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Merge pull request #371 from hms-dbmi-cellenics/fix-geosketch
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fix numpy version; update snaps
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@alexvpickering
alexvpickering authored Sep 18, 2024
2 parents 12f7dba + 1cfab7f commit 7819c16
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2 changes: 1 addition & 1 deletion pipeline-runner/Dockerfile
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Expand Up @@ -72,7 +72,7 @@ RUN echo ".libPaths(c('$RENV_LIB', .libPaths()))" >> $(R RHOME)/etc/Rprofile.sit
# install python packages in virtualenv
ENV WORKON_HOME=/src/.virtualenvs
RUN R -q -e "reticulate::virtualenv_create('r-reticulate', python='$(which python3)')" && \
R -q -e "reticulate::virtualenv_install('r-reticulate', c('geosketch==1.2', 'scanorama==1.7.3'), pip_options='--no-cache-dir')"
R -q -e "reticulate::virtualenv_install('r-reticulate', c('geosketch==1.2', 'scanorama==1.7.3', 'numpy<2'), pip_options='--no-cache-dir')"

# ---------------------------------------------------
# PRODUCTION BUILD
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61 changes: 21 additions & 40 deletions pipeline-runner/tests/testthat/_snaps/qc-6-integrate_scdata-seuratv4.md
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Expand Up @@ -6,64 +6,45 @@
Formal class 'Seurat' [package "SeuratObject"] with 13 slots
..@ assays :List of 2
.. ..$ RNA :Formal class 'Assay5' [package "SeuratObject"] with 8 slots
.. .. .. ..@ layers :List of 6
.. .. .. .. ..$ counts.1 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. .. .. .. .. .. ..@ i : int [1:6516] 1 5 8 11 22 30 33 34 36 38 ...
.. .. .. .. .. .. ..@ p : int [1:121] 0 47 99 149 205 258 306 342 387 423 ...
.. .. .. .. .. .. ..@ Dim : int [1:2] 230 120
.. .. .. ..@ layers :List of 3
.. .. .. .. ..$ scale.data: num [1:230, 1:240] -0.476 1.47 -0.487 -1.34 -0.374 ...
.. .. .. .. ..$ data :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. .. .. .. .. .. ..@ i : int [1:13368] 1 5 8 11 22 30 33 34 36 38 ...
.. .. .. .. .. .. ..@ p : int [1:241] 0 47 99 149 205 258 306 342 387 423 ...
.. .. .. .. .. .. ..@ Dim : int [1:2] 230 240
.. .. .. .. .. .. ..@ Dimnames:List of 2
.. .. .. .. .. .. .. ..$ : NULL
.. .. .. .. .. .. .. ..$ : NULL
.. .. .. .. .. .. ..@ x : num [1:6516] 1 1 3 1 1 4 1 5 1 1 ...
.. .. .. .. .. .. ..@ x : num [1:13368] 4.97 4.97 6.06 4.97 4.97 ...
.. .. .. .. .. .. ..@ factors : list()
.. .. .. .. ..$ counts.2 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. .. .. .. .. .. ..@ i : int [1:6852] 22 31 42 43 46 47 48 52 55 60 ...
.. .. .. .. .. .. ..@ p : int [1:121] 0 60 121 165 197 244 284 332 387 439 ...
.. .. .. .. .. .. ..@ Dim : int [1:2] 230 120
.. .. .. .. ..$ counts :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. .. .. .. .. .. ..@ i : int [1:13368] 1 5 8 11 22 30 33 34 36 38 ...
.. .. .. .. .. .. ..@ p : int [1:241] 0 47 99 149 205 258 306 342 387 423 ...
.. .. .. .. .. .. ..@ Dim : int [1:2] 230 240
.. .. .. .. .. .. ..@ Dimnames:List of 2
.. .. .. .. .. .. .. ..$ : NULL
.. .. .. .. .. .. .. ..$ : NULL
.. .. .. .. .. .. ..@ x : num [1:6852] 7 1 2 2 1 1 1 2 2 1 ...
.. .. .. .. .. .. ..@ x : num [1:13368] 1 1 3 1 1 4 1 5 1 1 ...
.. .. .. .. .. .. ..@ factors : list()
.. .. .. .. ..$ data.1 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. .. .. .. .. .. ..@ i : int [1:6516] 1 5 8 11 22 30 33 34 36 38 ...
.. .. .. .. .. .. ..@ p : int [1:121] 0 47 99 149 205 258 306 342 387 423 ...
