From f626041ff8debf55c4c8308a62f2da8b410a4a9d Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Thu, 29 Dec 2022 10:24:07 -0500
Subject: [PATCH 01/80] Install libcereal-dev (and thus rapidjson-dev) for the
 R CMD check call.

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index a4d3825354..a5df9a97a1 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -137,7 +137,7 @@ jobs:
         if: runner.os != 'Windows' && runner.os != 'macOS'
         run: |
             sudo apt-get update
-            sudo apt-get install -y --allow-unauthenticated libcurl4-openssl-dev
+            sudo apt-get install -y --allow-unauthenticated libcurl4-openssl-dev libcereal-dev
 
       - name: Install dependencies
         run: |

From eb1e7a5792fcd9d1617b190f30b04c43b8d23190 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Thu, 29 Dec 2022 10:37:36 -0500
Subject: [PATCH 02/80] Use mlpack-git for documentation of the git version.

---
 src/mlpack/bindings/R/CMakeLists.txt        | 5 +++++
 src/mlpack/bindings/R/mlpack/DESCRIPTION.in | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/mlpack/bindings/R/CMakeLists.txt b/src/mlpack/bindings/R/CMakeLists.txt
index 804528c099..b8ff0ca988 100644
--- a/src/mlpack/bindings/R/CMakeLists.txt
+++ b/src/mlpack/bindings/R/CMakeLists.txt
@@ -83,6 +83,11 @@ if (BUILD_R_BINDINGS)
       "\\1" MLPACK_VERSION_PATCH "${VERSION_HPP_CONTENTS}")
   set(PACKAGE_VERSION
       "${MLPACK_VERSION_MAJOR}.${MLPACK_VERSION_MINOR}.${MLPACK_VERSION_PATCH}")
+  if (USING_GIT)
+    set(PACKAGE_DOC_VERSION "git")
+  else ()
+    set(PACKAGE_DOC_VERSION "${PACKAGE_VERSION}")
+  endif ()
 
   string(TIMESTAMP PACKAGE_DATE "%Y-%m-%d")
 
diff --git a/src/mlpack/bindings/R/mlpack/DESCRIPTION.in b/src/mlpack/bindings/R/mlpack/DESCRIPTION.in
index 4745c42a17..f511fa6e5b 100644
--- a/src/mlpack/bindings/R/mlpack/DESCRIPTION.in
+++ b/src/mlpack/bindings/R/mlpack/DESCRIPTION.in
@@ -15,7 +15,7 @@ LinkingTo: Rcpp,
            RcppArmadillo (>= @RcppArmadillo_Version@),
            RcppEnsmallen (>= @RcppEnsmallen_Version@)
 Suggests: testthat (>= 2.1.0)
-URL: https://www.mlpack.org/doc/mlpack-@PACKAGE_VERSION@/r_documentation.html,
+URL: https://www.mlpack.org/doc/mlpack-@PACKAGE_DOC_VERSION@/r_documentation.html,
      https://github.com/mlpack/mlpack
 BugReports: https://github.com/mlpack/mlpack/issues
 RoxygenNote: 7.1.0

From e1d25565af8bf91ae5174e03b0157c92663d4c56 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Sun, 1 Jan 2023 12:02:05 -0500
Subject: [PATCH 03/80] Use qualified std::move() to fix clang warning.

---
 .../bindings/R/tests/test_r_binding_main.cpp  | 36 +++++++--------
 .../go/tests/test_go_binding_main.cpp         | 36 +++++++--------
 .../julia/tests/test_julia_binding_main.cpp   | 36 +++++++--------
 .../python/tests/test_python_binding_main.cpp | 44 +++++++++----------
 src/mlpack/tests/io_test.cpp                  |  4 +-
 src/mlpack/tests/main_tests/det_test.cpp      |  2 +-
 .../tests/main_tests/range_search_test.cpp    | 24 +++++-----
 7 files changed, 91 insertions(+), 91 deletions(-)

diff --git a/src/mlpack/bindings/R/tests/test_r_binding_main.cpp b/src/mlpack/bindings/R/tests/test_r_binding_main.cpp
index b12cafc771..290e7d1302 100644
--- a/src/mlpack/bindings/R/tests/test_r_binding_main.cpp
+++ b/src/mlpack/bindings/R/tests/test_r_binding_main.cpp
@@ -121,11 +121,11 @@ void BINDING_FUNCTION(util::Params& params, util::Timers& /* timers */)
   // the 3rd row will be multiplied by two.
   if (params.Has("matrix_in"))
   {
-    arma::mat out = move(params.Get<arma::mat>("matrix_in"));
+    arma::mat out = std::move(params.Get<arma::mat>("matrix_in"));
     out.shed_row(4);
     out.row(2) *= 2.0;
 
-    params.Get<arma::mat>("matrix_out") = move(out);
+    params.Get<arma::mat>("matrix_out") = std::move(out);
   }
 
   // Input matrices should be at least 5 rows; the 5th row will be dropped and
@@ -133,70 +133,70 @@ void BINDING_FUNCTION(util::Params& params, util::Timers& /* timers */)
   if (params.Has("umatrix_in"))
   {
     arma::Mat<size_t> out =
-        move(params.Get<arma::Mat<size_t>>("umatrix_in"));
+        std::move(params.Get<arma::Mat<size_t>>("umatrix_in"));
     out.shed_row(4);
     out.row(2) *= 2;
 
-    params.Get<arma::Mat<size_t>>("umatrix_out") = move(out);
+    params.Get<arma::Mat<size_t>>("umatrix_out") = std::move(out);
   }
 
   // An input column or row should have all elements multiplied by two.
   if (params.Has("col_in"))
   {
-    arma::vec out = move(params.Get<arma::vec>("col_in"));
+    arma::vec out = std::move(params.Get<arma::vec>("col_in"));
     out *= 2.0;
 
-    params.Get<arma::vec>("col_out") = move(out);
+    params.Get<arma::vec>("col_out") = std::move(out);
   }
 
   if (params.Has("ucol_in"))
   {
     arma::Col<size_t> out =
-        move(params.Get<arma::Col<size_t>>("ucol_in"));
+        std::move(params.Get<arma::Col<size_t>>("ucol_in"));
     out += 1;
 
-    params.Get<arma::Col<size_t>>("ucol_out") = move(out);
+    params.Get<arma::Col<size_t>>("ucol_out") = std::move(out);
   }
 
   if (params.Has("row_in"))
   {
-    arma::rowvec out = move(params.Get<arma::rowvec>("row_in"));
+    arma::rowvec out = std::move(params.Get<arma::rowvec>("row_in"));
     out *= 2.0;
 
-    params.Get<arma::rowvec>("row_out") = move(out);
+    params.Get<arma::rowvec>("row_out") = std::move(out);
   }
 
   if (params.Has("urow_in"))
   {
     arma::Row<size_t> out =
-        move(params.Get<arma::Row<size_t>>("urow_in"));
+        std::move(params.Get<arma::Row<size_t>>("urow_in"));
     out += 1;
 
-    params.Get<arma::Row<size_t>>("urow_out") = move(out);
+    params.Get<arma::Row<size_t>>("urow_out") = std::move(out);
   }
 
   // Vector arguments should have the last element removed.
   if (params.Has("vector_in"))
   {
-    vector<int> out = move(params.Get<vector<int>>("vector_in"));
+    vector<int> out = std::move(params.Get<vector<int>>("vector_in"));
     out.pop_back();
 
-    params.Get<vector<int>>("vector_out") = move(out);
+    params.Get<vector<int>>("vector_out") = std::move(out);
   }
 
   if (params.Has("str_vector_in"))
   {
-    vector<string> out = move(params.Get<vector<string>>("str_vector_in"));
+    vector<string> out = std::move(params.Get<vector<string>>("str_vector_in"));
     out.pop_back();
 
-    params.Get<vector<string>>("str_vector_out") = move(out);
+    params.Get<vector<string>>("str_vector_out") = std::move(out);
   }
 
   // All numeric elements should be multiplied by 3.
   if (params.Has("matrix_and_info_in"))
   {
     typedef tuple<data::DatasetInfo, arma::mat> TupleType;
-    TupleType tuple = move(params.Get<TupleType>("matrix_and_info_in"));
+    TupleType tuple = std::move(params.Get<TupleType>("matrix_and_info_in"));
 
     const data::DatasetInfo& di = std::get<0>(tuple);
     arma::mat& m = std::get<1>(tuple);
@@ -222,7 +222,7 @@ void BINDING_FUNCTION(util::Params& params, util::Timers& /* timers */)
       }
     }
 
-    params.Get<arma::mat>("matrix_and_info_out") = move(m);
+    params.Get<arma::mat>("matrix_and_info_out") = std::move(m);
   }
 
   // If we got a request to build a model, then build it.
diff --git a/src/mlpack/bindings/go/tests/test_go_binding_main.cpp b/src/mlpack/bindings/go/tests/test_go_binding_main.cpp
index 1e0f1ca930..92738bf2e9 100644
--- a/src/mlpack/bindings/go/tests/test_go_binding_main.cpp
+++ b/src/mlpack/bindings/go/tests/test_go_binding_main.cpp
@@ -117,11 +117,11 @@ void BINDING_FUNCTION(util::Params& params, util::Timers& /* timer */)
   // the 3rd row will be multiplied by two.
   if (params.Has("matrix_in"))
   {
-    arma::mat out = move(params.Get<arma::mat>("matrix_in"));
+    arma::mat out = std::move(params.Get<arma::mat>("matrix_in"));
     out.shed_row(4);
     out.row(2) *= 2.0;
 
-    params.Get<arma::mat>("matrix_out") = move(out);
+    params.Get<arma::mat>("matrix_out") = std::move(out);
   }
 
   // Input matrices should be at least 5 rows; the 5th row will be dropped and
@@ -129,70 +129,70 @@ void BINDING_FUNCTION(util::Params& params, util::Timers& /* timer */)
   if (params.Has("umatrix_in"))
   {
     arma::Mat<size_t> out =
-        move(params.Get<arma::Mat<size_t>>("umatrix_in"));
+        std::move(params.Get<arma::Mat<size_t>>("umatrix_in"));
     out.shed_row(4);
     out.row(2) *= 2;
 
-    params.Get<arma::Mat<size_t>>("umatrix_out") = move(out);
+    params.Get<arma::Mat<size_t>>("umatrix_out") = std::move(out);
   }
 
   // An input column or row should have all elements multiplied by two.
   if (params.Has("col_in"))
   {
-    arma::vec out = move(params.Get<arma::vec>("col_in"));
+    arma::vec out = std::move(params.Get<arma::vec>("col_in"));
     out *= 2.0;
 
-    params.Get<arma::vec>("col_out") = move(out);
+    params.Get<arma::vec>("col_out") = std::move(out);
   }
 
   if (params.Has("ucol_in"))
   {
     arma::Col<size_t> out =
-        move(params.Get<arma::Col<size_t>>("ucol_in"));
+        std::move(params.Get<arma::Col<size_t>>("ucol_in"));
     out *= 2;
 
-    params.Get<arma::Col<size_t>>("ucol_out") = move(out);
+    params.Get<arma::Col<size_t>>("ucol_out") = std::move(out);
   }
 
   if (params.Has("row_in"))
   {
-    arma::rowvec out = move(params.Get<arma::rowvec>("row_in"));
+    arma::rowvec out = std::move(params.Get<arma::rowvec>("row_in"));
     out *= 2.0;
 
-    params.Get<arma::rowvec>("row_out") = move(out);
+    params.Get<arma::rowvec>("row_out") = std::move(out);
   }
 
   if (params.Has("urow_in"))
   {
     arma::Row<size_t> out =
-        move(params.Get<arma::Row<size_t>>("urow_in"));
+        std::move(params.Get<arma::Row<size_t>>("urow_in"));
     out *= 2;
 
-    params.Get<arma::Row<size_t>>("urow_out") = move(out);
+    params.Get<arma::Row<size_t>>("urow_out") = std::move(out);
   }
 
   // Vector arguments should have the last element removed.
   if (params.Has("vector_in"))
   {
-    vector<int> out = move(params.Get<vector<int>>("vector_in"));
+    vector<int> out = std::move(params.Get<vector<int>>("vector_in"));
     out.pop_back();
 
-    params.Get<vector<int>>("vector_out") = move(out);
+    params.Get<vector<int>>("vector_out") = std::move(out);
   }
 
   if (params.Has("str_vector_in"))
   {
-    vector<string> out = move(params.Get<vector<string>>("str_vector_in"));
+    vector<string> out = std::move(params.Get<vector<string>>("str_vector_in"));
     out.pop_back();
 
-    params.Get<vector<string>>("str_vector_out") = move(out);
+    params.Get<vector<string>>("str_vector_out") = std::move(out);
   }
 
   // All numeric elements should be multiplied by 3.
   if (params.Has("matrix_and_info_in"))
   {
     typedef tuple<data::DatasetInfo, arma::mat> TupleType;
-    TupleType tuple = move(params.Get<TupleType>("matrix_and_info_in"));
+    TupleType tuple = std::move(params.Get<TupleType>("matrix_and_info_in"));
 
     const data::DatasetInfo& di = std::get<0>(tuple);
     arma::mat& m = std::get<1>(tuple);
@@ -218,7 +218,7 @@ void BINDING_FUNCTION(util::Params& params, util::Timers& /* timer */)
       }
     }
 
-    params.Get<arma::mat>("matrix_and_info_out") = move(m);
+    params.Get<arma::mat>("matrix_and_info_out") = std::move(m);
   }
 
   // If we got a request to build a model, then build it.
diff --git a/src/mlpack/bindings/julia/tests/test_julia_binding_main.cpp b/src/mlpack/bindings/julia/tests/test_julia_binding_main.cpp
index 127e304a5a..98e36074dc 100644
--- a/src/mlpack/bindings/julia/tests/test_julia_binding_main.cpp
+++ b/src/mlpack/bindings/julia/tests/test_julia_binding_main.cpp
@@ -119,11 +119,11 @@ void BINDING_FUNCTION(util::Params& params, util::Timers& /* timers */)
   // the 3rd row will be multiplied by two.
   if (params.Has("matrix_in"))
   {
-    arma::mat out = move(params.Get<arma::mat>("matrix_in"));
+    arma::mat out = std::move(params.Get<arma::mat>("matrix_in"));
     out.shed_row(4);
     out.row(2) *= 2.0;
 
-    params.Get<arma::mat>("matrix_out") = move(out);
+    params.Get<arma::mat>("matrix_out") = std::move(out);
   }
 
   // Input matrices should be at least 5 rows; the 5th row will be dropped and
@@ -131,70 +131,70 @@ void BINDING_FUNCTION(util::Params& params, util::Timers& /* timers */)
   if (params.Has("umatrix_in"))
   {
     arma::Mat<size_t> out =
-        move(params.Get<arma::Mat<size_t>>("umatrix_in"));
+        std::move(params.Get<arma::Mat<size_t>>("umatrix_in"));
     out.shed_row(4);
     out.row(2) *= 2;
 
-    params.Get<arma::Mat<size_t>>("umatrix_out") = move(out);
+    params.Get<arma::Mat<size_t>>("umatrix_out") = std::move(out);
   }
 
   // An input column or row should have all elements multiplied by two.
   if (params.Has("col_in"))
   {
-    arma::vec out = move(params.Get<arma::vec>("col_in"));
+    arma::vec out = std::move(params.Get<arma::vec>("col_in"));
     out *= 2.0;
 
-    params.Get<arma::vec>("col_out") = move(out);
+    params.Get<arma::vec>("col_out") = std::move(out);
   }
 
   if (params.Has("ucol_in"))
   {
     arma::Col<size_t> out =
-        move(params.Get<arma::Col<size_t>>("ucol_in"));
+        std::move(params.Get<arma::Col<size_t>>("ucol_in"));
     out *= 2;
 
-    params.Get<arma::Col<size_t>>("ucol_out") = move(out);
+    params.Get<arma::Col<size_t>>("ucol_out") = std::move(out);
   }
 
   if (params.Has("row_in"))
   {
-    arma::rowvec out = move(params.Get<arma::rowvec>("row_in"));
+    arma::rowvec out = std::move(params.Get<arma::rowvec>("row_in"));
     out *= 2.0;
 
-    params.Get<arma::rowvec>("row_out") = move(out);
+    params.Get<arma::rowvec>("row_out") = std::move(out);
   }
 
   if (params.Has("urow_in"))
   {
     arma::Row<size_t> out =
-        move(params.Get<arma::Row<size_t>>("urow_in"));
+        std::move(params.Get<arma::Row<size_t>>("urow_in"));
     out *= 2;
 
-    params.Get<arma::Row<size_t>>("urow_out") = move(out);
+    params.Get<arma::Row<size_t>>("urow_out") = std::move(out);
   }
 
   // Vector arguments should have the last element removed.
   if (params.Has("vector_in"))
   {
-    vector<int> out = move(params.Get<vector<int>>("vector_in"));
+    vector<int> out = std::move(params.Get<vector<int>>("vector_in"));
     out.pop_back();
 
-    params.Get<vector<int>>("vector_out") = move(out);
+    params.Get<vector<int>>("vector_out") = std::move(out);
   }
 
   if (params.Has("str_vector_in"))
   {
-    vector<string> out = move(params.Get<vector<string>>("str_vector_in"));
+    vector<string> out = std::move(params.Get<vector<string>>("str_vector_in"));
     out.pop_back();
 
-    params.Get<vector<string>>("str_vector_out") = move(out);
+    params.Get<vector<string>>("str_vector_out") = std::move(out);
   }
 
   // All numeric elements should be multiplied by 3.
   if (params.Has("matrix_and_info_in"))
   {
     typedef tuple<data::DatasetInfo, arma::mat> TupleType;
-    TupleType tuple = move(params.Get<TupleType>("matrix_and_info_in"));
+    TupleType tuple = std::move(params.Get<TupleType>("matrix_and_info_in"));
 
     const data::DatasetInfo& di = std::get<0>(tuple);
     arma::mat& m = std::get<1>(tuple);
@@ -224,7 +224,7 @@ void BINDING_FUNCTION(util::Params& params, util::Timers& /* timers */)
       }
     }
 
-    params.Get<arma::mat>("matrix_and_info_out") = move(m);
+    params.Get<arma::mat>("matrix_and_info_out") = std::move(m);
   }
 
   // If we got a request to build a model, then build it.
diff --git a/src/mlpack/bindings/python/tests/test_python_binding_main.cpp b/src/mlpack/bindings/python/tests/test_python_binding_main.cpp
index ce17cf217e..6ecea2910f 100644
--- a/src/mlpack/bindings/python/tests/test_python_binding_main.cpp
+++ b/src/mlpack/bindings/python/tests/test_python_binding_main.cpp
@@ -140,11 +140,11 @@ void BINDING_FUNCTION(util::Params& params, util::Timers& /* timer */)
   // the 3rd row will be multiplied by two.
   if (params.Has("matrix_in"))
   {
-    arma::mat out = move(params.Get<arma::mat>("matrix_in"));
+    arma::mat out = std::move(params.Get<arma::mat>("matrix_in"));
     out.shed_row(4);
     out.row(2) *= 2.0;
 
-    params.Get<arma::mat>("matrix_out") = move(out);
+    params.Get<arma::mat>("matrix_out") = std::move(out);
   }
 
