I can't work out how to get the %edit command working in Jupyter Notebook.
I type
%edit
and it returns with
IPython will make a temporary file named: /var/folders/dk/.../ipython_edit_JbS9ZC.py
My %EDITOR environment variable is
'EDITOR': '/usr/local/bin/subl -w'
I must be doing something wrong.
This feature issue appears to be well-known : https://github.com/ipython/ipython/issues/5879
A possible solution might be to use : Edit IPython cell in an external editor
Or you can embed the notebook in emacs (I don't use emacs) : https://github.com/tkf/emacs-ipython-notebook
Related
I try using a very light-weighted editor BowPad to edit and run codes.
Take running R as an example, which has been added to Windows PATH Environment Variable D:\R\R-3.6.2\bin\x64
I try to take some following steps:
I built a test.r writing some testing line codes as 1+2; plot(1:10)
Menu --> Run --> Configure custom commands
Command Name: run R
Command Line: D:\R\R-3.6.2\bin\R.exe $(SEL_TEXT)
$(LINE) The line where the cursor is
$(POS) the position where the cursor is
$(TAB_PATH) the path to the file of the active tab
$(TAB_NAME) the file name without extension of the current tab
$(TAB_EXT) the file extension of the current tab
$(TAB_DIR) the directory of the file of the active tab
$(SEL_TEXT) the selected text or the word at the cursor position
$(SEL_TEXT_ESCAPED) like $(SEL_TEXT) but escaped, useful for urls
When I press to choose run R to run the code, something wrong happens!
It will open a Rterm(64-bit) window each time when I run R!
it shows RGUMENT '1+2' __ignored__ or ARGUMENT 'plot(1:10)' __ignored__
Did I missing something ? BTW, can we set some shortcuts keys for running Python, R, Octave or Julia?
Also, when I reach the homepage of BowPad for more information, little usage of this software can be found!
R.exe refers to Rterm. You can use Rgui.exe instead but that won't automatically process arguments. I think what you likely want is to send the selected text to a running R session rather than starting up a new R session each time.
To do that
download this file and optionally place it on your path https://raw.githubusercontent.com/ggrothendieck/batchfiles/master/clip2r.js
in the Bowpad Run | Configure window configure a Run R command as the following (or if clip2r.js is not on your path use the entire pathname). It should be just like this with no arguments.
clip2r.js
From the Windows cmd line if Rgui is running we see that tasklist | findstr Rgui finds Rgui as the R gui process and you can create additional js scripts by editing clip2r.js replacing Rgui in the js script with whatever is the appropriate word to locate python, julia, octave or other R front end assuming again that they are running.
Now to invoke it from within Bowpad:
ensure that your Rgui session is already running and
from within Bowpad select the code you want to run and copy it to the clipboard and then invoke Run R. For example, to run everything use ctrl A ctrl C ctrl R 0 assuming that Run R is in position 0 in the configure menu. Alternately use the mouse with the Ribbon.
Regarding the comment about difficulty finding help, it looks like Bowpad is based on Scintilla so the documentation for it and the related SciTE editor likely apply to Bowpad too. You can also check the Bowpad source code on github.
I want to hide certain parts of a jupyter notebook and came across tags which can achieve this. I've tagged the cells with remove_cell in my notebook an tried to run
$ jupyter nbconvert test.ipynb --TagRemovePreprocessor.remove_input_tags="{'remove_cell'}"
however I always get the following error:
traitlets.traitlets.TraitError: The 'remove_input_tags' trait of a TagRemovePreprocessor instance must be a set, but a value of type 'unicode' (i.e. u'{remove_cell}') was specified.
I've tried to change the "{'remove_cell'}" to various format, e.g. {'remove_cell'} etc with the same result. Any help would be appreciated
According to nbconvert documentation it must be done as you have specified. But there seems to be some bug in command line parsing traitlets API, used internally by jupyter nbconvert. So i tried a slightly different approach of specifying Configuration in jupyter_nbconvert_config.py file.
Steps:
jupyter nbconvert --generate-config
This will generate default ~/.jupyter/jupyter_nbconvert_config.py.
Edit the configuration file and specify your configuration, in this case
c.TagRemovePreprocessor.remove_input_tags = set(['remove_cell'])
Run jupyter nbconvert test.ipynb This will remove the tagged cells and convert it to default HTML page.
I got this to work without editing the config file by using square brackets, which match the format of the tag in the cell metadata, instead of curly braces.
