v3.4.0

Release Notes

New features and changes

• The new bbi nonmem run slurm subcommand provides support for Slurm execution. (#338)

• bbi nonmem run now always writes the underlying command's output to {model}.out as opposed to doing so only when the command succeeds. (#336)

• bbi nonmem run now logs more details about failures. (#336)

• The executable bit is no longer set when writing files that are not intended to be executed, including bbi.yaml. (#335)

Bug fixes

• bbi nonmem run did not relay its --licfile command-line argument to the underlying nmfe call. (#339)

• Some spots that parse floats from NONMEM output files did not map NaN values to the -999999999 placeholder, causing bbi nonmem summary --json to abort. (#334)

v3.3.1

Release Notes

Documentation is now available at https://metrumresearchgroup.github.io/bbi/docs/.

Changes

• The documentation of many subcommands has been updated and expanded. (#329)

Bug fixes

• bbi nonmem probs did not correctly handle its optional directory argument. (#328)

• bbi nonmem clean failed to delete files extracted from *_copied.json files (enabled when --copiedRuns is used) due to incorrect path handling. (#331)

v3.3.1-rc.1

First release candidate for version 3.3.1

v3.3.0

Release Notes

bbi nonmem run now cleans up empty WK_* files. (#306)

Changelog

• 835953e Merge pull request #311 from metrumresearchgroup/release/3.3.0
• d06cb76 NEWS.md: add entry for v3.3.0
• 83c278c Merge pull request #308 from metrumresearchgroup/test-period-scenario
• c610e19 Merge pull request #310 from metrumresearchgroup/dependabot-yaml
• c59af7b Merge pull request #309 from metrumresearchgroup/test-fix-config-setup
• b204bb9 Merge pull request #306 from metrumresearchgroup/clean-up-wk
• a1982f4 Merge pull request #307 from metrumresearchgroup/tests-drop-mtp-mod
• 12aae8e dep: update yaml.v3
• b403a86 bbi_local_test.go: check more errors when copying config
• fa552e5 bbi_local_test.go: fix deferred close of files
• 4e76bbb bbi_local_test.go: reduce repeated construction of config path
• e128829 bbi_local_test.go: set up config for each scenario
• e4d1903 bbi_local_test.go: delete unnecessary comments
• c7c4901 bbi_local_test.go: extract common setup to helper function
• 8b64c93 integration: test period_test scenario
• d4ce315 local: add ignore pattern for WK_* files
• ff61d54 nonmem: add empty WK_ files to list of files to clean up
• 300a1c9 nonmem: avoid repeating a ReadDir call
• 58b3c45 integration: delete now failing MTP models

v3.2.3

Release Notes

Bug fixes

• bbi nonmem summary omitted the problem_text key from its JSON output when a model's $PROBLEM was empty, breaking the expectation of bbr. (#299)

• bbi nonmem summary did not permit leading whitespace before a $SIM directive despite that being valid NONMEM syntax. (#301)

• bbi nonmmem run and bbi nonmem summary did not ignore commented $DATA lines. (#301)

• bbi init now warns the user if there is a collision when generating identifiers under the "nonmem" entry of bbi.yaml. (#304)

• bbi init now support NONMEM installation directories that include a period in their name. (#304)

Changelog

• 8c65e31 Merge pull request #305 from metrumresearchgroup/news-3.2.3
• 1f36d23 NEWS.md: add entries for v3.2.3
• 4479c7c Merge pull request #304 from metrumresearchgroup/init-nm-period
• ff025b4 init: sanitize config identifier for nonmem entries
• e6b7236 init: detect collision due case insensitive keys
• a306987 init: warn on identifier collisions
• 66469dd init: generate NonMemDetail map directly
• ffd1939 init: extract logic for finding installation directories to function
• e4bcf12 init: convert a panic to a returned error
• e482117 init_test: check that error is non-nil before inspecting message
• 5bcfd56 init: rename variable for style consistency
• f8a2c83 Merge pull request #301 from metrumresearchgroup/commented-data
• c88dacd Merge pull request #299 from metrumresearchgroup/empty-problem-text
• 3a2cb7e run local: ignore commented data lines
• 717d42b parse_run_details: ignore commented $DATA lines
• 1d033b3 parse_run_details: allow $SIM to start with space
• 9fad389 summary: include empty problem_text in JSON

v3.2.2

Release Notes

Bug fixes

• The bbi nonmem summary check for incomplete .lst files (added in v3.2.0) has been reworked to use an approach that is less susceptible to misfires. (#294)

• bbi nonmem run local now invokes its shell script by calling bash directly rather than relying on the shebang for compatibility with Windows and with systems that have bash installed to a different spot. (#296)

