change the reticulate version

littlecabiria · littlecabiria · commit 7008d17da337 · 2025-03-14T11:58:26.000+11:00
diff --git a/src/methods/scdesign3_nb/config.vsh.yaml b/src/methods/scdesign3_nb/config.vsh.yaml
@@ -42,7 +42,15 @@ engines:
       - type: apt
         packages: [r-bioc-singlecellexperiment, git]
       - type: r
-        github: SONGDONGYUAN1994/scDesign3
+        github: 
+        - SONGDONGYUAN1994/scDesign3
+        - rstudio/reticulate@v1.40.0
+        cran:
+        - anndata
+        - reticulate==1.4.0
+      - type: python
+        packages:
+          - anndata
 
 runners:
   - type: executable
diff --git a/src/methods/scdesign3_nb/script.R b/src/methods/scdesign3_nb/script.R
@@ -13,7 +13,7 @@ meta <- list(
   name = "scdesign3"
 )
 ## VIASH END
-
+reticulate::py_config()
 cat("Read input files\n")
 input <- anndata::read_h5ad(par$input)
 
diff --git a/src/methods/scdesign3_poisson/config.vsh.yaml b/src/methods/scdesign3_poisson/config.vsh.yaml
@@ -42,7 +42,9 @@ engines:
       - type: apt
         packages: [r-bioc-singlecellexperiment, git]
       - type: r
-        github: SONGDONGYUAN1994/scDesign3
+        github: 
+        - SONGDONGYUAN1994/scDesign3
+        - rstudio/reticulate@v1.40.0
 
 runners:
   - type: executable
diff --git a/src/metrics/ks_statistic_sc_features/config.vsh.yaml b/src/metrics/ks_statistic_sc_features/config.vsh.yaml
@@ -71,10 +71,12 @@ engines:
           - resample
           - reshape2
           - spatstat
+          - anndata
         github: 
           - xuranw/MuSiC
           - YingMa0107/CARD
           - SydneyBioX/scFeatures
+          - rstudio/reticulate@v1.40.0
 
 runners:
   - type: executable
diff --git a/src/process_datasets/sc_features/config.vsh.yaml b/src/process_datasets/sc_features/config.vsh.yaml
@@ -33,7 +33,9 @@ engines:
     image: openproblems/base_r:1.0.0
     setup:
       - type: r
-        github: [SydneyBioX/scFeatures]
+        github:
+        - SydneyBioX/scFeatures
+        - rstudio/reticulate@v1.40.0
 
 runners:
   - type: executable

Original file line number	Diff line number	Diff line change
`@@ -13,7 +13,7 @@ meta <- list(`
`13`	`13`	`name = "scdesign3"`
`14`	`14`	`)`
`15`	`15`	`## VIASH END`
`16`		`-`
	`16`	`+reticulate::py_config()`
`17`	`17`	`cat("Read input files\n")`
`18`	`18`	`input <- anndata::read_h5ad(par$input)`
`19`	`19`