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Merge pull request #1 from FBartos/BayesTools-rewrite
updating to BayesTools & version 1.0.0
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^.*\.Rproj$ | ||
^RoBSA\.Rproj$ | ||
^\.Rproj\.user$ | ||
^trash$ | ||
^prefitted$ | ||
^tests/figs/.*$ | ||
^tests/results/.*$ | ||
^do-not-share$ | ||
^models$ | ||
^tests/results$ | ||
^tests/testthat/_snaps$ | ||
tests/testthat/test-1-load.R | ||
tests/testthat/test-2-distributions.R | ||
tests/testthat/test-3-setup.R | ||
tests/testthat/test-4-fit.R | ||
tests/testthat/test-5-methods.R | ||
tests/testthat/test-6-plots.R | ||
tests/testthat/test-7-diagnostics.R | ||
tests/testthat/test-8-predict.R | ||
tests/testthat/test-9-priors-calibration.R | ||
^..Rcheck | ||
^.*\.o | ||
^docs$ | ||
^doc$ | ||
^Meta$ | ||
^RoBSA.Rcheck$ | ||
README.Rmd | ||
README.Rmd | ||
^\.github$ | ||
^codecov\.yml$ |
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*.html |
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# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | ||
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | ||
on: | ||
push: | ||
branches: | ||
- main | ||
- master | ||
- pre-release | ||
pull_request: | ||
branches: | ||
- main | ||
- master | ||
- pre-release | ||
|
||
name: R-CMD-check | ||
|
||
jobs: | ||
R-CMD-check: | ||
runs-on: ${{ matrix.config.os }} | ||
|
||
name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
|
||
strategy: | ||
fail-fast: false | ||
matrix: | ||
config: | ||
- {os: windows-latest, r: 'release'} | ||
- {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||
- {os: ubuntu-devel, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" } | ||
- {os: macOS-latest, r: 'release'} | ||
|
||
env: | ||
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
RSPM: ${{ matrix.config.rspm }} | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
||
steps: | ||
- uses: actions/checkout@v2 | ||
|
||
- uses: r-lib/actions/setup-r@v1 | ||
with: | ||
r-version: ${{ matrix.config.r }} | ||
|
||
- uses: r-lib/actions/setup-pandoc@v1 | ||
|
||
- name: Query dependencies | ||
run: | | ||
install.packages('remotes') | ||
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
shell: Rscript {0} | ||
|
||
- name: Restore R package cache | ||
uses: actions/cache@v2 | ||
with: | ||
path: ${{ env.R_LIBS_USER }} | ||
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | ||
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | ||
|
||
- name: Install system dependencies | ||
if: runner.os == 'Linux' | ||
run: | | ||
while read -r cmd | ||
do | ||
eval sudo $cmd | ||
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | ||
- name: Install JAGS (windows-latest) | ||
if: runner.os == 'Windows' | ||
run: | | ||
curl.exe -o wjags.exe --url https://deac-fra.dl.sourceforge.net/project/mcmc-jags/JAGS/4.x/Windows/JAGS-4.2.0-Rtools33.exe | ||
wjags.exe /S | ||
del wjags.exe | ||
shell: cmd | ||
|
||
- name: Install JAGS (macOS-latest) | ||
if: runner.os == 'macOS' | ||
run : | | ||
rm '/usr/local/bin/gfortran' | ||
brew install automake jags | ||
- name: Install dependencies | ||
run: | | ||
remotes::install_deps(dependencies = TRUE) | ||
remotes::install_cran("rcmdcheck") | ||
#remotes::install_version("BayesTools", "0.2.10") | ||
remotes::install_github("FBartos/[email protected]") | ||
shell: Rscript {0} | ||
|
||
- name: Check | ||
if: runner.os != 'Windows' | ||
env: | ||
_R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
run: | | ||
options(crayon.enabled = TRUE) | ||
rcmdcheck::rcmdcheck( | ||
args = c("--no-manual", "--as-cran", "--ignore-vignettes"), | ||
build_args = c("--no-build-vignettes"), | ||
error_on = "warning", | ||
check_dir = "check") | ||
shell: Rscript {0}" | ||
|
||
- name: Check | ||
if: runner.os == 'Windows' | ||
env: | ||
_R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
JAGS_ROOT: "/c/progra~1/JAGS/JAGS-4.2.0" | ||
JAGS_MAJOR_VERSION: 4 | ||
run: | | ||
options(crayon.enabled = TRUE) | ||
rcmdcheck::rcmdcheck( | ||
args = c("--no-manual", "--as-cran", "--ignore-vignettes"), | ||
build_args = c("--no-build-vignettes"), | ||
error_on = "warning", | ||
check_dir = "check") | ||
shell: Rscript {0} | ||
|
||
|
||
- name: Upload check results | ||
if: failure() | ||
uses: actions/upload-artifact@main | ||
with: | ||
name: ${{ runner.os }}-r${{ matrix.config.r }}-results | ||
path: check |
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---|---|---|
@@ -0,0 +1,117 @@ | ||
# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | ||
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | ||
on: | ||
push: | ||
branches: | ||
- main | ||
- master | ||
- pre-release | ||
pull_request: | ||
branches: | ||
- main | ||
- master | ||
- pre-release | ||
|
||
name: R-CMD-tests | ||
|
||
jobs: | ||
R-CMD-check: | ||
runs-on: ${{ matrix.config.os }} | ||
|
||
name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
|
||
strategy: | ||
fail-fast: false | ||
matrix: | ||
config: | ||
- {os: windows-latest, r: 'release'} | ||
- {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||
