scverse / scverse/scanpy

Import performance part 3

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Description

In #406 we decided to get rid of scanpy.api, which worsened our import time. Thanks to @ivirshup (#703, #704), the main culprits to long import times are out of the game, but there’s still room for improvement.

I used profimp to identify the rest. I started with just profimp --html 'import scanpy', identified the external imports that take a while, and created a file in which I imported them before finally importing scanpy:

uvx --with=.[leiden] profimp --html "# anndata big imports
import numpy
import pandas
import zarr
import h5py

# scanpy big imports
import numba
import sklearn          # preprocessing._simple
#import sklearn.metrics  # neighbors
#import networkx         # diffmap, paga, plotting._utils
import leidenalg
import matplotlib.pyplot

# rest
import scanpy" | save -f dist/profimp-scanpy.html
Outdated: 1.4s with networkx and sklearn.metrics

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grafik

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 running the documented profimp command with the listed imports and inspect dist/profimp-scanpy.html. The issue provides no target files, tests, or specific optimization scope; completion would require identifying and reducing the remaining scanpy import-time costs.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
performance
Issue type
Refactor
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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