From 6b951035be8c6e7a21bfb64d88cb6a3bbb3827d2 Mon Sep 17 00:00:00 2001
From: luciorq <luciorqueiroz@gmail.com>
Date: Tue, 10 Dec 2024 12:09:22 -0500
Subject: [PATCH] docs: add package namespace to examples

---
 DESCRIPTION                | 2 +-
 NEWS.md                    | 6 +++++-
 R/create_env.R             | 2 +-
 R/env_exists.R             | 2 +-
 R/get_env_dir.R            | 2 +-
 R/get_install_dir.R        | 2 +-
 R/install_micromamba.R     | 2 +-
 R/install_packages.R       | 2 +-
 R/list_envs.R              | 2 +-
 R/list_packages.R          | 2 +-
 R/micromamba_bin_path.R    | 2 +-
 R/remove_env.R             | 2 +-
 R/run.R                    | 2 +-
 R/run_bin.R                | 2 +-
 R/with_sandbox_dir.R       | 4 ++--
 man/create_env.Rd          | 2 +-
 man/env_exists.Rd          | 2 +-
 man/get_env_dir.Rd         | 2 +-
 man/get_install_dir.Rd     | 2 +-
 man/install_micromamba.Rd  | 2 +-
 man/install_packages.Rd    | 2 +-
 man/list_envs.Rd           | 2 +-
 man/list_packages.Rd       | 2 +-
 man/micromamba_bin_path.Rd | 2 +-
 man/remove_env.Rd          | 2 +-
 man/run.Rd                 | 2 +-
 man/run_bin.Rd             | 2 +-
 man/with_sandbox_dir.Rd    | 4 ++--
 28 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a6b83bd..570b657 100644
--- 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", , "luciorqueiroz@gmail.com", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0002-6090-1834")),
diff --git a/NEWS.md b/NEWS.md
index d18f5da..735f14a 100644
--- 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
index 81ff472..ff21ad6 100644
--- 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
index 6b66be2..9ca2fb2 100644
--- 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
index dd89052..85dd896 100644
--- 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
index 8ba1230..2f82d5f 100644
--- 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
index c748bac..715364c 100644
--- 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
index f4237eb..fc4a674 100644
--- 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
index 31eb8d6..e9b06ed 100644
--- 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
index 1f2b5bd..a471a9a 100644
--- 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
index e7a3d40..781e122 100644
--- 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
index 7a67413..b63866f 100644
--- 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
index f3e28ee..f387ef4 100644
--- 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
index 4581fe8..2543bfc 100644
--- 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
index 40c7e2d..c8833df 100644
--- 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
index 2687fb1..bc67232 100644
--- a/man/create_env.Rd
+++ b/man/create_env.Rd
@@ -69,7 +69,7 @@ Create Conda Environment with specific packages installed to be used by \code{ru
 }
 \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/man/env_exists.Rd b/man/env_exists.Rd
index f38a729..21c3861 100644
--- a/man/env_exists.Rd
+++ b/man/env_exists.Rd
@@ -20,7 +20,7 @@ and \code{FALSE} otherwise.
 }
 \examples{
 \dontrun{
-with_sandbox_dir({
+condathis::with_sandbox_dir({
   # Create the environment
   condathis::create_env(
     packages = "fastqc",
diff --git a/man/get_env_dir.Rd b/man/get_env_dir.Rd
index 800fb8a..30c78c6 100644
--- a/man/get_env_dir.Rd
+++ b/man/get_env_dir.Rd
@@ -18,7 +18,7 @@ Retrieve path to where environment should be created.
 \strong{Note}: It retrieves the Path even if the environment is \strong{not} created yet.
 }
 \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/man/get_install_dir.Rd b/man/get_install_dir.Rd
index a7744bf..8901d97 100644
--- a/man/get_install_dir.Rd
+++ b/man/get_install_dir.Rd
@@ -22,7 +22,7 @@ as \verb{micromamba run} fails if there are spaces in the path (e.g., in \verb{~
 Therefore, Unix-style paths are used on macOS.
 }
 \examples{
-with_sandbox_dir({
+condathis::with_sandbox_dir({
   condathis::get_install_dir()
   #> /home/username/.local/share/condathis
 })
diff --git a/man/install_micromamba.Rd b/man/install_micromamba.Rd
index 47db467..9b61cb5 100644
--- a/man/install_micromamba.Rd
+++ b/man/install_micromamba.Rd
@@ -42,7 +42,7 @@ If the download fails, appropriate error messages are displayed.
 }
 \examples{
 \dontrun{
-with_sandbox_dir({
+condathis::with_sandbox_dir({
   # Install the default version of Micromamba
   condathis::install_micromamba()
 
