From d83e80f18d3e6069b45e58d85d8666211c633054 Mon Sep 17 00:00:00 2001 From: phauchamps Date: Fri, 23 Feb 2024 16:00:18 +0100 Subject: [PATCH] - updated unit tests to take into account new external package versions - updated copyrights in all R files - refactored package documentation file --- DESCRIPTION | 4 ++-- R/CytoPipeline-functions.R | 2 +- R/{CytoPipeline.R => CytoPipeline-package.R} | 13 ++++++++----- R/CytoPipelineClass.R | 2 +- R/CytoProcessingStep.R | 2 +- R/CytoProcessingStepImplementations.R | 2 +- R/data.R | 2 +- R/gating.R | 2 +- R/ggplots.R | 2 +- R/utils.R | 2 +- man/CytoPipeline.Rd | 18 +++++++++++++++++- tests/testthat.R | 2 +- ...ts-2d-x-logicle-y-logicle-translist-run.svg | 2 +- .../ggplotfilterevents-2d-translist-run.svg | 2 +- tests/testthat/test-CytoPipeline.R | 2 +- tests/testthat/test-CytoProcessingStep.R | 2 +- .../test-CytoProcessingStepImplementations.R | 2 +- tests/testthat/test-gating.R | 2 +- tests/testthat/test-ggplots.R | 3 ++- tests/testthat/test-utils.R | 2 +- 20 files changed, 45 insertions(+), 25 deletions(-) rename R/{CytoPipeline.R => CytoPipeline-package.R} (93%) diff --git a/DESCRIPTION b/DESCRIPTION index 039db16..dbc3212 100644 --- 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 index 919f18e..58a20fb 100644 --- a/R/CytoPipeline-functions.R +++ b/R/CytoPipeline-functions.R @@ -1,4 +1,4 @@ -# CytoPipeline - Copyright (C) <2022> +# CytoPipeline - Copyright (C) <2022-2024> # # # Description and complete License: see LICENSE file. diff --git a/R/CytoPipeline.R b/R/CytoPipeline-package.R similarity index 93% rename from R/CytoPipeline.R rename to R/CytoPipeline-package.R index 52ac756..bea8715 100644 --- a/R/CytoPipeline.R +++ b/R/CytoPipeline-package.R @@ -1,4 +1,4 @@ -# CytoPipeline - Copyright (C) <2022> +# CytoPipeline - Copyright (C) <2022-2024> # # # 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 (). - #' @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 \ No newline at end of file +#' +#' @keywords internal +"_PACKAGE" + +## usethis namespace: start +## usethis namespace: end +NULL diff --git a/R/CytoPipelineClass.R b/R/CytoPipelineClass.R index 517281e..39727d4 100644 --- a/R/CytoPipelineClass.R +++ b/R/CytoPipelineClass.R @@ -1,4 +1,4 @@ -# CytoPipeline - Copyright (C) <2022> +# CytoPipeline - Copyright (C) <2022-2024> # # # Description and complete License: see LICENSE file. diff --git a/R/CytoProcessingStep.R b/R/CytoProcessingStep.R index 64e04e9..0a1d313 100644 --- a/R/CytoProcessingStep.R +++ b/R/CytoProcessingStep.R @@ -1,4 +1,4 @@ -# CytoPipeline - Copyright (C) <2022> +# CytoPipeline - Copyright (C) <2022-2024> # # # Description and complete License: see LICENSE file. diff --git a/R/CytoProcessingStepImplementations.R b/R/CytoProcessingStepImplementations.R index a3a9e4f..237562e 100644 --- a/R/CytoProcessingStepImplementations.R +++ b/R/CytoProcessingStepImplementations.R @@ -1,4 +1,4 @@ -# CytoPipeline - Copyright (C) <2022> +# CytoPipeline - Copyright (C) <2022-2024> # # # Description and complete License: see LICENSE file. diff --git a/R/data.R b/R/data.R index e915c51..581a7f3 100644 --- a/R/data.R +++ b/R/data.R @@ -1,4 +1,4 @@ -# CytoPipeline - Copyright (C) <2022> +# CytoPipeline - Copyright (C) <2022-2024> # # # Description and complete License: see LICENSE file. diff --git a/R/gating.R b/R/gating.R index e7ffdb9..f1e277a 100644 --- a/R/gating.R +++ b/R/gating.R @@ -1,4 +1,4 @@ -# CytoPipeline - Copyright (C) <2022> +# CytoPipeline - Copyright (C) <2022-2024> # # # Description and complete License: see LICENSE file. diff --git a/R/ggplots.R b/R/ggplots.R index e3887ff..6944569 100644 --- a/R/ggplots.R +++ b/R/ggplots.R @@ -1,4 +1,4 @@ -# CytoPipeline - Copyright (C) <2022> +# CytoPipeline - Copyright (C) <2022-2024> # # # Description and complete License: see LICENSE file. diff --git a/R/utils.R b/R/utils.R index eb15ced..a29b7ab 100644 --- a/R/utils.R +++ b/R/utils.R @@ -1,4 +1,4 @@ -# CytoPipeline - Copyright (C) <2022> +# CytoPipeline - Copyright (C) <2022-2024> # # # Description and complete License: see LICENSE file. diff --git a/man/CytoPipeline.Rd b/man/CytoPipeline.Rd index e1a2332..c8fc759 100644 --- a/man/CytoPipeline.Rd +++ b/man/CytoPipeline.Rd @@ -1,7 +1,8 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/CytoPipeline.R +% Please edit documentation in R/CytoPipeline-package.R \docType{package} \name{CytoPipeline} +\alias{CytoPipeline-package} \alias{CytoPipeline} \title{CytoPipeline package} \description{ @@ -30,3 +31,18 @@ at the vignette! \seealso{ \link{CytoPipelineClass}, \link{CytoProcessingStep} } +\author{ +\strong{Maintainer}: Philippe Hauchamps \email{philippe.hauchamps@uclouvain.be} (\href{https://orcid.org/0000-0003-2865-1852}{ORCID}) + +Authors: +\itemize{ + \item Laurent Gatto \email{laurent.gatto@uclouvain.be} (\href{https://orcid.org/0000-0002-1520-2268}{ORCID}) +} + +Other contributors: +\itemize{ + \item Dan Lin \email{dan.8.lin@gsk.com} [contributor] +} + +} +\keyword{internal} diff --git a/tests/testthat.R b/tests/testthat.R index 531c9e6..d740c23 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -1,4 +1,4 @@ -# CytoPipeline - Copyright (C) <2022> +# CytoPipeline - Copyright (C) <2022-2024> # # # Description and complete License: see LICENSE file. diff --git a/tests/testthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-logicle-translist-run.svg b/tests/testthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-logicle-translist-run.svg index 425627a..0593d85 100644 --- a/tests/testthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-logicle-translist-run.svg +++ b/tests/testthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-logicle-translist-run.svg @@ -18,7 +18,7 @@ - + diff --git a/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-translist-run.svg b/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-translist-run.svg index 10b5da2..cd404ab 100644 --- a/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-translist-run.svg +++ b/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-translist-run.svg @@ -18,7 +18,7 @@ - + diff --git a/tests/testthat/test-CytoPipeline.R b/tests/testthat/test-CytoPipeline.R index bea2e09..9762a60 100644 --- 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> # # # Description and complete License: see LICENSE file. diff --git a/tests/testthat/test-CytoProcessingStep.R b/tests/testthat/test-CytoProcessingStep.R index 867f6bf..f923fcb 100644 --- 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> # # # Description and complete License: see LICENSE file. diff --git a/tests/testthat/test-CytoProcessingStepImplementations.R b/tests/testthat/test-CytoProcessingStepImplementations.R index 6c0a607..047114c 100644 --- 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> # # # Description and complete License: see LICENSE file. diff --git a/tests/testthat/test-gating.R b/tests/testthat/test-gating.R index 9342b9b..1a7584a 100644 --- 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> # # # Description and complete License: see LICENSE file. diff --git a/tests/testthat/test-ggplots.R b/tests/testthat/test-ggplots.R index 7de8971..caf5349 100644 --- 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> # # # 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 index aa9ea4e..5dbd830 100644 --- 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> # # # Description and complete License: see LICENSE file.