v2.3.0

Release Notes

All user-facing changes for this release only effect the bbi nonmem summary command and its output. There are also some changes to the CI configuration to facilitate rendering updated validation documents with babylontest and goProjectValidator.

Additions and changes

• bbi nonmem summary will no longer parse the .cov and .cor files
  • summary --json output will no longer have covariance_theta or correlation_theta elements
  • --no-cov-file and --no-cor-file flags are deprecated
• bbi nonmem covcor command now returns the json output that was formerly contained in the covariance_theta or correlation_theta elements. The --json flag is not needed for this command. It always returns json.
• The following fields were added or modified in the bbi nonmem summary --json output:
  • ofv -- Previously included the objective function value for only the last estimation method. Now includes all estimation methods.
  • condition_number -- The condition number. This will only be in the .lst file in certain cases (when scientists ask for it in the $COV block PRINT=E). There will be one for each estimation method. If any of them are large, the large_condition_number boolean under run_heuristics will be true.
  • eta_pval_significant -- Added to run_heuristics. true if any shrinkage_details.pval < 0.05. Will be false if no shrinkage file is present.
  • PRDERR -- Added to run_heuristics. Indicates whether a PRDERR file is present in the output directory.

Bug fixes

• Previously, the .shk file was not added to the files_used section of the bbi nonmem summary --json output, even when it was used. This has been fixed.

Changelog

d1dd901 Merge pull request #185 from metrumresearchgroup/develop
0907950 Merge pull request #182 from metrumresearchgroup/release/2.3.0
3fda07d changing to user-stories-230 babylontest branch for docs
550168f fix: reverting version because this is what it has on master
66e5649 fix: updated version to 2.3.0 from develop
8ae846b validation: updating story names in validation.json to match markdown in babylontest
c8057ca fix: pushing update to timeout to see if it will actually take effect
9f0bbae fix: Updating drone to use script to manually check for output that indicates failure
aa5ef72 pointing to babylontest/validation-2.3.0 branch to build validation docs
7ba072c fix: prederr to prderr in bbi summary --json
52193c0 release: added validation docs to validation.json
d15ef96 Merge pull request #176 from metrumresearchgroup/feature/new-summary-fields-2008
4ffd6cf Merge branch 'develop' of github.com:metrumresearchgroup/babylon into feature/new-summary-fields-2008
5292a7e Merge pull request #174 from metrumresearchgroup/refactor/cov-cor-out
430f72c feat: added better help messaging when nonexistent command is issued
3d1e93a fix: added explicit error msg when wrong file extension passed to summary
3433a87 fix: added PRIOR to constant parsing for Bayesian methods
be0d88a fix: fixed missing shrinkage bug in summary table method
4204a00 WIP: cleaning up old print statement
fb1d387 fix: catching empty .ext file when renamed with FILE in Janelles 1001 test model
12f2eea cleanup
855e188 WIP: made condition_number get each estimation method
0ea59f7 fix: changed so Bayesian doesnt expect shrinkage file
f9712d7 feat: added parsing objective function from multiple est methods
5ad8349 WIP: added PRDERR and answered p-value subpop question
7f8db5d WIP: adding eta_pval heuristic
e0253bc WIP: cleanup
cc25aa3 Merge pull request #173 from metrumresearchgroup/feature/add-condition-number
72aa981 WIP: added bbi nonmem covcor command, but still need to add tests
4621c4f Merge branch 'feature/add-condition-number' of github.com:metrumresearchgroup/babylon into refactor/cov-cor-out
7a5b686 fix: added main binary to .gitignore
017665d fix: fixed getConditionNumber to work with multiple lines and added test case
2f1592b cleanup: removing binary
7033041 WIP: fixed current tests
64c439d WIP: debugging testing
9ae1e27 WIP: removed cov and cor from summary and created
bc069ef Merge branch 'develop' of github.com:metrumresearchgroup/babylon into feature/add-condition-number
66fe297 WIP: first shot at condition number
f0962aa Merge pull request #171 from metrumresearchgroup/feature/custom-file-names
5a60341 fix: error if invalid modeloutput config present
21ca590 feat: implement parallel summarization of multiple models
c1d6914 feat: proper custom files and addition of total cpu time
61deae2 wip: first cut at adding custom file names for summary files
a18c7c2 fix: objective function importance sampling is not gradient based causing error due to no shrinkage
2882f34 fix: bad log statement
c607c86 Merge pull request #169 from metrumresearchgroup/fix/hash-equality