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nmfs-fish-tools / SSMSE

Management Strategy Evaluation (MSE) using Stock Synthesis (SS3)
https://nmfs-fish-tools.github.io/SSMSE
MIT License
18 stars 11 forks source link

Bug catcher #174

Closed CassidyPeterson-NOAA closed 9 months ago

CassidyPeterson-NOAA commented 9 months ago

Hey Kathryn and Nathan!

Finally pull requesting. Three main changes herein:

  1. allowing for recdevs that are labeled other than recdev1 in the par file (e.g., recdev2); edited in calc_par_trend() and match_parname() functions
  2. edited get_F() to correct a mistake in fleet labeling when there are fleets of type==3. Updated the function to include a fleetnames_all input, which contains all fleetnames (including those of type=3). I had to also change the test script to allow for an additional fleetnames_all input to the get_F() test functions. In the test script, I just set fleetnames_all = fleetnames.
  3. edit to run_SSMSE_iter() to adjust naming conventions from sample_struct to their standard column names (Yr, Seas, FltSvy, SE, etc). I originally thought this was simply an issue of the newer version of SS3, but I believe I also ran into trouble when running the cod example line-by-line. Not sure if it is related to the line-by-line method or what?

Thanks!

codecov[bot] commented 9 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (d1e7714) 69.82% compared to head (52f4d04) 69.83%. Report is 3 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #174 +/- ## ======================================= Coverage 69.82% 69.83% ======================================= Files 21 21 Lines 4384 4445 +61 ======================================= + Hits 3061 3104 +43 - Misses 1323 1341 +18 ```

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k-doering-NOAA commented 9 months ago

@CassidyPeterson-NOAA thanks so much for putting together this pull request! I definitely understand change 1 and the changes look good. 2. and 3. I had some questions on that you can see above. My SS3 knowledge is a little rusty, by the way (I forgot what fleet type 3 meant, for instance, and had to look it up!)

CassidyPeterson-NOAA commented 9 months ago

Thanks a bunch, Kathryn!

k-doering-NOAA commented 9 months ago

Thanks for submitting the PR!