Merge pull request #1 from FBartos/BayesTools-rewrite

updating to BayesTools & version 1.0.0

.Rbuildignore

@@ -1,13 +1,24 @@
-^.*\.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$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,124 @@
+# 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/BayesTools@v0.2.10")
+        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

.github/workflows/R-CMD-tests.yaml

@@ -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/BayesTools@v0.2.10")
+          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/BayesTools@v0.2.10")
+          install.packages("devtools")
+          install.packages("testthat")
+          install.packages("vdiffr")
+          devtools::install()
+          library(vdiffr)
+          library(testthat)
+          devtools::test()
+        shell: Rscript {0}

.github/workflows/pkgdown.yaml

@@ -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/BayesTools@v0.2.10")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'