very cool.
why do we need the --system flag ? for caching ?

So uv uses the setup-python-installed python and installs packages into that, instead of trying to use its own python and venv. That allows python args... commands to 'just work', instead of needing to do uv run python args.... Since not all maintainers are using uv lockfiles etc, I think this is the simplest way to use uv pip as a faster pip, instead of having to adopt uv's entire workflow.

Python is also cached on many of the github runners, so setup-python is quite a bit faster (it's already on the runner) than using uv to get python (download over network).

Put another way, pip install already installs into the system site packages if it's not run in a virtual environment. In contrast, uv pip install will install into a uv-maintained virtual environment even if it's not run in a virtual environment. To truly emulate pip install with uv, you need to tell uv you really want to mutate the system site packages with uv pip install --system, or set an equivalent environment variable (but that affects all other uv commands, which might not be what you want).

OK. Thanks. THis is super clear.

Thanks @galenlynch , looks like this cuts 20s or so off some of our test runs. Really really beneficial when doing the core tests, which can now take less than a minute to run in CI in full!!! Amazing.

Heads-up: looking at the nightly "Full spikeinterface tests codecov" runs on main, this PR seems to have made the full run slower, not faster.

Pre-merge (last 10 successful nightly runs, Apr 7 to Apr 16): average ~38 min (range 33 to 41).
Post-merge (Apr 17 to Apr 19, 3 runs): average ~46 min (43, 48, 48).

Small sample and the cache may not have fully warmed in the first few days, but there is no sign of a speedup so far on the full matrix. The core tests do seem faster, which matches what was reported in the thread.

Two things that might be worth checking:

1. Whether the cache is actually hitting on the full run, or whether the key changes on each run.
2. Whether uv pip install --system is resolving to different (newer) package versions than pip did. I have found two latent test failures that surfaced with this PR because uv pulled numpy 2.x and a newer scipy, which broke assert_array_equal(x=, y=) kwargs and a band=[single_value] call. Those were pre-existing bugs, but pinning or capping resolution would prevent the next one from landing silently.

Numbers pulled via gh run list --workflow="Full spikeinterface tests codecov".

I think this is because the caching is broken: https://github.com/SpikeInterface/spikeinterface/actions/runs/24653179008/job/72080347711

Looking at the individual test times in detail, the difference is almost entirely down to test_sorting_s3_nwb_zarr, which downloads a recording from the cloud. I don't see any caching logic here, so am a bit confused.
Timings for installing packages etc are down, which is a good sign!