Merge pull request hms-dbmi-cellenics#334 from biomage-org/update-tes…

…tthat-snapshots Upgrade testthat, update snapshots
biomage-org · Oct 17, 2023 · 44aa51c · 44aa51c
2 parents a594a67 + ad56718
commit 44aa51c
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diff --git a/pipeline-runner/renv.lock b/pipeline-runner/renv.lock
@@ -930,15 +930,10 @@
     },
     "brio": {
       "Package": "brio",
-      "Version": "1.1.2.9000",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteUsername": "r-lib",
-      "RemoteRepo": "brio",
-      "RemoteRef": "HEAD",
-      "RemoteSha": "94ebc6fd42afe5123b5f21254b857d704a4b6bbf",
-      "RemoteHost": "api.github.com",
-      "Hash": "171737b93dee71e0dd82e39998ff0223",
+      "Version": "1.1.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "976cf154dfb043c012d87cddd8bca363",
       "Requirements": []
     },
     "bslib": {
@@ -1115,13 +1110,13 @@
     },
     "desc": {
       "Package": "desc",
-      "Version": "1.3.0",
+      "Version": "1.4.2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "b6963166f7f10b970af1006c462ce6cd",
+      "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21",
       "Requirements": [
         "R6",
-        "crayon",
+        "cli",
         "rprojroot"
       ]
     },
@@ -1137,10 +1132,10 @@
     },
     "digest": {
       "Package": "digest",
-      "Version": "0.6.29",
+      "Version": "0.6.33",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "cf6b206a045a684728c3267ef7596190",
+      "Hash": "b18a9cf3c003977b0cc49d5e76ebe48d",
       "Requirements": []
     },
     "dplyr": {
@@ -1202,10 +1197,10 @@
     },
     "evaluate": {
       "Package": "evaluate",
-      "Version": "0.17",
+      "Version": "0.22",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "9171b012a55a1ef53f1442b1d798a3b4",
+      "Hash": "66f39c7a21e03c4dcb2c2d21d738d603",
       "Requirements": []
     },
     "fansi": {
@@ -1635,10 +1630,10 @@
     },
     "jsonlite": {
       "Package": "jsonlite",
-      "Version": "1.7.2",
+      "Version": "1.8.7",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "98138e0994d41508c7a6b84a0600cfcb",
+      "Hash": "266a20443ca13c65688b2116d5220f76",
       "Requirements": []
     },
     "labeling": {
@@ -1700,11 +1695,12 @@
     },
     "lifecycle": {
       "Package": "lifecycle",
-      "Version": "1.0.1",
+      "Version": "1.0.3",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "a6b6d352e3ed897373ab19d8395c98d0",
+      "Hash": "001cecbeac1cff9301bdc3775ee46a86",
       "Requirements": [
+        "cli",
         "glue",
         "rlang"
       ]
@@ -2135,16 +2131,17 @@
     },
     "pkgload": {
       "Package": "pkgload",
-      "Version": "1.3.2",
+      "Version": "1.3.3",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "6b0c222c5071efe0f3baf3dae9aa40e2",
+      "Hash": "903d68319ae9923fb2e2ee7fa8230b91",
       "Requirements": [
         "cli",
         "crayon",
         "desc",
         "fs",
         "glue",
+        "pkgbuild",
         "rlang",
         "rprojroot",
         "withr"
@@ -2224,10 +2221,10 @@
     },
     "processx": {
       "Package": "processx",
-      "Version": "3.8.0",
+      "Version": "3.8.2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "a33ee2d9bf07564efb888ad98410da84",
+      "Hash": "3efbd8ac1be0296a46c55387aeace0f3",
       "Requirements": [
         "R6",
         "ps"
@@ -2259,10 +2256,10 @@
     },
     "ps": {
       "Package": "ps",
-      "Version": "1.6.0",
+      "Version": "1.7.5",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "32620e2001c1dce1af49c49dccbb9420",
+      "Hash": "709d852d33178db54b17c722e5b1e594",
       "Requirements": []
     },
     "purrr": {
@@ -2415,10 +2412,10 @@
     },
     "rlang": {
       "Package": "rlang",
-      "Version": "1.0.6",
+      "Version": "1.1.1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "4ed1f8336c8d52c3e750adcdc57228a7",
+      "Hash": "a85c767b55f0bf9b7ad16c6d7baee5bb",
       "Requirements": []
     },
     "rpart": {
@@ -2864,10 +2861,10 @@
     },
     "testthat": {
       "Package": "testthat",
-      "Version": "3.1.6",
+      "Version": "3.2.0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "7910146255835c66e9eb272fb215248d",
+      "Hash": "877508719fcb8c9525eccdadf07a5102",
       "Requirements": [
         "R6",
         "brio",
@@ -3023,10 +3020,10 @@
     },
     "waldo": {
       "Package": "waldo",
-      "Version": "0.4.0",
+      "Version": "0.5.1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "035fba89d0c86e2113120f93301b98ad",
+      "Hash": "2c993415154cdb94649d99ae138ff5e5",
       "Requirements": [
         "cli",
         "diffobj",

