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Merged
jsstevenson merged 6 commits into from
Apr 3, 2025
Merged

Add missing dependencies #533

jsstevenson merged 6 commits into from
Apr 3, 2025

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@david4096
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@david4096 david4096 commented Mar 31, 2025

Was working on the annotator and these dependencies were missing. uv sync --extra extras

@david4096 david4096 requested review from a team as code owners March 31, 2025 20:45
@david4096 david4096 mentioned this pull request Mar 31, 2025
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jsstevenson requested changes Apr 1, 2025
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currently squinting at the commit history trying to understand why we would've pulled that pysam dependency in the first place...

@david4096 could you add a comment explaining the need for pinning setuptools/that specific version?

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david4096 commented Apr 1, 2025 •
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  1. Oh I wouldn't know!

  2. uv sync fails without it. A different version would probably work. The error is not having pkg_resources

https://stackoverflow.com/questions/7446187/no-module-named-pkg-resources

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jsstevenson commented Apr 1, 2025

Thanks! I'm not sure I'm precisely replicating your error (uv sync --extra extras works for me on python 3.10, 11, 12, and 13) but I do see a pkg_resources import during pytest setup:

________________________________________ ERROR collecting tests/extras/test_allele_translator.py ________________________________________         
ImportError while importing test module '/Users/jss009/code/vrs-python/tests/extras/test_allele_translator.py'.                                   
Hint: make sure your test modules/packages have valid Python names.      
Traceback:                                                               
../../.local/share/uv/python/cpython-3.11.11-macos-aarch64-none/lib/python3.11/importlib/__init__.py:126: in import_module                        
    return _bootstrap._gcd_import(name[level:], package, level)          
tests/extras/test_allele_translator.py:5: in <module>                    
    from ga4gh.vrs.extras.translator import AlleleTranslator             
src/ga4gh/vrs/extras/translator.py:17: in <module>                       
    from ga4gh.vrs.utils.hgvs_tools import HgvsTools                     
src/ga4gh/vrs/utils/hgvs_tools.py:6: in <module>                         
    import hgvs                                                          
.venv/lib/python3.11/site-packages/hgvs/__init__.py:60: in <module>      
    import pkg_resources                                                 
E   ModuleNotFoundError: No module named 'pkg_resources'                 
__________________________________________ ERROR collecting tests/extras/test_annotate_vcf.py ___________________________________________         
ImportError while importing test module '/Users/jss009/code/vrs-python/tests/extras/test_annotate_vcf.py'.                                        
Hint: make sure your test modules/packages have valid Python names.      
Traceback:                                                               
../../.local/share/uv/python/cpython-3.11.11-macos-aarch64-none/lib/python3.11/importlib/__init__.py:126: in import_module                        
    return _bootstrap._gcd_import(name[level:], package, level)          
tests/extras/test_annotate_vcf.py:12: in <module>                        
    from ga4gh.vrs.extras.annotator.vcf import VcfAnnotator, VcfAnnotatorError                                                                    
src/ga4gh/vrs/extras/annotator/vcf.py:17: in <module>                    
    from ga4gh.vrs.extras.translator import AlleleTranslator             
src/ga4gh/vrs/extras/translator.py:17: in <module>                       
    from ga4gh.vrs.utils.hgvs_tools import HgvsTools                     
src/ga4gh/vrs/utils/hgvs_tools.py:6: in <module>                         
    import hgvs                                                          
.venv/lib/python3.11/site-packages/hgvs/__init__.py:60: in <module>      
    import pkg_resources                                                 
E   ModuleNotFoundError: No module named 'pkg_resources'                 
_________________________________________ ERROR collecting tests/extras/test_cnv_translator.py __________________________________________         
ImportError while importing test module '/Users/jss009/code/vrs-python/tests/extras/test_cnv_translator.py'.                                      
Hint: make sure your test modules/packages have valid Python names.      
Traceback:                                                               
../../.local/share/uv/python/cpython-3.11.11-macos-aarch64-none/lib/python3.11/importlib/__init__.py:126: in import_module                        
    return _bootstrap._gcd_import(name[level:], package, level)          
tests/extras/test_cnv_translator.py:4: in <module>                                                                                                
    from ga4gh.vrs.extras.translator import CnvTranslator                
src/ga4gh/vrs/extras/translator.py:17: in <module>                       
    from ga4gh.vrs.utils.hgvs_tools import HgvsTools                     
src/ga4gh/vrs/utils/hgvs_tools.py:6: in <module>                         
    import hgvs                                                          
.venv/lib/python3.11/site-packages/hgvs/__init__.py:60: in <module>                                                                               
    import pkg_resources                                                 
E   ModuleNotFoundError: No module named 'pkg_resources'

It looks like the most proximal issue -- at least on my end -- is a needed fix in hgvs. Could you add a comment in pyproject.toml that this pin is temporary pending a fix there? Just want to make sure we have a sense of when we can unwind this in the future.

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jsstevenson commented Apr 1, 2025 •
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The other thing, which doesn't need to happen in this PR -- our CI/CD workflow installs setuptools upfront, which misses the proximal cause of this issue. I wonder if we should pull that step out so that we have more of a warning that this could be happening. @korikuzma

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david4096 commented Apr 1, 2025

@jsstevenson done

@david4096 david4096 requested a review from jsstevenson April 1, 2025 20:33
@korikuzma
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korikuzma commented Apr 3, 2025

Can we merge this?

@jsstevenson jsstevenson merged commit 27567b6 into ga4gh:main Apr 3, 2025
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