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Fix txt reading and improve performance#432

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smoia merged 14 commits intophysiopy:masterfrom
smoia:enh/txtread
Dec 14, 2022
Merged

Fix txt reading and improve performance#432
smoia merged 14 commits intophysiopy:masterfrom
smoia:enh/txtread

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@smoia smoia commented Dec 14, 2022

Closes #431

This PR sees a lot of refactoring of the io module.

Proposed Changes

  • check_multifreq performance has been massively improved.
  • A bug that was causing multi-frequency channels in txt files to be exported with the wrong frequency sampling has been fixed.
  • breaking API: read_header_and_channels provides a channel list that is already a list of numpy.ndarrays and a full header for acq
  • breaking API: extract_header_items requires only the header as input
  • breaking API: check_multifreq now returns also the list of channels with the right sampling.

Change Type

  • bugfix (+0.0.1)
  • minor (+0.1.0)
  • major (+1.0.0)
  • refactoring (no version update)
  • test (no version update)
  • infrastructure (no version update)
  • documentation (no version update)
  • other

Checklist before review

  • I added everything I wanted to add to this PR.
  • [Code or tests only] I wrote/updated the necessary docstrings.
  • [Code or tests only] I ran and passed tests locally.
  • [Documentation only] I built the docs locally.
  • My contribution is harmonious with the rest of the code: I'm not introducing repetitions.
  • My code respects the adopted style, especially linting conventions.
  • The title of this PR is explanatory on its own, enough to be understood as part of a changelog.
  • I added or indicated the right labels.
  • I added information regarding the timeline of completion for this PR.
  • Please, comment on my PR while it's a draft and give me feedback on the development!

@smoia smoia added Refactoring Improve nonfunctional attributes Minormod This PR generally closes an `Enhancement` issue. It increments the minor version (0.+1.0) BugFIX This PR generally closes a `Bug` issue, and increments the patch version (0.0.+1) Internal Changes affect the internal API. It doesn't increase the version, but produces a changelog labels Dec 14, 2022
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codecov bot commented Dec 14, 2022

Codecov Report

Merging #432 (79e495b) into master (4a4ee74) will increase coverage by 0.35%.
The diff coverage is 100.00%.

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #432      +/-   ##
==========================================
+ Coverage   94.42%   94.77%   +0.35%     
==========================================
  Files           8        8              
  Lines         879      881       +2     
==========================================
+ Hits          830      835       +5     
+ Misses         49       46       -3     
Impacted Files Coverage Δ
phys2bids/io.py 100.00% <100.00%> (+0.60%) ⬆️
phys2bids/viz.py 95.18% <0.00%> (+2.40%) ⬆️

@smoia smoia merged commit 201b3bd into physiopy:master Dec 14, 2022
@smoia smoia deleted the enh/txtread branch December 14, 2022 09:51
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smoia commented Dec 14, 2022

🚀 PR was released in 2.7.0 🚀

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BugFIX This PR generally closes a `Bug` issue, and increments the patch version (0.0.+1) Internal Changes affect the internal API. It doesn't increase the version, but produces a changelog Minormod This PR generally closes an `Enhancement` issue. It increments the minor version (0.+1.0) Refactoring Improve nonfunctional attributes

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phys2bids hanging (or taking more than 2 days to parse 1 file?)

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