ClavelLab / maldipickr

Dereplicate And Cherry-pick Mass Spectrometry Spectra
https://clavellab.github.io/maldipickr/
GNU General Public License v3.0
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add Targets factories to ease {maldipickr} workflow #46

Closed cpauvert closed 11 hours ago

cpauvert commented 4 months ago

This PR is to draft functions to facilitate reproducible and trustworthy workflow development {maldipickr} (using {targets}).

We invite readers unfamiliar with {targets} to read the short and well-written walk-through "How to use {targets}" to understand how {targets} help analysts "coordinate the pieces of computationally demanding analysis projects" and "skips costly runtime for tasks that are already up to date" (source: https://cran.r-project.org/package=targets).

These helpers in {maldipickr} are called {targets} factories, which means they return target objects or lists of target objects.

codecov[bot] commented 4 months ago

Codecov Report

Attention: Patch coverage is 56.66667% with 52 lines in your changes are missing coverage. Please review.

Project coverage is 89.40%. Comparing base (62ecd77) to head (875e2a2).

Files Patch % Lines
R/tar_pick_with_similarity.R 0.00% 52 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #46 +/- ## ========================================== - Coverage 96.67% 89.40% -7.27% ========================================== Files 17 20 +3 Lines 541 661 +120 ========================================== + Hits 523 591 +68 - Misses 18 70 +52 ```

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cpauvert commented 11 hours ago

This PR includes commits from what should have been a feature branch that I'm struggling to integrate properly. Even if I tried to find non-cherry-pick solutions with merge, I could not get it right: https://devblogs.microsoft.com/oldnewthing/20180323-01/?p=98325 So I'll close, rename the branch and create two proper feature branches: for gather_spectra_stats and targets-factories