• The logic used by bbi init to detect the NONMEM directory was broken on Windows. (#296)

• The bash scripts generated by bbi nonmem run now quote tokens when needed. (#297)

Changelog

• fb3a008 Merge pull request #298 from metrumresearchgroup/news-3.2.2
• cf83638 NEWS.md: add entries for v3.2.2

v3.2.2-rc2

Changelog

• fd9237d Merge pull request #297 from metrumresearchgroup/run-quote-for-bash
• e71dc47 run: quote tokens if needed when generating shell scripts

v3.2.2-rc1

Changelog

• f08dfc3 Merge pull request #296 from metrumresearchgroup/windows-fixups
• 60dc21b run local: make "bash not found" message more helpful
• 1613aa5 run local: invoke bash directly rather than relying on shebangs
• e09a001 init: make compatible with Windows
• 92cd1ab Merge pull request #294 from metrumresearchgroup/incomplete-check-stop-time
• e01d546 integration: example2_saemimp: send output to different ext files
• 43ac75e summary: use RunEnd for incomplete run check
• d318df8 parse_run_details: tighten RunEnd parsing
• c7923d7 parse_run_details_test: check 'Stop Time' parsing

v3.2.1

Release Notes

Bug fixes

• In v3.2.0, bbi nonmem summary gained a check for incomplete .lst files. This check was inappropriately triggered by models that specify an estimation record with METHOD=CHAIN. (#289)

Changelog

• 5df36d6 Merge pull request #292 from metrumresearchgroup/news
• cffdd87 NEWS.md: add entry for v3.2.1
• 71caa91 Merge pull request #289 from metrumresearchgroup/summary-chain-false-positive
• 5ce7dfb Merge pull request #290 from metrumresearchgroup/drone-path-precedence
• 9b2591a summary: account for chain method in incomplete run check
• e6435a1 drone: move built bbi's directory to front of PATH

v3.2.0

Release Notes

New features and changes

• -maxlim=2 is now passed to nmfe by default. To disable passing -maxlim to nmfe (the old default), set the value to 0 via the --maxlim option of bbi nonmem or with a bbi.yaml entry:

  nmfe_options:
    maxlim: 0
  

  Note that the maxlim value set in an existing bbi.yaml will be respected, and that, for compatibility reasons, 100 is treated the same as 0. (#279)

• To make bbi.yaml more portable across users, bbi init no longer writes the resolved path of the bbi binary in bbi.yaml. Instead it's resolved when generating the SGE submission script. Note that any bbi_binary values in existing bbi.yaml files will still be honored. (#278)

• As of v7.5, NONMEM generates an FDATA.csv file. bbi now gives this the same clean-up treatment as FDATA. (#282)

• The "Errors" field in the bbi nonmem summary --json output is now an array of integers that identify which, if any, items in the "Results" array were unable to be summarized. Each item in the "Results" array now includes a "success" field, and, for failures, an "error_msg" field. (#272)

• bbi nonmem summary --json no longer omits elapsed time values (estimation_time, covariance_time, and cpu_time) when they are zero. (#270, #274)

Bug fixes

• bbi nonmem summary (#272, #281)

  • gained more safeguards to catch incomplete .lst files.
  • tries harder to channel underlying failures into error messages that are propagated to JSON consumers.
  • reliably exits with a non-zero status on failure.

• The .lst parser didn't consider that "$PROB" could also be spelled as "$PROBLEM", leading to "LEM" sneaking into rendered problem descriptions. (#283)

• The .lst parser failed when it encountered NaN objective function values. (#268)

• Commands that support a --json flag did not consistently relay failures to encode the JSON output. (#268)

• Several issues around parsing elapsed time metadata (estimation_time, covariance_time, and postprocess_time) have been fixed. (#270)

• bbi nonmem was supposed to accept --prdefault and --tprdefault options and relay those to nmfe as -prdefault and -tprdefault, but the options on bbi's side weren't exposed. (#280)

• Calling bbi nonmem reclean with no positional arguments triggered an indexing error rather than showing the help message. (#276)

Changelog

• 9e9694d Merge pull request #287 from metrumresearchgroup/req-check
• 218e600 validation: eliminate requirement ID gaps
• 5d9b28b Merge pull request #286 from metrumresearchgroup/news
• 6434e07 validation: prune unlinked requirements
• 9f5778c validation: fix stories with single item requirements
• 1ce3773 NEWS.md: add entries for v3.2.0
• 916833c NEWS.md: fix a typo
• cc7a7fd NEWS.md: copy over GitHub release notes for previous versions
• 20df4bb cmd/NEWS.md: delete