Release v0.5.0 (#90)

This is the initial release to CRAN. * Use hypergeometric functions from RcppGSL (#21) * Consistent naming of R code files (#39) * Remove validity methods (#40) * Fix large batch of CRAN checks for first release (#44) * Default implementations of all clv.model methods stop() (#45) * CI setup (#52) * Remove single use generics (#53) * Bugfix: Fail CI if tests fail (#55) * Bugfix: lubridate definition of period years (#58) * clvtime epsilon (#57) * Bugfix: Disable GSL's error reporting (#59) * Setup vignettes (#60) * Dyncov "cheating for stability" use data.table (#62) * Parallelism setup and explanations (#66) * Push documentation (#67) * Feature new sampledata (#68) * Various important todos (#69) * vcov with Moore-Penrose and nearPD (#70) * Compare vs BTYD: fitting and prediction (#72) * Stubs for WIP models (#74) * Remove parameter 'complete' from coef() (#75) * Consistent internal names of class instances (#76) * Vcov: nearPD after back-transformation (#77) * Consistent constructors (#82) * Bugfix update walkthrough (#79) * Last ToDos before initial release (#84) * Plot values backward-looking (#87) * Setup github pages (#89) * Fixes as demanded by CRAN Co-authored-by: Patrick Bachmann <[email protected]> Co-authored-by: Markus Meierer <[email protected]>
bachmannpatrick · May 8, 2020 · 0396ef5 · 0396ef5
1 parent 04c6161
commit 0396ef5
Show file tree

Hide file tree

Showing 260 changed files with 7,683 additions and 9,515 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,2 +1,15 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^README\.md$
+^README\.rmd$
+^Walkthrough\.md$
+^Walkthrough\.rmd$
+^bibliography\.bib$
+^man-roxygen$
+^thoughts_parameterhandling\.rtf$
+^\.github$
+^cran-comments\.md$
+^_pkgdown\.yml$
+[.]o$
+[.]o.tmp$
+
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/Coverage.yaml b/.github/workflows/Coverage.yaml
@@ -0,0 +1,32 @@
+name: coverage
+on: pull_request # default to types [opened, synchronize, reopened]
+jobs:
+  coverage-ubuntu-16-04-R-release:
+    runs-on: ubuntu-16.04
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      # to install binaries on ubuntu
+      RSPM: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: 'release'
+      - name: Install system dependencies
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "install.packages(c('remotes', 'rcmdcheck'))"
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+      - name: Install package dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE) # installs binaries
+          # testthat and covr are part of package's Suggests and installed as package dependency.
+        shell: Rscript {0}
+
+      - name: Test coverage
+        # run: covr::codecov() # uploads to codecov.io
+        run: covr::package_coverage(type = "tests", quiet = FALSE)
+        shell: Rscript {0}
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,80 @@
+name: R-CMD-check
+on: push
+# CMD checks on win, mac, ubuntu
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    name: R-CMD-check-${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false # dont cancel if one fails, might have differen checks fail on different OS
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'devel'}
+          - {os: windows-latest, r: 'devel'}
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-16.04,   r: 'release', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+    env:
+        R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+        RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+        - uses: actions/checkout@v2
+        - uses: r-lib/actions/setup-r@master
+          with:
+            r-version: ${{ matrix.config.r }}
+        - name: Query dependencies
+          run: |
+            install.packages('remotes')
+            saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
+          shell: Rscript {0}
+
+        - name: Cache R packages
+          if: runner.os != 'Windows'
+          uses: actions/cache@v1
+          with:
+            path: ${{ env.R_LIBS_USER }}
+            key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
+            restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
+
+        - name: Install system dependencies
+          if: runner.os == 'Linux'
+          env:
+            RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+          run: |
+            Rscript -e "remotes::install_github('r-hub/sysreqs')"
+            sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+            sudo -s eval "$sysreqs"
+            sudo apt-get install -y qpdf # qpdf needed on ubuntu
+
+        - name: Install tinytex for linux (to build vignettes)
+          if: runner.os == 'Linux'
+          run: |
+            install.packages('tinytex')
+            tinytex::install_tinytex()
+          shell: Rscript {0}
+
+        - name: Install gsl for mac
+          if: runner.os == 'macOS'
+          run: |
+            brew install gsl
+
+        - name: Install package dependencies
+          run: |
+            remotes::install_deps(dependencies = TRUE)
+            # remotes::install_cran(c("RcppGSL", "stringi"), repos = "https://cran.rstudio.com")
+            remotes::install_cran("rcmdcheck", repos = "https://cran.rstudio.com")
+            # remove because leads to NOTE. Does not exist on windows
+            if(file.exists('depends.Rds')) {file.remove('depends.Rds')}
+          shell: Rscript {0}
+
+        - name: Check on Mac / ubuntu
+          if: runner.os != 'Windows'
+          run: rcmdcheck::rcmdcheck(args = c("--no-tests", "--as-cran", "--no-manual"), error_on = "warning", check_dir = "check")
+          shell: Rscript {0}
+
+        - name: Check on Windows, without install and vignette
+          if: runner.os == 'Windows'
+          run: rcmdcheck::rcmdcheck(args = c("--no-install", "--no-build-vignettes","--no-vignettes","--ignore-vignettes","--no-tests", "--as-cran", "--no-manual"), build_args = c("--no-build-vignettes"), error_on = "warning", check_dir = "check")
+          shell: Rscript {0}
diff --git a/.github/workflows/Tests.yaml b/.github/workflows/Tests.yaml
@@ -0,0 +1,36 @@
+name: testthat-tests
+on: pull_request # default to types [opened, synchronize, reopened]
+jobs:
+  tests-ubuntu-16-04-R-release:
+    runs-on: ubuntu-16.04
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      # to install binaries on ubuntu
+      RSPM: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: 'release'
+      - name: Install system dependencies
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "install.packages(c('remotes', 'rcmdcheck'))"
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+      - name: Install package dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE) # installs binaries
+          # Install testing stuff (testthat and covr are part of package's Suggests and installed as package dependency)
+          remotes::install_cran("devtools")
+        shell: Rscript {0}
+
+      - name: Run tests
+        run: |
+          library(testthat)
+          library(devtools)
+          reporter <- RstudioReporter$new() # has to be defined outside capture.output to still print
+          capture.output(devtools::test(reporter = reporter, stop_on_failure=TRUE, stop_on_warning=TRUE))
+        shell: Rscript {0}
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,46 @@
+on:
+  push:
+    branches: master
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Install gsl for mac
+        run: |
+          brew install gsl
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: macOS-r-4.0-0-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: macOS-r-4.0-0-
+
+      - name: Install dependencies
+        run: |
+          install.packages("remotes")
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_dev("pkgdown")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: pkgdown::deploy_to_branch(new_process = FALSE)
+        shell: Rscript {0}
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,8 @@
 src/*.o
 src/*.so
 src/*.dll
+src/*.gcda
+src/*.gcno
+src/*.o.tmp
+inst/doc
+.DS_Store
diff --git a/CLVTools.Rproj b/CLVTools.Rproj
@@ -18,5 +18,5 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageCheckArgs: --no-tests --no-install --as-cran
+PackageCheckArgs: --no-tests --as-cran
 PackageRoxygenize: rd,collate,namespace