diff --git a/pipeline-runner/tests/testthat/_snaps/handle_data.md b/pipeline-runner/tests/testthat/_snaps/handle_data.md
@@ -312,13 +312,13 @@
       [1] "KO"
       
       [[3]]$children[[1]]$rootNode
-      NULL
+      [1] FALSE
       
       [[3]]$children[[1]]$color
       [1] "#8c564b"
       
       [[3]]$children[[1]]$type
-      NULL
+      [1] "metadataCategorical"
       
       [[3]]$children[[1]]$cellIds
        [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
@@ -333,13 +333,13 @@
       [1] "WT1"
       
       [[3]]$children[[2]]$rootNode
-      NULL
+      [1] FALSE
       
       [[3]]$children[[2]]$color
       [1] "#d62728"
       
       [[3]]$children[[2]]$type
-      NULL
+      [1] "metadataCategorical"
       
       [[3]]$children[[2]]$cellIds
        [1] 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
@@ -370,13 +370,13 @@
       [1] "KMeta"
       
       [[4]]$children[[1]]$rootNode
-      NULL
+      [1] FALSE
       
       [[4]]$children[[1]]$color
       [1] "#8c564b"
       
       [[4]]$children[[1]]$type
-      NULL
+      [1] "metadataCategorical"
       
       [[4]]$children[[1]]$cellIds
        [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
@@ -391,13 +391,13 @@
       [1] "WMetaT"
       
       [[4]]$children[[2]]$rootNode
-      NULL
+      [1] FALSE
       
       [[4]]$children[[2]]$color
       [1] "#d62728"
       
       [[4]]$children[[2]]$type
-      NULL
+      [1] "metadataCategorical"
       
       [[4]]$children[[2]]$cellIds
        [1]  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59

diff --git a/pipeline-runner/tests/testthat/_snaps/qc-6-integrate_scdata-harmony.md b/pipeline-runner/tests/testthat/_snaps/qc-6-integrate_scdata-harmony.md
@@ -94,21 +94,21 @@
         .. .. .. ..@ misc                      :List of 1
         .. .. .. .. ..$ total.variance: num 10
         .. ..$ harmony        :Formal class 'DimReduc' [package "SeuratObject"] with 9 slots
-        .. .. .. ..@ cell.embeddings           : num [1:80, 1:2] -0.75 -0.75 2.042 -0.378 -0.75 ...
+        .. .. .. ..@ cell.embeddings           : num [1:80, 1:2] -0.7853 -0.7853 0.0789 -0.3166 -0.7853 ...
         .. .. .. .. ..- attr(*, "dimnames")=List of 2
         .. .. .. .. .. ..$ : chr [1:80] "ATGCCAGAACGACT" "CATGGCCTGTGCAT" "GAACCTGATGAACC" "TGACTGGATTCTCA" ...
         .. .. .. .. .. ..$ : chr [1:2] "harmony_1" "harmony_2"
-        .. .. .. ..@ feature.loadings          : num [1:10, 1:2] -12.3 -15 116.7 106.7 102.6 ...
+        .. .. .. ..@ feature.loadings          : num [1:10, 1:2] -13.1 -14.5 121.1 117.2 112.6 ...
         .. .. .. .. ..- attr(*, "dimnames")=List of 2
         .. .. .. .. .. ..$ : chr [1:10] "IGLL5" "CD1C" "PPBP" "PF4" ...
         .. .. .. .. .. ..$ : chr [1:2] "harmony_1" "harmony_2"
-        .. .. .. ..@ feature.loadings.projected: num [1:10, 1:2] -12.3 -15 116.7 106.7 102.6 ...
+        .. .. .. ..@ feature.loadings.projected: num [1:10, 1:2] -13.1 -14.5 121.1 117.2 112.6 ...
         .. .. .. .. ..- attr(*, "dimnames")=List of 2
         .. .. .. .. .. ..$ : chr [1:10] "IGLL5" "CD1C" "PPBP" "PF4" ...
         .. .. .. .. .. ..$ : chr [1:2] "harmony_1" "harmony_2"
         .. .. .. ..@ assay.used                : chr "RNA"
         .. .. .. ..@ global                    : logi FALSE
-        .. .. .. ..@ stdev                     : num [1:2] 1.55 1.17
+        .. .. .. ..@ stdev                     : num [1:2] 1.61 1.16
         .. .. .. ..@ key                       : chr "harmony_"
         .. .. .. ..@ jackstraw                 :Formal class 'JackStrawData' [package "SeuratObject"] with 4 slots
         .. .. .. .. .. ..@ empirical.p.values     : num[0 , 0 ] 

