Merge branch 'master' into windows-fixes

Author: rok-cesnovar

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/R-CMD-check.yaml

@@ -47,7 +47,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Install system dependencies
         if: runner.os == 'Linux'
@@ -78,7 +78,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
@@ -119,7 +119,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

.github/workflows/Test-coverage.yaml

@@ -32,7 +32,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
           workflow: Test-coverage.yml
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
       - uses: r-lib/actions/setup-pandoc@v1
@@ -50,7 +50,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ubuntu-r-4.0-1-${{ hashFiles('.github/depends.Rds') }}
@@ -83,7 +83,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       NOT_CRAN: true
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/cmdstan-tarball-check.yaml

@@ -32,7 +32,7 @@ jobs:
       NOT_CRAN: true
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set path for RTools 4.0
         if: runner.os == 'Windows'
@@ -76,7 +76,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
@@ -115,7 +115,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cmdstanr
 Title: R Interface to 'CmdStan'
-Version: 0.5.2
+Version: 0.5.2.1
 Date: 2022-04-24
 Authors@R: 
     c(person(given = "Jonah", family = "Gabry", role = c("aut", "cre"),

NEWS.md

@@ -1,3 +1,18 @@
+# cmdstanr 0.4.0.9000
+
+### Bug fixes
+
+* In `cmdstan_default_path()` we now ignore directories inside `.cmdstan` that don't start 
+with `"cmdstan-"`. (#651)
+
+* Fixed Windows issue related to not locating `grep.exe` or when it is located in a path
+with spaces. (@weshinsley, #661, #663)
+
+* Fixed a bug with diagnostic checks when ebfmi is NaN.
+
+* Fixed a bug that caused issues when using `~` or `.` in paths supplied to the 
+`cmdstanr_write_stan_file_dir` global option.
+
 # cmdstanr 0.5.2
 
 * Refactored toolchain installation and checks for R 4.x on Windows and added support

R/csv.R

@@ -236,9 +236,9 @@ read_cmdstan_csv <- function(files,
       grep_path_quotes <- paste0('"', grep_path_repaired, '"')
       fread_cmd <- paste0(
         grep_path_quotes,
-        " '^[#a-zA-Z]' --color=never '",
+        " -v \"^#\" --color=never \"",
         output_file,
-        "'"
+        "\""
       )
     } else {
       fread_cmd <- paste0("grep -v '^#' --color=never '", output_file, "'")
@@ -578,9 +578,9 @@ read_csv_metadata <- function(csv_file) {
     grep_path_quotes <- paste0('"', grep_path_repaired, '"')
     fread_cmd <- paste0(
       grep_path_quotes,
-      " '^[#a-zA-Z]' --color=never '",
+      " \"^[#a-zA-Z]\" --color=never \"",
       csv_file,
-      "'"
+      "\""
     )
   } else {
     fread_cmd <- paste0("grep '^[#a-zA-Z]' --color=never '", csv_file, "'")

R/example.R

@@ -148,6 +148,7 @@ write_stan_file <- function(code,
                             basename = NULL,
                             force_overwrite = FALSE,
                             hash_salt = "") {
+  dir <- absolute_path(dir)
   if (!dir.exists(dir)) {
     dir.create(dir, recursive = TRUE)
   }

R/install.R

@@ -509,7 +509,7 @@ check_rtools4x_windows_toolchain <- function(fix = FALSE, quiet = FALSE) {
     stop(
       "\n", rtools_version, " was not found but is required to run CmdStan with R version ",
       R.version$major, ".", R.version$minor, ".",
-      "\nPlease install ", rtools_version, " and run check_cmdstan_toolchain().",
+      "\nPlease install ", rtools_version, " and run cmdstanr::check_cmdstan_toolchain().",
       call. = FALSE
     )
   }
@@ -518,7 +518,7 @@ check_rtools4x_windows_toolchain <- function(fix = FALSE, quiet = FALSE) {
   if (grepl("\\(|)| ", rtools_path)) {
     stop(
       "\n", rtools_version, " is installed in a path with spaces or brackets, which is not supported.",
-      "\nPlease reinstall ", rtools_version, " to a valid path, restart R, and then run check_cmdstan_toolchain().",
+      "\nPlease reinstall ", rtools_version, " to a valid path, restart R, and then run cmdstanr::check_cmdstan_toolchain().",
       call. = FALSE
     )
   }
@@ -527,7 +527,7 @@ check_rtools4x_windows_toolchain <- function(fix = FALSE, quiet = FALSE) {
     if (!fix) {
       stop(
         "\n", rtools_version, " installation found but the toolchain was not installed.",
-        "\nRun check_cmdstan_toolchain(fix = TRUE) to fix the issue.",
+        "\nRun cmdstanr::check_cmdstan_toolchain(fix = TRUE) to fix the issue.",
         call. = FALSE
       )
     } else {
@@ -615,13 +615,13 @@ check_unix_make <- function() {
         "The 'make' tool was not found. ",
         "Please install the command line tools for Mac with 'xcode-select --install' ",
         "or install Xcode from the app store. ",
-        "Then restart R and run check_cmdstan_toolchain().",
+        "Then restart R and run cmdstanr::check_cmdstan_toolchain().",
         call. = FALSE
       )
     } else {
       stop(
         "The 'make' tool was not found. ",
-        "Please install 'make', restart R, and then run check_cmdstan_toolchain().",
+        "Please install 'make', restart R, and then run cmdstanr::check_cmdstan_toolchain().",
         call. = FALSE
       )
     }
@@ -638,14 +638,14 @@ check_unix_cpp_compiler <- function() {
         "A suitable C++ compiler was not found. ",
         "Please install the command line tools for Mac with 'xcode-select --install' ",
         "or install Xcode from the app store. ",
-        "Then restart R and run check_cmdstan_toolchain().",
+        "Then restart R and run cmdstanr::check_cmdstan_toolchain().",
         call. = FALSE
       )
     } else {
       stop(
         "A C++ compiler was not found. ",
         "Please install the 'clang++' or 'g++' compiler, restart R, ",
-        "and run check_cmdstan_toolchain().",
+        "and run cmdstanr::check_cmdstan_toolchain().",
         call. = FALSE
       )
     }

R/utils.R

@@ -308,9 +308,17 @@ ebfmi <- function(post_warmup_sampler_diagnostics) {
 
 check_ebfmi <- function(post_warmup_sampler_diagnostics, threshold = 0.2) {
   efbmi_per_chain <- ebfmi(post_warmup_sampler_diagnostics)
-  if (any(efbmi_per_chain < threshold)) {
+  nan_efbmi_count <- sum(is.nan(efbmi_per_chain))
+  efbmi_below_threshold <- sum(efbmi_per_chain < threshold)
+  if (nan_efbmi_count > 0) {
     message(
-      "Warning: ", sum(efbmi_per_chain < threshold), " of ", length(efbmi_per_chain),
+      "Warning: ", nan_efbmi_count, " of ", length(efbmi_per_chain),
+      " chains have a NaN E-BFMI.\n",
+      "See https://mc-stan.org/misc/warnings for details.\n"
+    )
+  } else if (efbmi_below_threshold > 0) {
+    message(
+      "Warning: ", efbmi_below_threshold, " of ", length(efbmi_per_chain),
       " chains had an E-BFMI less than ", threshold, ".\n",
       "See https://mc-stan.org/misc/warnings for details.\n"
     )