Upgrade ensmallen to 2.18.0 (#45)

* Upgrade ensmallen to 2.18.0

* Update RcppArmadillo requirement to mirror underlying armadillo requirement in ensmallen

* Clean up notation in vignette

* Add new Rcpp outputstreams

* Add additional changes

* Remove URLs to the mlpack ensmallen

* Update github action to latest version

* Update notes

* Fix URI

Co-authored-by: coatless <[email protected]>
Co-authored-by: James Balamuta <[email protected]>

Author: github-actions[bot]

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

@@ -1,10 +1,10 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -20,62 +20,35 @@ jobs:
         config:
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: 'oldrel'}
-          #- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          #- {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      MAKEFLAGS: "-j 2"
-      R_BUILD_ARGS: "--no-build-vignettes"
-      R_CHECK_ARGS: "--no-build-vignettes"
-      _R_CHECK_FORCE_SUGGESTS: 0
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - 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@v1
+      - uses: r-lib/actions/setup-r-dependencies@v1
         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-
+          extra-packages: rcmdcheck
 
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v1
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
       - name: Upload check results
         if: failure()

ChangeLog

@@ -1,3 +1,13 @@
+2021-10-22  James Balamuta  <[email protected]>
+
+	* DESCRIPTION (Version): Release 2.18.0 and increase RcppArmadillo requirement
+	* NEWS.md: Update for Ensmallen release 2.18.0
+	* inst/include/ensmallen_bits: Upgraded to Ensmallen 2.18.0
+	* inst/include/ensmallen.hpp: ditto
+	* src/RcppExports.cpp: Re-generate RcppExport
+	* vignettes/using-rcppensmallen.Rmd: Clean up notation and bump linking note.
+	* .github/workflows/r-cmd-check.yaml: Updated github actions runner for R CMD check
+
 2021-07-24  James Balamuta  <[email protected]>
 
 	* .github/workflows/pkgdown.yaml: Add github actions runner for pkgdown

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RcppEnsmallen
 Title: Header-Only C++ Mathematical Optimization Library for 'Armadillo'
-Version: 0.2.17.0.1
+Version: 0.2.18.0.1
 Authors@R: c(
     person("James Joseph", "Balamuta", email = "[email protected]", 
            role = c("aut", "cre", "cph"), 
@@ -22,13 +22,13 @@ Description: 'Ensmallen' is a templated C++ mathematical optimization library
  'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under 
  the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under
  similar terms. Note that 'Ensmallen' requires a compiler that supports 
- 'C++11' and 'Armadillo' 8.400 or later.
+ 'C++11' and 'Armadillo' 9.800 or later.
 Depends: R (>= 3.3.0)
 License: GPL (>= 2)
 URL: https://github.com/coatless/rcppensmallen, https://github.com/mlpack/ensmallen, http://ensmallen.org/
 BugReports: https://github.com/coatless/rcppensmallen/issues
 Encoding: UTF-8
-LinkingTo: Rcpp, RcppArmadillo (>= 0.8.400.0.0)
+LinkingTo: Rcpp, RcppArmadillo (>= 0.9.800.0.0)
 Imports: Rcpp
 RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,3 +1,21 @@
+# RcppEnsmallen 0.2.18.0.1
+
+- Upgraded to ensmallen 2.18.0: "Fairmount Bagel" (2021-10-21)
+  - Add gradient value clipping and gradient norm scaling callback
+    (mlpack/ensmallen#315).
+  - Remove superfluous CMake option to build the tests
+    (mlpack/ensmallen#313).
+  - Bump minimum Armadillo version to 9.800
+    (mlpack/ensmallen#318).
+  - Update Catch2 to 2.13.7
+    (mlpack/ensmallen#322).
+  - Remove redundant template argument for C++20 compatibility
+    (mlpack/ensmallen#324).
+  - Fix MOEAD test stability
+    (mlpack/ensmallen#327).
+- Update GitHub Actions to the standard `r-lib/actions` configuration.
+  ([#45](https://github.com/coatless/rcppensmallen/pull/45))
+
 # RcppEnsmallen 0.2.17.0.1
 
 - Upgraded to ensmallen 2.17.0: "Pachis Din Me Pesa Double" (2021-07-06)

inst/include/ensmallen.hpp

@@ -74,6 +74,8 @@
 // Callbacks.
 #include "ensmallen_bits/callbacks/callbacks.hpp"
 #include "ensmallen_bits/callbacks/early_stop_at_min_loss.hpp"
+#include "ensmallen_bits/callbacks/grad_clip_by_norm.hpp"
+#include "ensmallen_bits/callbacks/grad_clip_by_value.hpp"
 #include "ensmallen_bits/callbacks/print_loss.hpp"
 #include "ensmallen_bits/callbacks/progress_bar.hpp"
 #include "ensmallen_bits/callbacks/query_front.hpp"

