bugfixes for non-Rstudio

PredictiveEcology · Oct 24, 2024 · 3ad477a · 3ad477a
1 parent 92b6679
commit 3ad477a
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Showing 4 changed files with 102 additions and 87 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -5,8 +5,8 @@ Description: Quickly setup a 'SpaDES' project directories and add modules using
 URL:
     https://spades-project.predictiveecology.org/,
     https://github.com/PredictiveEcology/SpaDES.project
-Date: 2024-10-23
-Version: 0.1.0.9014
+Date: 2024-10-24
+Version: 0.1.0.9015
 Authors@R: c(
     person("Eliot J B", "McIntire", email = "[email protected]",
            role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6914-8316")),

diff --git a/R/setupProject.R b/R/setupProject.R
@@ -2432,8 +2432,12 @@ setupRestart <- function(updateRprofile, paths, name, inProject,
     }
   }
 
-  if ( (interactive() && (isTRUE(Restart) || is.character(Restart)) ) && isRstudio()
-       || !(useGit %in% FALSE)) {# getOption("SpaDES.project.Restart", TRUE))
+  if (!isRstudio()) {
+    Restart <- FALSE
+  }
+
+  if ( (interactive() && (isTRUE(Restart) || is.character(Restart)) ) && isRstudio() ||
+       !(useGit %in% FALSE)) {# getOption("SpaDES.project.Restart", TRUE))
 
     on.exit(setwd(origGetWd), add = TRUE)
 
@@ -2443,16 +2447,18 @@ setupRestart <- function(updateRprofile, paths, name, inProject,
     }
     pp <- path.expand(paths[["projectPath"]])
     isRstudioProj <- rprojroot::is_rstudio_project$testfun[[1]](pp)
-    curRstudioProj <- rstudioapi::getActiveProject()
-    isRstudioProj <- isRstudioProj && isTRUE(basename2(curRstudioProj) %in% basename(pp))
+    if (isRstudio()) {
+      curRstudioProj <- rstudioapi::getActiveProject()
+      isRstudioProj <- isRstudioProj && isTRUE(basename2(curRstudioProj) %in% basename(pp))
+    }
     # inProject <- isInProject(name)
 
-    if (!inProject || !isRstudioProj) {
-      if (requireNamespace("rstudioapi", lib.loc = paths[["packagePath"]])) {
-        messageVerbose("... restarting Rstudio inside the project",
-                       verbose = verbose)
+    if ((!inProject || !isRstudioProj)) {
+      if (requireNamespace("rstudioapi", lib.loc = paths[["packagePath"]]) && isRstudio() ) {
         wasUnsaved <- FALSE
         wasLastActive <- FALSE
+        messageVerbose("... restarting Rstudio inside the project",
+                       verbose = verbose)
         activeFile <- rstudioapi::getSourceEditorContext()$path
         if (!is.character(Restart)) {
           rstudioUnsavedFile <- "~/.active-rstudio-document"
@@ -2549,95 +2555,99 @@ setupRestart <- function(updateRprofile, paths, name, inProject,
                            ")")
         cat(addToTempFile, file = tempfileInOther, sep = "\n")
         cat(newRprofile, file = RprofileInOther, sep = "\n")
-        cloned <- FALSE
 
-        if (((!useGit %in% FALSE) && requireNamespace("usethis") && requireNamespace("gh") &&
-             requireNamespace("gitcreds")) && cloned %in% FALSE ) {
+      }
+
+      cloned <- FALSE
+      if (((!useGit %in% FALSE) && requireNamespace("usethis") && requireNamespace("gh") &&
+           requireNamespace("gitcreds")) && cloned %in% FALSE ) {
 
-          basenameName <- basename(name)
-          needGitUserName <- TRUE
-          if (is.character(useGit)) {
-            if (useGit != "sub") {
-              needGitUserName <- FALSE
-              gitUserName <- useGit
-            }
+        basenameName <- basename(name)
+        needGitUserName <- TRUE
+        if (is.character(useGit)) {
+          if (useGit != "sub") {
+            needGitUserName <- FALSE
+            gitUserName <- useGit
           }
+        }
 
