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feat: read_source #72

Merged
merged 20 commits into from
May 18, 2022
Merged

feat: read_source #72

merged 20 commits into from
May 18, 2022

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rohank63
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@rohank63 rohank63 commented Mar 30, 2021

Description

  • implement functionality to infer read source for single- and paired-ended libraries
  • most unit tests for new functionality missing

Type of change

Please delete options that are not relevant.

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality
    to not work as expected)
  • Documentation update

Checklist

Please carefully read these items and tick them off if the statements are true
or do not apply.

  • I have performed a self-review of my own code
  • My code follows the existing coding style, lints and generates no new
    warnings
  • I have added type annotations to all function/method signatures, and I
    have added type annotations for any local variables that are non-trivial,
    potentially ambiguous or might otherwise benefit from explicit typing.
  • I have commented my code in hard-to-understand areas
  • I have added ["Google-style docstrings"] to all new modules, classes,
    methods/functions or updated previously existing ones
  • I have added tests that prove my fix is effective or that my feature
    works
  • New and existing unit tests pass locally with my changes and I have not
    reduced the code coverage relative to the previous state
  • I have updated any sections of the app's documentation that are affected
    by the proposed changes

@uniqueg uniqueg self-assigned this Mar 14, 2022
@uniqueg uniqueg self-requested a review March 14, 2022 00:25
"Could not open abundance.tsv created by Kallisto quant"
) from exc

def _convert_dic_to_df(self) -> pd.DataFrame:
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Could you call htsinfer.utils.convert_dict_to_df instead?

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codecov-commenter commented May 18, 2022

Codecov Report

Merging #72 (7568e4c) into dev_v2 (35f6e2b) will not change coverage.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##            dev_v2       #72   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           10        10           
  Lines          602       611    +9     
=========================================
+ Hits           602       611    +9     
Impacted Files Coverage Δ
htsinfer/utils.py 100.00% <ø> (ø)
htsinfer/__init__.py 100.00% <100.00%> (ø)
htsinfer/cli.py 100.00% <100.00%> (ø)
htsinfer/exceptions.py 100.00% <100.00%> (ø)
htsinfer/get_read_layout.py 100.00% <100.00%> (ø)
htsinfer/htsinfer.py 100.00% <100.00%> (ø)
htsinfer/models.py 100.00% <100.00%> (ø)

Continue to review full report at Codecov.

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uniqueg
uniqueg previously approved these changes May 18, 2022
@uniqueg uniqueg self-requested a review May 18, 2022 11:38
@uniqueg uniqueg merged commit 6e6dc8c into dev_v2 May 18, 2022
@uniqueg uniqueg deleted the organisms_v2 branch May 18, 2022 11:38
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4 participants