New repo structure

R-package/targeted/.Rbuildignore → .Rbuildignore

@@ -1,15 +1,17 @@
 ^.github$
+^.lintr$
+^.gitignore$
 ^Dockerfile$
 ^Makefile$
 ^LICENSE$
 ^dependencies$
 ^tmp$
 ^\.travis\.yml$
 ^\.git$
-^\.lintr$
-^\.github$
-^\.gitignore$
+^Makefile$
+^src/target/lib$
 ^README\.Rmd$
+^LICENSE$
 ^examples$
 ^TODO$
 ^doc$

.github/workflows/r_check.yaml

@@ -1,49 +1,64 @@
-name: R tests
+# runs r cmd check + unit tests in inst/tinytest
+on:
+  pull_request:
+    branches: [main, develop]
 
-on: [push]
+name: r-cmd-check
 
 jobs:
-  r_targeted:
+  r-cmd-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
     strategy:
       fail-fast: false
       matrix:
         config:
           - {os: ubuntu-latest,   r: 'release'}
 
-    runs-on: ${{ matrix.config.os }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
     steps:
-      - name: Checkout repository incl. submodules
-        uses: actions/checkout@v2
-        with:
-          submodules: recursive
+      - uses: actions/checkout@v4
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-tinytex@v2
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-      - uses: r-lib/actions/setup-tinytex@v2
-      - run: tlmgr --version
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
       - name: Install dependencies
         run: |
-          sudo apt-get install -y pandoc libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libfontconfig1-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
-      - name: Cache R packages
-        uses: actions/cache@v2
+          sudo apt-get install -y pandoc libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libpoppler-cpp-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: |
-            ${{ env.R_LIBS_USER }}
-            !${{ env.R_LIBS_USER }}/pak
-          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
+          extra-packages: |
+            any::rcmdcheck
+            any::remotes
+            any::covr
+            any::pkgdown
+          needs: check
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes","covr","pkgdown","rcmdcheck"), repos="https://cloud.r-project.org")
-          remotes::install_deps("R-package/targeted", dep=T, upgrade=T)
-        shell: Rscript {0}
-      - name: Check
-        run: |
-          make r_check pkg=targeted
-      - name: Upload Coverage to Codecov
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          # args: 'c("--ignore-vignettes")'
+          # build_args: 'c("--no-build-vignettes")'
+
+      - name: Webpage deployment
+        if: success() && contains('refs/heads/main', github.ref)
         run: |
-          covr::codecov(path="R-package/targeted", type="all")
-        shell: Rscript {0}
+          Rscript -e 'remotes::install_github("kkholst/targeted")'
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
 
+      - name: Code Coverage
+        if: success() && contains('refs/heads/main', github.ref)
+        run: covr::codecov(type=c("tests", "examples"))
+        shell: Rscript {0}

.github/workflows/r_deploy.yaml

@@ -3,10 +3,10 @@ name: publish R package
 on:
   push:
     branches:
-      - develop
+      branches: [main]
 
 jobs:
-  r_targeted:
+  r_drat:
     if: github.event.pull_request.draft == false
     strategy:
       fail-fast: false
@@ -43,18 +43,18 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           cache: always
-          working-directory: R-package/targeted
+          working-directory: .
           extra-packages: any::drat
 
       - name: Build R package
         run: |
-          make r_export
-          cd build/R
-          R CMD build targeted
+          rm -Rf tmp; mkdir -p tmp/targeted
+          git archive HEAD | (cd tmp/targeted; tar x )
+          cd tmp; R CMD build targeted
 
       - name: Setting up R repository
         run: |
-          echo 'drat::insertPackage(action="archive", repodir="www/pkg", file=paste0("build/R/", list.files("build/R/", "gz$")))' | R --no-save --no-restore --silent
+          echo 'drat::insertPackage(action="archive", repodir="www/pkg", file=paste0(tmp/", list.files(tmp/", "gz$")))' | R --no-save --no-restore --silent
 
       - name: Deploy
         run: |

.github/workflows/target_check.yaml

@@ -1,56 +1,26 @@
-name: target tests
+name: target library tests
 
 on: [push]
 
 jobs:
-  python_package:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.10']
-
-    steps:
-      - name: Checkout repository incl. submodules
-        uses: actions/checkout@v3
-        with:
-          submodules: recursive
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install pytest-runner pytest-cov scipy patsy numpy pandas statsmodels codecov
-      - name: Check
-        run: |
-          cd python-package/targeted
-          python setup.py install
-          python setup.py test
-          python3 -m targeted
-          pytest --cov=targeted tests/
-          bin/test_targeted
-      - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v2
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          verbose: false
 
   cpp_library:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository incl. submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Install dependencies
         run: |
           sudo apt-get install -y lcov libblas-dev liblapack-dev
       - name: Unit tests
         run: |
+          cd src/target
           make test
       - name: Coverage
         run: |
+          cd src/target
           make coverage
           cd build/coverage; make coverage
           ./target_test -s

.gitignore

@@ -1,12 +1,55 @@
+.RDataTmp
+pkgdown
+man/figures/logo.*
+docs
+inst/doc
+vignettes/*.html
+vignettes/figure/*chunk*
+vignettes/*.R
+src/dependencies
+*.gcno
+TAGS
+*.o
+*.so
+*~
+test
+*.RData
+*.Rhistory
+*.Rcheck
+.Rproj.user/
+*.tar.gz
+*.zip
+*.tgz
+*.obsolete
+x.log
+nohup.out
+tmp
+valgrind*
+test
+*.tmp
+*.bbl
+*.blg
+*.bak
+*.snm
+*.aux
+*.log
+*~
+*.out
+*.swp
+*.nav
+*.toc
+*.vrb
+*.dvi
+_region*
+symbols.rds
+doc
+Meta
 www
 *.obs
 devel
 test.R
-
 autom4te.cache
 config.status
-R-package/targeted/configure
-.RDataTmp
 
 .ccls*
 .clangd
@@ -17,20 +60,14 @@ Debug
 citest
 notes.org
 *.tmp
-misc/*.csv
-misc/sgd/*.csv
-misc/functional
-misc/sgd/.ipynb_checkpoints/sgd_test-checkpoint.ipynb
-misc/sgd/sgd/.ropeproject/
-config/wheel.sh
-
-*.Rcheck
-symbols.rds
+src/target/misc/*.csv
+src/target/misc/sgd/*.csv
+src/target/misc/functional
+src/target/misc/sgd/.ipynb_checkpoints/sgd_test-checkpoint.ipynb
+src/target/misc/sgd/sgd/.ropeproject/
+src/target/config/wheel.sh
 Rplots*
 .#*
-examples/functional
-examples/test
-.Rhistory
 examples/*.csv
 doc/*guide*pdf
 doc/latex