-          if (needGitUserName) {
-            mess <- capture.output(
-              type = "message",
-              gitUserNamePoss <- gh::gh_whoami()$login)
-            if (is.null(gitUserNamePoss)) {
-              stop(paste(c(mess, "or try gitcreds::gitcreds_set()"), collapse = "\n"))
-            }
-            messageVerbose(msgNeedGitUserName(gitUserNamePoss), verbose = interactive() * 10)
-            gitUserName <- if (interactive()) readline() else gitUserNamePoss
-            if (!nzchar(gitUserName)) {
-              gitUserName <- gitUserNamePoss
-              needGitUserName <- FALSE
-            }
-
+        if (needGitUserName) {
+          mess <- capture.output(
+            type = "message",
+            gitUserNamePoss <- gh::gh_whoami()$login)
+          if (is.null(gitUserNamePoss)) {
+            stop(paste(c(mess, "or try gitcreds::gitcreds_set()"), collapse = "\n"))
           }
+          messageVerbose(msgNeedGitUserName(gitUserNamePoss), verbose = interactive() * 10)
+          gitUserName <- if (interactive()) readline() else gitUserNamePoss
+          if (!nzchar(gitUserName)) {
+            gitUserName <- gitUserNamePoss
+            needGitUserName <- FALSE
+          }
+
+        }
 
 
-          if (!rprojroot::is_rstudio_project$testfun[[1]](pp)) {
-            host <- "https://github.com"
-            tf <- tempfile2();
-            out <- .downloadFileMasterMainAuth(file.path("https://api.github.com/repos",gitUserName, basenameName),
-                                        destfile = tf, verbose = verbose - 10)
-            # The suppressWarnings is for "incomplete final line"
-            checkExists <- if (file.exists(tf)) suppressWarnings(readLines(tf)) else "Not Found"
+        if (!rprojroot::is_rstudio_project$testfun[[1]](pp)) {
+          host <- "https://github.com"
+          tf <- tempfile2();
+          out <- .downloadFileMasterMainAuth(file.path("https://api.github.com/repos",gitUserName, basenameName),
+                                             destfile = tf, verbose = verbose - 10)
+          # The suppressWarnings is for "incomplete final line"
+          checkExists <- if (file.exists(tf)) suppressWarnings(readLines(tf)) else "Not Found"
 
-            if (any(grepl("Not Found", checkExists))) {
-              usethis::create_project(pp, open = FALSE, rstudio = isRstudio())
+          if (any(grepl("Not Found", checkExists))) {
+            usethis::create_project(pp, open = FALSE, rstudio = isRstudio())
+          } else {
+            repo <- file.path(host, gitUserName, basenameName)
+            messageVerbose(.messages$gitRepoExistsCloneNowTxt(repo))
+            # messageVerbose(paste0("The github repository already exists: ", repo),
+            #                "\nWould you like to clone it now to ", getwd(), "\nType (y)es or any other key for no: ")
+            out <- if (interactive() && getOption("SpaDES.project.ask", TRUE)) readline() else "yes"
+            if (grepl("y|yes", tolower(out))) {
+              setwd(dirname(getwd()))
+              unlink(basenameName, recursive = TRUE)
+              gert::git_clone(repo, path = basenameName)
+              cloned <- TRUE
+              setwd(paths[["projectPath"]])
             } else {
-              repo <- file.path(host, gitUserName, basenameName)
-              messageVerbose(.messages$gitRepoExistsCloneNowTxt(repo))
-              # messageVerbose(paste0("The github repository already exists: ", repo),
-              #                "\nWould you like to clone it now to ", getwd(), "\nType (y)es or any other key for no: ")
-              out <- if (interactive() && getOption("SpaDES.project.ask", TRUE)) readline() else "yes"
-              if (grepl("y|yes", tolower(out))) {
-                setwd(dirname(getwd()))
-                unlink(basenameName, recursive = TRUE)
-                gert::git_clone(repo, path = basenameName)
-                cloned <- TRUE
-                setwd(paths[["projectPath"]])
-              } else {
-                stop("Can't proceed: either delete existing github repo, change the ",
-                     "project name, or change the Github account and try again")
-              }
+              stop("Can't proceed: either delete existing github repo, change the ",
+                   "project name, or change the Github account and try again")
             }
           }
+        }
 
-          if (!isFALSE(getOption("SpaDES.project.gitignore", TRUE))) {
-            igs <- gitIgnoreInitials(paths)
-            usethis::use_git_ignore(igs)
-            # gert::git_add(".gitignore")
-            # gert::git_commit("add more .gitignores")
-          }
+        if (!isFALSE(getOption("SpaDES.project.gitignore", TRUE))) {
+          igs <- gitIgnoreInitials(paths)
+          usethis::use_git_ignore(igs)
+          # gert::git_add(".gitignore")
+          # gert::git_commit("add more .gitignores")
+        }
 