- {os: macOS-latest, r: 'release'} | ||
|
||
env: | ||
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
RSPM: ${{ matrix.config.rspm }} | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
||
steps: | ||
- uses: actions/checkout@v2 | ||
|
||
- uses: r-lib/actions/setup-r@v1 | ||
with: | ||
r-version: ${{ matrix.config.r }} | ||
|
||
- uses: r-lib/actions/setup-pandoc@v1 | ||
|
||
- name: Query dependencies | ||
run: | | ||
install.packages('remotes') | ||
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
shell: Rscript {0} | ||
|
||
- name: Restore R package cache | ||
uses: actions/cache@v2 | ||
with: | ||
path: ${{ env.R_LIBS_USER }} | ||
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | ||
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | ||
|
||
- name: Install system dependencies | ||
if: runner.os == 'Linux' | ||
run: | | ||
while read -r cmd | ||
do | ||
eval sudo $cmd | ||
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | ||
- name: Install JAGS (windows-latest) | ||
if: runner.os == 'Windows' | ||
run: | | ||
curl.exe -o wjags.exe --url https://deac-fra.dl.sourceforge.net/project/mcmc-jags/JAGS/4.x/Windows/JAGS-4.2.0-Rtools33.exe | ||
wjags.exe /S | ||
del wjags.exe | ||
shell: cmd | ||
|
||
- name: Install JAGS (macOS-latest) | ||
if: runner.os == 'macOS' | ||
run : | | ||
rm '/usr/local/bin/gfortran' | ||
brew install automake jags | ||
- name: Install and test RoBSA (non-Windows) | ||
if: runner.os != 'Windows' | ||
env: | ||
_R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
run: | | ||
remotes::install_deps(dependencies = TRUE) | ||
remotes::install_cran("rcmdcheck") | ||
#remotes::install_version("BayesTools", "0.2.10") | ||
remotes::install_github("FBartos/[email protected]") | ||
install.packages("devtools") | ||
install.packages("testthat") | ||
install.packages("vdiffr") | ||
devtools::install() | ||
library(vdiffr) | ||
library(testthat) | ||
devtools::test() | ||
shell: Rscript {0}" | ||
|
||
- name: Install and test RoBSA (Windows) | ||
if: runner.os == 'Windows' | ||
env: | ||
_R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
JAGS_ROOT: "/c/progra~1/JAGS/JAGS-4.2.0" | ||
JAGS_MAJOR_VERSION: 4 | ||
run: | | ||
remotes::install_deps(dependencies = TRUE) | ||
remotes::install_cran("rcmdcheck") | ||
#remotes::install_version("BayesTools", "0.2.10") | ||
remotes::install_github("FBartos/[email protected]") | ||
install.packages("devtools") | ||
install.packages("testthat") | ||
install.packages("vdiffr") | ||
devtools::install() | ||
library(vdiffr) | ||
library(testthat) | ||
devtools::test() | ||
shell: Rscript {0} |
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Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,91 @@ | ||
on: | ||
push: | ||
branches: | ||
- main | ||
- master | ||
tags: | ||
-'*' | ||
|
||
name: pkgdown | ||
|
||
jobs: | ||
pkgdown: | ||
runs-on: ${{ matrix.config.os }} | ||
|
||
name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
|
||
strategy: | ||
fail-fast: false | ||
matrix: | ||
config: | ||
- {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||
|
||
env: | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
||
steps: | ||
- uses: actions/checkout@v2 | ||
|
||
- uses: r-lib/actions/setup-r@v1 | ||
with: | ||
r-version: ${{ matrix.config.r }} | ||
|
||
- uses: r-lib/actions/setup-pandoc@v1 | ||
|
||
- name: Install harfbuzz freetype2 fribidi Headers | ||
if: runner.os == 'Linux' | ||
run: sudo apt-get install libharfbuzz-dev libfribidi-dev | ||
|
||
|
||
- name: Query dependencies | ||
run: | | ||
install.packages('remotes') | ||
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
shell: Rscript {0} | ||
|
||
- name: Restore R package cache | ||
uses: actions/cache@v2 | ||
with: | ||
path: ${{ env.R_LIBS_USER }} | ||
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | ||
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | ||
|
||
- name: Install system dependencies | ||
if: runner.os == 'Linux' | ||
run: | | ||
while read -r cmd | ||
do | ||
eval sudo $cmd | ||
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | ||
- name: Install JAGS (windows-latest) | ||
if: runner.os == 'Windows' | ||
run: | | ||
curl.exe -o wjags.exe --url https://deac-fra.dl.sourceforge.net/project/mcmc-jags/JAGS/4.x/Windows/JAGS-4.2.0-Rtools33.exe | ||
wjags.exe /S | ||
del wjags.exe | ||
shell: cmd | ||
|
||
- name: Install JAGS (macOS-latest) | ||
if: runner.os == 'macOS' | ||
run : | | ||
rm '/usr/local/bin/gfortran' | ||
brew install automake jags | ||
- name: Install dependencies | ||
run: | | ||
remotes::install_deps(dependencies = TRUE) | ||
install.packages("pkgdown") | ||
#remotes::install_version("BayesTools", "0.2.10") | ||
remotes::install_github("FBartos/[email protected]") | ||
shell: Rscript {0} | ||
|
||
- name: Install package | ||
run: R CMD INSTALL . | ||
|
||
- name: Deploy package | ||
run: | | ||
git config --local user.email "[email protected]" | ||
git config --local user.name "GitHub Actions" | ||
Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' |
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