docs: add package namespace to examples

c1au6i0 · Dec 10, 2024 · 6b95103 · 6b95103
1 parent adb51f2
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: condathis
 Title: Run Any CLI Tool on a 'Conda' Environment
-Version: 0.0.8
+Version: 0.1.0
 Authors@R: c(
     person("Lucio", "Queiroz", , "[email protected]", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0002-6090-1834")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,10 +1,14 @@
+# condathis 0.1.0
+
+* Initial submission to CRAN.
+
 # condathis 0.0.8
 
 ## Breaking changes
 
 * `env_exists()` now error if no argument is supplied.
 
-* The base directory path used for creating the environments is now controlled by `tools::R_R_user_dir()` and accepts `R_USER_DATA_DIR`, and `XDG_DATA_HOME`, respectively as environment variables that can control that path. On Unix/Linux it should be `"${HOME}/.local/share/R/condathis"`.
+* The base directory path used for creating the environments is now controlled by `tools::R_user_dir()` and accepts `R_USER_DATA_DIR`, and `XDG_DATA_HOME`, respectively as environment variables that can control that path. On Unix/Linux it should be `"${HOME}/.local/share/R/condathis"`.
 
 * The default `TMPDIR` for all `run()` and `run_bin()` calls are clean after execution.
 

diff --git a/R/create_env.R b/R/create_env.R
@@ -43,7 +43,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' with_sandbox_dir({
+#' condathis::with_sandbox_dir({
 #'   # Create a Conda environment and install the CLI `fastqc` in it.
 #'   condathis::create_env(
 #'     packages = "fastqc==0.12.1",

diff --git a/R/env_exists.R b/R/env_exists.R
@@ -8,7 +8,7 @@
 #' @return Boolean. `TRUE` if the environment exists and `FALSE` otherwise.
 #' @examples
 #' \dontrun{
-#' with_sandbox_dir({
+#' condathis::with_sandbox_dir({
 #'   # Create the environment
 #'   condathis::create_env(
 #'     packages = "fastqc",

diff --git a/R/get_env_dir.R b/R/get_env_dir.R
@@ -7,7 +7,7 @@
 #' @return A character string indicating the path where environments will be created.
 
 #' @examples
-#' with_sandbox_dir({
+#' condathis::with_sandbox_dir({
 #'   # Get the default environment directory
 #'   condathis::get_env_dir()
 #'   #> "/path/to/condathis/envs/condathis-env"

diff --git a/R/get_install_dir.R b/R/get_install_dir.R
@@ -15,7 +15,7 @@
 #' A character string representing the normalized, real path to the `condathis` data directory.
 #'
 #' @examples
-#' with_sandbox_dir({
+#' condathis::with_sandbox_dir({
 #'   condathis::get_install_dir()
 #'   #> /home/username/.local/share/condathis
 #' })

diff --git a/R/install_micromamba.R b/R/install_micromamba.R
@@ -29,7 +29,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' with_sandbox_dir({
+#' condathis::with_sandbox_dir({
 #'   # Install the default version of Micromamba
 #'   condathis::install_micromamba()
 #'

diff --git a/R/install_packages.R b/R/install_packages.R
@@ -12,7 +12,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' with_sandbox_dir({
+#' condathis::with_sandbox_dir({
 #'   condathis::create_env(
 #'     packages = "fastqc",
 #'     env_name = "fastqc-env"

diff --git a/R/list_envs.R b/R/list_envs.R
@@ -13,7 +13,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' with_sandbox_dir({
+#' condathis::with_sandbox_dir({
 #'   # Create environments
 #'   condathis::create_env(
 #'     packages = "fastqc",

diff --git a/R/list_packages.R b/R/list_packages.R
@@ -20,7 +20,7 @@
 #' }
 #' @examples
 #' \dontrun{
-#' with_sandbox_dir({
+#' condathis::with_sandbox_dir({
 #'   # Creates a Conda environment with the CLI `fastqc`
 #'   condathis::create_env(
 #'     packages = "fastqc",

diff --git a/R/micromamba_bin_path.R b/R/micromamba_bin_path.R
@@ -12,7 +12,7 @@
 #'   }
 #'
 #' @examples
-#' with_sandbox_dir({
+#' condathis::with_sandbox_dir({
 #'   # Retrieve the path to where micromamba executable is searched
 #'   micromamba_path <- condathis::micromamba_bin_path()
 #'   print(micromamba_path)

diff --git a/R/remove_env.R b/R/remove_env.R
@@ -10,7 +10,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' with_sandbox_dir({
+#' condathis::with_sandbox_dir({
 #'   condathis::create_env(
 #'     packages = "fastqc",
 #'     env_name = "fastqc-env"

diff --git a/R/run.R b/R/run.R
@@ -41,7 +41,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' with_sandbox_dir({
+#' condathis::with_sandbox_dir({
 #'   ## Create env
 #'   create_env("samtools", env_name = "samtools-env")
 #'

diff --git a/R/run_bin.R b/R/run_bin.R
@@ -17,7 +17,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' with_sandbox_dir({
+#' condathis::with_sandbox_dir({
 #'   # Example assumes that 'my-env' exists and contains 'python'
 #'   # Run 'python' with a script in 'my-env' environment
 #'   condathis::run_bin(

diff --git a/R/with_sandbox_dir.R b/R/with_sandbox_dir.R
@@ -24,8 +24,8 @@
 #' Returns `NULL` invisibly.
 #'
 #' @examples
-#' with_sandbox_dir(print(fs::path_home()))
-#' with_sandbox_dir(print(tools::R_user_dir("condathis")))
+#' condathis::with_sandbox_dir(print(fs::path_home()))
+#' condathis::with_sandbox_dir(print(tools::R_user_dir("condathis")))
 #'
 #' @export
 with_sandbox_dir <- function(code, .local_envir = base::parent.frame()) {

diff --git a/man/create_env.Rd b/man/create_env.Rd
diff --git a/man/env_exists.Rd b/man/env_exists.Rd
diff --git a/man/get_env_dir.Rd b/man/get_env_dir.Rd
diff --git a/man/get_install_dir.Rd b/man/get_install_dir.Rd
diff --git a/man/install_micromamba.Rd b/man/install_micromamba.Rd
diff --git a/man/install_packages.Rd b/man/install_packages.Rd
diff --git a/man/list_envs.Rd b/man/list_envs.Rd
diff --git a/man/list_packages.Rd b/man/list_packages.Rd
diff --git a/man/micromamba_bin_path.Rd b/man/micromamba_bin_path.Rd
diff --git a/man/remove_env.Rd b/man/remove_env.Rd
diff --git a/man/run.Rd b/man/run.Rd
diff --git a/man/run_bin.Rd b/man/run_bin.Rd
diff --git a/man/with_sandbox_dir.Rd b/man/with_sandbox_dir.Rd