Release v3.3.0 #1096
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Release v3.3.0 #1096
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* FIx for namespace of characterization_view * Update server.R
* Added forced removal of cohorts with 0 counts from cohort definition set before analysis steps * Updated version number * Added utility to shiny deploy and updated shiny app aspects to enforce OhdsiShinyModules 2.0.0 * Added code to run on sampled cohorts * removed debug code * rcheck changes * fixes for errors and warnings * removal of warning * nchar fix for null sql * have cohort concept sets function exit cleanly * Fix for empty concept sets returned * Fix for empty concept sets returned * Fix exported null concepts in included_source_concept result * Fix exported null concepts in included_source_concept result * renamed migration file * renamed migration files * Fixes for export and migration of source concepts * Package Maintenance * removed broken migrations * concept_id instead of 0 where not set
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1096 +/- ##
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- Coverage 90.34% 88.53% -1.82%
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Files 19 19
Lines 3606 3682 +76
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+ Hits 3258 3260 +2
- Misses 348 422 +74 ☔ View full report in Codecov by Sentry. |
# Conflicts: # DESCRIPTION # NEWS.md # R/CohortCharacterizationDiagnostics.R # docs/404.html # docs/articles/CreatingAStudyPackage.html # docs/articles/DatabaseModeInDiagnosticsExplorer.html # docs/articles/RunningCohortDiagnostics.html # docs/articles/ViewingResultsUsingDiagnosticsExplorer.html # docs/articles/WhatIsCohortDiagnostics.html # docs/articles/index.html # docs/authors.html # docs/index.html # docs/news/index.html # docs/pkgdown.yml # docs/reference/CohortDiagnostics-package.html # docs/reference/checkInputFileEncoding.html # docs/reference/createDiagnosticsExplorerZip.html # docs/reference/createMergedResultsFile.html # docs/reference/createResultsDataModel.html # docs/reference/executeDiagnostics.html # docs/reference/getCdmDataSourceInformation.html # docs/reference/getCohortCounts.html # docs/reference/getDataMigrator.html # docs/reference/getDefaultCovariateSettings.html # docs/reference/getDefaultVocabularyTableNames.html # docs/reference/getResultsDataModelSpecifications.html # docs/reference/index.html # docs/reference/launchDiagnosticsExplorer.html # docs/reference/migrateDataModel.html # docs/reference/runCohortRelationshipDiagnostics.html # docs/reference/runCohortTimeSeriesDiagnostics.html # docs/reference/uploadResults.html # docs/sitemap.xml # extras/CohortDiagnostics.pdf # inst/doc/RunningCohortDiagnostics.pdf # inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf # inst/doc/WhatIsCohortDiagnostics.pdf # inst/sql/sql_server/UpdateVersionNumber.sql
# Conflicts: # DESCRIPTION # NEWS.md # docs/404.html # docs/articles/CreatingAStudyPackage.html # docs/articles/DatabaseModeInDiagnosticsExplorer.html # docs/articles/RunningCohortDiagnostics.html # docs/articles/ViewingResultsUsingDiagnosticsExplorer.html # docs/articles/WhatIsCohortDiagnostics.html # docs/articles/index.html # docs/authors.html # docs/index.html # docs/news/index.html # docs/pkgdown.yml # docs/reference/CohortDiagnostics-package.html # docs/reference/checkInputFileEncoding.html # docs/reference/createDiagnosticsExplorerZip.html # docs/reference/createMergedResultsFile.html # docs/reference/createResultsDataModel.html # docs/reference/executeDiagnostics.html # docs/reference/getCdmDataSourceInformation.html # docs/reference/getCohortCounts.html # docs/reference/getDataMigrator.html # docs/reference/getDefaultCovariateSettings.html # docs/reference/getDefaultVocabularyTableNames.html # docs/reference/getResultsDataModelSpecifications.html # docs/reference/index.html # docs/reference/launchDiagnosticsExplorer.html # docs/reference/migrateDataModel.html # docs/reference/runCohortRelationshipDiagnostics.html # docs/reference/runCohortTimeSeriesDiagnostics.html # docs/reference/uploadResults.html # docs/sitemap.xml # extras/CohortDiagnostics.pdf # inst/doc/RunningCohortDiagnostics.pdf # inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf # inst/doc/WhatIsCohortDiagnostics.pdf # inst/sql/sql_server/UpdateVersionNumber.sql
* Make data exportable handles empty data frame
* Update R_CMD_check_Hades.yaml * Create R_CMD_check_sqlite_only.yaml * skip test with unset variables * skip test with unset variables * skip on develop and main
* New branch for testing patch * Fixes for sampled usage and docs - changed api * removed parameter
* Fix subset conceptset analysis * Handle empty index event breakdown results * Fix tests failure when postgres is not configured --------- Co-authored-by: Gennadiy Anisimov <gennadiy.anisimov@softwarecountry.com>
…resolved in database connector
…n issue is resolved
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Please note that because you have this PR open, any push to the develop branch will trigger Github Actions twice, once for the push to develop, and once for the PR. This means all unit tests etc. are executed twice. Not only not a very efficient use of resources, but might also lead to errors because of concurrent runs (e.g. one process trying to run on cohorts the other process just deleted). I recommend either closing this PR until you are ready to release (I actually don't use PRs, I just merge into main when ready), or creating a separate release branch. |
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I created a v3.3.0 branch |
* Tidy up of cohort overlap/relationships tables * update specs and include descriptions
* Modified checksum calculation in cohort relationships * checksum test fix * Correct use of keys to overwrite old data * fix for tests * removed code changes that are out of scope
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This release resolves a large number of issues with the package but will Require a cohort generator release first for the sampling functionality (which should greatly speed up phenotype development).