From f14e25d79ab550fc8c37a90c01cb4a82a7f296fb Mon Sep 17 00:00:00 2001
From: b_falquet <64274616+BFalquet@users.noreply.github.com>
Date: Mon, 8 Apr 2024 18:03:34 +0200
Subject: [PATCH 1/2] error in pca snapshot (#377)

close #378

add timeout before setting input to ensure that update is performed
correctly.

thank you for the review

Co-authored-by: benoit <benoit.falquet@roche.com>
---
 tests/testthat/_snaps/pca.md | 18 +++++++++---------
 tests/testthat/test-pca.R    |  6 ++++++
 2 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/tests/testthat/_snaps/pca.md b/tests/testthat/_snaps/pca.md
index a3bee8c6..3158989b 100644
--- a/tests/testthat/_snaps/pca.md
+++ b/tests/testthat/_snaps/pca.md
@@ -44,15 +44,15 @@
       cat(res)
     Output
                   x           y PANEL group shape colour size fill alpha stroke
-      1 -0.68789565  0.04912578     1    -1    19  black  1.5   NA    NA    0.5
-      2 -0.37824954  0.19209841     1    -1    19  black  1.5   NA    NA    0.5
-      3  0.07502276 -0.31568702     1    -1    19  black  1.5   NA    NA    0.5
-      4  0.33995282 -0.26532014     1    -1    19  black  1.5   NA    NA    0.5
-      5  0.29004708  0.25038379     1    -1    19  black  1.5   NA    NA    0.5
-      6  0.08718694  0.09422278     1    -1    19  black  1.5   NA    NA    0.5
-      7  0.15015883  0.07932206     1    -1    19  black  1.5   NA    NA    0.5
-      8 -0.05952522 -0.58893592     1    -1    19  black  1.5   NA    NA    0.5
-      9  0.18330198  0.50479025     1    -1    19  black  1.5   NA    NA    0.5
+      1  0.22531097  0.04912578     1    -1    19  black  1.5   NA    NA    0.5
+      2 -0.32245662  0.19209841     1    -1    19  black  1.5   NA    NA    0.5
+      3  0.19042723 -0.31568702     1    -1    19  black  1.5   NA    NA    0.5
+      4 -0.12543919 -0.26532014     1    -1    19  black  1.5   NA    NA    0.5
+      5  0.29815055  0.25038379     1    -1    19  black  1.5   NA    NA    0.5
+      6  0.54809249  0.09422278     1    -1    19  black  1.5   NA    NA    0.5
+      7 -0.06706013  0.07932206     1    -1    19  black  1.5   NA    NA    0.5
+      8 -0.30521740 -0.58893592     1    -1    19  black  1.5   NA    NA    0.5
+      9 -0.44180789  0.50479025     1    -1    19  black  1.5   NA    NA    0.5
 
 ---
 
diff --git a/tests/testthat/test-pca.R b/tests/testthat/test-pca.R
index 0c2115a7..8234442b 100644
--- a/tests/testthat/test-pca.R
+++ b/tests/testthat/test-pca.R
@@ -112,12 +112,18 @@ test_that("pca module works as expected in the test app", {
   # label option and matrix option.
   app$set_inputs(!!ns("tab_selected") := "PCA")
   app$set_inputs(!!ns("assay-name") := "rpkm")
+  app$wait_for_idle(timeout = 30000) # Important to ensure update of x_var.
   app$set_inputs(!!ns("x_var") := "3")
   app$set_inputs(!!ns("y_var") := "4")
   app$set_inputs(!!ns("var_pct") := FALSE)
   app$set_inputs(!!ns("label") := FALSE)
 
   app$wait_for_idle(timeout = 30000)
+  res <- app$get_value(input = ns("x_var"))
+  expect_identical(res, "3")
+  res <- app$get_value(input = ns("y_var"))
+  expect_identical(res, "4")
+
   res <- app$get_value(output = ns("test_pca"))
   expect_snapshot(
     cat(res)

From 6dd18442b3700002984a5e74c97d33efab18fb53 Mon Sep 17 00:00:00 2001
From: BFalquet <BFalquet@users.noreply.github.com>
Date: Mon, 8 Apr 2024 16:04:41 +0000
Subject: [PATCH 2/2] [skip actions] Bump version to 0.1.6.9011

---
 .pre-commit-config.yaml | 2 +-
 DESCRIPTION             | 4 ++--
 NEWS.md                 | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 50710b55..d93d8523 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -122,7 +122,7 @@ repos:
           design/.*
           )$
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
         args: ["--maxkb=1000"]
diff --git a/DESCRIPTION b/DESCRIPTION
index 34c653ea..a5cba889 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.hermes
 Title: RNA-Seq Analysis Modules to Add to a Teal Application
-Version: 0.1.6.9010
-Date: 2024-04-02
+Version: 0.1.6.9011
+Date: 2024-04-08
 Authors@R: c(
     person("Daniel", "Sabanés Bové", , "daniel.sabanes_bove@roche.com", role = c("aut", "cre")),
     person("Nikolas", "Burkoff", role = "aut"),
diff --git a/NEWS.md b/NEWS.md
index de8aac06..cf962d76 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# teal.modules.hermes 0.1.6.9010
+# teal.modules.hermes 0.1.6.9011
 
 ### Miscellaneous
 * Added placeholders for `assaySpec`, `adtteSpec` and `geneSpec` inputs when no option is selected.