mkery / verdant Goto Github PK

JupyterLab v3 seems to be required to run Verdant. It might be nice to update README.md and link to how to install JupyterLab v3: https://blog.jupyter.org/jupyterlab-3-0-is-out-4f58385e25bb

Right now, assuming the cells are in the same position and, even with internal changes, are still the same cell. Need to drop that assumption.

Without the exact spacing the user had, it's messing up diff placement

All AST-based matching, extract out to a python-based API, so that all operations work as well and as stable as possible with and without it.

This extension looks amazing. However, it does not appear to be compatible with the latest versions of Jupyter Lab - I am getting the following errors when trying to install:

Conflicting Dependencies:
JupyterLab              Extension       Package
>=3.1.12 <3.2.0         >=3.0.0 <3.1.0  @jupyterlab/application
>=3.1.12 <3.2.0         >=3.0.0 <3.1.0  @jupyterlab/apputils
>=3.1.12 <3.2.0         >=3.0.0 <3.1.0  @jupyterlab/codemirror
>=3.1.12 <3.2.0         >=3.0.0 <3.1.0  @jupyterlab/docmanager
>=3.1.12 <3.2.0         >=3.0.0 <3.1.0  @jupyterlab/notebook
>=3.1.12 <3.2.0         >=3.0.0 <3.1.0  @jupyterlab/rendermime

Please upgrade this extension to be compatible with the latest version of Jupyter Lab. It would also be great it this could be installed via pip instead of relying on "jupyter labextension install".

Thanks!

Working on filters for the search tab

String is one, maybe others?
Note sometimes this is not completely a problem because the user is just writing code that does not compile yet since it's not valid python yet. But we still need to know whats there even if we can't parse it!!!!

When I try $ yarn build.
It just returns
yarn run v1.22.4
error Couldn't find a package.json file in "/Users/[username]"
info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command.

So do I need to git clone the whole project first?

Model keeps reinitializing itself on notebooks it has already loaded

@mkery In case you haven't seen this Nature post yet, there's a nice mention about Verdant. Here's the link: https://www.nature.com/articles/d41586-018-07196-1 second to last paragraph. 😄

Hi!

Your extension is amazing and extremely useful!
Could you please make it work on jupyter 2.x?

Thanks a million!

Hello, I would like to try this promising extension, but its installation fails with conflicting dependencies, such as here under Ubuntu 18

yarn start
yarn run v1.22.5
$ jupyter labextension install . && jupyter lab .
An error occured.
ValueError:
"[email protected]" is not compatible with the current JupyterLab
Conflicting Dependencies:
JupyterLab Extension Package

=3.0.2 <3.1.0 >=2.1.0 <3.0.0 @jupyterlab/application
=3.0.2 <3.1.0 >=2.1.0 <3.0.0 @jupyterlab/apputils
=3.0.2 <3.1.0 >=2.1.0 <3.0.0 @jupyterlab/codemirror
=5.0.1 <5.1.0 >=4.1.0 <5.0.0 @jupyterlab/coreutils
=3.0.2 <3.1.0 >=2.1.0 <3.0.0 @jupyterlab/docmanager
=3.0.2 <3.1.0 >=2.1.0 <2.2.0 @jupyterlab/notebook
=3.0.2 <3.1.0 >=2.1.0 <3.0.0 @jupyterlab/rendermime
=6.0.2 <6.1.0 >=5.1.0 <6.0.0 @jupyterlab/services
=17.0.1 <18.0.0 >=16.9.0 <16.10.0react
=17.0.1 <18.0.0 >=16.9.0 <16.10.0react-dom
See the log file for details: /tmp/jupyterlab-debug-3g59dvsp.log
error Command failed with exit code 1.

I tried it on Mac as well, same problem. Do you probably have a solution or could help me with installing the right versions? Thanks a lot, Doron

get inspector highlighting to work in both current notebook and ghost notebook

TODO

re-address storage. now store is modularized out, which is good. how can we improve performance so that it's not all in memory all the time

If a code cell contains the symbols """ (triple quote sign) or an escape character like \n inside of a string or comment then the parser throws an error. Have tried encoding string to utf-8 to avoid this but no luck so far.

• Start by decoupling the views from lilgit
• give each its own package

Need to write logic for those

fix parser so it's a server extension and not the hacky kernel thing it is now

From the paper, need to have

Need to check out py2ast.py to figure out how to avoid this problem. The ast provided by python has a start location for each node, but not an end location, making this tricky.

waiting on reliable method to do this, besides (hacky?) comparing timestamps

To make sure any new matches to the search query appear

Hello, thanks for the interesting package!

I was looking to try it out, but am having trouble with install, apparently due to versioning issues. Any chance you could provide assistance? Here are the full commands to reproduce from a clean conda environment:

conda create --name=verdant python=3 jupyterlab
conda activate verdant
git clone https://github.com/mkery/Verdant.git
cd Verdant/
pip install lilgit-parser
jupyter serverextension enable --py lilgit_parser
jupyter serverextension list
npm install
npm run build
jupyter labextension link .

At this point it dies with the following error:

$ jupyter labextension link .
An error occured.
ValueError: 
"[email protected]" is not compatible with the current JupyterLab
Conflicting Dependencies:
JupyterLab              Extension      Package
>=1.1.3 <1.2.0          >=0.19.1 <0.20.0@jupyterlab/application
>=1.1.3 <1.2.0          >=0.19.1 <0.20.0@jupyterlab/apputils
>=3.1.0 <3.2.0          >=2.2.1 <3.0.0 @jupyterlab/coreutils
>=1.1.3 <1.2.0          >=0.19.1 <0.20.0@jupyterlab/docmanager
>=1.1.3 <1.2.0          >=0.19.1 <0.20.0@jupyterlab/notebook
>=1.1.3 <1.2.0          >=0.19.1 <0.20.0@jupyterlab/rendermime
>=4.1.1 <4.2.0          >=3.2.1 <4.0.0 @jupyterlab/services
See the log file for details:  /var/folders/n9/8zbz_v_14ys5cdmn0vy0b9_w0000gn/T/jupyterlab-debug-qcke3yko.log

Looking in packages.json, it seems that a specific version for JupyterLab is specified, but I wasn't able to figure out how to install the specific version (the version numbers are different for different parts of the package, and it's not even possible to install 0.19.1 from pip at the moment). Would it be possible to get some directions about what to do to get this working? Thanks!

To reproduce:
open a ghost book
close it
open a different ghost book from the verdant checkpoint panel

• acknowledgments
• add links to papers
• show screenshot previews
• install instructions
• contributing guide