Prepare v0.8.0 release (#974)

* Prepare for v0.8.0 release

* Cherry-pick fix for Onedrive path issues

.Rbuildignore

@@ -12,3 +12,4 @@
 ^\.github$
 ^vignettes/articles-online-only$
 ^release-prep\.R$
+^\.vscode$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: cmdstanr
 Title: R Interface to 'CmdStan'
-Version: 0.7.1
-Date: 2024-01-09
+Version: 0.8.0
+Date: 2024-05-18
 Authors@R:
     c(person(given = "Jonah", family = "Gabry", role = "aut",
              email = "jsg2201@columbia.edu"),
@@ -36,7 +36,7 @@ RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE, r6 = FALSE)
 SystemRequirements: CmdStan (https://mc-stan.org/users/interfaces/cmdstan)
 Depends:
-    R (>= 4.0.0)
+    R (>= 3.5.0)
 Imports:
     checkmate,
     data.table,

NEWS.md

@@ -1,10 +1,46 @@
-# cmdstanr 0.7.0.9000
+# cmdstanr 0.8.0.9000
 
 Items for next release go here
 
+# cmdstanr 0.8.0
+
+## Major new features
+
+* Add functionality for passing `CmdStanFit` objects as initial values by @SteveBronder in #937
+
+## Other improvements
+
+* Add compatibility with CmdStan 2.35 by @andrjohns in #972
+* Add `show_messages` and `show_exceptions` arguments to all methods for controlling output by @andrjohns in #897
+* Drop RcppEigen dependency, implement basic Eigen -> C++ interop by @andrjohns in #899
+* Add compatibility with CmdStan 2.34 by @andrjohns in #905 #910
+* Add a format argument to the `unconstrain_draws()` method to specify draws format of return by @andrjohns in #886
+* Align `cmdstanr` EBFMI diagnostic threshold with CmdStan by @andrjohns in #892
+* Add global option `cmdstanr_print_line_numbers` to add line number to model printing by @sbfnk in #967
+* Add new CmdStan arguments `save_metric` and `save_cmdstan_config` by @venpopov in #932
+* Add documentation for CmdStanR global options by @jgabry in #951
+* Add documentation for how to obtain structured output similar to `rstan::extract()` using a combination of `cmdstanr` and `posterior` by @jgabry in #955
+* Added coercion generics for CmdStanFit objects by @gowerc in #943
+* `psis_resample` and `calculate_lp` arguments added to Pathfinder method by @SteveBronder in #903
+* Documentation and tests for LOO method updated by @jgabry in #923
+* Global option `cmdstanr_warn_inits` added to disable warnings about partially specified initial values by @jgabry in #913
+* Updates to MCMC `output_dir` documentation by @jgabry in #929
+
+## Bugfixes
+
+* Fix broken link in OpenCL documentation by @eipi10 in #908
+* Fix a minor typo in the README by @jgabry in #911
+* Make exported RNG functions respect changes to R's seed by @andrjohns in #973
+* Optimisations for model methods functions by @andrjohns in #960
+* Bugfix for passing function for initial values with Pathfinder method and default `num_paths` by @andrjohns in #964
+* Continue with compilation if `compile_stanalone=TRUE` but no functions are found by @jgabry in #956
+* Update tests and CI for compatibility with MacOS ARM64 by @andrjohns in #958
+* Fix handling of `inv_metric` argument with only 1 parameter by @venpopov in #935
+* Fixes for compatibility with RTools44 by @andrjohns in #952 #959
+
 # cmdstanr 0.7.0
 
-## Major new features 
+## Major new features
 
 * New `laplace` method by @jgabry in #800
 * New `pathfinder` method by @SteveBronder in #848
@@ -47,7 +83,7 @@ Items for next release go here
 ### Major new features
 
 * New `expose_functions()` method to expose Stan functions to R by @andrjohns in #702. See `?expose_functions`.
-* New methods for accessing log_prob, grad_log_prob, hessian, un/constrain variables by @andrjohns in #701. See `?init_model_methods`. 
+* New methods for accessing log_prob, grad_log_prob, hessian, un/constrain variables by @andrjohns in #701. See `?init_model_methods`.
 
 ### Other changes
 

R/model.R

@@ -212,7 +212,7 @@ cmdstan_model <- function(stan_file = NULL, exe_file = NULL, compile = TRUE, ...
 #'  |**Method**|**Description**|
 #'  |:----------|:---------------|
 #'  [`$sample()`][model-method-sample] |  Run CmdStan's `"sample"` method, return [`CmdStanMCMC`] object. |
-#'  [`$sample_mpi()`][model-method-sample_mpi] |  Run CmdStan's `"sample"` method with [MPI](https://mc-stan.org/math/mpi.html), return [`CmdStanMCMC`] object. |
+#'  [`$sample_mpi()`][model-method-sample_mpi] |  Run CmdStan's `"sample"` method with [MPI](https://mc-stan.org/math/md_doxygen_2parallelism__support_2mpi__parallelism.html), return [`CmdStanMCMC`] object. |
 #'  [`$optimize()`][model-method-optimize] |  Run CmdStan's `"optimize"` method, return [`CmdStanMLE`] object. |
 #'  [`$variational()`][model-method-variational] |  Run CmdStan's `"variational"` method, return [`CmdStanVB`] object. |
 #'  [`$pathfinder()`][model-method-pathfinder] |  Run CmdStan's `"pathfinder"` method, return [`CmdStanPathfinder`] object. |

R/path.R

@@ -115,9 +115,9 @@ cmdstan_default_install_path <- function(old = FALSE, wsl = FALSE) {
     file.path(paste0(wsl_dir_prefix(wsl = TRUE), wsl_home_dir()), ".cmdstan")
   } else {
     if (old) {
-      file.path(Sys.getenv("HOME"), ".cmdstanr")
+      file.path(.home_path(), ".cmdstanr")
     } else {
-      file.path(Sys.getenv("HOME"), ".cmdstan")
+      file.path(.home_path(), ".cmdstan")
     }
   }
 }
@@ -240,3 +240,16 @@ fake_cmdstan_version <- function(version) {
 reset_cmdstan_version <- function() {
   .cmdstanr$VERSION <- read_cmdstan_version(cmdstan_path())
 }
+
+.home_path <- function() {
+  home <- Sys.getenv("HOME")
+  if (os_is_windows()) {
+    userprofile <- Sys.getenv("USERPROFILE")
+    h_drivepath <- file.path(Sys.getenv("HOMEDRIVE"), Sys.getenv("HOMEPATH"))
+    win_home <- ifelse(userprofile == "", h_drivepath, userprofile)
+    if (win_home != "") {
+      home <- win_home
+    }
+  }
+  home
+}

README.md

@@ -27,7 +27,7 @@ releases.
 * Modularity: CmdStanR runs Stan's algorithms and lets downstream modules do the
 analysis.
 
-* Flexible [BSD-3 license](https://opensource.org/license/bsd-3-clause/).
+* Flexible [BSD-3 license](https://opensource.org/license/bsd-3-clause).
 
 
 ### Installation