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Run CI with uv #1423

Merged
merged 5 commits into from
Mar 14, 2024
Merged

Run CI with uv #1423

merged 5 commits into from
Mar 14, 2024

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flying-sheep
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@flying-sheep flying-sheep commented Mar 14, 2024 •
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@ivirshup --pre works:

 + scanpy==1.10.0rc2

@flying-sheep flying-sheep added this to the 0.10.7 milestone Mar 14, 2024
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codecov bot commented Mar 14, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.09%. Comparing base (20adb70) to head (39c9f0a).

Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #1423      +/-   ##
==========================================
- Coverage   86.29%   84.09%   -2.21%     
==========================================
  Files          36       36              
  Lines        5612     5602      -10     
==========================================
- Hits         4843     4711     -132     
- Misses        769      891     +122
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ivirshup
ivirshup reviewed Mar 14, 2024
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@ivirshup
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I think uv is able to resolve an environment before downloading wheels (not sure why pip can't if uv can though), so we could also get better caching behaviour with

  • An initial step that does uv pip install --dry-run --output-file requirements-lock.txt {env-specific}
  • Use requirements-lock.txt + python version as the cache key
  • Create environment with uv pip install -r requirements-lock.txt

But it's also fast enough already we don't really need to worry about it if we don't want. We're not getting charged for bandwidth.

@flying-sheep
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Pip will definitely resolve environments before downloading wheels, too. I’ve closely followed the path to get there, so I know. What makes you think it possibly doesn’t?

@ivirshup
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this 
pip install --no-cache-dir --dry-run ".[dev,test]"
Processing /mnt/workspace/repos/scanpy
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting anndata>=0.8 (from scanpy==1.10.0rc2.dev19+ga6126980)
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Collecting h5py>=3.1 (from scanpy==1.10.0rc2.dev19+ga6126980)
  Downloading h5py-3.10.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting joblib (from scanpy==1.10.0rc2.dev19+ga6126980)
  Downloading joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)
Collecting legacy-api-wrap>=1.4 (from scanpy==1.10.0rc2.dev19+ga6126980)
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Collecting matplotlib>=3.6 (from scanpy==1.10.0rc2.dev19+ga6126980)
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Would install PyYAML-6.0.1 anndata-0.10.6 array_api_compat-1.4.1 asciitree-0.3.3 attrs-23.2.0 cfgv-3.4.0 click-8.1.7 cloudpickle-3.0.0 contourpy-1.2.0 coverage-7.4.3 cycler-0.12.1 dask-2024.3.0 distlib-0.3.8 fasteners-0.19 filelock-3.13.1 fonttools-4.49.0 fsspec-2024.2.0 h5py-3.10.0 identify-2.5.35 igraph-0.11.4 imageio-2.34.0 iniconfig-2.0.0 joblib-1.3.2 kiwisolver-1.4.5 lazy_loader-0.3 legacy-api-wrap-1.4 leidenalg-0.10.2 llvmlite-0.42.0 locket-1.0.0 matplotlib-3.8.3 natsort-8.4.0 networkx-3.2.1 nodeenv-1.8.0 numba-0.59.0 numcodecs-0.12.1 numpy-1.26.4 packaging-24.0 pandas-2.2.1 partd-1.4.1 patsy-0.5.6 pbr-6.0.0 pillow-10.2.0 platformdirs-4.2.0 pluggy-1.4.0 pre-commit-3.6.2 profimp-0.1.0 pynndescent-0.5.11 pyparsing-3.1.2 pytest-8.1.1 pytest-cov-4.1.0 pytest-mock-3.12.0 pytest-nunit-1.0.7 python-dateutil-2.9.0.post0 pytz-2024.1 scanpy-1.10.0rc2.dev19+ga6126980 scikit-image-0.22.0 scikit-learn-1.4.1.post1 scipy-1.12.0 seaborn-0.13.2 session_info-1.0.0 setuptools-scm-8.0.4 six-1.16.0 statsmodels-0.14.1 stdlib-list-0.10.0 texttable-1.7.0 threadpoolctl-3.3.0 tifffile-2024.2.12 toolz-0.12.1 tqdm-4.66.2 typing_extensions-4.10.0 tzdata-2024.1 umap-learn-0.5.5 virtualenv-20.25.1 zarr-2.17.1

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flying-sheep commented Mar 14, 2024 •
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This … shows that it doesn’t download wheels until it has to:

Downloading anndata-0.10.6-py3-none-any.whl.metadata

uv uses the same metadata API, it’s just faster in some other way.

PyPI by now has backfilled metadata for everything that has wheels, excluding like 50 ancient releases with broken wheels.

@flying-sheep flying-sheep requested a review from ivirshup March 14, 2024 16:05
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This … shows that it doesn’t download wheels until it has to:

Downloading anndata-0.10.6-py3-none-any.whl.metadata

FWIW, pip was downloading the wheels in the --dry-run right after that, while uv doesn't.

ivirshup
ivirshup reviewed Mar 14, 2024
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FWIW, pip was downloading the wheels in the --dry-run right after that, while uv doesn't.

Yeah, I guess that’s a difference in their interpretation of “dry run”.

I think something like this should avoid downloading wheels in the end: pip install --dry-run --ignore-installed --no-cache-dir --quiet --report=- scanpy

@flying-sheep flying-sheep requested a review from ivirshup March 14, 2024 16:34
@ivirshup ivirshup enabled auto-merge (squash) March 14, 2024 16:45
@ivirshup ivirshup merged commit 920de97 into main Mar 14, 2024
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@ivirshup ivirshup deleted the uv branch March 14, 2024 16:46
meeseeksmachine pushed a commit to meeseeksmachine/anndata that referenced this pull request Mar 14, 2024
@flying-sheep @meeseeksmachine
Backport PR scverse#1423: Run CI with uv
3ba5d03
@meeseeksmachine meeseeksmachine mentioned this pull request Mar 14, 2024
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flying-sheep added a commit that referenced this pull request Mar 14, 2024
@meeseeksmachine @flying-sheep
Backport PR #1423 on branch 0.10.x (Run CI with uv) (#1424)
a8800ea 
Co-authored-by: Philipp A <[email protected]>
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