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ilan-gold
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ilan-gold
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- Why not
uv? It works fine foranndata - If that is the case (no reason to doubt it), and
runs-oncan be configurable, this does not need to be its own.ymlfile
| jobs: | ||
| test: | ||
| name: Integration test/ test (3.x rapids-singlecell) | ||
| runs-on: "cirun-aws-gpu--${{ github.run_id }}" |
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Is there no way to refactor the other workflow to make runs-on a configuration setting?
| - uses: mamba-org/setup-micromamba@v2 | ||
| with: | ||
| environment-file: rapids_singlecell/ci/environment.yml | ||
| init-shell: >- | ||
| bash | ||
| post-cleanup: 'all' | ||
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| - name: Install rapids-singlecell | ||
| id: install_pkg | ||
| run: >- | ||
| pip install -e .[test] | ||
| "scanpy @ git+https://github.com/scverse/scanpy.git" | ||
| "anndata @ git+https://github.com/scverse/anndata.git" |
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Why do we need conda? Why are you also installing the upstream of scanpy?
https://github.com/scverse/anndata/blob/main/.github/workflows/test-gpu.yml uses uv, as does the rest of the tests in this repo.
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I used uv for a while to do ci for rapids-singlecell. At some point every 5 runs there was an issue with installing rapids with uv so i switched back to conda
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Can we at least try it here? If not we can add an if-else statement to use conda for rapids in the unified CI, but I've never had an issue with the anndata CI
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I know I implemented the uv ci for anndata-GPU. But you "only" install cupy and not the other rapids-stuff. I always got timeout erros from the nvidia-index
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I don’t like that this duplicates the whole workflow.
I get that if we have to use conda, that would make it necessary because the differences between workflows are too big, but are you sure that’s the only option?
How about
- you share the error message from a failed uv install with us here (I should not have to say this, you know how hard it is to debug things when users don’t give you any details)
- let us brainstorm possible solutions:
UV_HTTP_TIMEOUT?UV_CONCURRENT_DOWNLOADS?- manual retry?
--native-tls?
- only if that doesn’t work, we should consider doing something totally different for one package than the others.
ilan-gold
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ilan-gold
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I get that if we have to use conda, that would make it necessary because the differences between workflows are too big, but maybe we can figure it out:
I'm not even sold on this. The difference between this and the other one really is just that micromamba line from what I can tell. Should be simple to turn it off for all the other ones, no?
| id: install_pkg | ||
| run: >- | ||
| pip install -e .[test] | ||
| "scanpy @ git+https://github.com/scverse/scanpy.git" |
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Why install the live version of scanpy?
ilan-gold
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ilan-gold
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Looks like it's doing its job - a bunch of issues caught!
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