test #4 for solving unit test issue with github actions

UCLouvain-CBIO · May 11, 2024 · 2402840 · 2402840
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diff --git a/tests/testthat/_snaps/gating/singletsgate-default-channels-with-fixed-nmad.svg b/tests/testthat/_snaps/gating/singletsgate-default-channels-with-fixed-nmad.svg
diff --git a/tests/testthat/_snaps/gating/singletsgate-default-channels.svg b/tests/testthat/_snaps/gating/singletsgate-default-channels.svg
diff --git a/tests/testthat/_snaps/gating/singletsgate-selected-channels.svg b/tests/testthat/_snaps/gating/singletsgate-selected-channels.svg
diff --git a/tests/testthat/_snaps/gating/singletsgates-one-after-the-other-fig1.svg b/tests/testthat/_snaps/gating/singletsgates-one-after-the-other-fig1.svg
diff --git a/tests/testthat/_snaps/gating/singletsgates-one-after-the-other-fig2.svg b/tests/testthat/_snaps/gating/singletsgates-one-after-the-other-fig2.svg
diff --git a/tests/testthat/_snaps/ggplots/ggplotevents-2d-linear-double.svg b/tests/testthat/_snaps/ggplots/ggplotevents-2d-linear-double.svg
diff --git a/tests/testthat/_snaps/ggplots/ggplotevents-2d-x-linear-y-logicle.svg b/tests/testthat/_snaps/ggplots/ggplotevents-2d-x-linear-y-logicle.svg
diff --git a/tests/testthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-linear.svg b/tests/testthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-linear.svg
diff --git a/tests/testthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-logicle-bins.svg b/tests/testthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-logicle-bins.svg
diff --git a/tests/testthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-logicle-by-markers.svg b/tests/testthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-logicle-by-markers.svg
diff --git a/...stthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-logicle-translist-not-run.svg b/...stthat/_snaps/ggplots/ggplotevents-2d-x-logicle-y-logicle-translist-not-run.svg
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-5000-points.svg b/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-5000-points.svg
diff --git a/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-all-points-interactive.svg b/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-all-points-interactive.svg
diff --git a/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-all-points.svg b/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-all-points.svg
diff --git a/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-infinite-nb-of-points.svg b/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-infinite-nb-of-points.svg
diff --git a/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-small-size.svg b/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-small-size.svg
diff --git a/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-translist-not-run.svg b/tests/testthat/_snaps/ggplots/ggplotfilterevents-2d-translist-not-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-gating.R b/tests/testthat/test-gating.R
@@ -13,114 +13,114 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details (<http://www.gnu.org/licenses/>).
 
-# # obtain OMIP021UTSamples, light-weight version used specifically for these 
-# # unit tests
-# path <- system.file("scripts",
-#                     package = "CytoPipeline"
-# )
-# 
-# source(file.path(path,"MakeOMIP021UTSamples.R"))
-# 
-# test_that("singletsGate works", {
-#     mySingletsGate <- singletsGate(OMIP021UTSamples[[1]])
-# 
-#     selectedSinglets <- flowCore::filter(
-#         OMIP021UTSamples[[1]],
-#         mySingletsGate
-#     )
-#     ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
-# 
-#     linRange <- c(0, 250000)
-#     p <- ggplotFilterEvents(
-#         ffPre = OMIP021UTSamples[[1]],
-#         ffPost = ff_l,
-#         seed = 1,
-#         xChannel = "FSC-A", xLinearRange = linRange,
-#         yChannel = "FSC-H", yLinearRange = linRange
-#     )
-# 
-#     vdiffr::expect_doppelganger("singletsGate default channels", fig = p)
-# 
-#     mySingletsGate <- singletsGate(OMIP021UTSamples[[1]], nmad = 3)
-# 
-#     selectedSinglets <- flowCore::filter(
-#         OMIP021UTSamples[[1]],
-#         mySingletsGate
-#     )
-#     ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
-# 
-#     p <- ggplotFilterEvents(
-#         ffPre = OMIP021UTSamples[[1]],
-#         ffPost = ff_l,
-#         seed = 1,
-#         xChannel = "FSC-A", xLinearRange = linRange,
-#         yChannel = "FSC-H", yLinearRange = linRange
-#     )
-# 
-#     vdiffr::expect_doppelganger(
-#         "singletsGate default channels with fixed nmad",
-#         fig = p
-#     )
-# 
-#     mySingletsGate <- singletsGate(OMIP021UTSamples[[1]],
-#         channel1 = "SSC-A",
-#         channel2 = "SSC-H"
-#     )
-# 
-#     selectedSinglets <- flowCore::filter(
-#         OMIP021UTSamples[[1]],
-#         mySingletsGate
