From 7ea302fc7268bb02a2cf40d8791e895d7a0954f8 Mon Sep 17 00:00:00 2001 From: jgabry Date: Wed, 13 Mar 2024 16:40:04 -0600 Subject: [PATCH 1/2] clarify that for MCMC output_dir will contain one file per chain closes #928 --- man-roxygen/model-common-args.R | 9 +++++---- man/model-method-diagnose.Rd | 9 +++++---- man/model-method-generate-quantities.Rd | 9 +++++---- man/model-method-laplace.Rd | 9 +++++---- man/model-method-optimize.Rd | 9 +++++---- man/model-method-pathfinder.Rd | 9 +++++---- man/model-method-sample.Rd | 9 +++++---- man/model-method-sample_mpi.Rd | 9 +++++---- man/model-method-variational.Rd | 9 +++++---- 9 files changed, 45 insertions(+), 36 deletions(-) diff --git a/man-roxygen/model-common-args.R b/man-roxygen/model-common-args.R index baf67777..ca609ebe 100644 --- a/man-roxygen/model-common-args.R +++ b/man-roxygen/model-common-args.R @@ -56,10 +56,11 @@ #' method. #' #' @param output_dir (string) A path to a directory where CmdStan should write -#' its output CSV files. For interactive use this can typically be left at -#' `NULL` (temporary directory) since CmdStanR makes the CmdStan output -#' (posterior draws and diagnostics) available in \R via methods of the fitted -#' model objects. The behavior of `output_dir` is as follows: +#' its output CSV files. For MCMC there will be one file per chain; for other +#' methods there will be a single file. For interactive use this can typically +#' be left at `NULL` (temporary directory) since CmdStanR makes the CmdStan +#' output (posterior draws and diagnostics) available in \R via methods of the +#' fitted model objects. The behavior of `output_dir` is as follows: #' * If `NULL` (the default), then the CSV files are written to a temporary #' directory and only saved permanently if the user calls one of the `$save_*` #' methods of the fitted model object (e.g., diff --git a/man/model-method-diagnose.Rd b/man/model-method-diagnose.Rd index dff6359c..9a0acd31 100644 --- a/man/model-method-diagnose.Rd +++ b/man/model-method-diagnose.Rd @@ -64,10 +64,11 @@ number of chains) when called to generate the initial values. See }} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-generate-quantities.Rd b/man/model-method-generate-quantities.Rd index c9173c30..bf25602e 100644 --- a/man/model-method-generate-quantities.Rd +++ b/man/model-method-generate-quantities.Rd @@ -58,10 +58,11 @@ transformed data and the goal is to generate \emph{different} data for each chain.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-laplace.Rd b/man/model-method-laplace.Rd index 2601f558..b033fbe3 100644 --- a/man/model-method-laplace.Rd +++ b/man/model-method-laplace.Rd @@ -79,10 +79,11 @@ number of chains) when called to generate the initial values. See \item{save_latent_dynamics}{Ignored for this method.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-optimize.Rd b/man/model-method-optimize.Rd index 9513db9f..dcf77444 100644 --- a/man/model-method-optimize.Rd +++ b/man/model-method-optimize.Rd @@ -93,10 +93,11 @@ temporary files created when \code{save_latent_dynamics=TRUE} see the method.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-pathfinder.Rd b/man/model-method-pathfinder.Rd index db3185a3..85fc9236 100644 --- a/man/model-method-pathfinder.Rd +++ b/man/model-method-pathfinder.Rd @@ -98,10 +98,11 @@ temporary files created when \code{save_latent_dynamics=TRUE} see the method.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-sample.Rd b/man/model-method-sample.Rd index ce21c60c..526c9c88 100644 --- a/man/model-method-sample.Rd +++ b/man/model-method-sample.Rd @@ -111,10 +111,11 @@ temporary files created when \code{save_latent_dynamics=TRUE} see the method.