Merge pull request #60 from bgreenwell/devel

Devel

.Rbuildignore

@@ -3,12 +3,16 @@
 ^\.github$
 ^_pkgdown\.yml$
 ^codecov\.yml$
+^data-raw$
 ^docs$
 ^lightgbm\.model$
 ^pkgdown$
 ^README\.Rmd$
 ^README\.md$
 ^README_cache$
+^rjarticle$
 ^slowtests$
+^tools$
 ^TODO\.md$
-^vignettes$
+^vignettes/fastshap\.Rmd\.orig$
+^vignettes/figure$

.Rproj.user/shared/notebooks/paths

@@ -0,0 +1,29 @@
+/Users/bgreenwell/Dropbox/devel/fastshap/.Rbuildignore="B0549DA2"
+/Users/bgreenwell/Dropbox/devel/fastshap/DESCRIPTION="300503D2"
+/Users/bgreenwell/Dropbox/devel/fastshap/NAMESPACE="0716B2F8"
+/Users/bgreenwell/Dropbox/devel/fastshap/NEWS.md="708C4D66"
+/Users/bgreenwell/Dropbox/devel/fastshap/R/RcppExports.R="B1345C4C"
+/Users/bgreenwell/Dropbox/devel/fastshap/R/data.R="BD5DD2F9"
+/Users/bgreenwell/Dropbox/devel/fastshap/R/explain.R="FC4A07AE"
+/Users/bgreenwell/Dropbox/devel/fastshap/R/gen_friedman.R="6639BB04"
+/Users/bgreenwell/Dropbox/devel/fastshap/R/print.R="6349C4C8"
+/Users/bgreenwell/Dropbox/devel/fastshap/R/utils.R="61254BF1"
+/Users/bgreenwell/Dropbox/devel/fastshap/README.Rmd="505F20E7"
+/Users/bgreenwell/Dropbox/devel/fastshap/_pkgdown.yml="25FDC3A7"
+/Users/bgreenwell/Dropbox/devel/fastshap/codecov.yml="B719EE43"
+/Users/bgreenwell/Dropbox/devel/fastshap/inst/tinytest/test-adjust.R="CD694D40"
+/Users/bgreenwell/Dropbox/devel/fastshap/inst/tinytest/test-baseline.R="67D83781"
+/Users/bgreenwell/Dropbox/devel/fastshap/inst/tinytest/test-convergence.R="0EB1809C"
+/Users/bgreenwell/Dropbox/devel/fastshap/inst/tinytest/test-copy-classes.R="709438B0"
+/Users/bgreenwell/Dropbox/devel/fastshap/inst/tinytest/test-exact.R="2A0B1DDE"
+/Users/bgreenwell/Dropbox/devel/fastshap/inst/tinytest/test-fastshap-vs-other-pkgs.R="F70E1DED"
+/Users/bgreenwell/Dropbox/devel/fastshap/inst/tinytest/test-genOMat.R="54612D12"
+/Users/bgreenwell/Dropbox/devel/fastshap/inst/tinytest/test_fastshap_ames.R="F485343A"
+/Users/bgreenwell/Dropbox/devel/fastshap/slowtests/fastshap-genOMat.cpp="99FEC81E"
+/Users/bgreenwell/Dropbox/devel/fastshap/slowtests/slowtest-benchmark.R="29ADFB84"
+/Users/bgreenwell/Dropbox/devel/fastshap/slowtests/slowtest-parallel.R="7B058F98"
+/Users/bgreenwell/Dropbox/devel/fastshap/slowtests/test-shapviz.R="7F402C66"
+/Users/bgreenwell/Dropbox/devel/fastshap/vignettes/ABC.Rmd="3B3641FE"
+/Users/bgreenwell/Dropbox/devel/fastshap/vignettes/fastshap.Rmd="536A2979"
+/Users/bgreenwell/Dropbox/devel/fastshap/vignettes/rjarticle/greenwell.Rmd="CF8A3E77"
+/Users/bgreenwell/Dropbox/trees/book.tex="4ECC8BA9"

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

@@ -1,86 +1,49 @@
-# 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
-  pull_request:
-    branches:
-      - main
-      - master
-
-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: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-
-    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: Cache R packages
-        if: runner.os != 'Windows'
-        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 dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), 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
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+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: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/pr-commands.yaml

@@ -0,0 +1,79 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  issue_comment:
+    types: [created]
+
+name: Commands
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -1,48 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
 
-      - name: Query dependencies
+      - name: Test coverage
         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")
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
 
-      - name: Cache R packages
-        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 dependencies
+      - name: Show testthat output
+        if: always()
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -8,3 +8,4 @@ lightgbm.model
 src/*.o
 src/*.so
 src/*.dll
+docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: fastshap
 Type: Package
 Title: Fast Approximate Shapley Values
-Version: 0.0.7.9000
+Version: 0.1.0
 Authors@R: person("Brandon", "Greenwell", email = "greenwell.brandon@gmail.com", role =
          c("aut", "cre"), comment = c(ORCID = "0000-0002-8120-0084"))
 Description: Computes fast (relative to other implementations) approximate 
@@ -19,21 +19,21 @@ Imports:
 Suggests: 
     AmesHousing,
     covr,
-    earth,
     knitr,
     lightgbm,
     ranger,
     rmarkdown,
     shapviz,
+    tibble,
     tinytest,
-    titanic,
     xgboost
 LinkingTo: 
     Rcpp,
     RcppArmadillo
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Encoding: UTF-8
 Depends: 
-    R (>= 2.10)
+    R (>= 3.5.0)
 LazyData: true
 Roxygen: list(markdown = TRUE)
+VignetteBuilder: knitr

NAMESPACE

@@ -4,10 +4,13 @@ S3method(explain,default)
 S3method(explain,lgb.Booster)
 S3method(explain,lm)
 S3method(explain,xgb.Booster)
+S3method(print,explain)
 export(explain)
 export(gen_friedman)
 importFrom(Rcpp,sourceCpp)
 importFrom(foreach,"%do%")
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
+importFrom(stats,var)
+importFrom(utils,object.size)
 useDynLib(fastshap, .registration = TRUE)