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andrjohnsandrjohns
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Merge branch 'master' into expose_new_stan_args
2 parents 695dba6 + 30c945c commit 6daf429

12 files changed

Lines changed: 196 additions & 21 deletions

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

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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2.8.2
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with:
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r-version: 'release'
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rtools-version: '42'
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- uses: r-lib/actions/setup-pandoc@v2.8.2
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- uses: r-lib/actions/setup-r@v2.8.7
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- uses: r-lib/actions/setup-pandoc@v2.8.7
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- name: Query dependencies
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run: |
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install.packages("curl")
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shell: Rscript {0}
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- uses: Vampire/setup-wsl@v2
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- uses: Vampire/setup-wsl@v3
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with:
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distribution: Ubuntu-22.04
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use-cache: 'false'

‎.github/workflows/R-CMD-check.yaml‎

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sudo apt-get install -y libcurl4-openssl-dev || true
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sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true
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- uses: r-lib/actions/setup-r@v2.8.2
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- uses: r-lib/actions/setup-r@v2.8.7
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with:
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r-version: ${{ matrix.config.r }}
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rtools-version: ${{ matrix.config.rtools }}
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- uses: r-lib/actions/setup-pandoc@v2.8.2
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- uses: r-lib/actions/setup-pandoc@v2.8.7
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- name: Query dependencies
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run: |

‎.github/workflows/Test-coverage.yaml‎

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if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2.8.2
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- uses: r-lib/actions/setup-pandoc@v2.8.2
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- uses: r-lib/actions/setup-r@v2.8.7
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- uses: r-lib/actions/setup-pandoc@v2.8.7
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- name: Install Ubuntu dependencies
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run: |
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2.8.2
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with:
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r-version: 'release'
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rtools-version: '42'
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- uses: r-lib/actions/setup-r@v2.8.7
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- uses: r-lib/actions/setup-pandoc@v2.8.2
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- uses: r-lib/actions/setup-pandoc@v2.8.7
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- name: Query dependencies
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run: |

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

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sudo apt-get install -y libcurl4-openssl-dev || true
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sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true
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- uses: r-lib/actions/setup-r@v2.8.2
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- uses: r-lib/actions/setup-r@v2.8.7
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with:
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r-version: ${{ matrix.config.r }}
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rtools-version: ${{ matrix.config.rtools }}
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- uses: r-lib/actions/setup-pandoc@v2.8.2
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- uses: r-lib/actions/setup-pandoc@v2.8.7
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- name: Query dependencies
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run: |

‎NAMESPACE‎

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@@ -6,6 +6,13 @@ S3method(as_draws,CmdStanMCMC)
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S3method(as_draws,CmdStanMLE)
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S3method(as_draws,CmdStanPathfinder)
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S3method(as_draws,CmdStanVB)
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export(as.CmdStanDiagnose)
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export(as.CmdStanGQ)
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export(as.CmdStanLaplace)
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export(as.CmdStanMCMC)
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export(as.CmdStanMLE)
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export(as.CmdStanPathfinder)
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export(as.CmdStanVB)
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export(as_cmdstan_fit)
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export(as_draws)
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export(as_mcmc.list)

‎R/args.R‎

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@@ -266,6 +266,9 @@ SampleArgs <- R6::R6Class(
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fileext = ".json"
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)
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for (i in seq_along(inv_metric_paths)) {
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if (length(inv_metric[[i]]) == 1 && metric == "diag_e") {
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inv_metric[[i]] <- array(inv_metric[[i]], dim = c(1))
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}
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write_stan_json(list(inv_metric = inv_metric[[i]]), inv_metric_paths[i])
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}
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‎R/fit.R‎

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@@ -1784,7 +1784,10 @@ inv_metric <- function(matrix = TRUE) {
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out <- private$inv_metric_
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if (matrix && !is.matrix(out[[1]])) {
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# convert each vector to a diagonal matrix
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out <- lapply(out, diag)
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out <- lapply(out, function(x) diag(x, nrow = length(x)))
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} else if (length(out[[1]]) == 1) {
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# convert each scalar to an array with dimension 1
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out <- lapply(out, array, dim = c(1))
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}
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out
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}

‎R/generics.R‎

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#' Coercion methods for CmdStan objects
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#'
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#' These methods are used to coerce objects into `cmdstanr` objects.
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#' Primarily intended for other packages to use when interfacing
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#' with `cmdstanr`.
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#'
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#' @param object to be coerced
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#' @param ... additional arguments
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#'
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#' @name cmdstan_coercion
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NULL
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanMCMC <- function(object, ...) {
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UseMethod("as.CmdStanMCMC")
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}
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanMLE <- function(object, ...) {
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UseMethod("as.CmdStanMLE")
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}
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanLaplace <- function(object, ...) {
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UseMethod("as.CmdStanLaplace")
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}
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanVB <- function(object, ...) {
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UseMethod("as.CmdStanVB")
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}
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanPathfinder <- function(object, ...) {
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UseMethod("as.CmdStanPathfinder")
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}
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanGQ <- function(object, ...) {
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UseMethod("as.CmdStanGQ")
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}
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanDiagnose <- function(object, ...) {
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UseMethod("as.CmdStanDiagnose")
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}

‎R/install.R‎

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rtools_ver <- "40"
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} else if (R.version$minor < "3.0") {
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rtools_ver <- "42"
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} else {
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} else if (R.version$minor < "5.0") {
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rtools_ver <- "43"
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} else {
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rtools_ver <- "44"
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}
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rtools_ver
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}

‎R/utils.R‎

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@@ -394,8 +394,9 @@ assert_valid_draws_format <- function(format) {
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}
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if (format %in% c("rvars", "draws_rvars")) {
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stop(
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"\nWe are fixing a bug in fit$draws(format = 'draws_rvars').",
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"\nFor now please use posterior::as_draws_rvars(fit$draws()) instead."
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"\nTo use the rvar format please convert after extracting the draws, ",
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"e.g., posterior::as_draws_rvars(fit$draws()).",
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call. = FALSE
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)
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}
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}

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