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Merged
merged 24 commits into from
Dec 29, 2022
Merged

[ENH] run QC on input data #113

merged 24 commits into from
Dec 29, 2022

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@Remi-Gau
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@Remi-Gau Remi-Gau commented Dec 27, 2022 •
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closes #110
closes #111
closes #112
closes #114

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sourcery-ai bot commented Dec 27, 2022 •
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Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 0.99%.

Quality metrics Before After Change
Complexity 2.68 ⭐ 2.52 ⭐ -0.16 👍
Method Length 67.12 🙂 73.47 🙂 6.35 👎
Working memory 6.25 🙂 6.91 🙂 0.66 👎
Quality 75.41% ⭐ 74.42% 🙂 -0.99% 👎
Other metrics Before After Change
Lines 2399 2044 -355
Changed files Quality Before Quality After Quality Change
bidsmreye/bidsmreye.py 59.51% 🙂 56.00% 🙂 -3.51% 👎
bidsmreye/download.py 67.98% 🙂 68.06% 🙂 0.08% 👍
bidsmreye/generalize.py 68.29% 🙂 66.55% 🙂 -1.74% 👎
bidsmreye/methods.py 62.07% 🙂 59.47% 🙂 -2.60% 👎
bidsmreye/prepare_data.py 68.35% 🙂 68.44% 🙂 0.09% 👍
bidsmreye/quality_control.py 61.40% 🙂 62.34% 🙂 0.94% 👍
bidsmreye/utils.py 76.08% ⭐ 81.92% ⭐ 5.84% 👍
docs/source/conf.py 78.03% ⭐ 77.66% ⭐ -0.37% 👎
tests/test_bidsmreye.py 91.92% ⭐ 91.92% ⭐ 0.00%
tests/test_generalize.py 85.83% ⭐ 85.83% ⭐ 0.00%
tests/test_methods.py 92.46% ⭐ 92.38% ⭐ -0.08% 👎
tests/test_prepare.py 85.92% ⭐ 85.92% ⭐ 0.00%
tests/test_quality_control.py 90.20% ⭐ 88.06% ⭐ -2.14% 👎
tests/test_utils.py 92.72% ⭐ 90.56% ⭐ -2.16% 👎
tests/test_visualize.py 93.69% ⭐ 93.69% ⭐ 0.00%
tests/utils.py 84.76% ⭐ 86.04% ⭐ 1.28% 👍

Here are some functions in these files that still need a tune-up:

File Function Complexity Length Working Memory Quality Recommendation
bidsmreye/bidsmreye.py bidsmreye 16 🙂 235 ⛔ 21 ⛔ 28.36% 😞 Try splitting into smaller methods. Extract out complex expressions
bidsmreye/quality_control.py compute_robust_outliers 6 ⭐ 300 ⛔ 14 😞 40.66% 😞 Try splitting into smaller methods. Extract out complex expressions
bidsmreye/generalize.py process_subject 6 ⭐ 231 ⛔ 12 😞 46.76% 😞 Try splitting into smaller methods. Extract out complex expressions
bidsmreye/quality_control.py perform_quality_control 5 ⭐ 188 😞 10 😞 54.39% 🙂 Try splitting into smaller methods. Extract out complex expressions
bidsmreye/download.py download 9 🙂 168 😞 8 🙂 56.60% 🙂 Try splitting into smaller methods

Legend and Explanation

The emojis denote the absolute quality of the code:

  • ⭐ excellent
  • 🙂 good
  • 😞 poor
  • ⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

Please see our documentation here for details on how these metrics are calculated.

We are actively working on this report - lots more documentation and extra metrics to come!

Help us improve this quality report!

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codecov bot commented Dec 27, 2022 •
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Codecov Report

Merging #113 (2f63be5) into main (dcd85d0) will increase coverage by 2.53%.
The diff coverage is 76.96%.

@@            Coverage Diff             @@
##             main     #113      +/-   ##
==========================================
+ Coverage   74.55%   77.08%   +2.53%     
==========================================
  Files           9       13       +4     
  Lines         786      851      +65     
  Branches      105      118      +13     
==========================================
+ Hits          586      656      +70     
- Misses        157      158       +1     
+ Partials       43       37       -6
Flag Coverage Δ
tests 76.96% <76.96%> (+2.54%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
bidsmreye/bidsmreye.py 56.62% <37.03%> (-3.94%) ⬇️
bidsmreye/prepare_data.py 52.00% <47.36%> (+2.00%) ⬆️
bidsmreye/generalize.py 51.16% <50.00%> (-0.65%) ⬇️
bidsmreye/bids_utils.py 71.28% <71.28%> (ø)
bidsmreye/configuration.py 84.11% <84.11%> (ø)
bidsmreye/logging.py 84.61% <84.61%> (ø)
bidsmreye/defaults.py 88.88% <88.88%> (ø)
bidsmreye/quality_control.py 96.45% <98.46%> (+2.23%) ⬆️
bidsmreye/download.py 80.39% <100.00%> (ø)
bidsmreye/methods.py 90.90% <100.00%> (ø)
... and 3 more

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@Remi-Gau Remi-Gau marked this pull request as ready for review December 28, 2022 23:06
@Remi-Gau Remi-Gau merged commit d828a56 into cpp-lln-lab:main Dec 29, 2022
@Remi-Gau Remi-Gau deleted the qc_on_input branch December 29, 2022 13:45
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[BUG] fix FAQ url Add doc coverage QA should be an independent action from generalize add badges

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