Adding Benchmarks

[selmanozleyen]

This PR adds benchmarks similar to the ones in https://github.com/scverse/scanpy/blob/main/benchmarks/benchmarks

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 24.20%. Comparing base (d8b8f91) to head (98b3dec).
⚠️ Report is 8 commits behind head on main.

❗ There is a different number of reports uploaded between BASE (d8b8f91) and HEAD (98b3dec). Click for more details.

HEAD has 3 uploads less than BASE

Flag	BASE (d8b8f91)	HEAD (98b3dec)
	4	1

Additional details and impacted files

@@             Coverage Diff             @@
##             main    #1016       +/-   ##
===========================================
- Coverage   66.63%   24.20%   -42.44%     
===========================================
  Files          40       41        +1     
  Lines        6060     6053        -7     
  Branches     1015     1012        -3     
===========================================
- Hits         4038     1465     -2573     
- Misses       1662     4571     +2909     
+ Partials      360       17      -343     

see 32 files with indirect coverage changes

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[scverse-benchmark]

No changes in benchmarks.

Comparison: https://github.com/scverse/squidpy/compare/662165070dcc38b424c9feb077c22fce69599c51..98b3deca6c60fc8df93b987345da8750ab7cb275
Last changed: Thu, 4 Sep 2025 14:11:36 +0000

More details: https://github.com/scverse/squidpy/pull/1016/checks?check_run_id=49604095778

[flying-sheep]

OK, silly me, it was RIGHT THERE in the “Usage” part of the readme: https://github.com/scverse/benchmark#usage

I improved that bit a little, but we should all have seen it immediately.

[flying-sheep]

I tried a lot of asv environment creation backends, but in the end, I just went with virtualenv and a custom install_command that uses uv instead of pip (which currently has resolution issues with squidpy’s deps)

One isse with asv is that it commits the one cardinal sin of environment management: It resolves dependencies more than once (i.e. in the install_command and from matrix.req), so there are two ways of using it:

1. don’t use matrix.req and install dependencies in install_command (making matrix.req useless)
2. list all dependencies in matrix.req and add --no-deps to the install_command (which forces you to maintain your dependency list in two spots)

that being said, I think you can use matrix.env variables install_command, e.g.:

{
  ...,
  "install_command": ["python -m uv pip install {r_numpy} {wheel_file}"],
  "matrix": {
    "env": {
      "R_NUMPY": ["numpy<2", "numpy>=2"],
    },
  },
}

[flying-sheep]

I made an issue about this: airspeed-velocity/asv#1542