Two layer neural networks (#80)

* new function for two layer models * two layer unit tests * avoid overflow issues * fix doc error * test when loss cannot be computed * tests for tunable values * update GHA * update spelling * use current CRAN torch * add missing snapshot and remove print snapshots (due to OS differences) * don't test on R 4.1 * test overflow on M1 mac --------- Co-authored-by: ‘topepo’ <‘[email protected]’>
tidymodels · Jul 16, 2024 · 631fe3c · 631fe3c
1 parent 9b01415
commit 631fe3c
Show file tree

Hide file tree

Showing 16 changed files with 1,562 additions and 555 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -12,6 +12,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -26,18 +28,20 @@ jobs:
 
           - {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'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
       TORCH_INSTALL: 1
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -55,4 +59,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          args: 'c("--no-multiarch", "--no-manual")'
+          build_args: 'c("--no-multiarch", "--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -8,6 +8,8 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
@@ -16,36 +18,45 @@ jobs:
       TORCH_INSTALL: 1
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -25,7 +25,7 @@ Imports:
     rlang (>= 1.1.1),
     stats,
     tibble,
-    torch (>= 0.11.0),
+    torch (>= 0.13.0),
     utils
 Suggests: 
     covr,
@@ -40,4 +40,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -19,6 +19,11 @@ S3method(brulee_mlp,default)
 S3method(brulee_mlp,formula)
 S3method(brulee_mlp,matrix)
 S3method(brulee_mlp,recipe)
+S3method(brulee_mlp_two_layer,data.frame)
+S3method(brulee_mlp_two_layer,default)
+S3method(brulee_mlp_two_layer,formula)
+S3method(brulee_mlp_two_layer,matrix)
+S3method(brulee_mlp_two_layer,recipe)
 S3method(brulee_multinomial_reg,data.frame)
 S3method(brulee_multinomial_reg,default)
 S3method(brulee_multinomial_reg,formula)
@@ -39,13 +44,15 @@ S3method(print,brulee_multinomial_reg)
 S3method(tunable,brulee_linear_reg)
 S3method(tunable,brulee_logistic_reg)
 S3method(tunable,brulee_mlp)
+S3method(tunable,brulee_mlp_two_layer)
 S3method(tunable,brulee_multinomial_reg)
 export("%>%")
 export(autoplot)
 export(brulee_activations)
 export(brulee_linear_reg)
 export(brulee_logistic_reg)
 export(brulee_mlp)
+export(brulee_mlp_two_layer)
 export(brulee_multinomial_reg)
 export(coef)
 export(matrix_to_dataset)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,7 @@
 # brulee (development version)
 
+* Added a convenience function, `brulee_mlp_two_layer()`, to more easily fit two-layer networks with parsnip.  
+
 # brulee 0.3.0
 
 * Fixed bug where `coef()` didn't would error if used on a `brulee_logistic_reg()` that was trained with a recipe. (#66)