I have a notebook script that I run on different datasets. I want to save the script, INCLUDING the output cells, in the data folder each time I run it.
I have the following command placed at the end of my script that I run in jupyter. I intend to save pretty much what I can see on the screen to a HTML file.
"here is my notebook script with inputs and ouput including graphs"
cmd='jupyter nbconvert --to html odnp_postprocessing.ipynb --output-dir '+dataFolder
os.system(cmd)
However, nbconvert does not export the actual cells. It will print out only the input cell without ouput the first time I run, but if I re-run, it will finally export both input and output. However then if I change something in the script, it will always export the first version. Then the only way around I found is to restart the kernel and re-run (twice) the new script with the modification.
Basically, it looks like nbconvert exports some kind of buffer that is not necesseraly the actual input and ouput cells that the user sees.
What I want to do, which is programmatically saved my notebook (inputs and ouputs) into HTML, each time I run it.
Is there a command to save the current version of the notebook? I tried to add %notebook before nbconvert command but a whole bunch of old inputs are saved as well.
I know I can run the notebook within nbconvert, but I'd like to avoid it as I already run it manually in jupyter.
Any idea?
I'm using jupyter through enthought canopy in Chrome browser.
Thanks
You're not telling us exactly how you are running nbconvert; from the current notebook ? Thus it is hard to figured things out.
Nbconvert converts the current file as it is on disk; as a wild guess: you haven't save your file. If you do not save your file then nbconvert will likely not have access to the outputs of cells; and wild guess again when you run it a second time autosave have kicked in.
Remember: - Nbconvert does not execute the file - Nbconvert is a separate process it can't magically access what is in your browser, which is potentially a different machine.
Usually think of it this way:
If you are using this command at the end of a notebook to save it in another format, then what you are looking for are save hooks that will trigger some code – server-side – every time you save a notebook.
Side note, learn about how to run shell command in IPython; ! can be used to execute shell command in CWD and does variable interpolation.