Remove the 'slendr_' prefix in the default Python environment

bodkan · Apr 12, 2022 · eb05180 · eb05180
1 parent 609cbcb
commit eb05180
Show file tree

Hide file tree

Showing 8 changed files with 9 additions and 9 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -110,7 +110,7 @@ jobs:
           mkdir ~/R_LIBS
           echo "R_LIBS_USER=~/R_LIBS" >> ~/.Renviron
           R -e 'install.packages("reticulate", repos = "http://cran.rstudio.com")'
-          R -e 'deps <- c("msprime==1.1.1", "tskit==0.4.1", "pyslim==0.700", "pandas"); PYTHON_ENV <- paste0("slendr_", paste(gsub("==", "-", deps), collapse = "_")); reticulate::conda_create(envname = PYTHON_ENV); reticulate::use_condaenv(PYTHON_ENV, required = TRUE); reticulate::conda_install(envname = PYTHON_ENV, packages = deps, pip = TRUE)'
+          R -e 'deps <- c("msprime==1.1.1", "tskit==0.4.1", "pyslim==0.700", "pandas"); PYTHON_ENV <- paste(gsub("==", "-", deps), collapse = "_"); reticulate::conda_create(envname = PYTHON_ENV); reticulate::use_condaenv(PYTHON_ENV, required = TRUE); reticulate::conda_install(envname = PYTHON_ENV, packages = deps, pip = TRUE)'
 
       - uses: r-lib/actions/setup-pandoc@v1
 

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -85,7 +85,7 @@ jobs:
           echo "R_LIBS_USER=~/R_LIBS" >> ~/.Renviron
           R -e 'install.packages(c("BiocManager", "reticulate"), repos = "http://cran.rstudio.com")'
           R -e 'BiocManager::install("ggtree")'
-          R -e 'deps <- c("msprime==1.1.1", "tskit==0.4.1", "pyslim==0.700", "pandas"); PYTHON_ENV <- paste0("slendr_", paste(gsub("==", "-", deps), collapse = "_")); reticulate::conda_create(envname = PYTHON_ENV); reticulate::use_condaenv(PYTHON_ENV, required = TRUE); reticulate::conda_install(envname = PYTHON_ENV, packages = deps, pip = TRUE)'
+          R -e 'deps <- c("msprime==1.1.1", "tskit==0.4.1", "pyslim==0.700", "pandas"); PYTHON_ENV <- paste(gsub("==", "-", deps), collapse = "_"); reticulate::conda_create(envname = PYTHON_ENV); reticulate::use_condaenv(PYTHON_ENV, required = TRUE); reticulate::conda_install(envname = PYTHON_ENV, packages = deps, pip = TRUE)'
 
       - uses: r-lib/actions/setup-r@v1
         with:

diff --git a/R/interface.R b/R/interface.R
@@ -1305,7 +1305,7 @@ setup_env <- function(quiet = FALSE, agree = FALSE, pip = TRUE) {
       # parse the Python env name back to the list of dependencies
       # (the environment is defined in .onAttach(), and this makes sure the
       # dependencies are defined all in one place)
-      deps <- gsub("slendr_", "", PYTHON_ENV) %>% gsub("-", "==", .) %>% strsplit("_") %>% .[[1]]
+      deps <- PYTHON_ENV %>% gsub("-", "==", .) %>% strsplit("_") %>% .[[1]]
       reticulate::conda_install(envname = PYTHON_ENV, packages = deps, pip = pip)
 
       if (!quiet)

diff --git a/R/zzz.R b/R/zzz.R
@@ -8,7 +8,7 @@ msp <- NULL
 # define slendr's required Python dependencies and compose an environment name
 # that will be used specifically for them
 deps <- c("msprime==1.1.1", "tskit==0.4.1", "pyslim==0.700", "pandas")
-PYTHON_ENV <- paste0("slendr_", paste(gsub("==", "-", deps), collapse = "_"))
+PYTHON_ENV <- paste(gsub("==", "-", deps), collapse = "_")
 
 .onAttach <- function(libname, pkgname) {
   # check for presence of the slim binary in user's PATH and display

diff --git a/tests/testthat/test-msprime-geneflow.R b/tests/testthat/test-msprime-geneflow.R
@@ -1,4 +1,4 @@
-skip_if(!slendr:::check_env_present() || Sys.getenv("local_build") != TRUE)
+skip_if(!slendr:::check_env_present())
 setup_env(quiet = TRUE)
 
 # Let's start by defining a couple of parameters for our simulations

diff --git a/tests/testthat/test-msprime.R b/tests/testthat/test-msprime.R
@@ -20,7 +20,7 @@
 # generated by two completely different pieces of software after all - SLiM
 # and msprime Python library), but they should be *nearly* the same.
 
-skip_if(!slendr:::check_env_present() || Sys.getenv("local_build") != TRUE)
+skip_if(!slendr:::check_env_present())
 setup_env(quiet = TRUE)
 
 seed <- 42

diff --git a/vignettes/vignette-05-tree-sequences.Rmd b/vignettes/vignette-05-tree-sequences.Rmd
@@ -232,7 +232,7 @@ tree
 
 This means that we have the whole R phylogenetic ecosystem at our disposal to analyze such trees. For instance we can use the powerful package *ggtree* to plot the tree we have just extracted:
 
-```{r, plot_ggtree, eval = Sys.which("slim") != "" && env_present && Sys.getenv("RUNNER_OS") != "macOS" && Sys.getenv("local_build") == TRUE}
+```{r, plot_ggtree, eval = Sys.which("slim") != "" && env_present && Sys.getenv("RUNNER_OS") != "macOS" && Sys.getenv("SLENDR_LOCAL") == TRUE}
 library(ggtree)
 
 ggtree(tree) +
@@ -242,7 +242,7 @@ ggtree(tree) +
 ```
 
 
-```{r, plot_apetree, eval = Sys.which("slim") != "" && env_present && Sys.getenv("RUNNER_OS") != "macOS" && Sys.getenv("local_build") != TRUE}
+```{r, plot_apetree, eval = Sys.which("slim") != "" && env_present && Sys.getenv("RUNNER_OS") != "macOS" && Sys.getenv("SLENDR_LOCAL") != TRUE}
 library(ape)
 plot(tree)
 nodelabels()

diff --git a/vignettes/vignette-08-paper.Rmd b/vignettes/vignette-08-paper.Rmd
@@ -466,7 +466,7 @@ ancestors <- ts_ancestors(ts, "EUR_599")
 
 ### Plotting code
 
-```{r, figure_ex4, eval = Sys.getenv("local_build") == TRUE && eval_chunk && file.exists("~/Documents/postdoc/slendr/slendr_models/ex3/output_slim.trees"), fig.height=9, fig.width=7, class.source = "fold-hide"}
+```{r, figure_ex4, eval = Sys.getenv("SLENDR_LOCAL") == TRUE && eval_chunk && file.exists("~/Documents/postdoc/slendr/slendr_models/ex3/output_slim.trees"), fig.height=9, fig.width=7, class.source = "fold-hide"}
 library(ggtree)
 
 # prepare annotation table for ggtree linking R phylo node ID (not tskit integer