43 hotfix lantern binaries (#44)

* test a different way of getting torch binaries * test a different way of getting torch binaries * fix tidyselect warnings * Update description and news
OHDSI · Dec 15, 2022 · 34320b7 · 34320b7
1 parent 23b8a5c
commit 34320b7
Show file tree

Hide file tree

Showing 5 changed files with 16 additions and 7 deletions.
diff --git a/.github/workflows/R_CDM_check_hades.yaml b/.github/workflows/R_CDM_check_hades.yaml
@@ -43,7 +43,6 @@ jobs:
       CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
       CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
       CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
-      TORCH_INSTALL: 1 # so torch runs torch::install_torch() 
 
     steps:
       - uses: actions/checkout@v2

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: DeepPatientLevelPrediction
 Type: Package
 Title: Deep Learning For Patient Level Prediction Using Data In The OMOP Common Data Model
-Version: 1.0.1
-Date: 09-10-2022
+Version: 1.0.2
+Date: 15-12-2022
 Authors@R: c(
     person("Jenna", "Reps", email = "jreps@its.jnj.com", role = c("aut")), 
     person("Egill", "Fridgeirsson", email = "e.fridgeirsson@erasmusmc.nl", role = c("aut", "cre")),
@@ -13,7 +13,7 @@ Authors@R: c(
 Maintainer: Egill Fridgeirsson <e.fridgeirsson@erasmusmc.nl>
 Description: A package for creating deep learning patient level prediction models following the OHDSI PatientLevelPrediction framework.
 License: Apache License 2.0
-URL: https://ohdsi.github.io/PatientLevelPrediction, https://github.com/OHDSI/DeepPatientLevelPrediction
+URL: https://github.com/OHDSI/DeepPatientLevelPrediction
 BugReports: https://github.com/OHDSI/DeepPatientLevelPrediction/issues
 VignetteBuilder: knitr
 Depends:

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+DeepPatientLevelPrediction 1.0.2
+======================
+- Fix torch binaries issue when running tests from other github actions
+- Fix link on website
+- Fix tidyselect to silence warnings.
+
 DeepPatientLevelPrediction 1.0.1
 ======================
 - Added changelog to website

diff --git a/R/Estimator.R b/R/Estimator.R
@@ -159,8 +159,8 @@ predictDeepEstimator <- function(plpModel,
       cohort = cohort,
       mapping = plpModel$covariateImportance %>%
         dplyr::select(
-          .data$columnId,
-          .data$covariateId
+          "columnId",
+          "covariateId"
         )
     )
     data <- Dataset(mappedData$covariates,
@@ -330,7 +330,7 @@ gridCvDeep <- function(mappedData,
   )
   # modify prediction
   prediction <- prediction %>%
-    dplyr::select(-.data$index)
+    dplyr::select(-"index")
 
   prediction$cohortStartDate <- as.Date(prediction$cohortStartDate, origin = "1970-01-01")
 

diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -1,5 +1,9 @@
 library(PatientLevelPrediction)
 
+if(Sys.getenv('GITHUB_ACTIONS') == 'true') {
+  torch::install_torch()
+}
+
 testLoc <- tempdir()
 
 # get connection and data from Eunomia