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Work done to support the human mitochondrial codon table in main, but missing from latest release 0.5.8.post1 #67

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bsgiles73 opened this issue Sep 6, 2024 · 5 comments
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@bsgiles73
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bsgiles73 commented Sep 6, 2024

Describe the bug
The latest build of bioutils does not include the recent work done to add the Human Mitochondrial translation table.

https://github.com/biocommons/bioutils/blob/main/src/bioutils/sequences.py#L605-L610

To Reproduce
Steps to reproduce the behavior:

  1. Install latest version of bioutils
  2. Run translate_cds method with vertebrate_mitochondrial translation table option.
(.venv) sgiles-MD6M:bioutils shane.giles$ pip freeze | grep bioutils
bioutils==0.5.8.post1
>>> from bioutils.sequences import translate_cds, TranslationTable
>>> translate_cds("ATACGA", translation_table=TranslationTable.standard)
'IR'
>>> translate_cds("ATACGA", translation_table=TranslationTable.vertebrate_mitochondrial)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/shane.giles/.pyenv/versions/3.11.4/lib/python3.11/enum.py", line 783, in __getattr__
    raise AttributeError(name) from None
AttributeError: vertebrate_mitochondrial

Expected behavior
Code does not throw exception using latest version, but uses the human mitochondrial translation table to generate the following.

>>> translate_cds("ATACGA", translation_table=TranslationTable.vertebrate_mitochondrial)
'MR'
@bsgiles73 bsgiles73 added the bug Something isn't working label Sep 6, 2024
@bsgiles73 bsgiles73 changed the title Work done to support the human mitochondrial codon table in main, but missing from latest build Work done to support the human mitochondrial codon table in main, but missing from latest release 0.5.8.post1 Sep 6, 2024
@bsgiles73 bsgiles73 changed the title Work done to support the human mitochondrial codon table in main, but missing from latest release 0.5.8.post1 Work done to support the human mitochondrial codon table in main, but missing from latest release 0.5.8.post1 Sep 6, 2024
@andreasprlic
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I think this makes sense: We merged the MR that adds mitochondrial support in ab6a9e4 which was in Jan 2024, but the 0.5.8 release was in July 2023. Solution should be to create a new release. I'll see if I can do that.

@andreasprlic
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I tried to create a new release, but it failed with the following. Looks like we need to update our release CI.

Checking dist/bioutils-0.6.0-py3-none-any.whl: PASSED
Uploading distributions to https://upload.pypi.org/legacy/
Uploading bioutils-0.6.0-py3-none-any.whl
WARNING  Error during upload. Retry with the --verbose option for more details. 
ERROR    HTTPError: 403 Forbidden from https://upload.pypi.org/legacy/          
         Invalid or non-existent authentication information. See                
         https://pypi.org/help/#invalid-auth for more information.   

@andreasprlic
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discussion for how to fix CI/CD on #68

@andreasprlic
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I rolled back the unfinished 0.6.0 release so we can restart it once #68 has been updated.

@andreasprlic
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bioutils 0.6.0 has been released. I consider this issue resolved.

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