Releases · NOAA-FIMS/FIMS

What's Changed

Summary of high level/breaking changes:

Added a pkgdown site for FIMS
Add code cov tests and site link
Remove recruitment bias correction and adjustment because we plan to use TMB (#185)
Improve logging coverage and separate logs into multiple files
Put recruitment deviations on the log scale when input
Report more values with standard errors
Code cleanup, documentation, and consistency improvements
Remove rapidjson dependence
Add start_year and end_year as slots to FIMSFrame
Make log_obs_error a vector
Load the Rcpp module upon package install so components don't need to be prefaced by fims$
Refactor vectors to use fims::Vector class
Add Newton steps to FIMS integration test to improve convergence in integration test

More detail:

Update issue forms by @k-doering-NOAA in #426
Update DESCRIPTION to match release number by @ChristineStawitz-NOAA in #425
resolved issues causing warnings by @MOshima-PIFSC in #430
#307: export age comp function by @k-doering-NOAA in #438
368 convert fims to a pkgdown site by @Bai-Li-NOAA in #437
#242 fix codecov calc and upload by @k-doering-NOAA in #436
391 feature find a file parser for c++ tests by @msupernaw in #434
fix: deploying pkgdown by @k-doering-NOAA in #448
fix: remove set() by @KyleShertzer-NOAA in #451
Update DESCRIPTION by @peterkuriyama-NOAA in #435
Remove bias correction/adjustment by @Bai-Li-NOAA in #452
doc: error and progress logging for information.hpp by @nathanvaughan-NOAA in #424
fix: refactor parameter constructor by @Bai-Li-NOAA in #455
doc: logit_steep correction by @ChristineStawitz-NOAA in #463
refactor add_tmb_to_fims_internal by @msupernaw in #459
Created get-gtest-codecov to create coverage.xml report for issue #242 by @MOshima-PIFSC in #470
#441: fix reviewer checklist build trigger, edit checklist by @k-doering-NOAA in #474
377 refactor call report f from modelhpp instead of fleet and population by @Andrea-Havron-NOAA in #466
Changed to by @MOshima-PIFSC in #487
411 refactor naming convention of member and local variables in the fleet class by @Bai-Li-NOAA in #476
Remove test data from fims deterministic folder by @Bai-Li-NOAA in #481
Update GHA workflows to enforce FIMS installation by @Bai-Li-NOAA in #489
renamed dimension folded indices to be clearer by @peterkuriyama-NOAA in #480
rm acomp/index nll tests objects by @ChristineStawitz-NOAA in #491
Delete test files by @ChristineStawitz-NOAA in #492
fix: update windows-2019 to windows-latest by @Bai-Li-NOAA in #495
Create multiple namespaces in FIMS by @k-doering-NOAA in #479
fix: use expect_equal() for deterministic tests by @Bai-Li-NOAA in #496
fix: build trigger only on pr being opened by @k-doering-NOAA in #498
407 updating log files by @nathanvaughan-NOAA in #499
Name refactoring for tests, growth, and median by @nathanvaughan-NOAA in #503
Fix the test for population.CalculateRecruitment() by @Bai-Li-NOAA in #508
fix: update run google test to use windows latest by @k-doering-NOAA in #511
refactor: move duplicated code into the test fixture section by @Bai-Li-NOAA in #497
Fims concurrent by @ChristineStawitz-NOAA in #520
Remove third party library rapidjson by @Bai-Li-NOAA in #519
Make Doxygen comment style the same by @k-doering-NOAA in #518
refactor recruitment deviations to log space by @Andrea-Havron-NOAA in #514
add documentation to test-fims-estimation by @Andrea-Havron-NOAA in #515
Added start_year and end_year as slots to FIMSFrame by @kellijohnson-NOAA in #501
New 464 load module by @Andrea-Havron-NOAA in #526
make log_obs_error a vector by @ChristineStawitz-NOAA in #532
Fims vector by @ChristineStawitz-NOAA in #517
Release mq by @ChristineStawitz-NOAA in #533