-#     )
-#     ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
-# 
-#     p <- ggplotFilterEvents(
-#         ffPre = OMIP021UTSamples[[1]],
-#         ffPost = ff_l,
-#         seed = 1,
-#         xChannel = "SSC-A", xLinearRange = linRange,
-#         yChannel = "SSC-H", yLinearRange = linRange
-#     )
-# 
-#     vdiffr::expect_doppelganger("singletsGate selected channels", fig = p)
-# 
-#     # test application of two gates one after the other
-#     singletsGate1 <- singletsGate(OMIP021UTSamples[[1]], nmad = 3)
-#     singletsGate2 <- singletsGate(OMIP021UTSamples[[1]],
-#         channel1 = "SSC-A",
-#         channel2 = "SSC-H",
-#         filterId = "Singlets2"
-#     )
-# 
-#     singletCombinedGate <- singletsGate1 & singletsGate2
-# 
-#     selectedSinglets <- flowCore::filter(
-#         OMIP021UTSamples[[1]],
-#         singletCombinedGate
-#     )
-# 
-#     ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
-# 
-#     p1 <- ggplotFilterEvents(
-#         ffPre = OMIP021UTSamples[[1]],
-#         ffPost = ff_l,
-#         seed = 1,
-#         xChannel = "FSC-A", xLinearRange = linRange,
-#         yChannel = "FSC-H", yLinearRange = linRange
-#     )
-# 
-#     p2 <- ggplotFilterEvents(
-#         ffPre = OMIP021UTSamples[[1]],
-#         ffPost = ff_l,
-#         seed = 1,
-#         xChannel = "SSC-A", xLinearRange = linRange,
-#         yChannel = "SSC-H", yLinearRange = linRange
-#     )
-# 
-# 
-#     vdiffr::expect_doppelganger("singletsGates one after the other - fig1",
-#         fig = p1
-#     )
-#     vdiffr::expect_doppelganger("singletsGates one after the other - fig2",
-#         fig = p2
-#     )
-# })
+# obtain OMIP021UTSamples, light-weight version used specifically for these
+# unit tests
+path <- system.file("scripts",
+                    package = "CytoPipeline"
+)
+
+source(file.path(path,"MakeOMIP021UTSamples.R"))
+
+test_that("singletsGate works", {
+    mySingletsGate <- singletsGate(OMIP021UTSamples[[1]])
+
+    selectedSinglets <- flowCore::filter(
+        OMIP021UTSamples[[1]],
+        mySingletsGate
+    )
+    ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
+
+    linRange <- c(0, 250000)
+    p <- ggplotFilterEvents(
+        ffPre = OMIP021UTSamples[[1]],
+        ffPost = ff_l,
+        seed = 1,
+        xChannel = "FSC-A", xLinearRange = linRange,
+        yChannel = "FSC-H", yLinearRange = linRange
+    )
+
+    vdiffr::expect_doppelganger("singletsGate default channels", fig = p)
+
+    mySingletsGate <- singletsGate(OMIP021UTSamples[[1]], nmad = 3)
+
+    selectedSinglets <- flowCore::filter(
+        OMIP021UTSamples[[1]],
+        mySingletsGate
+    )
+    ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
+
+    p <- ggplotFilterEvents(
+        ffPre = OMIP021UTSamples[[1]],
+        ffPost = ff_l,
+        seed = 1,
+        xChannel = "FSC-A", xLinearRange = linRange,
+        yChannel = "FSC-H", yLinearRange = linRange
+    )
+
+    vdiffr::expect_doppelganger(
+        "singletsGate default channels with fixed nmad",
+        fig = p
+    )
+
+    mySingletsGate <- singletsGate(OMIP021UTSamples[[1]],
+        channel1 = "SSC-A",
+        channel2 = "SSC-H"
+    )
+
+    selectedSinglets <- flowCore::filter(
+        OMIP021UTSamples[[1]],
+        mySingletsGate
+    )
+    ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
+
+    p <- ggplotFilterEvents(
+        ffPre = OMIP021UTSamples[[1]],
+        ffPost = ff_l,
+        seed = 1,
+        xChannel = "SSC-A", xLinearRange = linRange,
+        yChannel = "SSC-H", yLinearRange = linRange
+    )
+
+    vdiffr::expect_doppelganger("singletsGate selected channels", fig = p)
+
+    # test application of two gates one after the other
+    singletsGate1 <- singletsGate(OMIP021UTSamples[[1]], nmad = 3)
+    singletsGate2 <- singletsGate(OMIP021UTSamples[[1]],
+        channel1 = "SSC-A",
+        channel2 = "SSC-H",
+        filterId = "Singlets2"
+    )
+
+    singletCombinedGate <- singletsGate1 & singletsGate2
+
+    selectedSinglets <- flowCore::filter(
+        OMIP021UTSamples[[1]],
+        singletCombinedGate
+    )
+
+    ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
+
+    p1 <- ggplotFilterEvents(
+        ffPre = OMIP021UTSamples[[1]],
+        ffPost = ff_l,
+        seed = 1,
+        xChannel = "FSC-A", xLinearRange = linRange,
+        yChannel = "FSC-H", yLinearRange = linRange
+    )
+
+    p2 <- ggplotFilterEvents(
+        ffPre = OMIP021UTSamples[[1]],
+        ffPost = ff_l,
+        seed = 1,
+        xChannel = "SSC-A", xLinearRange = linRange,
+        yChannel = "SSC-H", yLinearRange = linRange
+    )
+
+
+    vdiffr::expect_doppelganger("singletsGates one after the other - fig1",
+        fig = p1
+    )
+    vdiffr::expect_doppelganger("singletsGates one after the other - fig2",
+        fig = p2
+    )
+})