   // Input matrices should be at least 5 rows; the 5th row will be dropped and
@@ -152,89 +152,89 @@ void BINDING_FUNCTION(util::Params& params, util::Timers& /* timer */)
   if (params.Has("umatrix_in"))
   {
     arma::Mat<size_t> out =
-        move(params.Get<arma::Mat<size_t>>("umatrix_in"));
+        std::move(params.Get<arma::Mat<size_t>>("umatrix_in"));
     out.shed_row(4);
     out.row(2) *= 2;
 
-    params.Get<arma::Mat<size_t>>("umatrix_out") = move(out);
+    params.Get<arma::Mat<size_t>>("umatrix_out") = std::move(out);
   }
 
   // An input matrix (pandas.Series) should have all elements multiplied by two.
   if (params.Has("smatrix_in"))
   {
-    arma::mat out = move(params.Get<arma::mat>("smatrix_in"));
+    arma::mat out = std::move(params.Get<arma::mat>("smatrix_in"));
     out *= 2.0;
 
-    params.Get<arma::mat>("smatrix_out") = move(out);
+    params.Get<arma::mat>("smatrix_out") = std::move(out);
   }
 
   // An input matrix (pandas.Series) should have all elements multiplied by two.
   if (params.Has("s_umatrix_in"))
   {
     arma::Mat<size_t> out =
-        move(params.Get<arma::Mat<size_t>>("s_umatrix_in"));
+        std::move(params.Get<arma::Mat<size_t>>("s_umatrix_in"));
     out *= 2;
 
-    params.Get<arma::Mat<size_t>>("s_umatrix_out") = move(out);
+    params.Get<arma::Mat<size_t>>("s_umatrix_out") = std::move(out);
   }
 
   // An input column or row should have all elements multiplied by two.
   if (params.Has("col_in"))
   {
-    arma::vec out = move(params.Get<arma::vec>("col_in"));
+    arma::vec out = std::move(params.Get<arma::vec>("col_in"));
     out *= 2.0;
 
-    params.Get<arma::vec>("col_out") = move(out);
+    params.Get<arma::vec>("col_out") = std::move(out);
   }
 
   if (params.Has("ucol_in"))
   {
     arma::Col<size_t> out =
-        move(params.Get<arma::Col<size_t>>("ucol_in"));
+        std::move(params.Get<arma::Col<size_t>>("ucol_in"));
     out *= 2;
 
-    params.Get<arma::Col<size_t>>("ucol_out") = move(out);
+    params.Get<arma::Col<size_t>>("ucol_out") = std::move(out);
   }
 
   if (params.Has("row_in"))
   {
-    arma::rowvec out = move(params.Get<arma::rowvec>("row_in"));
+    arma::rowvec out = std::move(params.Get<arma::rowvec>("row_in"));
     out *= 2.0;
 
-    params.Get<arma::rowvec>("row_out") = move(out);
+    params.Get<arma::rowvec>("row_out") = std::move(out);
   }
 
   if (params.Has("urow_in"))
   {
     arma::Row<size_t> out =
-        move(params.Get<arma::Row<size_t>>("urow_in"));
+        std::move(params.Get<arma::Row<size_t>>("urow_in"));
     out *= 2;
 
-    params.Get<arma::Row<size_t>>("urow_out") = move(out);
+    params.Get<arma::Row<size_t>>("urow_out") = std::move(out);
   }
 
   // Vector arguments should have the last element removed.
   if (params.Has("vector_in"))
   {
-    vector<int> out = move(params.Get<vector<int>>("vector_in"));
+    vector<int> out = std::move(params.Get<vector<int>>("vector_in"));
     out.pop_back();
 
-    params.Get<vector<int>>("vector_out") = move(out);
+    params.Get<vector<int>>("vector_out") = std::move(out);
   }
 
   if (params.Has("str_vector_in"))
   {
-    vector<string> out = move(params.Get<vector<string>>("str_vector_in"));
+    vector<string> out = std::move(params.Get<vector<string>>("str_vector_in"));
     out.pop_back();
 
-    params.Get<vector<string>>("str_vector_out") = move(out);
+    params.Get<vector<string>>("str_vector_out") = std::move(out);
   }
 
   // All numeric elements should be multiplied by 3.
   if (params.Has("matrix_and_info_in"))
   {
     typedef tuple<data::DatasetInfo, arma::mat> TupleType;
-    TupleType tuple = move(params.Get<TupleType>("matrix_and_info_in"));
+    TupleType tuple = std::move(params.Get<TupleType>("matrix_and_info_in"));
 
     const data::DatasetInfo& di = std::get<0>(tuple);
     arma::mat& m = std::get<1>(tuple);
@@ -260,7 +260,7 @@ void BINDING_FUNCTION(util::Params& params, util::Timers& /* timer */)
       }
     }
 
-    params.Get<arma::mat>("matrix_and_info_out") = move(m);
+    params.Get<arma::mat>("matrix_and_info_out") = std::move(m);
   }
 
   // If we got a request to build a model, then build it.
diff --git a/src/mlpack/tests/io_test.cpp b/src/mlpack/tests/io_test.cpp
index 21f69829ef..617b713055 100644
--- a/src/mlpack/tests/io_test.cpp
+++ b/src/mlpack/tests/io_test.cpp
@@ -1100,8 +1100,8 @@ TEST_CASE("MatrixAndDatasetInfoTest", "[IOTest]")
       "MatrixAndDatasetInfoTest");
 
   // Get the dataset and info.
-  DatasetInfo info = move(get<0>(p.Get<TupleType>("dataset")));
-  arma::mat dataset = move(get<1>(p.Get<TupleType>("dataset")));
+  DatasetInfo info = std::move(get<0>(p.Get<TupleType>("dataset")));
+  arma::mat dataset = std::move(get<1>(p.Get<TupleType>("dataset")));
 
   REQUIRE(info.Dimensionality() == 3);
 
diff --git a/src/mlpack/tests/main_tests/det_test.cpp b/src/mlpack/tests/main_tests/det_test.cpp
index 8ed8a9589e..69eb75d685 100644
--- a/src/mlpack/tests/main_tests/det_test.cpp
+++ b/src/mlpack/tests/main_tests/det_test.cpp
@@ -86,7 +86,7 @@ TEST_CASE_METHOD(DETTestFixture, "DETParamBoundTest",
 
   // Test for folds.
 
-  SetInputParam("training", move(trainingData));
+  SetInputParam("training", std::move(trainingData));
   SetInputParam("folds", (int) -1);
 
   REQUIRE_THROWS_AS(RUN_BINDING(), std::runtime_error);
diff --git a/src/mlpack/tests/main_tests/range_search_test.cpp b/src/mlpack/tests/main_tests/range_search_test.cpp
index 0a389c5758..1cd1b80e38 100644
--- a/src/mlpack/tests/main_tests/range_search_test.cpp
+++ b/src/mlpack/tests/main_tests/range_search_test.cpp
@@ -57,7 +57,7 @@ TEST_CASE_METHOD(RangeSearchTestFixture, "RangeSearchInputModelNoQuery",
   if (!data::Load("iris.csv", inputData))
     FAIL("Unable to load dataset iris.csv!");
 
-  SetInputParam("reference", move(inputData));
+  SetInputParam("reference", std::move(inputData));
   SetInputParam("min", minVal);
   SetInputParam("max", maxVal);
   SetInputParam("distances_file", distanceFile);
@@ -96,7 +96,7 @@ TEST_CASE_METHOD(RangeSearchTestFixture, "RangeSearchDifferentTree",
   if (!data::Load("iris.csv", inputData))
     FAIL("Unable to load dataset iris.csv!");
 
-  SetInputParam("reference", move(inputData));
+  SetInputParam("reference", std::move(inputData));
   SetInputParam("min", minVal);
   SetInputParam("max", maxVal);
   SetInputParam("distances_file", distanceFile);
@@ -125,7 +125,7 @@ TEST_CASE_METHOD(RangeSearchTestFixture, "RangeSearchBothReferenceAndModel",
   if (!data::Load("iris_test.csv", queryData))
     FAIL("Unable to load dataset iris_test.csv!");
 
-  SetInputParam("reference", move(inputData));
+  SetInputParam("reference", std::move(inputData));
   SetInputParam("min", minVal);
   SetInputParam("max", maxVal);
   SetInputParam("distances_file", distanceFile);
@@ -134,8 +134,8 @@ TEST_CASE_METHOD(RangeSearchTestFixture, "RangeSearchBothReferenceAndModel",
 
   RUN_BINDING();
 
-  SetInputParam("input_model", move(params.Get<RSModel*>("output_model")));
-  SetInputParam("query", move(queryData));
+  SetInputParam("input_model", std::move(params.Get<RSModel*>("output_model")));
+  SetInputParam("query", std::move(queryData));
 
   REQUIRE_THROWS_AS(RUN_BINDING(), std::runtime_error);
 
@@ -174,7 +174,7 @@ TEST_CASE_METHOD(RangeSearchTestFixture, "RangeSearchTest",
   vector<vector<size_t>> neighbors;
   vector<vector<double>> distances;
 
-  SetInputParam("reference", move(x));
+  SetInputParam("reference", std::move(x));
   SetInputParam("min", minVal);
   SetInputParam("max", maxVal);
   SetInputParam("distances_file", distanceFile);
@@ -219,7 +219,7 @@ TEST_CASE_METHOD(RangeSearchTestFixture, "RangeSeachTestwithQuery",
   double minVal = 0, maxVal = 5;
 
   SetInputParam("query", queryData);
-  SetInputParam("reference", move(x));
+  SetInputParam("reference", std::move(x));
   SetInputParam("min", minVal);
   SetInputParam("max", maxVal);
   SetInputParam("distances_file", distanceFile);
@@ -256,7 +256,7 @@ TEST_CASE_METHOD(RangeSearchTestFixture, "ModelCheck",
   if (!data::Load("iris_test.csv", queryData))
     FAIL("Unable to load dataset iris_test.csv!");
 
-  SetInputParam("reference", move(inputData));
+  SetInputParam("reference", std::move(inputData));
   SetInputParam("min", minVal);
   SetInputParam("max", maxVal);
   SetInputParam("distances_file", distanceFile);
@@ -275,7 +275,7 @@ TEST_CASE_METHOD(RangeSearchTestFixture, "ModelCheck",
   ResetSettings();
 
   SetInputParam("input_model", outputModel);
-  SetInputParam("query", move(queryData));
+  SetInputParam("query", std::move(queryData));
 
   RUN_BINDING();
 
@@ -455,7 +455,7 @@ TEST_CASE_METHOD(RangeSearchTestFixture, "RandomBasisTesting",
 
   RUN_BINDING();
 
-  RSModel* outputModel = move(params.Get<RSModel*>("output_model"));
+  RSModel* outputModel = std::move(params.Get<RSModel*>("output_model"));
 
   SetInputParam("min", minVal);
   SetInputParam("max", maxVal);
@@ -504,7 +504,7 @@ TEST_CASE_METHOD(RangeSearchTestFixture, "NaiveModeTest",
 
   neighbors = ReadData<size_t>(neighborsFile);
   distances = ReadData<double>(distanceFile);
-  RSModel* outputModel = move(params.Get<RSModel*>("output_model"));
+  RSModel* outputModel = std::move(params.Get<RSModel*>("output_model"));
 
   SetInputParam("min", minVal);
   SetInputParam("max", maxVal);
@@ -559,7 +559,7 @@ TEST_CASE_METHOD(RangeSearchTestFixture, "SingleModeTest",
 
   neighbors = ReadData<size_t>(neighborsFile);
   distances = ReadData<double>(distanceFile);
-  RSModel* outputModel = move(params.Get<RSModel*>("output_model"));
+  RSModel* outputModel = std::move(params.Get<RSModel*>("output_model"));
 
   SetInputParam("min", minVal);
   SetInputParam("max", maxVal);

From e02382746ae3fd6c677a57d22f2ba21cf33ef6cd Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Thu, 5 Jan 2023 09:38:21 -0500
Subject: [PATCH 04/80] Fix inaccurate documentation for DiscreteDistribution.

---
 src/mlpack/core/dists/discrete_distribution.hpp | 4 ----
 src/mlpack/methods/hmm/hmm.hpp                  | 5 ++++-
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/mlpack/core/dists/discrete_distribution.hpp b/src/mlpack/core/dists/discrete_distribution.hpp
index 5905028f0e..984cd63483 100644
--- a/src/mlpack/core/dists/discrete_distribution.hpp
+++ b/src/mlpack/core/dists/discrete_distribution.hpp
@@ -30,10 +30,6 @@ namespace mlpack {
  * observation is passed (i.e. observation > numObservations), a crash will
  * probably occur.
  *
- * This distribution only supports one-dimensional observations, so when
- * passing an arma::vec as an observation, it should only have one dimension
- * (vec.n_rows == 1).  Any additional dimensions will simply be ignored.
- *
  * @note
  * This class, like every other class in mlpack, uses arma::vec to represent
  * observations.  While a discrete distribution only has positive integers
diff --git a/src/mlpack/methods/hmm/hmm.hpp b/src/mlpack/methods/hmm/hmm.hpp
index 84a48fbf35..78cd244b15 100644
--- a/src/mlpack/methods/hmm/hmm.hpp
+++ b/src/mlpack/methods/hmm/hmm.hpp
@@ -88,7 +88,10 @@ class HMM
    * the given default distribution for emissions.  The dimensionality of the
    * observations is taken from the emissions variable, so it is important that
    * the given default emission distribution is set with the correct
-   * dimensionality.  Alternately, set the dimensionality with Dimensionality().
+   * dimensionality.  Alternately, set the dimensionality with Dimensionality(),
+   * and then use Emission() to access and set the dimensionality of each
+   * individual distribution correctly.
+   *
    * Optionally, the tolerance for convergence of the Baum-Welch algorithm can
    * be set.
    *

From 9a7fb8456ee40a7bc286b327ce9e832841c2f999 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Thu, 5 Jan 2023 10:41:51 -0500
Subject: [PATCH 05/80] Attempt to install cereal on OS X runner.

---
 .github/workflows/main.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index a5df9a97a1..aed62d44fe 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -121,7 +121,7 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-          
+
       - name: Query dependencies
         run: Rscript -e "install.packages('remotes')" -e "saveRDS(remotes::dev_package_deps('${{ needs.jobR.outputs.r_bindings }}', dependencies = TRUE), 'depends.Rds')"
 
@@ -139,6 +139,10 @@ jobs:
             sudo apt-get update
             sudo apt-get install -y --allow-unauthenticated libcurl4-openssl-dev libcereal-dev
 
+      - name: Install check dependencies
+        if: runner.os == 'macOS'
+        run: brew install cereal
+
       - name: Install dependencies
         run: |
           install.packages('remotes')

From 77d9d0361cb1a8c10c68a679ea1c3cf012efbd6a Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 9 Jan 2023 10:05:49 -0500
Subject: [PATCH 06/80] Add -lgfortran and -lquadmath when statically linking
 OpenBLAS on Linux.

---
 CMake/FindArmadillo.cmake | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/CMake/FindArmadillo.cmake b/CMake/FindArmadillo.cmake
index 8c5e0260ca..e59aa857e7 100644
--- a/CMake/FindArmadillo.cmake
+++ b/CMake/FindArmadillo.cmake
@@ -94,6 +94,20 @@ if(NOT _ARMA_USE_WRAPPER OR MSVC)
       endif()
     endif()
 
+    # On Linux, when statically linking against OpenBLAS, we must also manually
+    # link against -lgfortran and -lquadmath.  See
+    # https://gitlab.kitware.com/cmake/cmake/-/issues/23693 for more
+    # information.  When that issue is fixed, we may be able to remove this
+    # section.
+    if (NOT BUILD_SHARED_LIBS AND ${CMAKE_SYSTEM_NAME} MATCHES "Linux")
+      string(TOLOWER "${LAPACK_LIBRARIES}" _lower_lapack_libs)
+      string(FIND "${_lower_lapack_libs}" "openblas" _openblas_found_index)
+      if (${_openblas_found_index} GREATER_EQUAL 0)
+	message(STATUS "Using static OpenBLAS on Linux; adding -lgfortran and -lquadmath...")
+	set(LAPACK_LIBRARIES "${LAPACK_LIBRARIES};gfortran;quadmath")
+      endif ()
+    endif ()
+
     if(LAPACK_FOUND)
       set(_ARMA_SUPPORT_LIBRARIES "${_ARMA_SUPPORT_LIBRARIES}" "${LAPACK_LIBRARIES}")
     endif()

From f81359be02da2f7fdac1440af5558fbce17d0e26 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 9 Jan 2023 10:53:45 -0500
Subject: [PATCH 07/80] Try to bundle the upstream version of cereal directly.

---
 .github/workflows/main.yml | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index aed62d44fe..2e99fc3e62 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -57,7 +57,13 @@ jobs:
         - name: Install Build Dependencies
           run: |
             sudo apt-get update
-            sudo apt-get install -y --allow-unauthenticated libopenblas-dev liblapack-dev g++ libcereal-dev libensmallen-dev libhdf5-dev libarmadillo-dev libcurl4-openssl-dev
+            # We don't install cereal via apt, because the Debian packagers
+            # split the rapidjson dependency into a separate package.  We will
+            # bundle the cereal sources with the R package, so we want them to
+            # be exactly the upstream sources (with rapidjson included).
+            sudo apt-get install -y --allow-unauthenticated libopenblas-dev liblapack-dev g++ libensmallen-dev libhdf5-dev libarmadillo-dev libcurl4-openssl-dev
+            wget https://github.com/USCiLab/cereal/archive/refs/tags/v1.3.2.tar.gz
+            tar -xvzpf v1.3.2.tar.gz
 
         - name: Install R-bindings dependencies
           run: |
@@ -69,7 +75,7 @@ jobs:
         - name: CMake
           run: |
             mkdir build
-            cd build && cmake -DDEBUG=OFF -DPROFILE=OFF -DBUILD_CLI_EXECUTABLES=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=OFF -DBUILD_GO_BINDINGS=OFF -DBUILD_R_BINDINGS=ON -DDOWNLOAD_DEPENDENCIES=ON -DBUILD_TESTS=ON ..
+            cd build && cmake -DDEBUG=OFF -DPROFILE=OFF -DBUILD_CLI_EXECUTABLES=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=OFF -DBUILD_GO_BINDINGS=OFF -DBUILD_R_BINDINGS=ON -DDOWNLOAD_DEPENDENCIES=ON -DBUILD_TESTS=ON -DCEREAL_INCLUDE_DIR=../cereal-1.3.2/include/ ..
 
         - name: Build
           run: |
@@ -137,11 +143,7 @@ jobs:
         if: runner.os != 'Windows' && runner.os != 'macOS'
         run: |
             sudo apt-get update
-            sudo apt-get install -y --allow-unauthenticated libcurl4-openssl-dev libcereal-dev
-
-      - name: Install check dependencies
-        if: runner.os == 'macOS'
-        run: brew install cereal
+            sudo apt-get install -y --allow-unauthenticated libcurl4-openssl-dev
 
       - name: Install dependencies
         run: |

From 8fe18266d3199c415d6d1469cf87e08ed5abe2c4 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 10 Jan 2023 09:07:32 -0500
Subject: [PATCH 08/80] Try to work around Visual Studio bug.