.. .. .. .. .. .. ..@ Dim : int [1:2] 230 120
.. .. .. .. .. .. ..@ Dimnames:List of 2
.. .. .. .. .. .. .. ..$ : NULL
.. .. .. .. .. .. .. ..$ : NULL
.. .. .. .. .. .. ..@ x : num [1:6516] 4.97 4.97 6.06 4.97 4.97 ...
.. .. .. .. .. .. ..@ factors : list()
.. .. .. .. ..$ scale.data.1: num [1:230, 1:120] -0.476 1.47 -0.487 -1.34 -0.374 ...
.. .. .. .. ..$ data.2 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. .. .. .. .. .. ..@ i : int [1:6852] 22 31 42 43 46 47 48 52 55 60 ...
.. .. .. .. .. .. ..@ p : int [1:121] 0 60 121 165 197 244 284 332 387 439 ...
.. .. .. .. .. .. ..@ Dim : int [1:2] 230 120
.. .. .. .. .. .. ..@ Dimnames:List of 2
.. .. .. .. .. .. .. ..$ : NULL
.. .. .. .. .. .. .. ..$ : NULL
.. .. .. .. .. .. ..@ x : num [1:6852] 6.11 4.18 4.86 4.86 4.18 ...
.. .. .. .. .. .. ..@ factors : list()
.. .. .. .. ..$ scale.data.2: num [1:230, 1:120] -0.339 -0.571 -0.367 -1.417 -0.281 ...
.. .. .. ..@ cells :Formal class 'LogMap' [package "SeuratObject"] with 1 slot
.. .. .. .. .. ..@ .Data: logi [1:240, 1:6] TRUE TRUE TRUE TRUE TRUE TRUE ...
.. .. .. .. .. ..@ .Data: logi [1:240, 1:3] TRUE TRUE TRUE TRUE TRUE TRUE ...
.. .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
.. .. .. .. .. .. .. ..$ : chr [1:240] "ATGCCAGAACGACT" "CATGGCCTGTGCAT" "GAACCTGATGAACC" "TGACTGGATTCTCA" ...
.. .. .. .. .. .. .. ..$ : chr [1:6] "counts.1" "data.1" "scale.data.1" "counts.2" ...
.. .. .. .. .. ..$ dim : int [1:2] 240 6
.. .. .. .. .. .. .. ..$ : chr [1:3] "counts" "data" "scale.data"
.. .. .. .. .. ..$ dim : int [1:2] 240 3
.. .. .. .. .. ..$ dimnames:List of 2
.. .. .. .. .. .. ..$ : chr [1:240] "ATGCCAGAACGACT" "CATGGCCTGTGCAT" "GAACCTGATGAACC" "TGACTGGATTCTCA" ...
.. .. .. .. .. .. ..$ : chr [1:6] "counts.1" "data.1" "scale.data.1" "counts.2" ...
.. .. .. .. .. .. ..$ : chr [1:3] "counts" "data" "scale.data"
.. .. .. ..@ features :Formal class 'LogMap' [package "SeuratObject"] with 1 slot
.. .. .. .. .. ..@ .Data: logi [1:230, 1:6] TRUE TRUE TRUE TRUE TRUE TRUE ...
.. .. .. .. .. ..@ .Data: logi [1:230, 1:3] TRUE TRUE TRUE TRUE TRUE TRUE ...
.. .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
.. .. .. .. .. .. .. ..$ : chr [1:230] "MS4A1" "CD79B" "CD79A" "HLA-DRA" ...
.. .. .. .. .. .. .. ..$ : chr [1:6] "counts.1" "data.1" "scale.data.1" "counts.2" ...
.. .. .. .. .. ..$ dim : int [1:2] 230 6
.. .. .. .. .. .. .. ..$ : chr [1:3] "counts" "data" "scale.data"
.. .. .. .. .. ..$ dim : int [1:2] 230 3
.. .. .. .. .. ..$ dimnames:List of 2
.. .. .. .. .. .. ..$ : chr [1:230] "MS4A1" "CD79B" "CD79A" "HLA-DRA" ...
.. .. .. .. .. .. ..$ : chr [1:6] "counts.1" "data.1" "scale.data.1" "counts.2" ...
.. .. .. ..@ default : int 2
.. .. .. .. .. .. ..$ : chr [1:3] "counts" "data" "scale.data"
.. .. .. ..@ default : int 1
.. .. .. ..@ assay.orig: chr(0)
.. .. .. ..@ meta.data :'data.frame': 230 obs. of 14 variables:
.. .. .. .. ..$ vf_vst_counts.1_mean : num [1:230] 0.508 0.675 0.858 11.025 0.367 ...
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