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Feature/custom regex for index parsing #224

Merged
merged 10 commits into from
May 26, 2020
Merged

Feature/custom regex for index parsing #224

merged 10 commits into from
May 26, 2020

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MKoesters
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Fix bugs when parsing files with non numerical id

  • if groups in id can't be machted, return empty id_dict
  • if first scan is not an integer, set first scan to 0
  • remove debug print function
  • if no integer in spec_id, return full id string

@MKoesters
[WIP] custom regex for parsing index ids and only only use scan=x or …
0d6c89f 
…scanId=x as scan number
@MKoesters
remove print function
5a47fe0
@MKoesters
Fix bugs when parsing files with non numerical id
f06ba13 
- if groups in id can't be machted, return empty id_dict
- if first scan is not an integer, set first scan to 0
- remove debug print function
- if no integer in spec_id, return full id string
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codecov bot commented May 13, 2020 •
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Codecov Report

Merging #224 into dev will increase coverage by 0.16%.
The diff coverage is 69.84%.

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #224      +/-   ##
==========================================
+ Coverage   83.99%   84.15%   +0.16%     
==========================================
  Files          32       32              
  Lines        3673     3698      +25     
==========================================
+ Hits         3085     3112      +27     
+ Misses        588      586       -2
Impacted Files Coverage Δ
pymzml/spec.py 76.98% <29.41%> (+1.88%) ⬆️
pymzml/file_classes/standardMzml.py 69.60% <76.66%> (-0.08%) ⬇️
pymzml/file_interface.py 93.54% <100.00%> (+0.21%) ⬆️
pymzml/regex_patterns.py 100.00% <100.00%> (ø)
pymzml/run.py 86.04% <100.00%> (-3.43%) ⬇️
tests/main_reader_test.py 99.37% <100.00%> (-0.02%) ⬇️
tests/ms2_spec_test.py 98.14% <100.00%> (+0.14%) ⬆️

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@MKoesters MKoesters requested review from fu, StSchulze and JB-MS and removed request for fu May 15, 2020 12:49
StSchulze
StSchulze requested changes May 15, 2020
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@StSchulze StSchulze left a comment

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Looks good.
Remove debug code (that's commented out) and then it should be ready to go.

@MKoesters MKoesters mentioned this pull request May 26, 2020
Closed
@MKoesters MKoesters linked an issue May 26, 2020 that may be closed by this pull request
Support for VITEK MS (aka. Shimadzu Assurance) #216
Closed
@MKoesters MKoesters merged commit b110673 into dev May 26, 2020
@frederic-foucault frederic-foucault mentioned this pull request May 26, 2020
Closed
@StSchulze StSchulze deleted the feature/custom_regex_for_index_parsing branch June 4, 2021 13:10
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@StSchulze StSchulze StSchulze requested changes

@fu fu Awaiting requested review from fu

@JB-MS JB-MS Awaiting requested review from JB-MS

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Support for VITEK MS (aka. Shimadzu Assurance)
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@MKoesters @StSchulze