---
 src/mlpack/core/data/load_numeric_csv.hpp | 31 ++++++++++++++++++++---
 1 file changed, 27 insertions(+), 4 deletions(-)

diff --git a/src/mlpack/core/data/load_numeric_csv.hpp b/src/mlpack/core/data/load_numeric_csv.hpp
index a43bdd02de..83396b1af5 100644
--- a/src/mlpack/core/data/load_numeric_csv.hpp
+++ b/src/mlpack/core/data/load_numeric_csv.hpp
@@ -14,8 +14,32 @@
 
 #include "load_csv.hpp"
 
-namespace mlpack{
-namespace data{
+namespace mlpack {
+namespace data {
+
+/**
+ * A safe function to get negative or positive infinity, which avoids unary
+ * minus on an unsigned type.  This works around a Visual Studio bug.
+ * (TODO: add a link?)
+ */
+template<typename eT>
+inline eT SafeNegInf(
+    const bool neg,
+    const typename std::enable_if<std::is_unsigned<eT>::value>::type* = 0)
+{
+  // For an unsigned type, we cannot return negative infinity, so instead return
+  // 0.
+  return neg ? 0 : std::numeric_limits<eT>::infinity();
+}
+
+template<typename eT>
+inline eT SafeNegInf(
+    const bool neg,
+    const typename std::enable_if<!std::is_unsigned<eT>::value>::type* = 0)
+{
+  return neg ? -(std::numeric_limits<eT>::infinity()) :
+      std::numeric_limits<eT>::infinity();
+}
 
 template<typename eT>
 bool LoadCSV::ConvertToken(eT& val,
@@ -49,8 +73,7 @@ bool LoadCSV::ConvertToken(eT& val,
         ((sigB == 'n') || (sigB == 'N')) &&
         ((sigC == 'f') || (sigC == 'F')))
     {
-      val = neg ? -(std::numeric_limits<eT>
-                    ::infinity()) : std::numeric_limits<eT>::infinity();
+      val = SafeNegInf<eT>(neg);
       return true;
     }
     else if (((sigA == 'n') || (sigA == 'N')) &&

From 4ed41f45f3b8e0e6f6882168bdc5bebd423fa89e Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Wed, 11 Jan 2023 20:19:18 -0500
Subject: [PATCH 09/80] Be more paranoid in conditions.

---
 CMake/FindArmadillo.cmake | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/CMake/FindArmadillo.cmake b/CMake/FindArmadillo.cmake
index e59aa857e7..f494a5f931 100644
--- a/CMake/FindArmadillo.cmake
+++ b/CMake/FindArmadillo.cmake
@@ -99,12 +99,14 @@ if(NOT _ARMA_USE_WRAPPER OR MSVC)
     # https://gitlab.kitware.com/cmake/cmake/-/issues/23693 for more
     # information.  When that issue is fixed, we may be able to remove this
     # section.
-    if (NOT BUILD_SHARED_LIBS AND ${CMAKE_SYSTEM_NAME} MATCHES "Linux")
+    if (NOT BUILD_SHARED_LIBS AND
+        ${CMAKE_SYSTEM_NAME} MATCHES "Linux" AND
+        NOT CMAKE_CROSSCOMPILING)
       string(TOLOWER "${LAPACK_LIBRARIES}" _lower_lapack_libs)
       string(FIND "${_lower_lapack_libs}" "openblas" _openblas_found_index)
       if (${_openblas_found_index} GREATER_EQUAL 0)
-	message(STATUS "Using static OpenBLAS on Linux; adding -lgfortran and -lquadmath...")
-	set(LAPACK_LIBRARIES "${LAPACK_LIBRARIES};gfortran;quadmath")
+        message(STATUS "Using static OpenBLAS on Linux; adding -lgfortran and -lquadmath...")
+        set(LAPACK_LIBRARIES "${LAPACK_LIBRARIES};gfortran;quadmath")
       endif ()
     endif ()
 

From 45394e01c6ee1d050729f1ae23d4afb9801664d2 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Wed, 11 Jan 2023 20:21:18 -0500
Subject: [PATCH 10/80] Fix comment.

---
 src/mlpack/core/data/load_numeric_csv.hpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/mlpack/core/data/load_numeric_csv.hpp b/src/mlpack/core/data/load_numeric_csv.hpp
index 83396b1af5..6cfbbdd389 100644
--- a/src/mlpack/core/data/load_numeric_csv.hpp
+++ b/src/mlpack/core/data/load_numeric_csv.hpp
@@ -19,8 +19,7 @@ namespace data {
 
 /**
  * A safe function to get negative or positive infinity, which avoids unary
- * minus on an unsigned type.  This works around a Visual Studio bug.
- * (TODO: add a link?)
+ * minus on an unsigned type.  This works around a Visual Studio warning.
  */
 template<typename eT>
 inline eT SafeNegInf(

From 5d293871cef993cf0d7b9e151249829c848909d2 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Fri, 13 Jan 2023 14:37:24 -0500
Subject: [PATCH 11/80] Comment out pragmas in base64.hpp to fix CRAN warnings.

---
 .github/workflows/main.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 2e99fc3e62..64d851f11f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -64,6 +64,10 @@ jobs:
             sudo apt-get install -y --allow-unauthenticated libopenblas-dev liblapack-dev g++ libensmallen-dev libhdf5-dev libarmadillo-dev libcurl4-openssl-dev
             wget https://github.com/USCiLab/cereal/archive/refs/tags/v1.3.2.tar.gz
             tar -xvzpf v1.3.2.tar.gz
+            # These directives cause warnings on CRAN:
+            # https://github.com/USCiLab/cereal/blob/master/include/cereal/external/base64.hpp#L28-L31
+            # The command below comments them out.
+            sed -i 's|#pragma|// #pragma|' cereal-1.3.2/external/base64.hpp
 
         - name: Install R-bindings dependencies
           run: |

From 092c8e5ca804e077ebfc84d512d20b7a6d173c71 Mon Sep 17 00:00:00 2001
From: Yashwants19 <Yashwants19@users.noreply.github.com>
Date: Tue, 17 Jan 2023 10:00:33 +0000
Subject: [PATCH 12/80] Upgrade CLI11 to 2.3.2

---
 .../bindings/cli/third_party/CLI/CLI11.hpp    | 189 +++++++++++-------
 1 file changed, 119 insertions(+), 70 deletions(-)

diff --git a/src/mlpack/bindings/cli/third_party/CLI/CLI11.hpp b/src/mlpack/bindings/cli/third_party/CLI/CLI11.hpp
index 739fd8bd5e..3913fa9ca3 100644
--- a/src/mlpack/bindings/cli/third_party/CLI/CLI11.hpp
+++ b/src/mlpack/bindings/cli/third_party/CLI/CLI11.hpp
@@ -1,11 +1,11 @@
-// CLI11: Version 2.3.1
+// CLI11: Version 2.3.2
 // Originally designed by Henry Schreiner
 // https://github.com/CLIUtils/CLI11
 //
 // This is a standalone header file generated by MakeSingleHeader.py in CLI11/scripts
-// from: v2.3.1
+// from: v2.3.2
 //
-// CLI11 2.3.1 Copyright (c) 2017-2022 University of Cincinnati, developed by Henry
+// CLI11 2.3.2 Copyright (c) 2017-2022 University of Cincinnati, developed by Henry
 // Schreiner under NSF AWARD 1414736. All rights reserved.
 //
 // Redistribution and use in source and binary forms of CLI11, with or without
@@ -34,34 +34,34 @@
 #pragma once
 
 // Standard combined includes:
-#include <functional>
-#include <locale>
-#include <cstdint>
 #include <iomanip>
-#include <memory>
-#include <exception>
-#include <stdexcept>
-#include <string>
-#include <vector>
-#include <iterator>
-#include <algorithm>
-#include <sstream>
-#include <cmath>
-#include <type_traits>
-#include <limits>
 #include <set>
+#include <memory>
+#include <vector>
 #include <utility>
-#include <map>
+#include <stdexcept>
+#include <locale>
+#include <functional>
 #include <iostream>
+#include <iterator>
+#include <exception>
 #include <numeric>
 #include <fstream>
+#include <string>
+#include <type_traits>
 #include <tuple>
+#include <map>
+#include <algorithm>
+#include <cstdint>
+#include <sstream>
+#include <cmath>
+#include <limits>
 
 
 #define CLI11_VERSION_MAJOR 2
 #define CLI11_VERSION_MINOR 3
-#define CLI11_VERSION_PATCH 1
-#define CLI11_VERSION "2.3.1"
+#define CLI11_VERSION_PATCH 2
+#define CLI11_VERSION "2.3.2"
 
 
 
@@ -972,7 +972,9 @@ constexpr enabler dummy = {};
 template <bool B, class T = void> using enable_if_t = typename std::enable_if<B, T>::type;
 
 /// A copy of std::void_t from C++17 (helper for C++11 and C++14)
-template <typename... Ts> struct make_void { using type = void; };
+template <typename... Ts> struct make_void {
+    using type = void;
+};
 
 /// A copy of std::void_t from C++17 - same reasoning as enable_if_t, it does not hurt to redefine
 template <typename... Ts> using void_t = typename make_void<Ts...>::type;
@@ -1001,10 +1003,14 @@ template <typename T> struct is_copyable_ptr {
 };
 
 /// This can be specialized to override the type deduction for IsMember.
-template <typename T> struct IsMemberType { using type = T; };
+template <typename T> struct IsMemberType {
+    using type = T;
+};
 
 /// The main custom type needed here is const char * should be a string.
-template <> struct IsMemberType<const char *> { using type = std::string; };
+template <> struct IsMemberType<const char *> {
+    using type = std::string;
+};
 
 namespace detail {
 
@@ -1014,7 +1020,9 @@ namespace detail {
 /// pointer_traits<T> be valid.
 
 /// not a pointer
-template <typename T, typename Enable = void> struct element_type { using type = T; };
+template <typename T, typename Enable = void> struct element_type {
+    using type = T;
+};
 
 template <typename T> struct element_type<T, typename std::enable_if<is_copyable_ptr<T>::value>::type> {
     using type = typename std::pointer_traits<T>::element_type;
@@ -1022,7 +1030,9 @@ template <typename T> struct element_type<T, typename std::enable_if<is_copyable
 
 /// Combination of the element type and value type - remove pointer (including smart pointers) and get the value_type of
 /// the container
-template <typename T> struct element_value_type { using type = typename element_type<T>::type::value_type; };
+template <typename T> struct element_value_type {
+    using type = typename element_type<T>::type::value_type;
+};
 
 /// Adaptor for set-like structure: This just wraps a normal container in a few utilities that do almost nothing.
 template <typename T, typename _ = void> struct pair_adaptor : std::false_type {
@@ -1283,7 +1293,9 @@ auto value_string(const T &value) -> decltype(to_string(value)) {
 }
 
 /// template to get the underlying value type if it exists or use a default
-template <typename T, typename def, typename Enable = void> struct wrapped_type { using type = def; };
+template <typename T, typename def, typename Enable = void> struct wrapped_type {
+    using type = def;
+};
 
 /// Type size for regular object types that do not look like a tuple
 template <typename T, typename def> struct wrapped_type<T, def, typename std::enable_if<is_wrapper<T>::value>::type> {
@@ -1291,7 +1303,9 @@ template <typename T, typename def> struct wrapped_type<T, def, typename std::en
 };
 
 /// This will only trigger for actual void type
-template <typename T, typename Enable = void> struct type_count_base { static const int value{0}; };
+template <typename T, typename Enable = void> struct type_count_base {
+    static const int value{0};
+};
 
 /// Type size for regular object types that do not look like a tuple
 template <typename T>
@@ -1321,7 +1335,9 @@ template <typename T> struct subtype_count;
 template <typename T> struct subtype_count_min;
 
 /// This will only trigger for actual void type
-template <typename T, typename Enable = void> struct type_count { static const int value{0}; };
+template <typename T, typename Enable = void> struct type_count {
+    static const int value{0};
+};
 
 /// Type size for regular object types that do not look like a tuple
 template <typename T>
@@ -1372,7 +1388,9 @@ template <typename T> struct subtype_count {
 };
 
 /// This will only trigger for actual void type
-template <typename T, typename Enable = void> struct type_count_min { static const int value{0}; };
+template <typename T, typename Enable = void> struct type_count_min {
+    static const int value{0};
+};
 
 /// Type size for regular object types that do not look like a tuple
 template <typename T>
@@ -1421,7 +1439,9 @@ template <typename T> struct subtype_count_min {
 };
 
 /// This will only trigger for actual void type
-template <typename T, typename Enable = void> struct expected_count { static const int value{0}; };
+template <typename T, typename Enable = void> struct expected_count {
+    static const int value{0};
+};
 
 /// For most types the number of expected items is 1
 template <typename T>
@@ -1725,11 +1745,15 @@ inline std::string type_name() {
 /// Convert to an unsigned integral
 template <typename T, enable_if_t<std::is_unsigned<T>::value, detail::enabler> = detail::dummy>
 bool integral_conversion(const std::string &input, T &output) noexcept {
-    if(input.empty()) {
+    if(input.empty() || input.front() == '-') {
         return false;
     }
     char *val = nullptr;
+    errno = 0;
     std::uint64_t output_ll = std::strtoull(input.c_str(), &val, 0);
+    if(errno == ERANGE) {
+        return false;
+    }
     output = static_cast<T>(output_ll);
     if(val == (input.c_str() + input.size()) && static_cast<std::uint64_t>(output) == output_ll) {
         return true;
@@ -1750,7 +1774,11 @@ bool integral_conversion(const std::string &input, T &output) noexcept {
         return false;
     }
     char *val = nullptr;
+    errno = 0;
     std::int64_t output_ll = std::strtoll(input.c_str(), &val, 0);
+    if(errno == ERANGE) {
+        return false;
+    }
     output = static_cast<T>(output_ll);
     if(val == (input.c_str() + input.size()) && static_cast<std::int64_t>(output) == output_ll) {
         return true;
@@ -1867,18 +1895,18 @@ bool lexical_cast(const std::string &input, T &output) {
     bool worked = false;
     auto nloc = str1.find_last_of("+-");
     if(nloc != std::string::npos && nloc > 0) {
-        worked = detail::lexical_cast(str1.substr(0, nloc), x);
+        worked = lexical_cast(str1.substr(0, nloc), x);
         str1 = str1.substr(nloc);
         if(str1.back() == 'i' || str1.back() == 'j')
             str1.pop_back();
-        worked = worked && detail::lexical_cast(str1, y);
+        worked = worked && lexical_cast(str1, y);
     } else {
         if(str1.back() == 'i' || str1.back() == 'j') {
             str1.pop_back();
-            worked = detail::lexical_cast(str1, y);
+            worked = lexical_cast(str1, y);
             x = XC{0};
         } else {
-            worked = detail::lexical_cast(str1, x);
+            worked = lexical_cast(str1, x);
             y = XC{0};
         }
     }
@@ -2099,7 +2127,7 @@ template <typename AssignTo,
                       detail::enabler> = detail::dummy>
 bool lexical_assign(const std::string &input, AssignTo &output) {
     ConvertTo val{};
-    bool parse_result = (!input.empty()) ? lexical_cast<ConvertTo>(input, val) : true;
+    bool parse_result = (!input.empty()) ? lexical_cast(input, val) : true;
     if(parse_result) {
         output = val;
     }
@@ -2115,7 +2143,7 @@ template <
                 detail::enabler> = detail::dummy>
 bool lexical_assign(const std::string &input, AssignTo &output) {
     ConvertTo val{};
-    bool parse_result = input.empty() ? true : lexical_cast<ConvertTo>(input, val);
+    bool parse_result = input.empty() ? true : lexical_cast(input, val);
     if(parse_result) {
         output = AssignTo(val);  // use () form of constructor to allow some implicit conversions
     }
@@ -2193,7 +2221,7 @@ bool lexical_conversion(const std::vector<std::string> &strings, AssignTo &outpu
         if(str1.back() == 'i' || str1.back() == 'j') {
             str1.pop_back();
         }
-        auto worked = detail::lexical_cast(strings[0], x) && detail::lexical_cast(str1, y);
+        auto worked = lexical_cast(strings[0], x) && lexical_cast(str1, y);
         if(worked) {
             output = ConvertTo{x, y};
         }
@@ -2457,7 +2485,7 @@ inline std::string sum_string_vector(const std::vector<std::string> &values) {
     std::string output;
     for(const auto &arg : values) {
         double tv{0.0};
-        auto comp = detail::lexical_cast<double>(arg, tv);
+        auto comp = lexical_cast(arg, tv);
         if(!comp) {
             try {
                 tv = static_cast<double>(detail::to_flag_value(arg));
@@ -2475,8 +2503,7 @@ inline std::string sum_string_vector(const std::vector<std::string> &values) {
     } else {
         if(val <= static_cast<double>((std::numeric_limits<std::int64_t>::min)()) ||
            val >= static_cast<double>((std::numeric_limits<std::int64_t>::max)()) ||
-           // NOLINTNEXTLINE(clang-diagnostic-float-equal,bugprone-narrowing-conversions)
-           val == static_cast<std::int64_t>(val)) {
+           std::ceil(val) == std::floor(val)) {
             output = detail::value_string(static_cast<int64_t>(val));
         } else {
             output = detail::value_string(val);
@@ -2998,8 +3025,9 @@ template <typename DesiredType> class TypeValidator : public Validator {
   public:
     explicit TypeValidator(const std::string &validator_name)
         : Validator(validator_name, [](std::string &input_string) {
+              using CLI::detail::lexical_cast;
               auto val = DesiredType();
-              if(!detail::lexical_cast(input_string, val)) {
+              if(!lexical_cast(input_string, val)) {
                   return std::string("Failed parsing ") + input_string + " as a " + detail::type_name<DesiredType>();
               }
               return std::string();
@@ -3033,8 +3061,9 @@ class Range : public Validator {
         }
 
         func_ = [min_val, max_val](std::string &input) {
+            using CLI::detail::lexical_cast;
             T val;
-            bool converted = detail::lexical_cast(input, val);
+            bool converted = lexical_cast(input, val);
             if((!converted) || (val < min_val || val > max_val)) {
                 std::stringstream out;
                 out << "Value " << input << " not in range [";
@@ -3070,8 +3099,9 @@ class Bound : public Validator {
         description(out.str());
 
         func_ = [min_val, max_val](std::string &input) {
+            using CLI::detail::lexical_cast;
             T val;
-            bool converted = detail::lexical_cast(input, val);
+            bool converted = lexical_cast(input, val);
             if(!converted) {
                 return std::string("Value ") + input + " could not be converted";
             }
@@ -3262,8 +3292,9 @@ class IsMember : public Validator {
         // This is the function that validates
         // It stores a copy of the set pointer-like, so shared_ptr will stay alive
         func_ = [set, filter_fn](std::string &input) {
+            using CLI::detail::lexical_cast;
             local_item_t b;
-            if(!detail::lexical_cast(input, b)) {
+            if(!lexical_cast(input, b)) {
                 throw ValidationError(input);  // name is added later
             }
             if(filter_fn) {
@@ -3330,8 +3361,9 @@ class Transformer : public Validator {
         desc_function_ = [mapping]() { return detail::generate_map(detail::smart_deref(mapping)); };
 
         func_ = [mapping, filter_fn](std::string &input) {
+            using CLI::detail::lexical_cast;
             local_item_t b;
-            if(!detail::lexical_cast(input, b)) {
+            if(!lexical_cast(input, b)) {
                 return std::string();
                 // there is no possible way we can match anything in the mapping if we can't convert so just return
             }
@@ -3399,8 +3431,9 @@ class CheckedTransformer : public Validator {
         desc_function_ = tfunc;
 
         func_ = [mapping, tfunc, filter_fn](std::string &input) {
+            using CLI::detail::lexical_cast;
             local_item_t b;
-            bool converted = detail::lexical_cast(input, b);
+            bool converted = lexical_cast(input, b);
             if(converted) {
                 if(filter_fn) {
                     b = filter_fn(b);
@@ -3502,7 +3535,8 @@ class AsNumberWithUnit : public Validator {
                 unit = detail::to_lower(unit);
             }
             if(unit.empty()) {
-                if(!detail::lexical_cast(input, num)) {
+                using CLI::detail::lexical_cast;
+                if(!lexical_cast(input, num)) {
                     throw ValidationError(std::string("Value ") + input + " could not be converted to " +
                                           detail::type_name<Number>());
                 }
@@ -3520,7 +3554,8 @@ class AsNumberWithUnit : public Validator {
             }
 
             if(!input.empty()) {
-                bool converted = detail::lexical_cast(input, num);
+                using CLI::detail::lexical_cast;
+                bool converted = lexical_cast(input, num);
                 if(!converted) {
                     throw ValidationError(std::string("Value ") + input + " could not be converted to " +
                                           detail::type_name<Number>());
@@ -3829,7 +3864,8 @@ CLI11_INLINE IPV4Validator::IPV4Validator() : Validator("IPV4") {
         }
         int num = 0;
         for(const auto &var : result) {
-            bool retval = detail::lexical_cast(var, num);
+            using CLI::detail::lexical_cast;
+            bool retval = lexical_cast(var, num);
             if(!retval) {
                 return std::string("Failed parsing number (") + var + ')';
             }
@@ -5548,8 +5584,11 @@ struct AppFriend;
 }  // namespace detail
 
 namespace FailureMessage {
-std::string simple(const App *app, const Error &e);
-std::string help(const App *app, const Error &e);
+/// Printout a clean, simple message on error (the default in CLI11 1.5+)
+CLI11_INLINE std::string simple(const App *app, const Error &e);
+
+/// Printout the full help string on error (if this fn is set, the old default for CLI11)
+CLI11_INLINE std::string help(const App *app, const Error &e);
 }  // namespace FailureMessage
 