diff --git a/pipeline-runner/tests/testthat/_snaps/qc.md b/pipeline-runner/tests/testthat/_snaps/qc.md
@@ -465,7 +465,7 @@
     Code
       rlang::hash(snap_list$data)
     Output
-      [1] "a9264c1066779e6f23fbd8248f45cf59"
+      [1] "25e05c91587f1b98bab951258271ad1f"
     Code
       str(snap_list$data, vec.len = 20)
     Output
@@ -619,7 +619,7 @@
     Code
       rlang::hash(snap_list$guidata)
     Output
-      [1] "14aa0c10d29fb177b983c2b50bf7febb"
+      [1] "af7b2d35abd5a00b51907c07cbf87d27"
     Code
       str(snap_list$guidata, vec.len = 20)
     Output
@@ -1045,7 +1045,7 @@
     Code
       rlang::hash(snap_list$data)
     Output
-      [1] "a9264c1066779e6f23fbd8248f45cf59"
+      [1] "25e05c91587f1b98bab951258271ad1f"
     Code
       str(snap_list$data, vec.len = 20)
     Output
@@ -1625,7 +1625,7 @@
     Code
       rlang::hash(snap_list$data)
     Output
-      [1] "a9264c1066779e6f23fbd8248f45cf59"
+      [1] "25e05c91587f1b98bab951258271ad1f"
     Code
       str(snap_list$data, vec.len = 20)
     Output
@@ -2205,7 +2205,7 @@
     Code
       rlang::hash(snap_list$data)
     Output
-      [1] "a9264c1066779e6f23fbd8248f45cf59"
+      [1] "25e05c91587f1b98bab951258271ad1f"
     Code
       str(snap_list$data, vec.len = 20)
     Output
@@ -2359,7 +2359,7 @@
     Code
       rlang::hash(snap_list$guidata)
     Output
-      [1] "54e6e5937573a7cb22e708fb3bc860c2"
+      [1] "56772520d5c0c75ad75f00b75cef4cff"
     Code
       str(snap_list$guidata, vec.len = 20)
     Output
@@ -6746,7 +6746,7 @@
     Code
       rlang::hash(snap_list$data)
     Output
-      [1] "a9264c1066779e6f23fbd8248f45cf59"
+      [1] "25e05c91587f1b98bab951258271ad1f"
     Code
       str(snap_list$data, vec.len = 20)
     Output
@@ -6900,7 +6900,7 @@
     Code
       rlang::hash(snap_list$guidata)
     Output
-      [1] "7da115cc2757c7c3236acca7ec5cedc5"
+      [1] "669b3e222d74861d9845bacb04201108"
     Code
       str(snap_list$guidata, vec.len = 20)
     Output
@@ -7126,7 +7126,7 @@
     Code
       rlang::hash(snap_list$data)
     Output
-      [1] "6a4475546557490ee2b612312dc66290"
+      [1] "204d12cf36b5f4f4e752334b59d98597"
     Code
       str(snap_list$data, vec.len = 20)
     Output
@@ -7234,11 +7234,11 @@
         .. .. .. .. ..- attr(*, "dimnames")=List of 2
         .. .. .. .. .. ..$ : chr [1:584] "CGATGGCAGACTCGAG-1" "ACCGTTCGTGGTCAAG-1" "CATCCGTGTCAGTCCG-1" "GTTGCTCAGTAGCCAG-1" "CATGCTCTCTCTCGCA-1" "GGAGATGGTCTCAGAT-1" "GCAGCCATCCTGCCAT-1" "GACTCTCAGATACATG-1" "CTGGCAGGTTGCCAAT-1" "AGTAGTCAGGTGATAT-1" "TTACCGCCAACCCGCA-1" "GACTCAAAGAAGTCCG-1" "TTCACGCGTCTCGGGT-1" "ATCAGGTAGACTAAGT-1" "AACGAAAAGGAACGAA-1" "ATCCGTCGTGGCTACC-1" "TCGTGGGTCGTGTCAA-1" "GGGAGATCAGTTCACA-1" "TATCCTAAGACATACA-1" "CATCAAGTCAAAGGTA-1" ...
