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update liana #52188

Merged
merged 4 commits into from
Nov 21, 2024
Merged

update liana #52188

merged 4 commits into from
Nov 21, 2024

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nilchia
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@nilchia nilchia commented Nov 19, 2024 •
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This pull request adjusts the version constraints.

The anndata 0.10.9 is not compatible with liana

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/nilchia/miniconda3/envs/liana/lib/python3.9/site-packages/liana/__init__.py", line 3, in <module>
    from liana import method as mt, plotting as pl, resource as rs, multi as mu, utils as ut, testing
  File "/home/nilchia/miniconda3/envs/liana/lib/python3.9/site-packages/liana/method/__init__.py", line 3, in <module>
    from liana.method.sc._Method import Method, MethodMeta, _show_methods
  File "/home/nilchia/miniconda3/envs/liana/lib/python3.9/site-packages/liana/method/sc/__init__.py", line 1, in <module>
    from ._rank_aggregate import _rank_aggregate_meta
  File "/home/nilchia/miniconda3/envs/liana/lib/python3.9/site-packages/liana/method/sc/_rank_aggregate.py", line 3, in <module>
    from liana.method.sc._Method import MethodMeta
  File "/home/nilchia/miniconda3/envs/liana/lib/python3.9/site-packages/liana/method/sc/_Method.py", line 3, in <module>
    from liana.method.sc._liana_pipe import liana_pipe
  File "/home/nilchia/miniconda3/envs/liana/lib/python3.9/site-packages/liana/method/sc/_liana_pipe.py", line 20, in <module>
    from mudata import MuData
  File "/home/nilchia/miniconda3/envs/liana/lib/python3.9/site-packages/mudata/__init__.py", line 3, in <module>
    from ._core.mudata import MuData
  File "/home/nilchia/miniconda3/envs/liana/lib/python3.9/site-packages/mudata/_core/mudata.py", line 21, in <module>
    from anndata._core.aligned_mapping import (
ImportError: cannot import name 'AlignedViewMixin' from 'anndata._core.aligned_mapping' (/home/nilchia/miniconda3/envs/liana/lib/python3.9/site-packages/anndata/_core/aligned_mapping.py)

decoupler from Bioconda is not updated and I did not find its recipe folder. however, decoupler-py from conda-forge is updated and works fine.

@nilchia nilchia marked this pull request as ready for review November 19, 2024 13:01
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nilchia commented Nov 19, 2024

I can't see the error. This passes locally.

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coderabbitai bot commented Nov 19, 2024 •
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📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request introduces modifications to the meta.yaml file for the "liana" package. Key changes include an increment in the version number from 0 to 1 in the build section. The run requirements have been updated to impose a maximum version constraint on the anndata package, changing it from >=0.7.4 to >=0.7.4,<=0.10.8. Additionally, the decoupler package has been renamed to decoupler-py, and a new requirement for pandas has been added, specifying a version range of >=2.2.2,<3.0.0. All other dependencies and sections of the file remain unchanged.

Possibly related PRs

  • update cell2cell #51790: This PR updates the cell2cell package to ensure compatibility with the corneto package, which is a requirement for the liana package, indicating a direct relationship with the main PR's focus on the liana package.

Suggested labels

please review & merge

Suggested reviewers

  • bgruening
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📥 Commits

Reviewing files that changed from the base of the PR and between b6851b1 and b006e4e.

📒 Files selected for processing (1)
  • recipes/liana/meta.yaml (2 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
  • recipes/liana/meta.yaml

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@nilchia
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nilchia commented Nov 21, 2024

@bioconda-bot please fetch artifacts!

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
noarch liana-1.4.0-pyhdfd78af_1.tar.bz2 noarch.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
liana 1.4.0--pyhdfd78af_1 GitHub Actions
showImages are in the linux-64 zip file above.gzip -dc images/liana---1.4.0--pyhdfd78af_1.tar.gz | docker load

@martin-g martin-g merged commit 5fdae71 into bioconda:master Nov 21, 2024
6 checks passed
@nilchia nilchia deleted the liana_1 branch November 21, 2024 07:56
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@martin-g martin-g martin-g approved these changes

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