From 699480b2777ce62c17ac0a188eab293dc28cc6df Mon Sep 17 00:00:00 2001
From: Steve Bronder <sbronder@flatironinstitute.org>
Date: Wed, 20 Mar 2024 10:24:04 -0400
Subject: [PATCH] update docs and remove checks for possibly failed output
 files

---
 DESCRIPTION                             |  2 +-
 R/args.R                                |  1 +
 R/run.R                                 | 21 +++------------------
 man/model-method-check_syntax.Rd        |  2 +-
 man/model-method-compile.Rd             |  2 +-
 man/model-method-diagnose.Rd            |  2 +-
 man/model-method-expose_functions.Rd    |  2 +-
 man/model-method-format.Rd              |  2 +-
 man/model-method-generate-quantities.Rd |  2 +-
 man/model-method-laplace.Rd             |  2 +-
 man/model-method-optimize.Rd            |  2 +-
 man/model-method-pathfinder.Rd          |  2 +-
 man/model-method-variables.Rd           |  2 +-
 man/model-method-variational.Rd         |  2 +-
 14 files changed, 16 insertions(+), 30 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3d55cb48..7ce3e65e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -29,7 +29,7 @@ URL: https://mc-stan.org/cmdstanr/, https://discourse.mc-stan.org
 BugReports: https://github.com/stan-dev/cmdstanr/issues
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE, r6 = FALSE)
 SystemRequirements: CmdStan (https://mc-stan.org/users/interfaces/cmdstan)
 Depends:
diff --git a/R/args.R b/R/args.R
index dd233cac..d6851852 100644
--- a/R/args.R
+++ b/R/args.R
@@ -2,6 +2,7 @@
 
 #' Returns the number of inner processes for a given method
 #' @param args An args object
+#' @noRd
 get_num_inner_processes <- function(args) {
   x <- NULL
   if (inherits(args, "SampleArgs")) {
diff --git a/R/run.R b/R/run.R
index d0fd9d36..43cbedb8 100644
--- a/R/run.R
+++ b/R/run.R
@@ -3,6 +3,7 @@
 #' Parse a file from end to beginning looking for the elapsed time.
 #' @param file A file path.
 #' @return A list of numeric warmup, sampling, and total times.
+#' @noRd
 .sample_file_time = function(file) {
   bufferSize <- 256
   size <- file.info(file)$size
@@ -117,21 +118,10 @@ CmdStanRun <- R6::R6Class(
           call. = FALSE
         )
       }
-      if (include_failed) {
-        private$latent_dynamics_files_
-      } else {
-        # FIXME: I'm not sure what to do when chains fail since they are all in one file?
-#        ok <- self$procs$is_finished() | self$procs$is_queued()
-        private$latent_dynamics_files_
-      }
+      private$latent_dynamics_files_
     },
     output_files = function(include_failed = FALSE) {
-      if (include_failed) {
         private$output_files_
-      } else {
-        ok <- self$procs$is_finished() | self$procs$is_queued()
-        private$output_files_[ok]
-      }
     },
     profile_files = function(include_failed = FALSE) {
       files <- private$profile_files_
@@ -142,12 +132,7 @@ CmdStanRun <- R6::R6Class(
           call. = FALSE
         )
       }
-      if (include_failed) {
-        files
-      } else {
-        ok <- self$procs$is_finished() | self$procs$is_queued()
-        files[ok]
-      }
+      files
     },
     save_output_files = function(dir = ".",
                                  basename = NULL,
diff --git a/man/model-method-check_syntax.Rd b/man/model-method-check_syntax.Rd
index a646a5e1..68366fb5 100644
--- a/man/model-method-check_syntax.Rd
+++ b/man/model-method-check_syntax.Rd
@@ -86,8 +86,8 @@ Other CmdStanModel methods:
 \code{\link{model-method-laplace}},
 \code{\link{model-method-optimize}},
 \code{\link{model-method-pathfinder}},
-\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-sample}},
+\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-variables}},
 \code{\link{model-method-variational}}
 }
diff --git a/man/model-method-compile.Rd b/man/model-method-compile.Rd
index d295eedc..7bfa47d7 100644
--- a/man/model-method-compile.Rd
+++ b/man/model-method-compile.Rd
@@ -157,8 +157,8 @@ Other CmdStanModel methods:
 \code{\link{model-method-laplace}},
 \code{\link{model-method-optimize}},
 \code{\link{model-method-pathfinder}},
-\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-sample}},
+\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-variables}},
 \code{\link{model-method-variational}}
 }
diff --git a/man/model-method-diagnose.Rd b/man/model-method-diagnose.Rd
index 9a0acd31..99043501 100644
--- a/man/model-method-diagnose.Rd
+++ b/man/model-method-diagnose.Rd
@@ -129,8 +129,8 @@ Other CmdStanModel methods:
