PyCharm modifying every notebook in repo.

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Brett Zibilich
Created

I do not use pycharm to work with notebooks and have never opened these notebooks in PyCharm.

We have hundreds stored in a repo along with other non-Jupyter python. Pycharm continually modifies notebooks by either replacing /u001b with /u001B or adding lines tot he end of the file.

How do I disable this? Or tell pycharm to leave notebooks alone altogether? It's incredibly annoying. The only other option will be to revert to an older version.

This behavior did not happen before 2022.3.2 for me.

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Daniil Bogdanov
Created
Hi,

If you are not using PyCharm to edit Jupyter notebooks, you can exclude them from PyCharm. To do so, please navigate Settings | Editor | File Types, Ignored Files and Folders tab and add the .ipynb extension to the list.

Also, please take screenshots of unexpected additions/edits from PyCharm so I can fill out a bug report.
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Javlopez
Created

We are also seeing this with `2022.3.2`. Is there an existing bug for me to comment on?

1
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Daniil Bogdanov
Created
There are existing threads regarding Jupyter notebooks, but an example is needed to distinguish the correct one. The best option is to take screenshots of the diffs in Git with the PyCharm edits.
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Javlopez
Created

Can I email an example to you? These are internal company files that I’d rather not post publicly.

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Javlopez
Created

Here's an example

 

diff --git a/lab/notebook.ipynb b/lab/notebook.ipynb
index 6807255dcf..d735e2e134 100644
--- a/lab/notebook.ipynb
+++ b/lab/notebook.ipynb
@@ -12,14 +12,14 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "── \u001b[1mAttaching packages\u001b[22m ─────────────────────────────────────── tidyverse 1.3.2 ──\n",
-      "\u001b[32m✔\u001b[39m \u001b[34mggplot2\u001b[39m 3.4.0      \u001b[32m✔\u001b[39m \u001b[34mpurrr  \u001b[39m 1.0.1 \n",
-      "\u001b[32m✔\u001b[39m \u001b[34mtibble \u001b[39m 3.1.8      \u001b[32m✔\u001b[39m \u001b[34mdplyr  \u001b[39m 1.0.10\n",
-      "\u001b[32m✔\u001b[39m \u001b[34mtidyr  \u001b[39m 1.2.1      \u001b[32m✔\u001b[39m \u001b[34mstringr\u001b[39m 1.5.0 \n",
-      "\u001b[32m✔\u001b[39m \u001b[34mreadr  \u001b[39m 2.1.3      \u001b[32m✔\u001b[39m \u001b[34mforcats\u001b[39m 0.5.2 \n",
-      "── \u001b[1mConflicts\u001b[22m ────────────────────────────────────────── tidyverse_conflicts() ──\n",
-      "\u001b[31m✖\u001b[39m \u001b[34mdplyr\u001b[39m::\u001b[32mfilter()\u001b[39m masks \u001b[34mstats\u001b[39m::filter()\n",
-      "\u001b[31m✖\u001b[39m \u001b[34mdplyr\u001b[39m::\u001b[32mlag()\u001b[39m    masks \u001b[34mstats\u001b[39m::lag()\n"
+      "── \u001B[1mAttaching packages\u001B[22m ─────────────────────────────────────── tidyverse 1.3.2 ──\n",
+      "\u001B[32m✔\u001B[39m \u001B[34mggplot2\u001B[39m 3.4.0      \u001B[32m✔\u001B[39m \u001B[34mpurrr  \u001B[39m 1.0.1 \n",
+      "\u001B[32m✔\u001B[39m \u001B[34mtibble \u001B[39m 3.1.8      \u001B[32m✔\u001B[39m \u001B[34mdplyr  \u001B[39m 1.0.10\n",
+      "\u001B[32m✔\u001B[39m \u001B[34mtidyr  \u001B[39m 1.2.1      \u001B[32m✔\u001B[39m \u001B[34mstringr\u001B[39m 1.5.0 \n",
+      "\u001B[32m✔\u001B[39m \u001B[34mreadr  \u001B[39m 2.1.3      \u001B[32m✔\u001B[39m \u001B[34mforcats\u001B[39m 0.5.2 \n",
+      "── \u001B[1mConflicts\u001B[22m ────────────────────────────────────────── tidyverse_conflicts() ──\n",
+      "\u001B[31m✖\u001B[39m \u001B[34mdplyr\u001B[39m::\u001B[32mfilter()\u001B[39m masks \u001B[34mstats\u001B[39m::filter()\n",
+      "\u001B[31m✖\u001B[39m \u001B[34mdplyr\u001B[39m::\u001B[32mlag()\u001B[39m    masks \u001B[34mstats\u001B[39m::lag()\n"
      ]
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Brett Zibilich
Created

Unfortunately I'm in a similar situation where a screenshot would be contrary to company policy.

I can say that Javlopez's example is exactly what I'm seeing too. Your answer on how to exclude Jupyter notebooks works for me; I think most of our Jupyter users use the browser UI, but I'll suggest holding off on them updating for now.

 

Thank you for the reply Daniil!

 

 

1
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Jon L
Created

Also happening for me on 2022.3.2. I excluded .ipynb but it's still occurring.

0
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Daniil Bogdanov
Created

Hello there, 

I've reproduced the issue; here is a related thread on Youtrack. Please vote for it to raise its relevance and receive updates.

1
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Jieliu
Created

I tried the workaround but it does not work at all. This severally hurts my work progress. Where is the instruction for reverting back to the previous version? 

0
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Tomerbd1
Created

After full download and install from 2022.3.2 back to 2022.3.1 then this workaround fixed.  Just searched for this intellij version and did full install.

2
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Jieliu
Created

I switched to the community edition and the issue is gone now. 

0
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Nimish
Created

This is happening again with 24.1.1

5
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Javlopez
Created

Yup seeing it with `2024.1.1`

2
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Nimish
Created

Is there a workaround here? it's making PyCharm nearly unusable.

3
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Willie
Created

I have had this problem for a while too.  I keep getting the following popup in my browser:

I tried the solution above suggested by daniil and it did stop PyCharm from updating my Jupyter notebooks.  The only thing I don't like about the solution is now when I do ctrl+shift+F in PyCharm, the notebooks in my project aren't included in the search.  This makes sense I suppose, however, I have lots of notebooks and I use the “find in files…” search quite regularly.

So instead of adding the *.ipynb extension to the “Ignored Files and Folders” tab, I just removed the *.ipynb extension from the Jupyter notebooks entry under the first tab, “Recognized File Types”.  If all your notebooks lose their cute little orange icon, you'll know you did it right.

Now my Jupyter notebooks are included in searches and PyCharm isn't trying to update my notebooks in the background.  Win, Win.

Hope this helps

[PyCharm version: 2024.1.1]

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Nimish
Created

Still happening with 2024.1.2

6
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Yotamcons
Created

I find myself adding `git checkout @ -- notebooks/*.ipynb` before every commit :/
it seems pycharm is somehow examening the notebooks in the background, and thus the output fields change… 
 

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