 /// enumeration of modes of how to deal with extras in config files
@@ -6122,7 +6161,8 @@ class App {
                      std::string flag_description = "") {
 
         CLI::callback_t fun = [&flag_result](const CLI::results_t &res) {
-            return CLI::detail::lexical_cast(res[0], flag_result);
+            using CLI::detail::lexical_cast;
+            return lexical_cast(res[0], flag_result);
         };
         auto *opt = _add_flag_internal(flag_name, std::move(fun), std::move(flag_description));
         return detail::default_flag_modifiers<T>(opt);
@@ -6138,8 +6178,9 @@ class App {
         CLI::callback_t fun = [&flag_results](const CLI::results_t &res) {
             bool retval = true;
             for(const auto &elem : res) {
+                using CLI::detail::lexical_cast;
                 flag_results.emplace_back();
-                retval &= detail::lexical_cast(elem, flag_results.back());
+                retval &= lexical_cast(elem, flag_results.back());
             }
             return retval;
         };
@@ -6851,16 +6892,6 @@ CLI11_INLINE void retire_option(App *app, const std::string &option_name);
 /// Helper function to mark an option as retired
 CLI11_INLINE void retire_option(App &app, const std::string &option_name);
 
-namespace FailureMessage {
-
-/// Printout a clean, simple message on error (the default in CLI11 1.5+)
-CLI11_INLINE std::string simple(const App *app, const Error &e);
-
-/// Printout the full help string on error (if this fn is set, the old default for CLI11)
-CLI11_INLINE std::string help(const App *app, const Error &e);
-
-}  // namespace FailureMessage
-
 namespace detail {
 /// This class is simply to allow tests access to App's protected functions
 struct AppFriend {
@@ -7143,8 +7174,9 @@ CLI11_INLINE Option *App::add_flag_callback(std::string flag_name,
                                             std::string flag_description) {
 
     CLI::callback_t fun = [function](const CLI::results_t &res) {
+        using CLI::detail::lexical_cast;
         bool trigger{false};
-        auto result = CLI::detail::lexical_cast(res[0], trigger);
+        auto result = lexical_cast(res[0], trigger);
         if(result && trigger) {
             function();
         }
@@ -7159,8 +7191,9 @@ App::add_flag_function(std::string flag_name,
                        std::string flag_description) {
 
     CLI::callback_t fun = [function](const CLI::results_t &res) {
+        using CLI::detail::lexical_cast;
         std::int64_t flag_count{0};
-        CLI::detail::lexical_cast(res[0], flag_count);
+        lexical_cast(res[0], flag_count);
         function(flag_count);
         return true;
     };
@@ -7544,7 +7577,7 @@ CLI11_NODISCARD CLI11_INLINE std::string App::help(std::string prev, AppFormatMo
     // Delegate to subcommand if needed
     auto selected_subcommands = get_subcommands();
     if(!selected_subcommands.empty()) {
-        return selected_subcommands.at(0)->help(prev, mode);
+        return selected_subcommands.back()->help(prev, mode);
     }
     return formatter_->make_help(this, prev, mode);
 }
@@ -8274,7 +8307,22 @@ CLI11_INLINE bool App::_parse_single_config(const ConfigItem &item, std::size_t
             if(item.inputs.size() <= 1) {
                 // Flag parsing
                 auto res = config_formatter_->to_flag(item);
-                res = op->get_flag_value(item.name, res);
+                bool converted{false};
+                if(op->get_disable_flag_override()) {
+
+                    try {
+                        auto val = detail::to_flag_value(res);
+                        if(val == 1) {
+                            res = op->get_flag_value(item.name, "{}");
+                            converted = true;
+                        }
+                    } catch(...) {
+                    }
+                }
+
+                if(!converted) {
+                    res = op->get_flag_value(item.name, res);
+                }
 
                 op->add_result(res);
                 return true;
@@ -8998,8 +9046,9 @@ CLI11_INLINE std::string convert_arg_for_ini(const std::string &arg, char string
     }
     // floating point conversion can convert some hex codes, but don't try that here
     if(arg.compare(0, 2, "0x") != 0 && arg.compare(0, 2, "0X") != 0) {
+        using CLI::detail::lexical_cast;
         double val = 0.0;
-        if(detail::lexical_cast(arg, val)) {
+        if(lexical_cast(arg, val)) {
             return arg;
         }
     }
@@ -9420,7 +9469,7 @@ CLI11_INLINE std::string Formatter::make_description(const App *app) const {
         if(min_options == 1) {
             desc += " \n[Exactly 1 of the following options is required]";
         } else {
-            desc += " \n[Exactly " + std::to_string(min_options) + "options from the following list are required]";
+            desc += " \n[Exactly " + std::to_string(min_options) + " options from the following list are required]";
         }
     } else if(max_options > 0) {
         if(min_options > 0) {

From 7aa6cbd2ba8a2a7d356b76c97207bf8d6353f195 Mon Sep 17 00:00:00 2001
From: aadi-raj <b21081@students.iitmandi.ac.in>
Date: Wed, 18 Jan 2023 23:52:23 +0530
Subject: [PATCH 13/80] A small typo fix in the doc hpt.md

---
 doc/user/hpt.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/user/hpt.md b/doc/user/hpt.md
index 88bcb28e23..881d60923b 100644
--- a/doc/user/hpt.md
+++ b/doc/user/hpt.md
@@ -216,6 +216,6 @@ Optimization" section for more details.
 
 ## Further documentation
 
-For more information on the `HyperParameterTuner` class, see the source code fro
+For more information on the `HyperParameterTuner` class, see the source code of 
 the `HyperParameterTuner` class (it is very well commented!), and the
 [cross-validation tutorial](cv.md).

From e1bdbfc99fe894a1b80ac5eb8ee048a42c49242e Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 23 Jan 2023 03:23:51 -0500
Subject: [PATCH 14/80] Fix path.

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 64d851f11f..757975ec0e 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -67,7 +67,7 @@ jobs:
             # These directives cause warnings on CRAN:
             # https://github.com/USCiLab/cereal/blob/master/include/cereal/external/base64.hpp#L28-L31
             # The command below comments them out.
-            sed -i 's|#pragma|// #pragma|' cereal-1.3.2/external/base64.hpp
+            sed -i 's|#pragma|// #pragma|' cereal-1.3.2/include/cereal/external/base64.hpp
 
         - name: Install R-bindings dependencies
           run: |

From 3d3df8f646f9bd3c64accbf7d5036593360ead7f Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 24 Jan 2023 03:18:55 -0500
Subject: [PATCH 15/80] Fix name of class.

---
 doc/quickstart/cpp.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/doc/quickstart/cpp.md b/doc/quickstart/cpp.md
index 3f92b2b15f..213d0917fd 100644
--- a/doc/quickstart/cpp.md
+++ b/doc/quickstart/cpp.md
@@ -105,11 +105,11 @@ int main()
       testLabels, 0.3);
 
   // Create the RandomForest object and train it on the training data.
-  RandomForest r(trainDataset,
-                 trainLabels,
-                 7 /* number of classes */,
-                 10 /* number of trees */,
-                 3 /* minimum leaf size */);
+  RandomForest<> r(trainDataset,
+                   trainLabels,
+                   7 /* number of classes */,
+                   10 /* number of trees */,
+                   3 /* minimum leaf size */);
 
   // Compute and print the training error.
   Row<size_t> trainPredictions;

From d2fee6a262b083dd9a8275ceac5acb9628804e38 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 24 Jan 2023 11:16:25 -0500
Subject: [PATCH 16/80] Add missing files to list of includes.

---
 src/mlpack.hpp | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/mlpack.hpp b/src/mlpack.hpp
index 91038d4c2e..47ee571b48 100644
--- a/src/mlpack.hpp
+++ b/src/mlpack.hpp
@@ -48,6 +48,7 @@
 #include "mlpack/methods/kmeans.hpp"
 #include "mlpack/methods/lars.hpp"
 #include "mlpack/methods/linear_regression.hpp"
+#include "mlpack/methods/linear_svm.hpp"
 #include "mlpack/methods/lmnn.hpp"
 #include "mlpack/methods/local_coordinate_coding.hpp"
 #include "mlpack/methods/logistic_regression.hpp"
@@ -57,8 +58,11 @@
 #include "mlpack/methods/naive_bayes.hpp"
 #include "mlpack/methods/nca.hpp"
 #include "mlpack/methods/neighbor_search.hpp"
+#include "mlpack/methods/nmf.hpp"
+#include "mlpack/methods/nystroem_method.hpp"
 #include "mlpack/methods/pca.hpp"
 #include "mlpack/methods/perceptron.hpp"
+#include "mlpack/methods/preprocess.hpp"
 #include "mlpack/methods/quic_svd.hpp"
 #include "mlpack/methods/radical.hpp"
 #include "mlpack/methods/random_forest.hpp"

From 47fd0b6a8d504ca82ce9ebd6bf6c2c5fc332ac5e Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 24 Jan 2023 11:52:55 -0500
Subject: [PATCH 17/80] Add missing include file.

---
 src/mlpack/methods/preprocess/preprocess.hpp | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 src/mlpack/methods/preprocess/preprocess.hpp

diff --git a/src/mlpack/methods/preprocess/preprocess.hpp b/src/mlpack/methods/preprocess/preprocess.hpp
new file mode 100644
index 0000000000..ba5ceead0e
--- /dev/null
+++ b/src/mlpack/methods/preprocess/preprocess.hpp
@@ -0,0 +1,17 @@
+/**
+ * @file methods/preprocess/preprocess.hpp
+ * @author Ryan Curtin
+ *
+ * Convenience include for preprocessing utilities.
+ *
+ * mlpack 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 mlpack.  If not, see
+ * http://www.opensource.org/licenses/BSD-3-Clause for more information.
+ */
+#ifndef MLPACK_METHODS_PREPROCESSING_PREPROCESSING_HPP
+#define MLPACK_METHODS_PREPROCESSING_PREPROCESSING_HPP
+
+#include "scaling_model.hpp"
+
+#endif

From 9bffe7839d4cefd682be98054b0032daea149221 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 24 Jan 2023 11:53:07 -0500
Subject: [PATCH 18/80] Fix functions that need to be inlined.

---
 .../methods/preprocess/scaling_model_impl.hpp    | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/mlpack/methods/preprocess/scaling_model_impl.hpp b/src/mlpack/methods/preprocess/scaling_model_impl.hpp
index 6da36e6f49..78f4bf5645 100644
--- a/src/mlpack/methods/preprocess/scaling_model_impl.hpp
+++ b/src/mlpack/methods/preprocess/scaling_model_impl.hpp
@@ -19,9 +19,9 @@
 namespace mlpack {
 namespace data {
 
-ScalingModel::ScalingModel(const int minvalue,
-                           const int maxvalue,
-                           double epsilonvalue) :
+inline ScalingModel::ScalingModel(const int minvalue,
+                                  const int maxvalue,
+                                  double epsilonvalue) :
     scalerType(0),
     minmaxscale(NULL),
     maxabsscale(NULL),
@@ -37,7 +37,7 @@ ScalingModel::ScalingModel(const int minvalue,
 }
 
 //! Copy constructor.
-ScalingModel::ScalingModel(const ScalingModel& other) :
+inline ScalingModel::ScalingModel(const ScalingModel& other) :
     scalerType(other.scalerType),
     minmaxscale(other.minmaxscale == NULL ? NULL :
         new data::MinMaxScaler(*other.minmaxscale)),
@@ -59,7 +59,7 @@ ScalingModel::ScalingModel(const ScalingModel& other) :
 }
 
 //! Move constructor.
-ScalingModel::ScalingModel(ScalingModel&& other) :
+inline ScalingModel::ScalingModel(ScalingModel&& other) :
     scalerType(other.scalerType),
     minmaxscale(other.minmaxscale),
     maxabsscale(other.maxabsscale),
@@ -84,7 +84,7 @@ ScalingModel::ScalingModel(ScalingModel&& other) :
 }
 
 //! Copy assignment operator.
-ScalingModel& ScalingModel::operator=(const ScalingModel& other)
+inline ScalingModel& ScalingModel::operator=(const ScalingModel& other)
 {
   if (this == &other)
   {
@@ -124,7 +124,7 @@ ScalingModel& ScalingModel::operator=(const ScalingModel& other)
 }
 
 //! Move assignment operator.
-ScalingModel& ScalingModel::operator=(ScalingModel&& other)
+inline ScalingModel& ScalingModel::operator=(ScalingModel&& other)
 {
   if (this != &other)
   {
@@ -153,7 +153,7 @@ ScalingModel& ScalingModel::operator=(ScalingModel&& other)
   return *this;
 }
 
-ScalingModel::~ScalingModel()
+inline ScalingModel::~ScalingModel()
 {
   delete minmaxscale;
   delete maxabsscale;

From cb58b5858eb355b46ed27da844e50b0ccfc06572 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 24 Jan 2023 11:56:05 -0500
Subject: [PATCH 19/80] Update HISTORY.

---
 HISTORY.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/HISTORY.md b/HISTORY.md
index 30a213c70c..0bec69304d 100644
--- a/HISTORY.md
+++ b/HISTORY.md
@@ -1,5 +1,6 @@
 ### mlpack ?.?.?
 ###### ????-??-??
+  * Fix a few missing includes in `<mlpack.hpp>` (#3374).
 
 ### mlpack 4.0.1
 ###### 2022-12-23

From 70ae814f186a0e85f27be3fdf11c6164ea9a5c8f Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 24 Jan 2023 12:07:53 -0500
Subject: [PATCH 20/80] Adapt reinforcement learning tutorial to mlpack 4 API.

---
 doc/tutorials/reinforcement_learning.md | 29 +++++++++++++------------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/doc/tutorials/reinforcement_learning.md b/doc/tutorials/reinforcement_learning.md
index 477258a17b..02e627b28e 100644
--- a/doc/tutorials/reinforcement_learning.md
+++ b/doc/tutorials/reinforcement_learning.md
@@ -143,13 +143,13 @@ can't pass mlpack's `FFN` network directly. Instead, we have to wrap it into
 int main()
 {
   // Set up the network.
-  FFN<MeanSquaredError<>, GaussianInitialization> network(MeanSquaredError<>(),
+  FFN<MeanSquaredError, GaussianInitialization> network(MeanSquaredError(),
       GaussianInitialization(0, 0.001));
-  network.Add<Linear<>>(4, 128);
-  network.Add<ReLULayer<>>();
-  network.Add<Linear<>>(128, 128);
-  network.Add<ReLULayer<>>();
-  network.Add<Linear<>>(128, 2);
+  network.Add<Linear>(128);
+  network.Add<ReLU>();
+  network.Add<Linear>(128);
+  network.Add<ReLU>();
+  network.Add<Linear>(2);
 
   SimpleDQN<> model(network);
 
@@ -159,7 +159,7 @@ The next step would be to setup the other components of the Q-learning agent,
 namely its policy, replay method and hyperparameters.
 
 ```c++
- // Set up the policy and replay method.
+  // Set up the policy and replay method.
   GreedyPolicy<CartPole> policy(1.0, 1000, 0.1, 0.99);
   RandomReplay<CartPole> replayMethod(10, 10000);
 
@@ -314,6 +314,7 @@ auto measure = [&returns, &position, &episode](double episodeReturn)
   std::cout << "Episode No.: " << episode
       << "; Episode Return: " << episodeReturn
       << "; Average Return: " << arma::mean(returns) << std::endl;
+  return false;
 };
 ```
 
@@ -328,17 +329,16 @@ Here is the full code to try this right away:
 #include <mlpack.hpp>
 
 using namespace mlpack;
-using namespace mlpack::rl;
 
 int main()
 {
   // Set up the network.
-  FFN<MeanSquaredError<>, GaussianInitialization> model(MeanSquaredError<>(), GaussianInitialization(0, 0.001));
-  model.Add<Linear<>>(4, 128);
-  model.Add<ReLULayer<>>();
-  model.Add<Linear<>>(128, 128);
-  model.Add<ReLULayer<>>();
-  model.Add<Linear<>>(128, 2);
+  FFN<MeanSquaredError, GaussianInitialization> model(MeanSquaredError(), GaussianInitialization(0, 0.001));
+  model.Add<Linear>(128);
+  model.Add<ReLU>();
+  model.Add<Linear>(128);
+  model.Add<ReLU>();
+  model.Add<Linear>(2);
 
   AggregatedPolicy<GreedyPolicy<CartPole>> policy({GreedyPolicy<CartPole>(0.7, 5000, 0.1),
                                                    GreedyPolicy<CartPole>(0.7, 5000, 0.01),
@@ -371,6 +371,7 @@ int main()
     std::cout << "Episode No.: " << episode
         << "; Episode Return: " << episodeReturn
         << "; Average Return: " << arma::mean(returns) << std::endl;
+    return false;
   };
 
   for (int i = 0; i < 100; i++)

From 7c0b56bd8eca245df55e4eafd5d522b3b3f47445 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 24 Jan 2023 12:27:28 -0500
Subject: [PATCH 21/80] The rotated filters have the same size as the original
 filters.