So, in my cell metadata I have this:
{
"tags": ["remove_cell"]
}
and on the command line I used:
jupyter nbconvert test.ipynb --TagRemovePreprocessor.remove_input_tags="['remove_cell']"
which successfully removed any cells with this tag from the HTML output.
nbconvert did not hide the cells with tags while also executing the notebook, and this is the most useful example I found here https://github.com/jupyter/nbconvert/issues/1300:
So the underlying issue is that the preprocessors being added on your behalf are un-ordered, so by unlikely chance the --execute turning on the ExecutePreprocessor is getting applied after the TagRemovePreprocessor. To fix this you can set the preprocessors to use in an explicit order by doing:
jupyter nbconvert notebooks/demo_notebook.ipynb \
--TagRemovePreprocessor.remove_input_tags='{"remove-input"}' \
--TagRemovePreprocessor.remove_all_outputs_tags='{"remove-output"}' \
--Exporter.preprocessors='["nbconvert.preprocessors.ExecutePreprocessor","nbconvert.preprocessors.TagRemovePreprocessor"]' \
--to notebook
This has been an ongoing issue for me, as I would love to use Jupyter Notebook to write my research reports, but have found it very difficult to export my Jupyter Notebooks to PDF without code and without large formatting errors.
I am able to download the notebooks as PDF, but have not found a way to hide the code, or have the PDF resemble the formatting of the notebook.
No solution I've found on SO has been sufficient for my issue, so it may be possible that this is not the intended functionality of Jupyter Notebook.
Have you tried this:
jupyter nbconvert path/to/your/ipynb --to=pdf --TemplateExporter.exclude_input=True
For more on the flags, you can refer to nbconvert config options
I have successfully converted .ipynb to .html exclude the code blocks
I followed the suggestion by 0xffff above but the PDF output did not behave as intended (code blocks were still included).
However, their suggestion inspired me to try converting to html first using the following call:
jupyter nbconvert path/to/your/ipynb --to=html --TemplateExporter.exclude_input=True
This behaved as intended, and from there, it was straightforward to print the output to PDF in a browser.
Regarding the issue with the --to=pdf flag, I've opened up an issue on the Jupyter Notebook git repo: https://github.com/jupyter/notebook/issues/3804. Will report back once I get a response.
nbconvert
nbconvert is an official package, and other answers have mentioned it. However, they did not mention there are two ways to convert to PDF.
The default option uses LaTeX, and it's often a pain to install:
jupyter nbconvert notebook.ipynb --to=pdf
A newer option is to use the webpdf converter, this does not require LaTeX
jupyter nbconvert notebook.ipynb --to=webpdf
Quarto
Quarto is the newest option. The defaults are prettier than nbconvert, and it has advanced features to customize the output PDF. However, it uses pandoc (and pandoc uses LaTeX), so you must install both first.
quarto render notebook.ipynb --to pdf
Quarto is a new project, and I often run into problems (I couldn't convert the sample notebook); however, the project is in active development and I'm sure it will get better.
Online converters
The last option is to use one of the many online services. The two main caveats are 1) You might not want to upload your notebooks to some random website, and 2) It's often unclear what engine they use to convert the notebooks. I've tried many of them with mostly negative results.
I created one online converter that uses nbconvert and deletes your notebook as soon as it's converted.
If you manually create the PDF, there is a simpler solution: add the following code block & execute it
from IPython.core.display import HTML
HTML('<style>.input, .jp-InputArea {display: none !important}</style>')
Code will disappear both in the "normal" UI and in print preview / export to HTML. Open print preview, generate the PDF - it looks great now, clear the output of this one cell to bring the code back, done
How can I select matching keywords in a Jupyter notebook via a keyboard shortcut? For example, in the Atom/Sublime editor I can hit cmd + D on a mac (or Ctrl + d on Windows) while the cursor is over 'var' and each time I do that the next 'var' will be highlighted. I can then type the new variable name and 'var' is replaced with whatever I typed.
var = "hello"
print(var)
print(var)
Is there an equivalent in a Jupyter notebook?
Add custom.js to
C:\Users\username\.jupyter\custom # for Windows and
~/.jupyter/custom/ # for Mac
with content
require(["codemirror/keymap/sublime", "notebook/js/cell", "base/js/namespace"],
function(sublime_keymap, cell, IPython) {
cell.Cell.options_default.cm_config.keyMap = 'sublime';
cell.Cell.options_default.cm_config.extraKeys["Ctrl-Enter"] = function(cm) {}
var cells = IPython.notebook.get_cells();
for(var cl=0; cl< cells.length ; cl++){
cells[cl].code_mirror.setOption('keyMap', 'sublime');
cells[cl].code_mirror.setOption("extraKeys", {
"Ctrl-Enter": function(cm) {}
});
}
}
);
and restart jupyter. Now Ctrl+D should work like it does in Sublime.
