Merge pull request #9 from OHDSI/develop

Develop
OHDSI · Jan 22, 2024 · cb807fa · cb807fa
2 parents c3c513a + 894eb60
commit cb807fa
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diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml
diff --git a/.github/workflows/nightly_cleanup_Hades.yml b/.github/workflows/nightly_cleanup_Hades.yml
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,5 @@
 .DS_Store
 inst/doc
 scratch
+hidden
+inst/templates/in_develop
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Ulysses
 Title: Automate OHDSI Study Setup
-Version: 0.0.2
+Version: 0.0.3
 Authors@R: 
     person("Martin", "Lavallee", , "[email protected]", role = c("aut", "cre"))
 Description: Automates setup of OHDSI study and provides functions to assist on improving organization

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,36 +1,39 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(addCohortFolder)
 export(addConfig)
-export(addScratchFolder)
+export(buildStudyHub)
 export(checkConfig)
 export(checkDatabaseCredential)
+export(cohortManifest)
 export(defaultCredentials)
 export(isOhdsiStudy)
+export(makeAnalysisPlan)
 export(makeAnalysisScript)
 export(makeCaprScript)
 export(makeCohortDetails)
 export(makeConfig)
 export(makeContributionGuidelines)
-export(makeExample)
 export(makeHowToRun)
 export(makeInternals)
 export(makeKeyringSetup)
 export(makeMeetingMinutes)
 export(makeNews)
 export(makeOhdsiProtocol)
-export(makePassProtocol)
 export(makeReadMe)
 export(makeResultsReport)
-export(makeStudySAP)
+export(makeStudySettings)
+export(makeTechSpecs)
 export(makeWebApiScript)
+export(moduleTable)
 export(newOhdsiStudy)
+export(previewStudyHub)
 export(publishStudyToRepository)
 export(requestStudyRepository)
 export(setCredential)
 export(setMultipleCredentials)
 export(setStudyKeyring)
+export(zipResults)
 import(fs)
 import(rlang)
 import(usethis)

diff --git a/NEWS.md b/NEWS.md
@@ -1,11 +1,24 @@
-# Ulysses 0.0.2
+Ulysses 0.0.3
+=============
+
+* add study hub builder
+* convert all documents to qmd
+* add functions to define study settings prior to build
+* add cohort functions
+    - `cohortManifest` lists cohorts used in study
+    - `makeCohortDetails` renders human-readable file to convey cohort definitions
+    - add versioning to cohort definitions
+
+Ulysses 0.0.2
+=============
 
 * Add keyring functions and update SetupKeyring.R template
 * Update repository request email template
 * Add git function to publish repo to remote
 * Fix bugs in HowToRun and KeyringSetup template
 
-# Ulysses 0.0.1
+Ulysses 0.0.1
+=============
 
 * Add initial functionality
     * file templates for: