I know folk who are major contributors to the Jupyter ecosystem and they seem incredibly open and enthusiastic towards implementing whatever the scientists need to make it more usable. At the time, I was a few weeks away from submitting my thesis, and so was spending a lot of time re-running my various codes and plotting the results. Indeed, the online interactive textbook for another Berkeley course, DS — Principles and Techniques of Data Science [ repo ] — uses both both Gitbook and nbinteract , so the setup guide may be worth a look…. Notify me of new posts via email. The notebook is generating the figures with a consistent style, as well as the bib keys list. Plots for the same dataset can be generated in the same document, making it easier to explore the data and find the best way to present it. The name of each notebook roughly gives the topic or question the plots were made to address, prefixed with the date when the notebook was most recently overhauled.
From the textbook repo, it looks as if the recipe could quite easily be separated from the actual book. Being able to see the resulting figure right next to the code that generates it is incredibly useful for this. Another possible approach would be to use a gitbook workflow. You are commenting using your Google account. Here is how it works. I do all my writing in Sublime Text , boosted with a couple of packages. View all posts by Tony Hirst.
I believe they have much potential to turn into a tool that could in the not so distant future rival standard IDEs.
Of particular interest in this case: The suggested use for these notebooks is that you scan through some until you find a plot whose format you want to use, then look back within that notebook to see how it was programed. Monday, April 20, 6: CSL file for the bibliography styles you want to use.
Fragment: From Jupyter Notebooks to Online Interactive Textbooks
The Jupyter notebook generates the figures and saves them in a folder. This workflow was particularly suitable for this paper, since all the data analysis was done in the Jupyter notebook and there were many citations in particular for each plots that I did not wanted to input manually.
You can build from the command line. I never tried, though. Post was not sent – check your email addresses!
Writing academic papers in plain text with Markdown and Jupyter notebook
I was instantly won over by the fact that I could have multiple panes open in a single window, and so no longer needed to have ioython tabs open on my browser in order to run multiple notebooks. Especially when generating plots for my thesis, I often wanted to rerun the same plotting script many times with small tweaks until I got the figure that I wanted.
Ice templating has been applied to all classes of materials, but particularly ceramics over the past 15 years. As I run the notebook, the figures are generated and saved in a folder.
Fragment: From Jupyter Notebooks to Online Interactive Textbooks – , the blog…
These cells can then be run individually and not necessarily in sequence. As mentioned above, I often have multiple notebooks open at once. I also saved the pandoc command line argument as a text file in the folder where the markdown file is, so that I do not depend on Sublime Text in case I change my mind, and do not have to remember the exact command line to type lazy, I told you. Another possible approach would be to use a gitbook workflow. This mix of code noteboko and rich text make them much more human-readable than source code alone: From the textbook repo, it looks as if the recipe could quite easily be separated from the actual book.
I am not sure how you managed to do with the YAML at the beginning. The main selling points for me were the following:. As discussed above, the real advantage is that Authorea articles are web-native and data-driven.
Filed nottebook software engineering. I do all my writing in Sublime Textboosted with a couple of packages. I am not a physicist, so my papers are usually light in terms of maths. Pandoc takes the paper.
Plotting my thesis with Jupyter | Alice Harpole
All the analysis was done in a Jupyter notebook, that I nottebook later on FigShare when the paper was published. A Masters thesis about nbinteract is available here: Ipythoh Facebook More Email. May 12, at 3: Essentially, I’m just wondering if anyone out there has figured out a good way or even a not-so-good way that at least works to include Jupyter notebooks as pages in large LaTeX documents.
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In that case, I wrote almost everything. I updated the CSV file with the new data plots, ran the notebook, and the figures were instantaneously updated.