You can see that Ctrl-Enter functionality is disabled as it would be very convenient to run current cell rather than creating new line for most users. You can choose to have that functionality by commenting that line out.
You can disable other key config that you don't want in a similar way.
Most recent (and easy) way
The best way right now to achieve Sublime-like keymapping in Jupyter Notebook: Select CodeMirror Keymap from jupyter-contrib-nbextensions. As reported in the homepage:
The jupyter_contrib_nbextensions package contains a collection of community-contributed unofficial extensions that add functionality to the Jupyter notebook.
I personally use several extensions from this package and I find them very useful.
As reported in the installation docs, you simply need to run:
pip install jupyter_contrib_nbextensions
to install the extensions (or better, I would suggest:
python -m pip install jupyter_contrib_nbextensions
where python points to the python executable of the installation you are using within Jupyter Notebook). You can also use conda if you prefer.
Anyway, you then need to copy some JS and CSS stuff to make the extensions work within Jupyter Notebook, which you can achieve through:
jupyter contrib nbextension install --user
again, assuming that jupyter points to the jupyter executable you are using to run your notebooks.
At this point, you simply need to enable the extension: navigate the nbextensions_configurator (that comes as a dependency with the jupyter_contrib_nbextensions package), which you can easily do through the Jupyter Notebook dashboard (to be clear, the page you open to run your notebooks) by browsing the Nbextensions tab and check the box corresponding to Select CodeMirror Keymap.
Done! Launching a notebook it will be sufficient to click on Edit>Keymaps>Sublime to achieve the desired behaviour.
I know this is a rather old question, but I happened to come across it before finding out about jupyter_contrib_nbextensions (and in particular the Select CodeMirror Keymap extension). Thus, I decided to post this answer, hopefully to help other people like me and to let them avoid some further search or messing up with customized JS files (which could scary someone).
In jupyter lab now you can add in the extension by searching sublime
Click install and rebuild jupyter.
**Notice: when you click install look at the terminal console, the building result will be shown there
The above solution worked for me, but I found that it had the undesirable effect of entering a "tab" character when I hit enter. Here is the associated GitHub issue: https://github.com/jupyter/notebook/issues/4769#issuecomment-511935127
Per that post, I found that this solution gives the right ctrl + d behavior, and keeps tabs-as-spaces.
require(["codemirror/keymap/sublime", "notebook/js/cell", "base/js/namespace"],
function(sublime_keymap, cell, IPython) {
// setTimeout(function(){ // uncomment line to fake race-condition
cell.Cell.options_default.cm_config.keyMap = 'sublime';
var cells = IPython.notebook.get_cells();
for(var c=0; c< cells.length ; c++){
cells[c].code_mirror.setOption('keyMap', 'sublime');
}
// }, 1000)// uncomment line to fake race condition
}
);
In Jupyter Lab, this can now be set in Settings > Text Editor Key Map > Sublime Text.
The only solution which made this work for me is
pip install jupyterlab_sublime
How do I run %%magic in R inside Jupyter?
%%javascript
IPython.OutputArea.auto_scroll_threshold = 99999;
The auto scroll feature on longer output is vastly annoying as I have several functions and scripts that spit out a lot of output.
The above Javascript works fine in python notebooks but not in R notebooks.
When I run the %% magic command in R, it barfs:
Error in parse(text = x, srcfile = src): <text>:1:1: unexpected SPECIAL
1: %%
Any suggestions?
According to this post disable_autoscroll.py, it may be possible to put that Javascript into a profile_dir/static/js/custom.js file. Pray tell, where is the profile_dir on a Windows box?
I found: c:/Anaconda2/Lib/site-packages/notebook/static/custom/custom.js but that is the central custom.js file.
References:
Auto-scrolling of long output should be configurable in the UI
In my anaconda install of the notebook, the custom.js file is in %USERPROFILE%\.jupyter\custom\custom.js.
For the "magics": magics are a thing of the python kernel, not the notebook. The R kernel does not implement a magic system and so these don't work. As mentioned above, use IRdisplay::display_javascript('IPython.OutputArea.auto_scroll_threshold = 99999;') for your usecase.