diff --git a/man/install_packages.Rd b/man/install_packages.Rd
index b25b28a..782d208 100644
--- a/man/install_packages.Rd
+++ b/man/install_packages.Rd
@@ -45,7 +45,7 @@ Install Packages in a Existing Conda Environment
 }
 \examples{
 \dontrun{
-with_sandbox_dir({
+condathis::with_sandbox_dir({
   condathis::create_env(
     packages = "fastqc",
     env_name = "fastqc-env"
diff --git a/man/list_envs.Rd b/man/list_envs.Rd
index de28e6d..c33b52e 100644
--- a/man/list_envs.Rd
+++ b/man/list_envs.Rd
@@ -22,7 +22,7 @@ to Condathis, such as the base Conda environment itself.
 }
 \examples{
 \dontrun{
-with_sandbox_dir({
+condathis::with_sandbox_dir({
   # Create environments
   condathis::create_env(
     packages = "fastqc",
diff --git a/man/list_packages.Rd b/man/list_packages.Rd
index 73b0e7d..958bde4 100644
--- a/man/list_packages.Rd
+++ b/man/list_packages.Rd
@@ -40,7 +40,7 @@ each package, including its name, version, and source details.
 }
 \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/man/micromamba_bin_path.Rd b/man/micromamba_bin_path.Rd
index 9c1fdcc..3a3b56e 100644
--- a/man/micromamba_bin_path.Rd
+++ b/man/micromamba_bin_path.Rd
@@ -20,7 +20,7 @@ by the \code{condathis} package. The path is determined based on the system's
 operating system and architecture.
 }
 \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/man/remove_env.Rd b/man/remove_env.Rd
index e65c379..8dbd2f2 100644
--- a/man/remove_env.Rd
+++ b/man/remove_env.Rd
@@ -29,7 +29,7 @@ Remove a Conda environment previously created by \code{create_env()}.
 }
 \examples{
 \dontrun{
-with_sandbox_dir({
+condathis::with_sandbox_dir({
   condathis::create_env(
     packages = "fastqc",
     env_name = "fastqc-env"
diff --git a/man/run.Rd b/man/run.Rd
index a5f6138..55e5ad3 100644
--- a/man/run.Rd
+++ b/man/run.Rd
@@ -60,7 +60,7 @@ This is particularly useful for reproducible research and ensuring that specific
 }
 \examples{
 \dontrun{
-with_sandbox_dir({
+condathis::with_sandbox_dir({
   ## Create env
   create_env("samtools", env_name = "samtools-env")
 
diff --git a/man/run_bin.Rd b/man/run_bin.Rd
index 37ed343..c38a08f 100644
--- a/man/run_bin.Rd
+++ b/man/run_bin.Rd
@@ -59,7 +59,7 @@ load environment variables and scripts defined in the environment
 }
 \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/man/with_sandbox_dir.Rd b/man/with_sandbox_dir.Rd
index 01651af..ea3855d 100644
--- a/man/with_sandbox_dir.Rd
+++ b/man/with_sandbox_dir.Rd
@@ -31,7 +31,7 @@ used to create an isolated environment during examples and tests. The temporary
 directories are created automatically and cleaned up after execution.
 }
 \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")))
 
 }