-          if (!rprojroot::is_git_root$testfun[[1]](pp)) {
-            if (needGitUserName) {
-              messageVerbose(msgNeedGitUserName(gitUserNamePoss), verbose = interactive() * 10)
-              gitUserName <- readline()
-            }
-            if (!nzchar(gitUserName))
-              gitUserName <- NULL
-            bbb <- try(usethis::use_git())
-            if (!(exists("gitUserNamePoss", inherits = FALSE)))
-              gitUserNamePoss <- gh::gh_whoami()$login
-            if (identical(gitUserName, gitUserNamePoss))
-              gitUserName <- NULL
-
-            githubRepoExists <- usethis::use_github(gitUserName) # This will fail if not an organization
+        if (!rprojroot::is_git_root$testfun[[1]](pp)) {
+          if (needGitUserName) {
+            messageVerbose(msgNeedGitUserName(gitUserNamePoss), verbose = interactive() * 10)
+            gitUserName <- readline()
           }
+          if (!nzchar(gitUserName))
+            gitUserName <- NULL
+          bbb <- try(usethis::use_git())
+          if (!(exists("gitUserNamePoss", inherits = FALSE)))
+            gitUserNamePoss <- gh::gh_whoami()$login
+          if (identical(gitUserName, gitUserNamePoss))
+            gitUserName <- NULL
+
+          githubRepoExists <- usethis::use_github(gitUserName) # This will fail if not an organization
         }
+      }
+      if (isRstudio()) {
         on.exit(rstudioapi::openProject(path = paths[["projectPath"]], newSession = TRUE))
         message("Starting a new Rstudio session with projectPath (", green(paths[["projectPath"]]), ") as its root")
         stop_quietly()
-      } else {
-        stop("Please open this in a new Rstudio project at ", paths[["projectPath"]])
       }
+      #} else {
+      #  stop("Please open this in a new Rstudio project at ", paths[["projectPath"]])
+      #}
     }
   } else {
     if (!Restart %in% FALSE) {

diff --git a/man/spadesProjectOptions.Rd b/man/spadesProjectOptions.Rd
diff --git a/vignettes/i-getting-started.Rmd b/vignettes/i-getting-started.Rmd
@@ -12,6 +12,12 @@ editor_options:
   chunk_output_type: console
 ---
 
+```{r setCRAN,echo=FALSE}
+# cleanup / restore state
+if (is.null(getOption("repos")) || !"CRAN" %in% names(getOption("repos"))) {
+ options(repos = c(CRAN = "https://cloud.r-project.org"))
+}
+```
 
 
 ```{r setup, include = FALSE}
@@ -22,6 +28,7 @@ knitr::opts_chunk$set(
 )
 
 # Most are eval=FALSE within each chunk; but a few are not. Those must be eval=FALSE on GA and CRAN
+if (is.null(getOption("repos"))) chooseCRANmirror(ind = 1)
 SuggestedPkgsNeeded <- c("SpaDES.core", "igraph", "visNetwork", "ellipsis", "terra")
 hasSuggests <- all(sapply(SuggestedPkgsNeeded, requireNamespace, quietly = TRUE))
 useSuggests <- !(tolower(Sys.getenv("_R_CHECK_DEPENDS_ONLY_")) == "true")
@@ -46,12 +53,6 @@ origLibPath = .libPaths()[1]
 
 
 
-```{r setCRAN,echo=FALSE}
-# cleanup / restore state
-if (is.null(getOption("repos")) || !"CRAN" %in% names(getOption("repos"))) {
- options(repos = c(CRAN = "https://cloud.r-project.org"))
-}
-```
 
 `SpaDES` is a collection of R packages designed to provide a flexible framework for ecological analysis, simulations, forecasting, and other ecological tasks. At its core, a `SpaDES` analysis revolves around the concept of a "module" - a self-contained unit of code that performs a specific function and includes both machine-readable and human-readable metadata. In a typical `SpaDES` project, users often employ multiple modules, whether they've authored them or they've been contributed by others. This scalability introduces several challenges, including managing file paths (e.g., for data inputs, outputs, figures, modules, and packages), handling package dependencies, and coordinating the development of multiple modules simultaneously. While it is possible to develop a `SpaDES` project using methods familiar to the user, the `SpaDES.project` package streamlines this process, facilitating a clean, reproducible and reusable project setup for any project. Default settings ensure that project files and packages are kept isolated, preventing potential conflicts with other projects on the same computer.