---
 src/mlpack/methods/ann/layer/convolution_impl.hpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mlpack/methods/ann/layer/convolution_impl.hpp b/src/mlpack/methods/ann/layer/convolution_impl.hpp
index a4bcb367a6..567cc85f85 100644
--- a/src/mlpack/methods/ann/layer/convolution_impl.hpp
+++ b/src/mlpack/methods/ann/layer/convolution_impl.hpp
@@ -384,8 +384,8 @@ void ConvolutionType<
       (padWLeft != 0 || padWRight != 0 || padHTop != 0 || padHBottom != 0);
 
   // To perform the backward pass, we need to rotate all the filters.
-  arma::Cube<typename MatType::elem_type> rotatedFilters(weight.n_cols,
-      weight.n_rows, weight.n_slices);
+  arma::Cube<typename MatType::elem_type> rotatedFilters(weight.n_rows,
+      weight.n_cols, weight.n_slices);
 
   // To perform the backward pass, we need to dilate all the mappedError.
   arma::Cube<typename MatType::elem_type> dilatedMappedError;

From addeffb1110fea1a89445e94765c278724a57a45 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 24 Jan 2023 12:30:33 -0500
Subject: [PATCH 22/80] Update HISTORY.

---
 HISTORY.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/HISTORY.md b/HISTORY.md
index 30a213c70c..ad52cf3ba1 100644
--- a/HISTORY.md
+++ b/HISTORY.md
@@ -1,5 +1,6 @@
 ### mlpack ?.?.?
 ###### ????-??-??
+  * Bugfix for non-square convolution kernels (#3376).
 
 ### mlpack 4.0.1
 ###### 2022-12-23

From 563a45864cbe970b9e5d911643b960d6ad468229 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 24 Jan 2023 12:33:07 -0500
Subject: [PATCH 23/80] Apply the fix to grouped convolutions, too.

---
 src/mlpack/methods/ann/layer/grouped_convolution_impl.hpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mlpack/methods/ann/layer/grouped_convolution_impl.hpp b/src/mlpack/methods/ann/layer/grouped_convolution_impl.hpp
index e40ca6968d..5c946014bb 100644
--- a/src/mlpack/methods/ann/layer/grouped_convolution_impl.hpp
+++ b/src/mlpack/methods/ann/layer/grouped_convolution_impl.hpp
@@ -402,8 +402,8 @@ void GroupedConvolutionType<
       (padWLeft != 0 || padWRight != 0 || padHTop != 0 || padHBottom != 0);
 
   // To perform the backward pass, we need to rotate all the filters.
-  arma::Cube<typename MatType::elem_type> rotatedFilters(weight.n_cols,
-      weight.n_rows, weight.n_slices);
+  arma::Cube<typename MatType::elem_type> rotatedFilters(weight.n_rows,
+      weight.n_cols, weight.n_slices);
 
   #pragma omp parallel for
   for (size_t map = 0; map < ((maps * inMaps) / groups); ++map)

From 5d2d1918799da2fbda3b4942c0b40aa900bd8de4 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 24 Jan 2023 12:57:52 -0500
Subject: [PATCH 24/80] Add some simple tests for non-square filters.

---
 src/mlpack/tests/ann/layer/convolution.cpp    | 20 +++++++++++++++++++
 .../tests/ann/layer/grouped_convolution.cpp   | 20 +++++++++++++++++++
 2 files changed, 40 insertions(+)

diff --git a/src/mlpack/tests/ann/layer/convolution.cpp b/src/mlpack/tests/ann/layer/convolution.cpp
index bb40ca8e9d..85e102516c 100644
--- a/src/mlpack/tests/ann/layer/convolution.cpp
+++ b/src/mlpack/tests/ann/layer/convolution.cpp
@@ -441,3 +441,23 @@ TEST_CASE("AdvancedConvolutionLayerWithStrideTest", "[ANNLayerTest]")
   layer.Backward(input, output, delta);
   REQUIRE(arma::accu(delta) == Approx(115.3515701294).epsilon(1e-5));
 }
+
+// Make a simple convolutional layer with non-square filters, and make sure the
+// forward and backward and gradient passes all return a result.  (This checks
+// that we don't have any shape errors.)
+TEST_CASE("NonSquareConvolutionTest", "[ANNLayerTest]")
+{
+  Convolution module1(1, 5, 3);
+  module1.InputDimensions() = std::vector<size_t>({ 7, 7 });
+  module1.ComputeOutputDimensions();
+  arma::mat weights1(module1.WeightSize(), 1);
+  module1.SetWeights(weights1.memptr());
+
+  arma::mat data(49, 10, arma::fill::randu);
+  arma::mat forwardResult(module1.OutputSize(), 10, arma::fill::zeros);
+  REQUIRE_NOTHROW(module1.Forward(data, forwardResult));
+  arma::mat backwardResult(49, 10);
+  REQUIRE_NOTHROW(module1.Backward(data, forwardResult, backwardResult));
+  arma::mat gradientResult(module1.WeightSize(), 1);
+  REQUIRE_NOTHROW(module1.Gradient(data, backwardResult, gradientResult));
+}
diff --git a/src/mlpack/tests/ann/layer/grouped_convolution.cpp b/src/mlpack/tests/ann/layer/grouped_convolution.cpp
index 09e7e4dc4b..391b520c06 100644
--- a/src/mlpack/tests/ann/layer/grouped_convolution.cpp
+++ b/src/mlpack/tests/ann/layer/grouped_convolution.cpp
@@ -202,3 +202,23 @@ TEST_CASE("GradientGroupedConvolutionLayerTest", "[ANNLayerTest]")
 
   REQUIRE(CheckGradient(function) < 1e-1);
 }
+
+// Make a simple grouped convolutional layer with non-square filters, and make
+// sure the forward and backward and gradient passes all return a result.  (This
+// checks that we don't have any shape errors.)
+TEST_CASE("NonSquareGroupedConvolutionTest", "[ANNLayerTest]")
+{
+  GroupedConvolution module1(1, 5, 3, 1);
+  module1.InputDimensions() = std::vector<size_t>({ 7, 7 });
+  module1.ComputeOutputDimensions();
+  arma::mat weights1(module1.WeightSize(), 1);
+  module1.SetWeights(weights1.memptr());
+
+  arma::mat data(49, 10, arma::fill::randu);
+  arma::mat forwardResult(module1.OutputSize(), 10, arma::fill::zeros);
+  REQUIRE_NOTHROW(module1.Forward(data, forwardResult));
+  arma::mat backwardResult(49, 10);
+  REQUIRE_NOTHROW(module1.Backward(data, forwardResult, backwardResult));
+  arma::mat gradientResult(module1.WeightSize(), 1);
+  REQUIRE_NOTHROW(module1.Gradient(data, backwardResult, gradientResult));
+}

From ad2325fd532364c54adc12c1b9cd7bf62aca529c Mon Sep 17 00:00:00 2001
From: James J Balamuta <coatless@users.noreply.github.com>
Date: Tue, 24 Jan 2023 17:31:36 -0800
Subject: [PATCH 25/80] Update COPYRIGHT.txt

---
 COPYRIGHT.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt
index 4cec03a865..dbb4ed45ac 100644
--- a/COPYRIGHT.txt
+++ b/COPYRIGHT.txt
@@ -7,7 +7,7 @@ Source:
 
 Files: *
 Copyright:
-  Copyright 2008-2022, Ryan Curtin <ryan@ratml.org>
+  Copyright 2008-2023, Ryan Curtin <ryan@ratml.org>
   Copyright 2008-2013, Bill March <march@gatech.edu>
   Copyright 2008-2012, Dongryeol Lee <dongryel@cc.gatech.edu>
   Copyright 2008-2013, Nishant Mehta <niche@cc.gatech.edu>
@@ -147,6 +147,7 @@ Copyright:
   Copyright 2021, Roshan Nrusing Swain <swainroshan001@gmail.com>
   Copyright 2021, Suvarsha Chennareddy <suvarshachennareddy@gmail.com>
   Copyright 2021, Shubham Agrawal <shubham.agra1206@gmail.com>
+  Copyright 2020 - 2022, James Joseph Balamuta <balamut2@illinois.edu>  
   Copyright 2022, Sri Madhan M <srimadhan11@gmail.com>
   Copyright 2022, Zhuojin Liu <zhuojinliu.cs@gmail.com>
   Copyright 2022, Richèl Bilderbeek <richel@richelbilderbeek.nl>

From ed882bd12f28c827eca7b2b43718ab1d518f7f92 Mon Sep 17 00:00:00 2001
From: James J Balamuta <coatless@users.noreply.github.com>
Date: Tue, 24 Jan 2023 17:43:05 -0800
Subject: [PATCH 26/80] Update COPYRIGHT.txt

---
 COPYRIGHT.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt
index dbb4ed45ac..bde6e3e60c 100644
--- a/COPYRIGHT.txt
+++ b/COPYRIGHT.txt
@@ -83,6 +83,7 @@ Copyright:
   Copyright 2017, Samikshya Chand <samikshya289@gmail.com>
   Copyright 2017, N Rajiv Vaidyanathan <rajivvaidyanathan4@gmail.com>
   Copyright 2017, Kartik Nighania <kartiknighania@gmail.com>
+  Copyright 2017 - 2023, Dirk Eddelbuettel <edd@debian.org>
   Copyright 2017-2018, Eugene Freyman <evg.freyman@gmail.com>
   Copyright 2017-2019, Manish Kumar <manish887kr@gmail.com>
   Copyright 2017-2018, Haritha Sreedharan Nair <haritha1313@gmail.com>

From a208e4967b13cf382cb24b2ff61cf7cc9ff994f7 Mon Sep 17 00:00:00 2001
From: James J Balamuta <coatless@users.noreply.github.com>
Date: Tue, 24 Jan 2023 17:44:59 -0800
Subject: [PATCH 27/80] Spacing [ci skip]

---
 COPYRIGHT.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt
index bde6e3e60c..55b361c5e4 100644
--- a/COPYRIGHT.txt
+++ b/COPYRIGHT.txt
@@ -83,7 +83,7 @@ Copyright:
   Copyright 2017, Samikshya Chand <samikshya289@gmail.com>
   Copyright 2017, N Rajiv Vaidyanathan <rajivvaidyanathan4@gmail.com>
   Copyright 2017, Kartik Nighania <kartiknighania@gmail.com>
-  Copyright 2017 - 2023, Dirk Eddelbuettel <edd@debian.org>
+  Copyright 2017-2023, Dirk Eddelbuettel <edd@debian.org>
   Copyright 2017-2018, Eugene Freyman <evg.freyman@gmail.com>
   Copyright 2017-2019, Manish Kumar <manish887kr@gmail.com>
   Copyright 2017-2018, Haritha Sreedharan Nair <haritha1313@gmail.com>
@@ -148,7 +148,7 @@ Copyright:
   Copyright 2021, Roshan Nrusing Swain <swainroshan001@gmail.com>
   Copyright 2021, Suvarsha Chennareddy <suvarshachennareddy@gmail.com>
   Copyright 2021, Shubham Agrawal <shubham.agra1206@gmail.com>
-  Copyright 2020 - 2022, James Joseph Balamuta <balamut2@illinois.edu>  
+  Copyright 2020-2022, James Joseph Balamuta <balamut2@illinois.edu>  
   Copyright 2022, Sri Madhan M <srimadhan11@gmail.com>
   Copyright 2022, Zhuojin Liu <zhuojinliu.cs@gmail.com>
   Copyright 2022, Richèl Bilderbeek <richel@richelbilderbeek.nl>

From 1f30b5a9eb782260c3792025ea73e974e2df3d6f Mon Sep 17 00:00:00 2001
From: James J Balamuta <coatless@users.noreply.github.com>
Date: Tue, 24 Jan 2023 20:38:45 -0800
Subject: [PATCH 28/80] Add @iamshnoo

---
 COPYRIGHT.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt
index 55b361c5e4..96aec3e942 100644
--- a/COPYRIGHT.txt
+++ b/COPYRIGHT.txt
@@ -142,6 +142,7 @@ Copyright:
   Copyright 2020, Alex Nguyen <alexvn.edu@gmail.com>
   Copyright 2020, Gaurav Ghati <gauravghatii@gmail.com>
   Copyright 2020, Anmolpreet Singh <anmol323c@gmail.com>
+  Copyright 2020, Anjishnu Mukherjee <amukher6@gmu.edu>
   Copyright 2021, Tru Hoang <trugiahoang@gmail.com>
   Copyright 2021, Mark Fischinger <markfischinger@gmail.com>
   Copyright 2021, Muhammad Fawwaz Mayda <maydafawwaz@gmail.com>

From b453cc0d5e8cf1a0542722f5cb7d4b7a4d86f950 Mon Sep 17 00:00:00 2001
From: James J Balamuta <coatless@users.noreply.github.com>
Date: Wed, 25 Jan 2023 10:22:35 -0800
Subject: [PATCH 29/80] Added @shrit

---
 COPYRIGHT.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt
index 96aec3e942..bbed09b471 100644
--- a/COPYRIGHT.txt
+++ b/COPYRIGHT.txt
@@ -143,6 +143,7 @@ Copyright:
   Copyright 2020, Gaurav Ghati <gauravghatii@gmail.com>
   Copyright 2020, Anmolpreet Singh <anmol323c@gmail.com>
   Copyright 2020, Anjishnu Mukherjee <amukher6@gmu.edu>
+  Copyright 2020-2023, Omar Shrit <omar@shrit.me>
   Copyright 2021, Tru Hoang <trugiahoang@gmail.com>
   Copyright 2021, Mark Fischinger <markfischinger@gmail.com>
   Copyright 2021, Muhammad Fawwaz Mayda <maydafawwaz@gmail.com>

From d3d597f678f9b470f8f6b96e46bb1935d1f08a3b Mon Sep 17 00:00:00 2001
From: Rodo <rodonguyendd@gmail.com>
Date: Thu, 26 Jan 2023 12:00:50 +0000
Subject: [PATCH 30/80] Add more info

---
 README.md | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 8ea0dcc058..d86c8b13b9 100644
--- a/README.md
+++ b/README.md
@@ -103,11 +103,12 @@ Citations are beneficial for the growth and improvement of mlpack.
 
 ## 2. Dependencies
 
-mlpack requires a C++14 compiler and has the following additional dependencies:
-
- - Armadillo      >= 9.800
- - ensmallen      >= 2.10.0
- - cereal         >= 1.1.2
+**mlpack** requires following additional dependencies:
+ - C++14 Compiler
+ - [Armadillo](https://arma.sourceforge.net/docs.html)      &nbsp;&emsp;>= 9.800
+ - [ensmallen](https://ensmallen.org)      &emsp;>= 2.10.0
+ - [cereal](http://uscilab.github.io/cereal/)         &ensp;&nbsp;
+&emsp;&emsp;>= 1.1.2
 
 If the STB library headers are available, image loading support will be
 available.
@@ -119,12 +120,14 @@ If you are compiling Armadillo by hand, ensure that LAPACK and BLAS are enabled.
 *See also the [C++ quickstart](doc/quickstart/cpp.md).*
 
 Since mlpack is a header-only library, installing just the headers for use in a
-C++ application is trivial.  From the root of the sources, configure and install
+C++ application is trivial. However, should an error occurs due to uninstalled dependencies, take a look at [Section 3.1](#31-additional-build-options) for this particular error and more.
+
+From the root of the sources, configure and install
 in the standard CMake way:
 
 ```sh
 mkdir build && cd build/
-cmake ../
+cmake ..
 sudo make install
 ```
 
