Update versions of Python dependencies

bodkan · Oct 15, 2023 · 001ee58 · 001ee58
1 parent cc070e8
commit 001ee58
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -124,7 +124,7 @@ jobs:
           mkdir ~/R_LIBS
           echo "R_LIBS_USER=~/R_LIBS" >> ~/.Renviron
           R -e 'install.packages("reticulate", repos = "http://cran.rstudio.com"); reticulate::install_miniconda()'
-          R -e 'deps <- c("msprime==1.2.0", "tskit==0.5.5", "pyslim==1.0.3", "jsonschema==4.18.6"); PYTHON_ENV <- paste0("Python-3.11_", paste(gsub("==", "-", deps), collapse = "_")); reticulate::conda_create(envname = PYTHON_ENV, python_version = '3.11'); reticulate::use_condaenv(PYTHON_ENV, required = TRUE); reticulate::conda_install(envname = PYTHON_ENV, packages = c(deps, "pandas"), pip = TRUE)'
+          R -e 'deps <- c("msprime==1.2.0", "tskit==0.5.6", "pyslim==1.0.4"); PYTHON_ENV <- paste0("Python-3.11_", paste(gsub("==", "-", deps), collapse = "_")); reticulate::conda_create(envname = PYTHON_ENV, python_version = '3.11'); reticulate::use_condaenv(PYTHON_ENV, required = TRUE); reticulate::conda_install(envname = PYTHON_ENV, packages = c(deps, "pandas"), pip = TRUE)'
 
       - uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -93,7 +93,7 @@ jobs:
           mkdir ~/R_LIBS
           echo "R_LIBS_USER=~/R_LIBS" >> ~/.Renviron
           R -e 'install.packages("reticulate", repos = "http://cran.rstudio.com"); reticulate::install_miniconda()'
-          R -e 'deps <- c("msprime==1.2.0", "tskit==0.5.5", "pyslim==1.0.3", "jsonschema==4.18.6"); PYTHON_ENV <- paste0("Python-3.11_", paste(gsub("==", "-", deps), collapse = "_")); reticulate::conda_create(envname = PYTHON_ENV, python_version = '3.11'); reticulate::use_condaenv(PYTHON_ENV, required = TRUE); reticulate::conda_install(envname = PYTHON_ENV, packages = c(deps, "pandas"), pip = TRUE)'
+          R -e 'deps <- c("msprime==1.2.0", "tskit==0.5.6", "pyslim==1.0.4"); PYTHON_ENV <- paste0("Python-3.11_", paste(gsub("==", "-", deps), collapse = "_")); reticulate::conda_create(envname = PYTHON_ENV, python_version = '3.11'); reticulate::use_condaenv(PYTHON_ENV, required = TRUE); reticulate::conda_install(envname = PYTHON_ENV, packages = c(deps, "pandas"), pip = TRUE)'
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/R/interface.R b/R/interface.R
@@ -1446,7 +1446,7 @@ setup_env <- function(quiet = FALSE, agree = FALSE, pip = NULL) {
       # dependencies are defined all in one place)
       versions <- PYTHON_ENV %>% gsub("-", "==", .) %>% strsplit("_") %>% .[[1]]
       python_version <- gsub("Python==", "", versions[1])
-      package_versions <- c(versions[-1], "pandas", "jsonschema==4.18.6")
+      package_versions <- c(versions[-1], "pandas")
 
       reticulate::conda_create(envname = PYTHON_ENV, python_version = python_version)
       reticulate::use_condaenv(PYTHON_ENV, required = TRUE)

diff --git a/R/zzz.R b/R/zzz.R
@@ -9,7 +9,7 @@ msp <- NULL
 # define slendr's required Python dependencies and compose an environment name
 # that will be used specifically for them
 PYTHON_ENV <-
-  c("msprime==1.2.0", "tskit==0.5.5", "pyslim==1.0.3") %>%
+  c("msprime==1.2.0", "tskit==0.5.6", "pyslim==1.0.4") %>%
   gsub("==", "-", .) %>%
   paste(collapse = "_") %>%
   paste0("Python-3.11_", .)