- updated unit tests to take into account new external package versions

- updated copyrights in all R files - refactored package documentation file
UCLouvain-CBIO · Feb 23, 2024 · d83e80f · d83e80f
1 parent 97e31fc
commit d83e80f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -32,14 +32,14 @@ Description: This package provides support for automation and visualization of
 License: GPL-3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 BugReports: https://github.com/UCLouvain-CBIO/CytoPipeline/issues
 URL: https://uclouvain-cbio.github.io/CytoPipeline
 biocViews: FlowCytometry, Preprocessing, QualityControl, WorkflowStep,
  ImmunoOncology, Software, Visualization
 Collate:
     'CytoPipeline-functions.R'
-    'CytoPipeline.R'
+    'CytoPipeline-package.R'
     'CytoPipelineClass.R'
     'CytoProcessingStep.R'
     'CytoProcessingStepImplementations.R'

diff --git a/R/CytoPipeline-functions.R b/R/CytoPipeline-functions.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/R/CytoPipeline.R → R/CytoPipeline-package.R b/R/CytoPipeline.R → R/CytoPipeline-package.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.
@@ -13,11 +13,8 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details (<http://www.gnu.org/licenses/>).
 
-
 #' @title CytoPipeline package
 #' 
-#' @docType package
-#' 
 #' @name CytoPipeline
 #'
 #' @rdname CytoPipeline
@@ -47,4 +44,10 @@
 #' 
 #' For a step by step example using `CytoPipeline`, please have a look 
 #' at the vignette!
-NULL
+#' 
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL
diff --git a/R/CytoPipelineClass.R b/R/CytoPipelineClass.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/R/CytoProcessingStep.R b/R/CytoProcessingStep.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/R/CytoProcessingStepImplementations.R b/R/CytoProcessingStepImplementations.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/R/data.R b/R/data.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/R/gating.R b/R/gating.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/R/ggplots.R b/R/ggplots.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/R/utils.R b/R/utils.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/man/CytoPipeline.Rd b/man/CytoPipeline.Rd
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/...s/testthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-logicle-translist-run.svg b/...s/testthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-logicle-translist-run.svg
diff --git a/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-translist-run.svg b/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-translist-run.svg
diff --git a/tests/testthat/test-CytoPipeline.R b/tests/testthat/test-CytoPipeline.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/tests/testthat/test-CytoProcessingStep.R b/tests/testthat/test-CytoProcessingStep.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/tests/testthat/test-CytoProcessingStepImplementations.R b/tests/testthat/test-CytoProcessingStepImplementations.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/tests/testthat/test-gating.R b/tests/testthat/test-gating.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.

diff --git a/tests/testthat/test-ggplots.R b/tests/testthat/test-ggplots.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.
@@ -416,6 +416,7 @@ test_that("ggplotFilterEvents works", {
     ) +
         ggtitle("Live gate filter")
 
+    # temporary deactivation of one unit test to have the test passed on GHA
     vdiffr::expect_doppelganger(
         "ggplotFilterEvents 2D - transList - run",
         fig = p

diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
@@ -1,4 +1,4 @@
-# CytoPipeline - Copyright (C) <2022>
+# CytoPipeline - Copyright (C) <2022-2024>
 # <Université catholique de Louvain (UCLouvain), Belgique>
 #
 #   Description and complete License: see LICENSE file.