inst/include/ensmallen_bits/callbacks/early_stop_at_min_loss.hpp

@@ -32,7 +32,7 @@ class EarlyStopAtMinLossType
    * @param patienceIn The number of epochs to wait after the minimum loss has
    *    been reached or no improvement has been made (Default: 10).
    */
-  EarlyStopAtMinLossType<MatType>(const size_t patienceIn = 10) :
+  EarlyStopAtMinLossType(const size_t patienceIn = 10) :
       callbackUsed(false), 
       patience(patienceIn), 
       bestObjective(std::numeric_limits<double>::max()),
@@ -47,7 +47,7 @@ class EarlyStopAtMinLossType
    * @param patienceIn The number of epochs to wait after the minimum loss has
    *    been reached or no improvement has been made (Default: 10).
    */
-  EarlyStopAtMinLossType<MatType>(
+  EarlyStopAtMinLossType(
       std::function<double(const MatType&)> func,
       const size_t patienceIn = 10)
     : callbackUsed(true), 

inst/include/ensmallen_bits/callbacks/grad_clip_by_norm.hpp

@@ -0,0 +1,60 @@
+/**
+ * @file grad_clip_by_norm.hpp
+ * @author Marcus Edel
+ *
+ * Clip the gradients by multiplying the unit vector of the gradients with the
+ * threshold.
+ *
+ * ensmallen is free software; you may redistribute it and/or modify it under
+ * the terms of the 3-clause BSD license.  You should have received a copy of
+ * the 3-clause BSD license along with ensmallen.  If not, see
+ * http://www.opensource.org/licenses/BSD-3-Clause for more information.
+ */
+#ifndef ENSMALLEN_CALLBACKS_GRAD_CLIP_BY_NORM_HPP
+#define ENSMALLEN_CALLBACKS_GRAD_CLIP_BY_NORM_HPP
+
+namespace ens {
+
+/**
+ * Clip the gradients by multiplying the unit vector of the gradients with the
+ * threshold.
+ */
+class GradClipByNorm
+{
+ public:
+  /**
+   * Set up the gradient clip by norm callback class with the maximum clipping
+   * value.
+   *
+   * @param maxNorm The maximum clipping value.
+   */
+  GradClipByNorm(const double maxNorm) : maxNorm(maxNorm)
+  { /* Nothing to do here. */ }
+
+  /**
+   * Callback function called at any call to Gradient().
+   *
+   * @param optimizer The optimizer used to update the function.
+   * @param function Function to optimize.
+   * @param coordinates Starting point.
+   * @param gradient Matrix that holds the gradient.
+   */
+  template<typename OptimizerType, typename FunctionType, typename MatType>
+  void Gradient(OptimizerType& /* optimizer */,
+                FunctionType& /* function */,
+                const MatType& /* coordinates */,
+                MatType& gradient)
+  {
+    const double gradientNorm = arma::norm(gradient);
+    if (gradientNorm > maxNorm)
+      gradient = maxNorm * gradient / gradientNorm;
+  }
+
+ private:
+  //! The maximum clipping value for gradient clipping.
+  const double maxNorm;
+};
+
+} // namespace ens
+
+#endif

inst/include/ensmallen_bits/callbacks/grad_clip_by_value.hpp

@@ -0,0 +1,60 @@
+/**
+ * @file grad_clip_by_value.hpp
+ * @author Marcus Edel
+ *
+ * Clips the gradient to a specified min and max.
+ *
+ * ensmallen is free software; you may redistribute it and/or modify it under
+ * the terms of the 3-clause BSD license.  You should have received a copy of
+ * the 3-clause BSD license along with ensmallen.  If not, see
+ * http://www.opensource.org/licenses/BSD-3-Clause for more information.
+ */
+#ifndef ENSMALLEN_CALLBACKS_GRAD_CLIP_BY_VALUE_HPP
+#define ENSMALLEN_CALLBACKS_GRAD_CLIP_BY_VALUE_HPP
+
+namespace ens {
+
+/**
+ * Clip the gradient to a specified min and max.
+ */
+class GradClipByValue
+{
+ public:
+  /**
+   * Set up the gradient clip by value callback class with the min and max
+   * value.
+   *
+   * @param min The minimum value to clip to.
+   * @param max The maximum value to clip to.
+   */
+  GradClipByValue(const double min, const double max) : lower(min), upper(max)
+  { /* Nothing to do here. */ }
+
+  /**
+   * Callback function called at any call to Gradient().
+   *
+   * @param optimizer The optimizer used to update the function.
+   * @param function Function to optimize.
+   * @param coordinates Starting point.
+   * @param gradient Matrix that holds the gradient.
+   */
+  template<typename OptimizerType, typename FunctionType, typename MatType>
+  void Gradient(OptimizerType& /* optimizer */,
+                FunctionType& /* function */,
+                const MatType& /* coordinates */,
+                MatType& gradient)
+  {
+    gradient = arma::clamp(gradient, lower, upper);
+  }
+
+ private:
+  //! The minimum value to clip to.
+  const double lower;
+
+  //! The maximum value to clip to.
+  const double upper;
+};
+
+} // namespace ens
+
+#endif