@@ -136,14 +139,16 @@ cmake -S . -B build
 sudo cmake --build build --target install
 ```
 
+### 3.1. Additional build options
+
 You can add a few arguments to the `cmake` command to control the behavior of
 the configuration and build process.  Simply add these to the `cmake` command.
 Some options are given below:
 
- - `-DCMAKE_INSTALL_PREFIX=/install/root/` will set the root of the install
-   directory to `/install/root` when `make install` is run.
  - `-DDOWNLOAD_DEPENDENCIES=ON` will automatically download mlpack's
    dependencies (ensmallen, Armadillo, and cereal).
+ - `-DCMAKE_INSTALL_PREFIX=/install/root/` will set the root of the install
+   directory to `/install/root` when `make install` is run.
  - `-DDEBUG=ON` will enable debugging symbols in any compiled bindings or tests.
 
 There are also options to enable building bindings to each language that mlpack
@@ -171,7 +176,7 @@ See the [C++ quickstart](doc/quickstart/cpp.md) and the
 [examples](https://github.com/mlpack/examples) repository for some examples of
 mlpack applications in C++, with corresponding `Makefile`s.
 
-### 3.1. Including mlpack and improving compile time
+### 3.2. Improving compile time
 
 mlpack is a template-heavy library, and if care is not used, compilation time of
 a project can be increased greatly.  Fortunately, there are a number of ways to

From 9d84c387569e2dd1fbdd31fa3bb045527b0dd586 Mon Sep 17 00:00:00 2001
From: Rodo <rodonguyendd@gmail.com>
Date: Thu, 26 Jan 2023 12:19:16 +0000
Subject: [PATCH 31/80] Fix grammars

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index d86c8b13b9..021b0c54f6 100644
--- a/README.md
+++ b/README.md
@@ -103,7 +103,7 @@ Citations are beneficial for the growth and improvement of mlpack.
 
 ## 2. Dependencies
 
-**mlpack** requires following additional dependencies:
+**mlpack** requires the following additional dependencies:
  - C++14 Compiler
  - [Armadillo](https://arma.sourceforge.net/docs.html)      &nbsp;&emsp;>= 9.800
  - [ensmallen](https://ensmallen.org)      &emsp;>= 2.10.0

From 874d45ffc5b4ca89c4ce76b3c0321a8089d56051 Mon Sep 17 00:00:00 2001
From: James J Balamuta <coatless@users.noreply.github.com>
Date: Thu, 26 Jan 2023 07:15:39 -0800
Subject: [PATCH 32/80] Add @SuryodayBasak

---
 COPYRIGHT.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt
index bbed09b471..09609b83be 100644
--- a/COPYRIGHT.txt
+++ b/COPYRIGHT.txt
@@ -126,6 +126,7 @@ Copyright:
   Copyright 2019, Rohit Kartik <rohit.audrey@gmail.com>
   Copyright 2019, Aditya Viki <adityaviki01@gmail.com>
   Copyright 2019-2020 Kartik Dutt <kartikdutt@live.in>
+  Copyright 2019, Suryoday Basak <suryodaybasak@gmail.com>
   Copyright 2020, Sriram S K <sriramsk1999@gmail.com>
   Copyright 2020, Manoranjan Kumar Bharti ( Nakul Bharti ) <knakul853@gmail.com>
   Copyright 2020, Saraansh Tandon <saraanshtandon1999@gmail.com>

From 280c443d15ca0f67f9ed7fe41735ae62b4b9d59a Mon Sep 17 00:00:00 2001
From: James J Balamuta <coatless@users.noreply.github.com>
Date: Thu, 26 Jan 2023 07:17:10 -0800
Subject: [PATCH 33/80] Added missing commas

---
 COPYRIGHT.txt | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt
index 09609b83be..4740e37fbc 100644
--- a/COPYRIGHT.txt
+++ b/COPYRIGHT.txt
@@ -26,7 +26,7 @@ Copyright:
   Copyright 2013, Mudit Raj Gupta <mudit.raaj.gupta@gmail.com>
   Copyright 2013-2018, Sumedh Ghaisas <sumedhghaisas@gmail.com>
   Copyright 2014, Michael Fox <michaelfox99@gmail.com>
-  Copyright 2014,2020 Ryan Birmingham <birm@gatech.edu>
+  Copyright 2014,2020, Ryan Birmingham <birm@gatech.edu>
   Copyright 2014, Siddharth Agrawal <siddharth.950@gmail.com>
   Copyright 2014, Saheb Motiani <saheb210692@gmail.com>
   Copyright 2014, Yash Vadalia <yashdv@gmail.com>
@@ -90,9 +90,9 @@ Copyright:
   Copyright 2017-2018, Sourabh Varshney <sourabhvarshney111@gmail.com>
   Copyright 2018, Projyal Dev <projyal@gmail.com>
   Copyright 2018, Nikhil Goel <nikhilgoel199797@gmail.com>
-  Copyright 2018-2020 Shikhar Jaiswal <jaiswalshikhar87@gmail.com>
+  Copyright 2018-2020, Shikhar Jaiswal <jaiswalshikhar87@gmail.com>
   Copyright 2018, B Kartheek Reddy <bkartheekreddy@gmail.com>
-  Copyright 2018-2019 Atharva Khandait <akhandait45@gmail.com>
+  Copyright 2018-2019, Atharva Khandait <akhandait45@gmail.com>
   Copyright 2018, Wenhao Huang <wenhao.huang.work@gmail.com>
   Copyright 2018-2019, Roberto Hueso <robertohueso96@gmail.com>
   Copyright 2018, Prabhat Sharma <prabhatsharma7298@gmail.com>
@@ -115,9 +115,9 @@ Copyright:
   Copyright 2019, Miguel Canteras <mcanteras@gmail.com>
   Copyright 2019, Bishwa Karki <karkeebishwa1@gmail.com>
   Copyright 2019, Mehul Kumar Nirala <mehulkumarnirala@gmail.com>
-  Copyright 2019-2020 Yashwant Singh Parihar <yashwantsingh.sngh@gmail.com>
+  Copyright 2019-2020, Yashwant Singh Parihar <yashwantsingh.sngh@gmail.com>
   Copyright 2019, Heet Sankesara <heetsankesara3@gmail.com>
-  Copyright 2019-2020 Jeffin Sam <sam.jeffin@gmail.com>
+  Copyright 2019-2020, Jeffin Sam <sam.jeffin@gmail.com>
   Copyright 2019, Vikas S Shetty <shettyvikas209@gmail.com>
   Copyright 2019, Khizir Siddiqui <khizirsiddiqui@gmail.com>
   Copyright 2019, Tejasvi Tomar <tstomar@outlook.com>
@@ -125,7 +125,7 @@ Copyright:
   Copyright 2019, Ziyang Jiang <zij004@alumni.stanford.edu>
   Copyright 2019, Rohit Kartik <rohit.audrey@gmail.com>
   Copyright 2019, Aditya Viki <adityaviki01@gmail.com>
-  Copyright 2019-2020 Kartik Dutt <kartikdutt@live.in>
+  Copyright 2019-2020, Kartik Dutt <kartikdutt@live.in>
   Copyright 2019, Suryoday Basak <suryodaybasak@gmail.com>
   Copyright 2020, Sriram S K <sriramsk1999@gmail.com>
   Copyright 2020, Manoranjan Kumar Bharti ( Nakul Bharti ) <knakul853@gmail.com>

From 2207d93ad80c6247921b5f5befcacacafe79604c Mon Sep 17 00:00:00 2001
From: conradsnicta <conradsnicta@users.noreply.github.com>
Date: Fri, 27 Jan 2023 05:01:22 +0000
Subject: [PATCH 34/80] remove unused define (#3381)

---
 src/mlpack/core.hpp | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/src/mlpack/core.hpp b/src/mlpack/core.hpp
index 44d3eefce3..f016df2f88 100644
--- a/src/mlpack/core.hpp
+++ b/src/mlpack/core.hpp
@@ -61,9 +61,4 @@
   #include <omp.h>
 #endif
 
-// Use Armadillo's C++ version detection.
-#ifdef ARMA_USE_CXX11
-  #define MLPACK_USE_CX11
-#endif
-
 #endif

From b3784759548896b9cc1a41f5a14aeb154ba1b215 Mon Sep 17 00:00:00 2001
From: Rodo <rodonguyendd@gmail.com>
Date: Fri, 27 Jan 2023 15:11:39 +1000
Subject: [PATCH 35/80] Update README.md

Co-authored-by: Ryan Curtin <ryan@ratml.org>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 021b0c54f6..45fe9ee252 100644
--- a/README.md
+++ b/README.md
@@ -104,7 +104,7 @@ Citations are beneficial for the growth and improvement of mlpack.
 ## 2. Dependencies
 
 **mlpack** requires the following additional dependencies:
- - C++14 Compiler
+ - C++14 compiler
  - [Armadillo](https://arma.sourceforge.net/docs.html)      &nbsp;&emsp;>= 9.800
  - [ensmallen](https://ensmallen.org)      &emsp;>= 2.10.0
  - [cereal](http://uscilab.github.io/cereal/)         &ensp;&nbsp;

From 9cd061013995295bac1752f5ffa73d106840c4c6 Mon Sep 17 00:00:00 2001
From: Rodo <rodonguyendd@gmail.com>
Date: Fri, 27 Jan 2023 15:11:46 +1000
Subject: [PATCH 36/80] Update README.md

Co-authored-by: Ryan Curtin <ryan@ratml.org>
---
 README.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 45fe9ee252..6347bb7414 100644
--- a/README.md
+++ b/README.md
@@ -107,8 +107,7 @@ Citations are beneficial for the growth and improvement of mlpack.
  - C++14 compiler
  - [Armadillo](https://arma.sourceforge.net/docs.html)      &nbsp;&emsp;>= 9.800
  - [ensmallen](https://ensmallen.org)      &emsp;>= 2.10.0
- - [cereal](http://uscilab.github.io/cereal/)         &ensp;&nbsp;
-&emsp;&emsp;>= 1.1.2
+ - [cereal](http://uscilab.github.io/cereal/)         &ensp;&nbsp;&emsp;&emsp;>= 1.1.2
 
 If the STB library headers are available, image loading support will be
 available.

From b5a8540cd581947deb893f014ad602c17c2618de Mon Sep 17 00:00:00 2001
From: Rodo <rodonguyendd@gmail.com>
Date: Fri, 27 Jan 2023 15:14:27 +1000
Subject: [PATCH 37/80] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 6347bb7414..99dbcc0298 100644
--- a/README.md
+++ b/README.md
@@ -105,7 +105,7 @@ Citations are beneficial for the growth and improvement of mlpack.
 
 **mlpack** requires the following additional dependencies:
  - C++14 compiler
- - [Armadillo](https://arma.sourceforge.net/docs.html)      &nbsp;&emsp;>= 9.800
+ - [Armadillo](https://arma.sourceforge.net)      &nbsp;&emsp;>= 9.800
  - [ensmallen](https://ensmallen.org)      &emsp;>= 2.10.0
  - [cereal](http://uscilab.github.io/cereal/)         &ensp;&nbsp;&emsp;&emsp;>= 1.1.2
 

From 6d0b788b48978beb59fc5f78c17dd52feb299c3a Mon Sep 17 00:00:00 2001
From: Rodo <rodonguyendd@gmail.com>
Date: Fri, 27 Jan 2023 15:15:50 +1000
Subject: [PATCH 38/80] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 99dbcc0298..0775c7a49a 100644
--- a/README.md
+++ b/README.md
@@ -175,7 +175,7 @@ See the [C++ quickstart](doc/quickstart/cpp.md) and the
 [examples](https://github.com/mlpack/examples) repository for some examples of
 mlpack applications in C++, with corresponding `Makefile`s.
 
-### 3.2. Improving compile time
+### 3.2. Reducing compile time
 
 mlpack is a template-heavy library, and if care is not used, compilation time of
 a project can be increased greatly.  Fortunately, there are a number of ways to

From 194f629604b9cddf83a482202c753044acc11ee3 Mon Sep 17 00:00:00 2001
From: Rodo <rodonguyendd@gmail.com>
Date: Fri, 27 Jan 2023 15:22:45 +1000
Subject: [PATCH 39/80] Update README.md

Improving and moving instructions for cmake error
---
 README.md | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 0775c7a49a..b2cfdc56db 100644
--- a/README.md
+++ b/README.md
@@ -119,7 +119,7 @@ If you are compiling Armadillo by hand, ensure that LAPACK and BLAS are enabled.
 *See also the [C++ quickstart](doc/quickstart/cpp.md).*
 
 Since mlpack is a header-only library, installing just the headers for use in a
-C++ application is trivial. However, should an error occurs due to uninstalled dependencies, take a look at [Section 3.1](#31-additional-build-options) for this particular error and more.
+C++ application is trivial. 
 
 From the root of the sources, configure and install
 in the standard CMake way:
@@ -130,7 +130,13 @@ cmake ..
 sudo make install
 ```
 
-Note: Since CMake v3.14.0 the `cmake` command can create the build folder itself.
+If the `cmake ..` command fails due to unavailable dependencies, consider either using the
+`-DDOWNLOAD_DEPENDENCIES=ON` option as detailed in
+[the following subsection](#31-additional-build-options), or ensure that mlpack's dependencies
+are installed, e.g. using the system package manager.  For example, on Debian and Ubuntu,
+all relevant dependencies can be installed with `sudo apt-get install libarmadillo-dev libensmallen-dev libcereal-dev g++ cmake`.
+
+Alternatively, CMake v3.14.0 the `cmake` command can create the build folder itself.
 The above commands can be rewritten as follows:
 
 ```sh

From 13fafb43e98a686de833a9bbd8c0d80aa50561c4 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Fri, 27 Jan 2023 12:11:46 +0530
Subject: [PATCH 40/80] Fix a typo

---
 doc/user/formats.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/user/formats.md b/doc/user/formats.md
index f7c6daae42..e80e3b8cf5 100644
--- a/doc/user/formats.md
+++ b/doc/user/formats.md
@@ -177,7 +177,7 @@ matrix = matrix.t(); // We must transpose after load!
 The transposition after loading is necessary if the coordinate list is in
 row-major format (that is, if each row in the matrix represents a point and each
 column represents a feature).  Be sure that the matrix you use with mlpack
-methods has points as columns and features as rows!  See \ref matrices for more
+methods has points as columns and features as rows!  See [matrices](matrices.md) for more
 information.
 
 ## Categorical features and command line programs

From 2f1845401f1213e78730219214c2b1024efa36ec Mon Sep 17 00:00:00 2001
From: Aditya Raj <96882869+aadi-raj@users.noreply.github.com>
Date: Sat, 28 Jan 2023 11:23:32 +0530
Subject: [PATCH 41/80] Update serialization.pxd

---
 src/mlpack/bindings/python/mlpack/serialization.pxd | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/mlpack/bindings/python/mlpack/serialization.pxd b/src/mlpack/bindings/python/mlpack/serialization.pxd
index b82c9e73a5..19c8b72e74 100644
--- a/src/mlpack/bindings/python/mlpack/serialization.pxd
+++ b/src/mlpack/bindings/python/mlpack/serialization.pxd
@@ -4,6 +4,11 @@ serialization.pxd: serialization functions for mlpack classes.
 
 This simply makes the utility serialization functions from serialization.hpp
 available from Python.
+
+mlpack 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 mlpack.  If not, see
+http://www.opensource.org/licenses/BSD-3-Clause for more information.
 """
 cimport cython
 

From 0f010e745aa71a30fb4b9120f989cfb01db349de Mon Sep 17 00:00:00 2001
From: Aditya Raj <96882869+aadi-raj@users.noreply.github.com>
Date: Sat, 28 Jan 2023 11:26:25 +0530
Subject: [PATCH 42/80] Update generate_R.cpp.in

---
 src/mlpack/bindings/R/generate_R.cpp.in | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/mlpack/bindings/R/generate_R.cpp.in b/src/mlpack/bindings/R/generate_R.cpp.in
index dfef755e84..0a52e1cd80 100644
--- a/src/mlpack/bindings/R/generate_R.cpp.in
+++ b/src/mlpack/bindings/R/generate_R.cpp.in
@@ -3,6 +3,11 @@
  * @author Yashwant Singh Parihar
  *
  * This is a template file to call the PrintR() function for a given binding.
+ * 
+ * mlpack 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 mlpack.  If not, see
+ * http://www.opensource.org/licenses/BSD-3-Clause for more information.
  */
 #define BINDING_TYPE BINDING_TYPE_R
 // Disable debug output.

From 34c5cede3b19035db4db4adf8f89e8a2d3dfeefb Mon Sep 17 00:00:00 2001
From: Aditya Raj <96882869+aadi-raj@users.noreply.github.com>
Date: Sat, 28 Jan 2023 11:27:54 +0530
Subject: [PATCH 43/80] Update generate_jl.cpp.in

---
 src/mlpack/bindings/julia/generate_jl.cpp.in | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/mlpack/bindings/julia/generate_jl.cpp.in b/src/mlpack/bindings/julia/generate_jl.cpp.in
index 34d93b89f8..ae94440129 100644
--- a/src/mlpack/bindings/julia/generate_jl.cpp.in
+++ b/src/mlpack/bindings/julia/generate_jl.cpp.in
@@ -3,6 +3,11 @@
  * @author Ryan Curtin
  *
  * This is a template file to call the PrintJL() function for a given binding.
+ *
+ * mlpack 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 mlpack.  If not, see
+ * http://www.opensource.org/licenses/BSD-3-Clause for more information.
  */
 #define BINDING_TYPE BINDING_TYPE_JL
 // Disable debug output.

From 8e6799d730d7c0b245f9ed3440c9cda20c0b500b Mon Sep 17 00:00:00 2001
From: Aditya Raj <96882869+aadi-raj@users.noreply.github.com>
Date: Sat, 28 Jan 2023 11:29:24 +0530
Subject: [PATCH 44/80] Update julia_util.h

---
 src/mlpack/bindings/julia/julia_util.h | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/mlpack/bindings/julia/julia_util.h b/src/mlpack/bindings/julia/julia_util.h
index b3e01620b1..3a8bf27413 100644
--- a/src/mlpack/bindings/julia/julia_util.h
+++ b/src/mlpack/bindings/julia/julia_util.h
@@ -4,6 +4,11 @@
  *
  * Some utility functions in C that can be called from Julia with ccall() in
  * order to interact with the IO interface.
+ *
+ * mlpack 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 mlpack.  If not, see
+ * http://www.opensource.org/licenses/BSD-3-Clause for more information.
  */
 #ifndef MLPACK_BINDINGS_JULIA_JULIA_UTIL_H
 #define MLPACK_BINDINGS_JULIA_JULIA_UTIL_H

From e748efcdaa6c03738b023949be555892781dc4cb Mon Sep 17 00:00:00 2001
From: Aditya Raj <96882869+aadi-raj@users.noreply.github.com>
Date: Sat, 28 Jan 2023 11:30:47 +0530
Subject: [PATCH 45/80] Update runtests.jl

---
 src/mlpack/bindings/julia/tests/runtests.jl | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/mlpack/bindings/julia/tests/runtests.jl b/src/mlpack/bindings/julia/tests/runtests.jl
index 189995f944..49517782c2 100644
--- a/src/mlpack/bindings/julia/tests/runtests.jl
+++ b/src/mlpack/bindings/julia/tests/runtests.jl
@@ -2,6 +2,12 @@
 # @author Ryan Curtin
 #
 # Tests for the Julia bindings.
+
+# mlpack 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 mlpack.  If not, see
+# http://www.opensource.org/licenses/BSD-3-Clause for more information.
+
 using Pkg
 Pkg.activate(".")
 using Test

From 0760b338785f9d0e29a46653d326d25a7e923409 Mon Sep 17 00:00:00 2001
From: Aditya Raj <96882869+aadi-raj@users.noreply.github.com>
Date: Sat, 28 Jan 2023 11:32:49 +0530
Subject: [PATCH 46/80] Update generate_markdown.cpp.in

---
 src/mlpack/bindings/markdown/generate_markdown.cpp.in | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/mlpack/bindings/markdown/generate_markdown.cpp.in b/src/mlpack/bindings/markdown/generate_markdown.cpp.in
index 77f9e60541..eb8a343925 100644
--- a/src/mlpack/bindings/markdown/generate_markdown.cpp.in
+++ b/src/mlpack/bindings/markdown/generate_markdown.cpp.in
@@ -4,6 +4,11 @@
  *
  * This file is configured by CMake to generate all of the Markdown required by
  * the project.
+ *
+ * mlpack 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 mlpack.  If not, see
+ * http://www.opensource.org/licenses/BSD-3-Clause for more information.
  */
 #include <mlpack/core.hpp>
 #include "binding_info.hpp"

From 61dfdef88ddeff75ceef35c5bc515777c07e86b4 Mon Sep 17 00:00:00 2001
From: Rodo <rodonguyendd@gmail.com>
Date: Mon, 30 Jan 2023 08:52:57 +1000
Subject: [PATCH 47/80] Fix wording

Co-authored-by: Ryan Curtin <ryan@ratml.org>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index b2cfdc56db..2c91d6925c 100644
--- a/README.md
+++ b/README.md
@@ -136,7 +136,7 @@ If the `cmake ..` command fails due to unavailable dependencies, consider either
 are installed, e.g. using the system package manager.  For example, on Debian and Ubuntu,
 all relevant dependencies can be installed with `sudo apt-get install libarmadillo-dev libensmallen-dev libcereal-dev g++ cmake`.
 
-Alternatively, CMake v3.14.0 the `cmake` command can create the build folder itself.
+Alternatively, since CMake v3.14.0 the `cmake` command can create the build folder itself.
 The above commands can be rewritten as follows:
 
 ```sh

From d656c22a15d655f7f82f81f2aec0f8498067fe21 Mon Sep 17 00:00:00 2001
From: Rodo <rodonguyendd@gmail.com>
Date: Mon, 30 Jan 2023 08:54:26 +1000
Subject: [PATCH 48/80] Fix wording

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 2c91d6925c..af04e8128b 100644
--- a/README.md
+++ b/README.md
@@ -136,8 +136,8 @@ If the `cmake ..` command fails due to unavailable dependencies, consider either
 are installed, e.g. using the system package manager.  For example, on Debian and Ubuntu,
 all relevant dependencies can be installed with `sudo apt-get install libarmadillo-dev libensmallen-dev libcereal-dev g++ cmake`.
 
