Add cell type annotation GUI to ChatGSE platform

[slobentanzer]

Here's the repo: https://github.com/biocypher/ChatGSE

[RM7]

Hey Sebastian,

i tried the chatGSE and i like the idea. So i added it to our project and tried my first experiments with text2term and chatGSE.

But at the moment the is one problem. We need to add text2term to the poetry enviroment. But the versions of the libaries text2term and chatGSE depend on are different. Because we can not change the libaries of text2term we need to change the libaries of chatGSE.

Here is the output of my try:

poetry add text2term
Using version ^2.3.2 for text2term

Updating dependencies
Resolving dependencies...

The current project's Python requirement (>=3.10,<4.0) is not compatible with some of the required packages Python requirement:

• scipy requires Python <3.12,>=3.8, so it will not be satisfied for Python >=3.12,<4.0

Because no versions of text2term match >2.3.2,<3.0.0
and text2term (2.3.2) depends on scipy (1.10.1), text2term (>=2.3.2,<3.0.0) requires scipy (1.10.1).
So, because scipy (1.10.1) requires Python <3.12,>=3.8
and chatgse depends on text2term (^2.3.2), version solving failed.

• Check your dependencies Python requirement: The Python requirement can be specified via the python or markers properties

For scipy, a possible solution would be to set the `python` property to ">=3.10,<3.12"

https://python-poetry.org/docs/dependency-specification/#python-restricted-dependencies,
https://python-poetry.org/docs/dependency-specification/#using-environment-markers

Am we allowed to change it and should we try it?

[slobentanzer]

You can try out anything on a fork of the repo, for that you don't need permissions.

However, I would first look into whether this error is actually legit. From what I see, it does not make sense:

scipy requires Python <3.12,>=3.8, so it will not be satisfied for Python >=3.12,<4.0

None of the packages in ChatGSE should require Python >=3.12. We require 3.10 at least, but that should be fine with text2term. Maybe you can try to figure out what the actual problem there is.

[RM7]

I found the problem.
The Problem is that in your pyproject.toml file you have specified the python version ^3.10. This indicates that the version can be between >=3.10 <4.0. But scipy can only work with python versions between >=3.8 <3.12.

For scipy the range is to big and because of this we are getting the error.
When you specify the version in the .toml file in the range of scipy the error goes away.

So now it is working.

[slobentanzer]

Good that it's working, but I still don't understand the issue.

But scipy can only work with python versions between >=3.8 <3.12.

3.10 is >=3.8, <3.12. I don't get it.

[slobentanzer]

When you specify the version in the .toml file in the range of scipy the error goes away.

What exactly did you change?

[RM7]

I don't understand the issue, too. But according to the internet such prolems appear sometimes.

In the pyproject.toml I changed the version from:

[tool.poetry.dependencies]
python = "^3.10

to:

python = ">=3.10, <3.12"

[slobentanzer]

great. can you file a pull request?

[RM7]

Additionally I added text2term to poetry. This added some points to the poetry.lock file.

I pushed it to the repository. How do I file a pull request.
I did not work with github that much before

[slobentanzer]

I don't understand, which repository did you push it to? You can look these things up, you know? GitHub issues are not the place to discuss basic usage. It takes 5 minutes of googling...

[RM7]

I pushed it to the sc2sc repository under the folder ChatGSE-main. It contains a full copy of the ChatGSE Project.

According to the pull request I have to go now. So I will do it later.

[simonmoedinger]

Hei Sebastian,
could you give me permisson that I can edit this issue? (e.g. assignees etc.)

[slobentanzer]

See if it works for you now. I gave the WFT team triage access to the repo.

[simonmoedinger]

Final Status