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-sample_mpi.Rd b/man/model-method-sample_mpi.Rd index 8b0c3ddb..ca7203da 100644 --- a/man/model-method-sample_mpi.Rd +++ b/man/model-method-sample_mpi.Rd @@ -110,10 +110,11 @@ temporary files created when \code{save_latent_dynamics=TRUE} see the method.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-variational.Rd b/man/model-method-variational.Rd index 6b894b74..3678f11e 100644 --- a/man/model-method-variational.Rd +++ b/man/model-method-variational.Rd @@ -94,10 +94,11 @@ temporary files created when \code{save_latent_dynamics=TRUE} see the method.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} From 714e6903c16d6e29dbf1d6a737457eb506727c86 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 18 Mar 2024 18:12:03 +0000 Subject: [PATCH 2/2] Bump r-lib/actions from 2.7.2 to 2.8.2 Bumps [r-lib/actions](https://github.com/r-lib/actions) from 2.7.2 to 2.8.2. - [Release notes](https://github.com/r-lib/actions/releases) - [Commits](https://github.com/r-lib/actions/compare/v2.7.2...v2.8.2) --- updated-dependencies: - dependency-name: r-lib/actions dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/R-CMD-check-wsl.yaml | 4 ++-- .github/workflows/R-CMD-check.yaml | 4 ++-- .github/workflows/Test-coverage.yaml | 8 ++++---- .github/workflows/cmdstan-tarball-check.yaml | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/R-CMD-check-wsl.yaml b/.github/workflows/R-CMD-check-wsl.yaml index b7300f9d..b24a728c 100644 --- a/.github/workflows/R-CMD-check-wsl.yaml +++ b/.github/workflows/R-CMD-check-wsl.yaml @@ -37,11 +37,11 @@ jobs: - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v2.7.2 + - uses: r-lib/actions/setup-r@v2.8.2 with: r-version: 'release' rtools-version: '42' - - uses: r-lib/actions/setup-pandoc@v2.7.2 + - uses: r-lib/actions/setup-pandoc@v2.8.2 - name: Query dependencies run: | diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 9803aa06..1ff60668 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -57,11 +57,11 @@ jobs: sudo apt-get install -y libcurl4-openssl-dev || true sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true - - uses: r-lib/actions/setup-r@v2.7.2 + - uses: r-lib/actions/setup-r@v2.8.2 with: r-version: ${{ matrix.config.r }} rtools-version: ${{ matrix.config.rtools }} - - uses: r-lib/actions/setup-pandoc@v2.7.2 + - uses: r-lib/actions/setup-pandoc@v2.8.2 - name: Query dependencies run: | diff --git a/.github/workflows/Test-coverage.yaml b/.github/workflows/Test-coverage.yaml index 462f4add..69c19fdc 100644 --- a/.github/workflows/Test-coverage.yaml +++ b/.github/workflows/Test-coverage.yaml @@ -34,8 +34,8 @@ jobs: if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'" - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v2.7.2 - - uses: r-lib/actions/setup-pandoc@v2.7.2 + - uses: r-lib/actions/setup-r@v2.8.2 + - uses: r-lib/actions/setup-pandoc@v2.8.2 - name: Install Ubuntu dependencies run: | @@ -85,12 +85,12 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v2.7.2 + - uses: r-lib/actions/setup-r@v2.8.2 with: r-version: 'release' rtools-version: '42' - - uses: r-lib/actions/setup-pandoc@v2.7.2 + - uses: r-lib/actions/setup-pandoc@v2.8.2 - name: Query dependencies run: | diff --git a/.github/workflows/cmdstan-tarball-check.yaml b/.github/workflows/cmdstan-tarball-check.yaml index 57eb8a5c..fd995436 100644 --- a/.github/workflows/cmdstan-tarball-check.yaml +++ b/.github/workflows/cmdstan-tarball-check.yaml @@ -40,12 +40,12 @@ jobs: sudo apt-get install -y libcurl4-openssl-dev || true sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true - - uses: r-lib/actions/setup-r@v2.7.2 + - uses: r-lib/actions/setup-r@v2.8.2 with: r-version: ${{ matrix.config.r }} rtools-version: ${{ matrix.config.rtools }} - - uses: r-lib/actions/setup-pandoc@v2.7.2 + - uses: r-lib/actions/setup-pandoc@v2.8.2 - name: Query dependencies run: |