Releases: metrumresearchgroup/bbi
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
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 theproblem_text
key from its JSON output when a model's$PROBLEM
was empty, breaking the expectation ofbbr
. (#299) -
bbi nonmem summary
did not permit leading whitespace before a$SIM
directive despite that being valid NONMEM syntax. (#301) -
bbi nonmmem run
andbbi 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 ofbbi.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 callingbash
directly rather than relying on the shebang for compatibility with Windows and with systems that havebash
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
v3.2.2-rc2
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 withMETHOD=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 tonmfe
by default. To disable passing-maxlim
tonmfe
(the old default), set the value to 0 via the--maxlim
option ofbbi nonmem
or with abbi.yaml
entry:nmfe_options: maxlim: 0
Note that the
maxlim
value set in an existingbbi.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 inbbi.yaml
. Instead it's resolved when generating the SGE submission script. Note that anybbi_binary
values in existingbbi.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
, andcpu_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.
- gained more safeguards to catch incomplete
-
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 encounteredNaN
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
, andpostprocess_time
) have been fixed. (#270) -
bbi nonmem
was supposed to accept--prdefault
and--tprdefault
options and relay those tonmfe
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
v3.2.0-rc.1
Changelog
- 9fdf0af Merge pull request #282 from metrumresearchgroup/fdata-csv
- 103d6a8 Merge pull request #283 from metrumresearchgroup/nmparser-prob
- 8209989 AssertNonMemCreatedOutputFiles: check more complete list of files
- 5a8e41c Merge pull request #284 from metrumresearchgroup/help-typos
- 0c8ea9e nonmem: fix two help output typos
- c0aff14 nmparser: handle $PROBLEM in addition to $PROB
- 35a31df TestParseRunDetails: make input differences clearer
- 921763e TestParseRunDetails: drop a comment
- c062ae9 nonmem: clean up FDATA.csv
- 81d9651 integration: add and wire up AssertNonMemCleanedUpFiles
- 6c2d71f integration: specify NONMEM version for NMQUAL tests separately
- c46a4e2 Merge pull request #281 from metrumresearchgroup/invalid-lst-check
- 64d3ca4 GetModelOutput: return error if lst does not have $DATA line
- 4bfb420 integration: allow specifying bbi args in TestSummaryErrors cases
- 1d60a24 summary: sort Errors field
- 1471131 Merge pull request #278 from metrumresearchgroup/unresolve-bbi-binary
- 148f501 Merge pull request #279 from metrumresearchgroup/maxlim
- 6825e7d Merge pull request #280 from metrumresearchgroup/fix-unlinked-nfme-cli-opts
- 75e5020 Merge pull request #272 from metrumresearchgroup/summary-json-errors
- 39ac45d Merge pull request #276 from metrumresearchgroup/reclean-oob
- 98e28bc Merge pull request #277 from metrumresearchgroup/drone-update-lint
- 9887958 nonmem: expose PRDefault and TPRDefault as command line options
- 3a3229a configlib: drop inaccurate MaxLim comment
- b30413e nonmem: pass -maxlim=2 to nmfe by default
- c6e66f7 validation: add orphan requirement to BBI-RUN-004
- 6a08483 integration/init_test.go: test default maxlim value
- a697fff nonmem: tweak --maxlim description
- 4ac396e nonmem: also treat maxlim=0 as special case
- dfaa9da nonmem: tighten maxlim value special casing
- 807cbf8 sge: use process bbi executable in scripts unless overridden
- f09283b sge: clarify description of bbi_binary flag
- 636264a drone: update to latest golangci-lint
- f5d4d9e cmd: don't double print error return by cmd.Execute
- c0bf4b0 reclean: add positional argument to usage output
- 19a1da7 reclean: avoid index error if no positional argument is specified
- 8a7b589 integration: add simple test for reclean command