         .. .. .. .. .. ..$ : chr [1:30] "harmony_1" "harmony_2" "harmony_3" "harmony_4" "harmony_5" "harmony_6" "harmony_7" "harmony_8" "harmony_9" "harmony_10" "harmony_11" "harmony_12" "harmony_13" "harmony_14" "harmony_15" "harmony_16" "harmony_17" "harmony_18" "harmony_19" "harmony_20" ...
-        .. .. .. ..@ feature.loadings          : num [1:970, 1:30] 371.13 301.5 48.43 219.98 607.9 -64.65 -259.19 -257.95 35.78 -233.64 -25.87 -1092.49 63.73 -84.32 -791.32 159.95 | __truncated__ ...
+        .. .. .. ..@ feature.loadings          : num [1:970, 1:30] 371.13 301.5 48.43 219.98 607.9 -64.65 -259.19 -257.96 35.78 -233.64 -25.87 -1092.49 63.73 -84.32 -791.31 159.95 | __truncated__ ...
         .. .. .. .. ..- attr(*, "dimnames")=List of 2
         .. .. .. .. .. ..$ : chr [1:970] "CERNA1" "GPR174" "DCLK2" "AC001226.2" "PAX5" "SMG6" "EDF1" "ZNF605" "LINC02413" "ACTR3B" "AC004067.1" "HSD17B4" "AC007881.3" "KCNAB3" "PSMA3" "LIPE" "FOXJ1" "PTX3" "DCBLD1" "FUNDC1" ...
         .. .. .. .. .. ..$ : chr [1:30] "harmony_1" "harmony_2" "harmony_3" "harmony_4" "harmony_5" "harmony_6" "harmony_7" "harmony_8" "harmony_9" "harmony_10" "harmony_11" "harmony_12" "harmony_13" "harmony_14" "harmony_15" "harmony_16" "harmony_17" "harmony_18" "harmony_19" "harmony_20" ...
-        .. .. .. ..@ feature.loadings.projected: num [1:970, 1:30] 371.13 301.5 48.43 219.98 607.9 -64.65 -259.19 -257.95 35.78 -233.64 -25.87 -1092.49 63.73 -84.32 -791.32 159.95 | __truncated__ ...
+        .. .. .. ..@ feature.loadings.projected: num [1:970, 1:30] 371.13 301.5 48.43 219.98 607.9 -64.65 -259.19 -257.96 35.78 -233.64 -25.87 -1092.49 63.73 -84.32 -791.31 159.95 | __truncated__ ...
         .. .. .. .. ..- attr(*, "dimnames")=List of 2
         .. .. .. .. .. ..$ : chr [1:970] "CERNA1" "GPR174" "DCLK2" "AC001226.2" "PAX5" "SMG6" "EDF1" "ZNF605" "LINC02413" "ACTR3B" "AC004067.1" "HSD17B4" "AC007881.3" "KCNAB3" "PSMA3" "LIPE" "FOXJ1" "PTX3" "DCBLD1" "FUNDC1" ...
         .. .. .. .. .. ..$ : chr [1:30] "harmony_1" "harmony_2" "harmony_3" "harmony_4" "harmony_5" "harmony_6" "harmony_7" "harmony_8" "harmony_9" "harmony_10" "harmony_11" "harmony_12" "harmony_13" "harmony_14" "harmony_15" "harmony_16" "harmony_17" "harmony_18" "harmony_19" "harmony_20" ...
@@ -7376,7 +7376,7 @@
     Code
       rlang::hash(snap_list$guidata)
     Output
-      [1] "73c43ae03e7c42b9460bd303f65b2808"
+      [1] "0741c84a670e10c6722500ba279c0439"
     Code
       str(snap_list$guidata, vec.len = 20)
     Output
@@ -7493,7 +7493,7 @@
     Code
       rlang::hash(snap_list$data)
     Output
-      [1] "6a4475546557490ee2b612312dc66290"
+      [1] "204d12cf36b5f4f4e752334b59d98597"
     Code
       str(snap_list$data, vec.len = 20)
     Output
@@ -7601,11 +7601,11 @@
