scverse / scverse/spatialdata

Overwriting issue when rerunning code

Open
#265 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
394
Forks
95
Avg merge
4d 3h
Merged PRs (30d)
7

Description

When creating objects in spatialData, you cannot rerun all code, as overwiting objects in spatialData is difficult.
A workaround is to use the add_x function and use the overwrite=True. But this might not be the best option.
It would be handy to just be able to rerun your code without overwriting every time.

Also, for layer that aren't loaded in memory, such as the points layer, the overwrite doesn't work. It can be handy when taking a subset of the data and thus a subset of the points.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by tracing the add_x functions and their overwrite handling, including behavior for the points layer when it is not loaded in memory. Check how rerunning object-creation code and taking a subset of points currently behave. Done means rerunning the code safely replaces the intended objects without requiring overwrite=True, including unloaded points layers.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.