From 34320b79d5a27b81fd89f365c10c50bfdd9b7ef3 Mon Sep 17 00:00:00 2001
From: Egill Axfjord Fridgeirsson <egillax@gmail.com>
Date: Thu, 15 Dec 2022 15:44:10 +0100
Subject: [PATCH] 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
---
 .github/workflows/R_CDM_check_hades.yaml | 1 -
 DESCRIPTION                              | 6 +++---
 NEWS.md                                  | 6 ++++++
 R/Estimator.R                            | 6 +++---
 tests/testthat/setup.R                   | 4 ++++
 5 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/R_CDM_check_hades.yaml b/.github/workflows/R_CDM_check_hades.yaml
index 7445265..3278c1a 100644
--- 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
index 13c063b..9e6c69f 100644
--- 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
index bc0a4c7..39db33a 100644
--- 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
index 00d78c5..1023113 100644
--- 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
index 93c9232..775e7e5 100644
--- 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