         .. .. .. .. ..- attr(*, "dimnames")=List of 2
         .. .. .. .. .. ..$ : chr [1:584] "CGATGGCAGACTCGAG-1" "ACCGTTCGTGGTCAAG-1" "CATCCGTGTCAGTCCG-1" "GTTGCTCAGTAGCCAG-1" "CATGCTCTCTCTCGCA-1" "GGAGATGGTCTCAGAT-1" "GCAGCCATCCTGCCAT-1" "GACTCTCAGATACATG-1" "CTGGCAGGTTGCCAAT-1" "AGTAGTCAGGTGATAT-1" "TTACCGCCAACCCGCA-1" "GACTCAAAGAAGTCCG-1" "TTCACGCGTCTCGGGT-1" "ATCAGGTAGACTAAGT-1" "AACGAAAAGGAACGAA-1" "ATCCGTCGTGGCTACC-1" "TCGTGGGTCGTGTCAA-1" "GGGAGATCAGTTCACA-1" "TATCCTAAGACATACA-1" "CATCAAGTCAAAGGTA-1" ...
         .. .. .. .. .. ..$ : chr [1:30] "harmony_1" "harmony_2" "harmony_3" "harmony_4" "harmony_5" "harmony_6" "harmony_7" "harmony_8" "harmony_9" "harmony_10" "harmony_11" "harmony_12" "harmony_13" "harmony_14" "harmony_15" "harmony_16" "harmony_17" "harmony_18" "harmony_19" "harmony_20" ...
-        .. .. .. ..@ feature.loadings          : num [1:970, 1:30] 371.13 301.5 48.43 219.98 607.9 -64.65 -259.19 -257.95 35.78 -233.64 -25.87 -1092.49 63.73 -84.32 -791.32 159.95 | __truncated__ ...
+        .. .. .. ..@ feature.loadings          : num [1:970, 1:30] 371.13 301.5 48.43 219.98 607.9 -64.65 -259.19 -257.96 35.78 -233.64 -25.87 -1092.49 63.73 -84.32 -791.31 159.95 | __truncated__ ...
         .. .. .. .. ..- attr(*, "dimnames")=List of 2
         .. .. .. .. .. ..$ : chr [1:970] "CERNA1" "GPR174" "DCLK2" "AC001226.2" "PAX5" "SMG6" "EDF1" "ZNF605" "LINC02413" "ACTR3B" "AC004067.1" "HSD17B4" "AC007881.3" "KCNAB3" "PSMA3" "LIPE" "FOXJ1" "PTX3" "DCBLD1" "FUNDC1" ...
         .. .. .. .. .. ..$ : chr [1:30] "harmony_1" "harmony_2" "harmony_3" "harmony_4" "harmony_5" "harmony_6" "harmony_7" "harmony_8" "harmony_9" "harmony_10" "harmony_11" "harmony_12" "harmony_13" "harmony_14" "harmony_15" "harmony_16" "harmony_17" "harmony_18" "harmony_19" "harmony_20" ...
-        .. .. .. ..@ feature.loadings.projected: num [1:970, 1:30] 371.13 301.5 48.43 219.98 607.9 -64.65 -259.19 -257.95 35.78 -233.64 -25.87 -1092.49 63.73 -84.32 -791.32 159.95 | __truncated__ ...
+        .. .. .. ..@ feature.loadings.projected: num [1:970, 1:30] 371.13 301.5 48.43 219.98 607.9 -64.65 -259.19 -257.96 35.78 -233.64 -25.87 -1092.49 63.73 -84.32 -791.31 159.95 | __truncated__ ...
         .. .. .. .. ..- attr(*, "dimnames")=List of 2
         .. .. .. .. .. ..$ : chr [1:970] "CERNA1" "GPR174" "DCLK2" "AC001226.2" "PAX5" "SMG6" "EDF1" "ZNF605" "LINC02413" "ACTR3B" "AC004067.1" "HSD17B4" "AC007881.3" "KCNAB3" "PSMA3" "LIPE" "FOXJ1" "PTX3" "DCBLD1" "FUNDC1" ...
         .. .. .. .. .. ..$ : chr [1:30] "harmony_1" "harmony_2" "harmony_3" "harmony_4" "harmony_5" "harmony_6" "harmony_7" "harmony_8" "harmony_9" "harmony_10" "harmony_11" "harmony_12" "harmony_13" "harmony_14" "harmony_15" "harmony_16" "harmony_17" "harmony_18" "harmony_19" "harmony_20" ...