is indicated with special comments and there is a header indicating the
554 format version. All output is stripped out when exporting to python.
546 format version. All output is stripped out when exporting to Python.
555
547
556 Here is an example of a simple notebook with one text cell and one code input
548 Here is an example of the Python output from a simple notebook with one text cell and one code input cell::
557 cell, when exported to python format::
558
549
559 # <nbformat>2</nbformat>
550 # <nbformat>2</nbformat>
560
551
561 # <markdowncell>
552 # <markdowncell>
562
553
563 # A text cell
554 # A text cell
564
555
565 # <codecell>
556 # <codecell>
566
557
567 print "hello IPython"
558 print "Hello, IPython!"
568
559
569
560
570 Known issues
561 Known issues
571 ============
562 ============
572
563
573 When behind a proxy, especially if your system or browser is set to autodetect
564 When behind a proxy, especially if your system or browser is set to autodetect
574 the proxy, the html notebook might fail to connect to the server's websockets,
565 the proxy, the Notebook app might fail to connect to the server's websockets,
575 and present you with a warning at startup. In this case, you need to configure
566 and present you with a warning at startup. In this case, you need to configure
576 your system not to use the proxy for the server's address.
567 your system not to use the proxy for the server's address.
577
568
578 In Firefox, for example, go to the Preferences panel, Advanced section,
569 In Firefox, for example, go to the Preferences panel, Advanced section,
579 Network tab, click 'Settings...', and add the address of the notebook server
570 Network tab, click 'Settings...', and add the address of the notebook server
580 to the 'No proxy for' field.
571 to the 'No proxy for' field.
581
572
582
573
583 .. _Markdown: http://daringfireball.net/projects/markdown/basics
574 .. _Markdown: http://daringfireball.net/projects/markdown/basics
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