-Alternatively, since CMake v3.14.0 the `cmake` command can create the build folder itself.
-The above commands can be rewritten as follows:
+Alternatively, since CMake v3.14.0 the `cmake` command can create the build folder itself,
+the above commands can be rewritten as follows:
 
 ```sh
 cmake -S . -B build

From 094d9b6a16b58a120b4f046859b14871867e1a84 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 11:19:41 +0530
Subject: [PATCH 49/80] Update doc/user/formats.md

Co-authored-by: Ryan Curtin <ryan@ratml.org>
---
 doc/user/formats.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/user/formats.md b/doc/user/formats.md
index e80e3b8cf5..eaf928edba 100644
--- a/doc/user/formats.md
+++ b/doc/user/formats.md
@@ -177,8 +177,8 @@ matrix = matrix.t(); // We must transpose after load!
 The transposition after loading is necessary if the coordinate list is in
 row-major format (that is, if each row in the matrix represents a point and each
 column represents a feature).  Be sure that the matrix you use with mlpack
-methods has points as columns and features as rows!  See [matrices](matrices.md) for more
-information.
+methods has points as columns and features as rows!  See [matrices](matrices.md)
+for more information.
 
 ## Categorical features and command line programs
 

From 3efbe0b2606ea81e2f76684798382c5138996b02 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 11:34:14 +0530
Subject: [PATCH 50/80] "updating codes"

---
 doc/tutorials/amf.md | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/doc/tutorials/amf.md b/doc/tutorials/amf.md
index 32c7d56913..6d6cb8951b 100644
--- a/doc/tutorials/amf.md
+++ b/doc/tutorials/amf.md
@@ -137,7 +137,8 @@ int main()
   NMFALSFactorizer nmf;
   mat W, H;
   mat V = randu<mat>(100, 100);
-  double residue = nmf.Apply(V, W, H);
+  size_t r = 90;
+  double residue = nmf.Apply(V, r, W, H);
 }
 ```
 
@@ -169,11 +170,12 @@ using namespace mlpack;
 
 int main()
 {
-  sp_mat V = randu<sp_mat>(100,100);
+  sp_mat V = sprandu<sp_mat>(100,100,0.1);
+  size_t r = 90;
   mat W, H;
 
   SVDBatchFactorizer<sp_mat> svd;
-  double residue = svd.Apply(V, W, H);
+  double residue = svd.Apply(V, r, W, H);
 }
 ```
 

From 0327f2edf8ff483e6ed4a090dc951333cde85a7c Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 16:46:47 +0530
Subject: [PATCH 51/80] fixing links in trees.md

---
 doc/developer/trees.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/developer/trees.md b/doc/developer/trees.md
index 97c76c5418..6321e1ebe8 100644
--- a/doc/developer/trees.md
+++ b/doc/developer/trees.md
@@ -90,7 +90,7 @@ mlpack algorithms, each \c TreeType itself must be a template class taking three
 parameters:
 
  - `MetricType` -- the underlying metric that the tree will be built on (see
-[the MetricType policy documentation](metrictype.md))
+[the MetricType policy documentation](metrics.md))
  - `StatisticType` -- holds any auxiliary information that individual
 algorithms may need
  - `MatType` -- the type of the matrix used to represent the data

From b4f7222af0c6e8dfb86013371edab41fbcba1603 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 16:50:57 +0530
Subject: [PATCH 52/80] fixing links in metrics.md

---
 doc/developer/metrics.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/developer/metrics.md b/doc/developer/metrics.md
index b4cec62526..4a6ec5bc6a 100644
--- a/doc/developer/metrics.md
+++ b/doc/developer/metrics.md
@@ -35,7 +35,7 @@ Note that for metrics that do not hold any state, the `Evaluate()` method can
 be marked as `static`.
 
 Overall, the `MetricType` template policy is quite simple (much like the
-[KernelType policy](kerneltype.md)).  Below is an example metric class, which
+[KernelType policy](kernels.md)).  Below is an example metric class, which
 implements the L2 distance:
 
 ```c++
@@ -105,4 +105,4 @@ policy:
  - `ChebyshevDistance`
  - `MahalanobisDistance`
  - `LMetric` (for arbitrary L-metrics)
- - `IPMetric` (requires a [KernelType](kerneltype.md) parameter)
+ - `IPMetric` (requires a [KernelType](kernels.md) parameter)

From 152837ffd22e3e5c35b0ca8f12619dba357e4d51 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 16:53:40 +0530
Subject: [PATCH 53/80] fixing links in kernels.md

---
 doc/developer/kernels.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/developer/kernels.md b/doc/developer/kernels.md
index 7bd65bd293..09aa23c39a 100644
--- a/doc/developer/kernels.md
+++ b/doc/developer/kernels.md
@@ -16,7 +16,7 @@ including
 
 mlpack implements a number of kernel methods and, accordingly, each of these
 methods allows arbitrary kernels to be used via the `KernelType` template
-parameter.  Like the [MetricType policy](metrictype.md), the requirements are
+parameter.  Like the [MetricType policy](metrics.md), the requirements are
 quite simple: a class implementing the `KernelType` policy must have
 
  - an `Evaluate()` function
@@ -42,7 +42,7 @@ Note that for kernels that do not hold any state, the `Evaluate()` method can be
 marked as `static`.
 
 Overall, the `KernelType` template policy is quite simple (much like the
-[MetricType policy](metrictype.md)).  Below is an example kernel class, which
+[MetricType policy](metrics.md)).  Below is an example kernel class, which
 outputs `1` if the vectors are close and `0` otherwise.
 
 ```c++

From a9616cef3160cc5541a3b8c1bea49ad46ee25bed Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 16:56:04 +0530
Subject: [PATCH 54/80] fix typo in Image Utilities

---
 doc/tutorials/image.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/image.md b/doc/tutorials/image.md
index dc08a085dd..01169e7afb 100644
--- a/doc/tutorials/image.md
+++ b/doc/tutorials/image.md
@@ -2,7 +2,7 @@
 
 Image datasets are becoming increasingly popular in deep learning.
 
-mlpack's image saving/loading functionality is based on [stb/](https://github.com/nothings/stb).
+mlpack's image saving/loading functionality is based on [stb](https://github.com/nothings/stb).
 
 ## Model API
 

From 54ec3046c47958c6de072be599efb88f49eec4e4 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 17:02:45 +0530
Subject: [PATCH 55/80] fixing typo in trees.md

---
 doc/developer/trees.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/developer/trees.md b/doc/developer/trees.md
index 6321e1ebe8..19e6c490e4 100644
--- a/doc/developer/trees.md
+++ b/doc/developer/trees.md
@@ -86,7 +86,7 @@ restatement of the fourth part of the definition).
 
 Most everything in mlpack is decomposed into a series of configurable template
 parameters, and trees are no exception.  In order to ease usage of high-level
-mlpack algorithms, each \c TreeType itself must be a template class taking three
+mlpack algorithms, each TreeType itself must be a template class taking three
 parameters:
 
  - `MetricType` -- the underlying metric that the tree will be built on (see
@@ -424,7 +424,7 @@ This constructor should be called with `(*this)` after the node is constructed
 The last template parameter is the `MatType` parameter.  This is generally
 `arma::mat` or `arma::sp_mat`, but could be any Armadillo type, including
 matrices that hold data points of different precisions (such as `float` or even
-`int`).  It generally suffices to write \c MatType assuming that `arma::mat`
+`int`).  It generally suffices to write MatType assuming that `arma::mat`
 will be used, since the vast majority of the time this will be what is used.
 
 ### Constructors and destructors

From 53909b3f9db7aa0e3df622af189e7f1895355ece Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 17:45:08 +0530
Subject: [PATCH 56/80] fixing typo in range_search.md

---
 doc/tutorials/range_search.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/range_search.md b/doc/tutorials/range_search.md
index 55dd98acae..6f62762bf5 100644
--- a/doc/tutorials/range_search.md
+++ b/doc/tutorials/range_search.md
@@ -3,7 +3,7 @@
 Range search is a simple machine learning task which aims to find all the
 neighbors of a point that fall into a certain range of distances.  In this
 setting, we have a *query* and a *reference* dataset.  Given a certain range,
-for each point in the *query* dataset, we wish to know all points in the \b
+for each point in the *query* dataset, we wish to know all points in the
 reference dataset which have distances within that given range to the given
 query point.
 

From 94fa2971cd80a53d5196ac307a43d5a99dd7b734 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 17:49:20 +0530
Subject: [PATCH 57/80] fixing typo in cf.md

---
 doc/tutorials/cf.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/cf.md b/doc/tutorials/cf.md
index 2d4a313ba8..eed525140b 100644
--- a/doc/tutorials/cf.md
+++ b/doc/tutorials/cf.md
@@ -389,7 +389,7 @@ number of rows equal to the number of items and the number of columns equal to
 the number of users, and each nonzero element in the matrix corresponds to a
 non-missing rating.
 
-The method that the factorizer implements is specified via the \c
+The method that the factorizer implements is specified via the
 FactorizerTraits class, which is a template metaprogramming traits class:
 
 ```c++

From fa73dbb444fcbd4b2dc2dfc27f9670c43798e466 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 17:54:58 +0530
Subject: [PATCH 58/80] fixing links in approx_kfn.md

---
 doc/tutorials/approx_kfn.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/tutorials/approx_kfn.md b/doc/tutorials/approx_kfn.md
index c703aefa45..8d0f5eb581 100644
--- a/doc/tutorials/approx_kfn.md
+++ b/doc/tutorials/approx_kfn.md
@@ -114,8 +114,8 @@ search:
 
 These two programs allow a large number of algorithms to be used to find
 approximate furthest neighbors.  Note that the `mlpack_kfn` program is also
-documented in the [KNN tutorial](knn.md) page, as it shares options with the
-`mlpack_knn` program.
+documented in the [KNN tutorial](neighbor_search.md) page, as it shares options 
+with the `mlpack_knn` program.
 
 Below are several examples of how the `mlpack_approx_kfn` and `mlpack_kfn`
 programs might be used.  The first examples focus on the `mlpack_approx_kfn`
@@ -869,7 +869,7 @@ qdafn.Search(querySet, 3, neighbors, distances);
 The extensive `NeighborSearch` class also provides a way to search for
 approximate furthest neighbors using a different, tree-based technique.  For
 full documentation on this class, see the [NeighborSearch
-tutorial](nstutorial.md).  The `KFN` class is a convenient typedef of the
+tutorial](neighbor_search.md).  The `KFN` class is a convenient typedef of the
 `NeighborSearch` class that can be used to perform the furthest neighbors task
 with `kd`-trees.
 
@@ -982,6 +982,6 @@ kfn.Search(querySet, 2, neighbors, distances);
 ## Further documentation
 
 For further documentation on the approximate furthest neighbor facilities
-offered by mlpack, see also [the NeighborSearch tutorial](nstutorial.md).  Also,
+offered by mlpack, see also [the NeighborSearch tutorial](neighbor_search.md).  Also,
 each class (`QDAFN`, `DrusillaSelect`, `NeighborSelect`) are well-documented,
 and more details can be found in the source code documentation.

From c37d9f74ef118a7b8fc8ae6cb852a6d23bbc0dec Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 17:57:27 +0530
Subject: [PATCH 59/80] fixing typo in approx_kfn.md

---
 doc/tutorials/approx_kfn.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/approx_kfn.md b/doc/tutorials/approx_kfn.md
index 8d0f5eb581..bfd306f57e 100644
--- a/doc/tutorials/approx_kfn.md
+++ b/doc/tutorials/approx_kfn.md
@@ -682,7 +682,7 @@ std::cout << ds.CandidateSet().col(4).t();
 
 It is possible to retrain a `DrusillaSelect` model with new parameters or with a
 new reference set.  This is functionally equivalent to creating a new model.
-The example code below creates a first \c DrusillaSelect model using 3 tables
+The example code below creates a first DrusillaSelect model using 3 tables
 and 10 projections, and then retrains this with the same reference set using 10
 tables and 3 projections.
 

From 09011dd799c1a15ac328b410a7da069110dfe697 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 18:16:46 +0530
Subject: [PATCH 60/80] fixing error in hpt.md

---
 doc/user/hpt.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/user/hpt.md b/doc/user/hpt.md
index 881d60923b..b7cb55cbe8 100644
--- a/doc/user/hpt.md
+++ b/doc/user/hpt.md
@@ -179,7 +179,7 @@ HyperParameterTuner<LinearRegression, MSE, SimpleCV> hpt(0.2, dataset,
 ```
 
 Next, we must set up the hyperparameters to be optimized.  If we are doing a
-grid search with the \c ens::GridSearch optimizer (the
+grid search with the ens::GridSearch optimizer (the
 default), then we only need to pass a `std::vector` (for non-numeric
 hyperparameters) or an `arma::vec` (for numeric hyperparameters) containing all
 of the possible choices that we wish to search over.

From ce849fd9dd08eb23134cd897fb86e65adf8b38dd Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Wed, 1 Feb 2023 18:19:16 +0530
Subject: [PATCH 61/80] fixing typo in cv.md

---
 doc/user/cv.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/user/cv.md b/doc/user/cv.md
index be392c2b0f..7a4584a764 100644
--- a/doc/user/cv.md
+++ b/doc/user/cv.md
@@ -70,7 +70,7 @@ SoftmaxRegression(const arma::mat& data,
 ```
 
 which has the parameter `lambda` after three conventional arguments (`data`,
-\c labels and \c numClasses). We can skip passing `fitIntercept` and
+labels and numClasses). We can skip passing `fitIntercept` and
 `optimizer` since there are the default values.  (Technically, we don't even
 need to pass `lambda` since there is a default value.)
 

From 430d071d11844855fb14247a006c625dab93e569 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Thu, 2 Feb 2023 01:17:45 +0530
Subject: [PATCH 62/80] Update doc/developer/trees.md

Co-authored-by: Ryan Curtin <ryan@ratml.org>
---
 doc/developer/trees.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/developer/trees.md b/doc/developer/trees.md
index 19e6c490e4..06fd665dcc 100644
--- a/doc/developer/trees.md
+++ b/doc/developer/trees.md
@@ -424,7 +424,7 @@ This constructor should be called with `(*this)` after the node is constructed
 The last template parameter is the `MatType` parameter.  This is generally
 `arma::mat` or `arma::sp_mat`, but could be any Armadillo type, including
 matrices that hold data points of different precisions (such as `float` or even
-`int`).  It generally suffices to write MatType assuming that `arma::mat`
+`int`).  It generally suffices to write `MatType` assuming that `arma::mat`
 will be used, since the vast majority of the time this will be what is used.
 
 ### Constructors and destructors

From 32637d532578fa45fe4f5f87c0f9055255b7de43 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Thu, 2 Feb 2023 01:18:07 +0530
Subject: [PATCH 63/80] Update doc/tutorials/approx_kfn.md

Co-authored-by: Ryan Curtin <ryan@ratml.org>
---
 doc/tutorials/approx_kfn.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/approx_kfn.md b/doc/tutorials/approx_kfn.md
index bfd306f57e..33a4237d98 100644
--- a/doc/tutorials/approx_kfn.md
+++ b/doc/tutorials/approx_kfn.md
@@ -682,7 +682,7 @@ std::cout << ds.CandidateSet().col(4).t();
 
 It is possible to retrain a `DrusillaSelect` model with new parameters or with a
 new reference set.  This is functionally equivalent to creating a new model.
-The example code below creates a first DrusillaSelect model using 3 tables
+The example code below creates a first `DrusillaSelect` model using 3 tables
 and 10 projections, and then retrains this with the same reference set using 10
 tables and 3 projections.
 

From 0641deb0c537a1976725d14b5c002e1292e5d2b2 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Thu, 2 Feb 2023 01:18:16 +0530
Subject: [PATCH 64/80] Update doc/tutorials/cf.md

Co-authored-by: Ryan Curtin <ryan@ratml.org>
---
 doc/tutorials/cf.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/cf.md b/doc/tutorials/cf.md
index eed525140b..9452ebfdd0 100644
--- a/doc/tutorials/cf.md
+++ b/doc/tutorials/cf.md
@@ -390,7 +390,7 @@ the number of users, and each nonzero element in the matrix corresponds to a
 non-missing rating.
 
 The method that the factorizer implements is specified via the
-FactorizerTraits class, which is a template metaprogramming traits class:
+`FactorizerTraits` class, which is a template metaprogramming traits class:
 
 ```c++
 template<typename FactorizerType>

From 1801b4d55a4881081a857362b871eb714db1c4b3 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Thu, 2 Feb 2023 01:18:35 +0530
Subject: [PATCH 65/80] Update doc/tutorials/range_search.md

Co-authored-by: Ryan Curtin <ryan@ratml.org>
---
 doc/tutorials/range_search.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/range_search.md b/doc/tutorials/range_search.md
index 6f62762bf5..42fa5b6526 100644
--- a/doc/tutorials/range_search.md
+++ b/doc/tutorials/range_search.md
@@ -4,7 +4,7 @@ Range search is a simple machine learning task which aims to find all the
 neighbors of a point that fall into a certain range of distances.  In this
 setting, we have a *query* and a *reference* dataset.  Given a certain range,
 for each point in the *query* dataset, we wish to know all points in the
-reference dataset which have distances within that given range to the given
+*reference* dataset which have distances within that given range to the given
 query point.
 
 Alternately, if the query and reference datasets are the same, the problem can

From 58d3f1f51561aa57a775de51274e3dfd6682fa73 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Thu, 2 Feb 2023 01:19:07 +0530
Subject: [PATCH 66/80] Update doc/developer/trees.md

Co-authored-by: Ryan Curtin <ryan@ratml.org>
---
 doc/developer/trees.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/developer/trees.md b/doc/developer/trees.md
index 06fd665dcc..17e9525939 100644
--- a/doc/developer/trees.md
+++ b/doc/developer/trees.md
@@ -86,7 +86,7 @@ restatement of the fourth part of the definition).
 
 Most everything in mlpack is decomposed into a series of configurable template
 parameters, and trees are no exception.  In order to ease usage of high-level
-mlpack algorithms, each TreeType itself must be a template class taking three
+mlpack algorithms, each `TreeType` itself must be a template class taking three
 parameters:
 
  - `MetricType` -- the underlying metric that the tree will be built on (see

From 267b11116cbe490b7522749ae0fc828a2cb2de5f Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Thu, 2 Feb 2023 01:19:21 +0530
Subject: [PATCH 67/80] Update doc/user/cv.md

Co-authored-by: Ryan Curtin <ryan@ratml.org>
---
 doc/user/cv.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/user/cv.md b/doc/user/cv.md
index 7a4584a764..53067911d7 100644
--- a/doc/user/cv.md
+++ b/doc/user/cv.md
@@ -70,7 +70,7 @@ SoftmaxRegression(const arma::mat& data,
 ```
 
 which has the parameter `lambda` after three conventional arguments (`data`,
-labels and numClasses). We can skip passing `fitIntercept` and
+`labels` and `numClasses`). We can skip passing `fitIntercept` and
 `optimizer` since there are the default values.  (Technically, we don't even
 need to pass `lambda` since there is a default value.)
 

