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Commit c36f280

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andrjohnsandrjohns
committedMay 4, 2024
Merge branch 'master' into expose_new_stan_args
·
v0.9.0v0.8.0
2 parents e90fda4 + cc2e36d commit c36f280

28 files changed

+759
-160
lines changed
 

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

+4-17
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@@ -40,20 +40,9 @@ jobs:
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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('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Install dependencies
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run: |
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("rcmdcheck")
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remotes::install_local(path = ".", INSTALL_opts = "--no-test-load")
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install.packages("curl")
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shell: Rscript {0}
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- uses: r-lib/actions/setup-r-dependencies@v2.8.7
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with:
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extra-packages: any::rcmdcheck, local::.
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- uses: Vampire/setup-wsl@v3
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with:
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sessioninfo::session_info(pkgs, include_base = TRUE)
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shell: Rscript {0}
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- name: Check
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- uses: r-lib/actions/check-r-package@v2.8.7
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env:
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_R_CHECK_CRAN_INCOMING_: false
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run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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shell: Rscript {0}
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- name: Show testthat output
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if: always()

‎.github/workflows/R-CMD-check.yaml

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@@ -25,12 +25,12 @@ jobs:
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config:
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- {os: macOS-latest, r: 'devel', rtools: ''}
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- {os: macOS-latest, r: 'release', rtools: ''}
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- {os: windows-latest, r: 'devel', rtools: ''}
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- {os: windows-latest, r: 'release', rtools: ''}
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- {os: windows-latest, r: 'oldrel', rtools: '42'}
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- {os: ubuntu-20.04, r: 'devel', rtools: ''}
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- {os: ubuntu-20.04, r: 'release', rtools: ''}
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- {os: ubuntu-20.04, r: 'oldrel', rtools: ''}
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- {os: windows-latest, r: 'devel', rtools: '44'}
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- {os: windows-latest, r: 'release', rtools: '44'}
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- {os: windows-latest, r: 'oldrel', rtools: '43'}
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- {os: ubuntu-latest, r: 'devel', rtools: ''}
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- {os: ubuntu-latest, r: 'release', rtools: ''}
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- {os: ubuntu-latest, r: 'oldrel', rtools: ''}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -49,42 +49,16 @@ jobs:
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- uses: actions/checkout@v4
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- name: Install system dependencies
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update
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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@v2.8.7
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with:
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r-version: ${{ matrix.config.r }}
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rtools-version: ${{ matrix.config.rtools }}
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- uses: r-lib/actions/setup-pandoc@v2.8.7
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- uses: r-lib/actions/setup-pandoc@v2.8.7
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- name: Cache R packages
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if: runner.os != 'Windows'
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uses: actions/cache@v4
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- uses: r-lib/actions/setup-r-dependencies@v2.8.7
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install dependencies
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run: |
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Sys.setenv("MAKEFLAGS"="-j2")
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("rcmdcheck")
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remotes::install_local(path = ".")
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install.packages("curl")
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shell: Rscript {0}
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extra-packages: any::rcmdcheck, local::.
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- name: Install cmdstan
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run: |
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sessioninfo::session_info(pkgs, include_base = TRUE)
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shell: Rscript {0}
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- name: Check
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- uses: r-lib/actions/check-r-package@v2.8.7
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env:
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_R_CHECK_CRAN_INCOMING_: false
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run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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shell: Rscript {0}
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- name: Show testthat output
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if: always()