 \code{\link{model-method-laplace}},
 \code{\link{model-method-optimize}},
 \code{\link{model-method-pathfinder}},
-\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-sample}},
+\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-variables}},
 \code{\link{model-method-variational}}
 }
diff --git a/man/model-method-expose_functions.Rd b/man/model-method-expose_functions.Rd
index a62f7bb8..b7d42231 100644
--- a/man/model-method-expose_functions.Rd
+++ b/man/model-method-expose_functions.Rd
@@ -77,8 +77,8 @@ Other CmdStanModel methods:
 \code{\link{model-method-laplace}},
 \code{\link{model-method-optimize}},
 \code{\link{model-method-pathfinder}},
-\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-sample}},
+\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-variables}},
 \code{\link{model-method-variational}}
 }
diff --git a/man/model-method-format.Rd b/man/model-method-format.Rd
index 2aa34f18..d24010a4 100644
--- a/man/model-method-format.Rd
+++ b/man/model-method-format.Rd
@@ -106,8 +106,8 @@ Other CmdStanModel methods:
 \code{\link{model-method-laplace}},
 \code{\link{model-method-optimize}},
 \code{\link{model-method-pathfinder}},
-\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-sample}},
+\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-variables}},
 \code{\link{model-method-variational}}
 }
diff --git a/man/model-method-generate-quantities.Rd b/man/model-method-generate-quantities.Rd
index eeb2f010..ef7c2a33 100644
--- a/man/model-method-generate-quantities.Rd
+++ b/man/model-method-generate-quantities.Rd
@@ -168,8 +168,8 @@ Other CmdStanModel methods:
 \code{\link{model-method-laplace}},
 \code{\link{model-method-optimize}},
 \code{\link{model-method-pathfinder}},
-\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-sample}},
+\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-variables}},
 \code{\link{model-method-variational}}
 }
diff --git a/man/model-method-laplace.Rd b/man/model-method-laplace.Rd
index b033fbe3..253d67f5 100644
--- a/man/model-method-laplace.Rd
+++ b/man/model-method-laplace.Rd
@@ -214,8 +214,8 @@ Other CmdStanModel methods:
 \code{\link{model-method-generate-quantities}},
 \code{\link{model-method-optimize}},
 \code{\link{model-method-pathfinder}},
-\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-sample}},
+\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-variables}},
 \code{\link{model-method-variational}}
 }
diff --git a/man/model-method-optimize.Rd b/man/model-method-optimize.Rd
index dcf77444..b9b53454 100644
--- a/man/model-method-optimize.Rd
+++ b/man/model-method-optimize.Rd
@@ -332,8 +332,8 @@ Other CmdStanModel methods:
 \code{\link{model-method-generate-quantities}},
 \code{\link{model-method-laplace}},
 \code{\link{model-method-pathfinder}},
-\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-sample}},
+\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-variables}},
 \code{\link{model-method-variational}}
 }
diff --git a/man/model-method-pathfinder.Rd b/man/model-method-pathfinder.Rd
index 383bbac0..bd1b4f3d 100644
--- a/man/model-method-pathfinder.Rd
+++ b/man/model-method-pathfinder.Rd
@@ -357,8 +357,8 @@ Other CmdStanModel methods:
 \code{\link{model-method-generate-quantities}},
 \code{\link{model-method-laplace}},
 \code{\link{model-method-optimize}},
-\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-sample}},
+\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-variables}},
 \code{\link{model-method-variational}}
 }
diff --git a/man/model-method-variables.Rd b/man/model-method-variables.Rd
index dc80ed9a..87e9d73e 100644
--- a/man/model-method-variables.Rd
+++ b/man/model-method-variables.Rd
@@ -46,8 +46,8 @@ Other CmdStanModel methods:
 \code{\link{model-method-laplace}},
 \code{\link{model-method-optimize}},
 \code{\link{model-method-pathfinder}},
-\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-sample}},
+\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-variational}}
 }
 \concept{CmdStanModel methods}
diff --git a/man/model-method-variational.Rd b/man/model-method-variational.Rd
index 3678f11e..1b2d9a74 100644
--- a/man/model-method-variational.Rd
+++ b/man/model-method-variational.Rd
@@ -333,8 +333,8 @@ Other CmdStanModel methods:
 \code{\link{model-method-laplace}},
 \code{\link{model-method-optimize}},
 \code{\link{model-method-pathfinder}},
-\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-sample}},
+\code{\link{model-method-sample_mpi}},
 \code{\link{model-method-variables}}
 }
 \concept{CmdStanModel methods}