‎.github/workflows/Test-coverage.yaml

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@@ -13,10 +13,18 @@ name: Test coverage
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- master
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jobs:
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test-coverage-ubuntu:
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name: "Linux"
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test-coverage:
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if: "! contains(github.event.head_commit.message, '[ci skip]')"
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runs-on: ubuntu-20.04
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }}
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strategy:
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fail-fast: false
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matrix:
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config:
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- { os: windows-latest }
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- { os: ubuntu-latest }
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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NOT_CRAN: true
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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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sudo apt-get update
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sudo apt-get install -y libcurl4-openssl-dev
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sudo apt-get install -y openmpi-bin openmpi-common openmpi-doc libopenmpi-dev
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v4
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- uses: r-lib/actions/setup-r-dependencies@v2.8.7
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ubuntu-r-4.0-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ubuntu-r-4.0-1-
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- name: Install dependencies
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run: |
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install.packages(c("remotes", "curl"), dependencies = TRUE)
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remotes::install_local(path = ".", INSTALL_opts = "--no-test-load")
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("covr")
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remotes::install_cran("gridExtra")
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shell: Rscript {0}
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extra-packages: any::rcmdcheck, local::., any::covr, any::gridExtra
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- name: Install cmdstan
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run: |
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cmdstanr::check_cmdstan_toolchain(fix = TRUE)
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cmdstanr::install_cmdstan(cores = 2)
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shell: Rscript {0}
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- name: Test coverage
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- name: Test coverage (Linux)
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if: runner.os == 'Linux'
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run: covr::codecov(type = "tests")
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shell: Rscript {0}
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test-coverage-windows:
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name: "Windows"
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if: "! contains(github.event.head_commit.message, '[ci skip]')"
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runs-on: windows-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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NOT_CRAN: true
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2.8.7
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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('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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shell: Rscript {0}
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- name: Install dependencies
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run: |
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install.packages(c("remotes", "curl"), dependencies = TRUE)
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remotes::install_local(path = ".")
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cmdstanr::check_cmdstan_toolchain(fix = TRUE)
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cmdstanr::install_cmdstan(cores = 2, overwrite = TRUE)
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("covr")
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remotes::install_cran("gridExtra")
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shell: Rscript {0}
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- name: Test coverage
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- name: Test coverage (Windows)
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if: runner.os == 'Windows'
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run: |
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options(covr.gcov = 'C:/rtools40/mingw64/bin/gcov.exe');
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options(covr.gcov = 'C:/rtools44/mingw64/bin/gcov.exe');
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covr::codecov(type = "tests", function_exclusions = "sample_mpi")
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shell: Rscript {0}

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

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@@ -23,7 +23,7 @@ jobs:
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matrix:
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config:
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- {os: macOS-latest, r: 'release', rtools: ''}
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- {os: windows-latest, r: 'release', rtools: '42'}
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- {os: windows-latest, r: 'release', rtools: '44'}
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- {os: ubuntu-20.04, r: 'release', rtools: ''}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

‎DESCRIPTION

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@@ -10,6 +10,7 @@ Authors@R:
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person(given = "Andrew", family = "Johnson", role = c("aut", "cre"),
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email = "andrew.johnson@arjohnsonau.com",
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comment = c(ORCID = "0000-0001-7000-8065")),
13+
person(given = "Steve", family = "Bronder", role = "aut"),
1314
person(given = "Ben", family = "Bales", role = "ctb"),
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person(given = "Mitzi", family = "Morris", role = "ctb"),
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person(given = "Mikhail", family = "Popov", role = "ctb"),
@@ -18,7 +19,8 @@ Authors@R:
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email = "will.landau@gmail.com", comment = c(ORCID = "0000-0003-1878-3253")),
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person(given = "Jacob", family = "Socolar", role = "ctb"),
2021
person(given = "Martin", family = "Modrák", role = "ctb"),
21-
person(given = "Steve", family = "Bronder", role = "ctb"))
22+
person(given = "Ven", family = "Popov", role = "ctb")
23+
)
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Description: A lightweight interface to 'Stan' <https://mc-stan.org>.
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The 'CmdStanR' interface is an alternative to 'RStan' that calls the command
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line interface for compilation and running algorithms instead of interfacing

‎NAMESPACE

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@@ -6,6 +6,15 @@ S3method(as_draws,CmdStanMCMC)
66
S3method(as_draws,CmdStanMLE)
77
S3method(as_draws,CmdStanPathfinder)
88
S3method(as_draws,CmdStanVB)
9+
S3method(process_init,"function")
10+
S3method(process_init,CmdStanLaplace)
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S3method(process_init,CmdStanMCMC)
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S3method(process_init,CmdStanMLE)
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S3method(process_init,CmdStanPathfinder)
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S3method(process_init,CmdStanVB)
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S3method(process_init,default)
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S3method(process_init,draws)
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S3method(process_init,list)
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export(as.CmdStanDiagnose)
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export(as.CmdStanGQ)
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export(as.CmdStanLaplace)
@@ -40,3 +49,4 @@ export(write_stan_json)
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export(write_stan_tempfile)
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import(R6)
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importFrom(posterior,as_draws)
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importFrom(stats,aggregate)

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