From dad54d29d429c8f396079dcaad797abaabb34803 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Thu, 2 Feb 2023 01:19:33 +0530
Subject: [PATCH 68/80] Update doc/user/hpt.md

Co-authored-by: Ryan Curtin <ryan@ratml.org>
---
 doc/user/hpt.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/user/hpt.md b/doc/user/hpt.md
index b7cb55cbe8..738a9c6f26 100644
--- a/doc/user/hpt.md
+++ b/doc/user/hpt.md
@@ -179,7 +179,7 @@ HyperParameterTuner<LinearRegression, MSE, SimpleCV> hpt(0.2, dataset,
 ```
 
 Next, we must set up the hyperparameters to be optimized.  If we are doing a
-grid search with the ens::GridSearch optimizer (the
+grid search with the `ens::GridSearch` optimizer (the
 default), then we only need to pass a `std::vector` (for non-numeric
 hyperparameters) or an `arma::vec` (for numeric hyperparameters) containing all
 of the possible choices that we wish to search over.

From 648bba07007bd17f2213052db8b3db816679a83b Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Thu, 2 Feb 2023 01:33:39 +0530
Subject: [PATCH 69/80] changing value of rank of factorization

Reason behind the change is to make the example code more realistic for many problems.
---
 doc/tutorials/amf.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/tutorials/amf.md b/doc/tutorials/amf.md
index 6d6cb8951b..5579b169b2 100644
--- a/doc/tutorials/amf.md
+++ b/doc/tutorials/amf.md
@@ -137,7 +137,7 @@ int main()
   NMFALSFactorizer nmf;
   mat W, H;
   mat V = randu<mat>(100, 100);
-  size_t r = 90;
+  size_t r = 10;
   double residue = nmf.Apply(V, r, W, H);
 }
 ```
@@ -171,7 +171,7 @@ using namespace mlpack;
 int main()
 {
   sp_mat V = sprandu<sp_mat>(100,100,0.1);
-  size_t r = 90;
+  size_t r = 10;
   mat W, H;
 
   SVDBatchFactorizer<sp_mat> svd;

From 6d3336da0a39428acd78289e0214f970269d3b9f Mon Sep 17 00:00:00 2001
From: conradsnicta <conradsnicta@users.noreply.github.com>
Date: Thu, 2 Feb 2023 11:44:14 +0100
Subject: [PATCH 70/80] update citation details (#3393)

---
 README.md | 26 +++++++++++++++-----------
 1 file changed, 15 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index af04e8128b..3cc3641897 100644
--- a/README.md
+++ b/README.md
@@ -85,18 +85,22 @@ variety of other needs.
 If you use mlpack in your research or software, please cite mlpack using the
 citation below (given in BibTeX format):
 
-    @article{mlpack2018,
-        title     = {mlpack 3: a fast, flexible machine learning library},
-        author    = {Curtin, Ryan R. and Edel, Marcus and Lozhnikov, Mikhail and
-                     Mentekidis, Yannis and Ghaisas, Sumedh and Zhang,
-                     Shangtong},
+    @article{mlpack2023,
+        title     = {mlpack 4: a fast, header-only C++ machine learning library},
+        author    = {Ryan R. Curtin and Marcus Edel and Omar Shrit and 
+                     Shubham Agrawal and Suryoday Basak and James J. Balamuta and 
+                     Ryan Birmingham and Kartik Dutt and Dirk Eddelbuettel and 
+                     Rishabh Garg and Shikhar Jaiswal and Aakash Kaushik and 
+                     Sangyeon Kim and Anjishnu Mukherjee and Nanubala Gnana Sai and 
+                     Nippun Sharma and Yashwant Singh Parihar and Roshan Swain and 
+                     Conrad Sanderson},
         journal   = {Journal of Open Source Software},
-        volume    = {3},
-        issue     = {26},
-        pages     = {726},
-        year      = {2018},
-        doi       = {10.21105/joss.00726},
-        url       = {https://doi.org/10.21105/joss.00726}
+        volume    = {8},
+        number    = {82},
+        pages     = {5026},
+        year      = {2023},
+        doi       = {10.21105/joss.05026},
+        url       = {https://doi.org/10.21105/joss.05026}
     }
 
 Citations are beneficial for the growth and improvement of mlpack.

From 46bcedff8139ea7da713bca813e4a10c02bbe8a6 Mon Sep 17 00:00:00 2001
From: Aditya Raj <96882869+aadi-raj@users.noreply.github.com>
Date: Fri, 3 Feb 2023 19:10:28 +0530
Subject: [PATCH 71/80] Minor doc fix in bindings.md

I have encountered some minor doc issues while going through the file.
I have tried to fix some of them.

Thanks
Adi
---
 doc/developer/bindings.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/developer/bindings.md b/doc/developer/bindings.md
index cd3c4720db..53f6e11b02 100644
--- a/doc/developer/bindings.md
+++ b/doc/developer/bindings.md
@@ -254,7 +254,7 @@ links above for further documentation.
 In order to write a new binding, then, you simply must define `BINDING_NAME`,
 then write `BINDING_USER_NAME()`, `BINDING_SHORT_DESC()`, `BINDING_LONG_DESC()`,
 `BINDING_EXAMPLE()` and `BINDING_SEE_ALSO()` definitions of the program with
-some docuentation, define the input and output parameters as `PARAM` macros, and
+some documentation, define the input and output parameters as `PARAM` macros, and
 then write a `BINDING_FUNCTION()` function that actually performs the
 functionality of the binding.
 
@@ -695,7 +695,7 @@ There are numerous different macros that can be used:
  - `PARAM_TMATRIX_OUT()` - transposed double-valued matrix (`arma::mat`) output
        parameter
  - `PARAM_MATRIX_AND_INFO_IN()` - matrix with categoricals input parameter
-       (`std::tuple<data::DatasetInfo, arma::mat`)
+       (`std::tuple<data::DatasetInfo, arma::mat>`)
  - `PARAM_COL_IN()` - double-valued column vector (`arma::vec`) input parameter
  - `PARAM_COL_OUT()` - double-valued column vector (`arma::vec`) output
        parameter
@@ -1322,7 +1322,7 @@ If this is the route that is desired, a large amount of CMake boilerplate may be
 necessary.  The Python CMake configuration can be referred to as an example, but
 probably a large amount of adaptation to other languages will be necessary.
 
-Lastly, when adding a new language, be sure to make sure it works with the
+Lastly, when adding a new language, make sure it works with the
 Markdown documentation generator.  In order to make this happen, you will need
 to modify all of the `add_markdown_docs()` calls in
 `src/mlpack/methods/CMakeLists.txt` to contain the name of the language you have

From 2d7b72768f01b02525edf6050a1060988909872e Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Sat, 4 Feb 2023 19:03:45 +0530
Subject: [PATCH 72/80] removing repeatation in neighbor_search.md

---
 doc/tutorials/neighbor_search.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/doc/tutorials/neighbor_search.md b/doc/tutorials/neighbor_search.md
index 8180b46bba..f1389645bb 100644
--- a/doc/tutorials/neighbor_search.md
+++ b/doc/tutorials/neighbor_search.md
@@ -418,8 +418,7 @@ The `RuleType` class provides the following functions for use in the traverser:
 // Evaluate the base case between two points.
 double BaseCase(const size_t queryIndex, const size_t referenceIndex);
 
-// Score the two nodes to see if they can be pruned, returning DBL_MAX if they
-// can be pruned.
+// Score the two nodes to see if they can be pruned, returning DBL_MAX
 double Score(TreeType& queryNode, TreeType& referenceNode);
 ```
 

From f8ea15a15af016d288ab05be84f8f6e271c10cff Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Sat, 4 Feb 2023 19:06:44 +0530
Subject: [PATCH 73/80] fix typo in approx_kfn.md

---
 doc/tutorials/approx_kfn.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/approx_kfn.md b/doc/tutorials/approx_kfn.md
index 33a4237d98..01613b11a0 100644
--- a/doc/tutorials/approx_kfn.md
+++ b/doc/tutorials/approx_kfn.md
@@ -80,7 +80,7 @@ In order to solve this problem, mlpack provides a number of interfaces.
 
  - two simple command-line executables to calculate approximate furthest
    neighbors
- - a simple C++ class for QDAFN"
+ - a simple C++ class for QDAFN
  - a simple C++ class for DrusillaSelect
  - a simple C++ class for tree-based and brute-force search
 

From 291b170d8c491b3ec5ab5c4cc92cf536aaae086b Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Sat, 4 Feb 2023 19:08:38 +0530
Subject: [PATCH 74/80] fix typo in emst.md

---
 doc/tutorials/emst.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/emst.md b/doc/tutorials/emst.md
index 115e91f9df..60be3ab8b7 100644
--- a/doc/tutorials/emst.md
+++ b/doc/tutorials/emst.md
@@ -18,7 +18,7 @@ via templates.  For more details, see the following paper:
 
 ```
 @inproceedings{march2010fast,
-  title={Fast {E}uclidean minimum spanning tree: algorithm, analysis, and
+  title={Fast Euclidean minimum spanning tree: algorithm, analysis, and
 applications},
   author={March, William B. and Ram, Parikshit and Gray, Alexander G.},
   booktitle={Proceedings of the 16th ACM SIGKDD International Conference on

From 1e7e2aea642cf2467a271c7186d67e1453b8905a Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Sat, 4 Feb 2023 19:11:36 +0530
Subject: [PATCH 75/80] fix typo in neighbor_search.md

---
 doc/tutorials/neighbor_search.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/neighbor_search.md b/doc/tutorials/neighbor_search.md
index f1389645bb..7424805d3f 100644
--- a/doc/tutorials/neighbor_search.md
+++ b/doc/tutorials/neighbor_search.md
@@ -363,7 +363,7 @@ covariance matrix).  Therefore, you can write a non-static MetricType class and
 use it seamlessly with `NeighborSearch`.
 
 For more information on the `MetricType` policy, see the [documentation for
-`MetricType`s](../developer/metrics.md).
+`MetricType`](../developer/metrics.md).
 
 ### `MatType` policy class
 

From b2213238c1ec36bcb3020d96bf3dffe8cbc09914 Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Sat, 4 Feb 2023 19:21:12 +0530
Subject: [PATCH 76/80] fixing links in kmeans.md

---
 doc/tutorials/kmeans.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/kmeans.md b/doc/tutorials/kmeans.md
index 559327a399..28f8b30112 100644
--- a/doc/tutorials/kmeans.md
+++ b/doc/tutorials/kmeans.md
@@ -449,7 +449,7 @@ section in the [NeighborSearch tutorial](neighbor_search.md)), any of mlpack's
 metric classes (found in `mlpack/core/metrics/`) can be given as an argument.
 The `LMetric` class is a good example implementation.
 
-A class fulfilling the [MetricType policy](../developer/metrictype.md) must
+A class fulfilling the [MetricType policy](../developer/metrics.md) must
 provide the following two functions:
 
 ```c++

From 87c106e15a7922972445564213d2ae972dee190c Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Sat, 4 Feb 2023 19:34:19 +0530
Subject: [PATCH 77/80] improve efficiency of statement in kmeans.md

---
 doc/tutorials/kmeans.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/doc/tutorials/kmeans.md b/doc/tutorials/kmeans.md
index 28f8b30112..afbcdb6ca5 100644
--- a/doc/tutorials/kmeans.md
+++ b/doc/tutorials/kmeans.md
@@ -445,7 +445,8 @@ how to modify them.
 
 Most machine learning algorithms in mlpack support modifying the distance
 metric, and `KMeans<>` is no exception.  Similar to `NeighborSearch` (see the
-section in the [NeighborSearch tutorial](neighbor_search.md)), any of mlpack's
+"MetricType policy class" section in the
+[NeighborSearch tutorial](neighbor_search.md)), any of mlpack's
 metric classes (found in `mlpack/core/metrics/`) can be given as an argument.
 The `LMetric` class is a good example implementation.
 

From a58b2a8472107ee80c8943e92f4f2d75522115cd Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Sun, 5 Feb 2023 01:11:13 +0530
Subject: [PATCH 78/80] delete undesired commit

---
 doc/tutorials/emst.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/emst.md b/doc/tutorials/emst.md
index 60be3ab8b7..115e91f9df 100644
--- a/doc/tutorials/emst.md
+++ b/doc/tutorials/emst.md
@@ -18,7 +18,7 @@ via templates.  For more details, see the following paper:
 
 ```
 @inproceedings{march2010fast,
-  title={Fast Euclidean minimum spanning tree: algorithm, analysis, and
+  title={Fast {E}uclidean minimum spanning tree: algorithm, analysis, and
 applications},
   author={March, William B. and Ram, Parikshit and Gray, Alexander G.},
   booktitle={Proceedings of the 16th ACM SIGKDD International Conference on

From a299fc323d2f6738640d594197721208b0381b2b Mon Sep 17 00:00:00 2001
From: Adarsh Santoria <108261986+AdarshSantoria@users.noreply.github.com>
Date: Sun, 5 Feb 2023 01:12:01 +0530
Subject: [PATCH 79/80] Update doc/tutorials/neighbor_search.md

Co-authored-by: Ryan Curtin <ryan@ratml.org>
---
 doc/tutorials/neighbor_search.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tutorials/neighbor_search.md b/doc/tutorials/neighbor_search.md
index 7424805d3f..153acf93ed 100644
--- a/doc/tutorials/neighbor_search.md
+++ b/doc/tutorials/neighbor_search.md
@@ -418,7 +418,7 @@ The `RuleType` class provides the following functions for use in the traverser:
 // Evaluate the base case between two points.
 double BaseCase(const size_t queryIndex, const size_t referenceIndex);
 
-// Score the two nodes to see if they can be pruned, returning DBL_MAX
+// Score the two nodes to see if they can be pruned, returning DBL_MAX if so.
 double Score(TreeType& queryNode, TreeType& referenceNode);
 ```
 

From 79276c6efbbca010ccae7626e86862ee639e8e3d Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 6 Feb 2023 19:34:10 -0500
Subject: [PATCH 80/80] Fix DBSCAN handling of non-core points (#3346)

---
 HISTORY.md                                |  2 +
 src/mlpack/methods/dbscan/dbscan_impl.hpp | 88 ++++++++++++++++++++---
 src/mlpack/tests/dbscan_test.cpp          | 33 +++++++++
 3 files changed, 115 insertions(+), 8 deletions(-)

diff --git a/HISTORY.md b/HISTORY.md
index 5abe54ee22..36232c4eeb 100644
--- a/HISTORY.md
+++ b/HISTORY.md
@@ -4,6 +4,8 @@
 
   * Fix a few missing includes in `<mlpack.hpp>` (#3374).
 
+  * Fix DBSCAN handling of non-core points (#3346).
+
 ### mlpack 4.0.1
 ###### 2022-12-23
   * Fix mapping of categorical data for Julia bindings (#3305).
diff --git a/src/mlpack/methods/dbscan/dbscan_impl.hpp b/src/mlpack/methods/dbscan/dbscan_impl.hpp
index a49d63e8bf..bb240ccd5d 100644
--- a/src/mlpack/methods/dbscan/dbscan_impl.hpp
+++ b/src/mlpack/methods/dbscan/dbscan_impl.hpp
@@ -154,18 +154,68 @@ void DBSCAN<RangeSearchType, PointSelectionPolicy>::PointwiseCluster(
   std::vector<std::vector<size_t>> neighbors;
   std::vector<std::vector<double>> distances;
 
+  // Note that the strategy here is somewhat different from the original DBSCAN
+  // paper.  The original DBSCAN paper grows each cluster individually to its
+  // fullest extent; here, we use a UnionFind structure to grow each point into
+  // a local cluster (if it has enough points), and we combine with other local
+  // clusters.  The end result is the same.
+  //
+  // Define points as being either core points, or non-core points.  Core points
+  // have more than `minPoints` neighbors.  Non-core points are included into
+  // the first core point cluster that encounters them; if they are not included
+  // by anything, they are labeled as noise.
+  //
+  // We maintain a list of non-core points so that we can handle that logic
+  // correctly.
+
+  std::vector<bool> visited(data.n_cols, false);
+  std::vector<bool> nonCorePoints(data.n_cols, false);
+
   for (size_t i = 0; i < data.n_cols; ++i)
   {
     if (i % 10000 == 0 && i > 0)
       Log::Info << "DBSCAN clustering on point " << i << "..." << std::endl;
 
+    // Get the next index.
+    const size_t index = pointSelector.Select(i, data);
+    visited[index] = true;
+
     // Do the range search for only this point.
-    rangeSearch.Search(data.col(i), Range(0.0, epsilon), neighbors,
+    rangeSearch.Search(data.col(index), Range(0.0, epsilon), neighbors,
         distances);
 
-    // Union to all neighbors.
-    for (size_t j = 0; j < neighbors[0].size(); ++j)
-      uf.Union(i, neighbors[0][j]);
+    // Union to all neighbors if the point is not noise.
+    //
+    // If the point is noise, we leave its label as undefined (i.e. we do no
+    // unioning).
+    if (neighbors[0].size() >= minPoints)
+    {
+      for (size_t j = 0; j < neighbors[0].size(); ++j)
+      {
+        // Union to all neighbors that either do not have a label, or are core
+        // points of other clusters.  (When we union to another core point, we
+        // are merging clusters.)
+        if (uf.Find(neighbors[0][j]) == neighbors[0][j])
+        {
+          // This unions unlabeled points.
+          uf.Union(index, neighbors[0][j]);
+        }
+        else if (!nonCorePoints[neighbors[0][j]] && visited[neighbors[0][j]])
+        {
+          // This unions core points of other clusters.  Note that we only union
+          // with other clusters that have already been visited---this is
+          // because we do not know whether unvisited points are core or
+          // non-core points.  (If an unvisited point is a core point, it'll
+          // merge with us later.)
+          uf.Union(index, neighbors[0][j]);
+        }
+      }
+    }
+    else
+    {
+      // This is not a core point---it does not have enough neighbors.
+      nonCorePoints[index] = true;
+    }
   }
 }
 
@@ -180,21 +230,43 @@ void DBSCAN<RangeSearchType, PointSelectionPolicy>::BatchCluster(
     const MatType& data,
     UnionFind& uf)
 {
-  // For each point, find the points in epsilon-nighborhood and their distances.
+  // For each point, find the points in epsilon-neighborhood and their distances.
   std::vector<std::vector<size_t>> neighbors;
   std::vector<std::vector<double>> distances;
   Log::Info << "Performing range search." << std::endl;
   rangeSearch.Train(data);
-  rangeSearch.Search(data, Range(0.0, epsilon), neighbors, distances);
+  rangeSearch.Search(Range(0.0, epsilon), neighbors, distances);
   Log::Info << "Range search complete." << std::endl;
 
+  // See the description of the algorithm in `PointwiseCluster()`.  The strategy
+  // is the same here, but we have cached all range search results already.
+  // That means we already have computed whether each point is or is not a core
+  // point, just based on the size of its neighbors; so we don't need an
+  // auxiliary std::vector<bool> for that.
+
   // Now loop over all points.
   for (size_t i = 0; i < data.n_cols; ++i)
   {
     // Get the next index.
     const size_t index = pointSelector.Select(i, data);
-    for (size_t j = 0; j < neighbors[index].size(); ++j)
-      uf.Union(index, neighbors[index][j]);
+    // Monochromatic dual-tree range search does not return the point as its own
+    // neighbor, so we are looking for `minPoints - 1` instead.
+    if (neighbors[index].size() >= minPoints - 1)
+    {
+      for (size_t j = 0; j < neighbors[index].size(); ++j)
+      {
+        if (uf.Find(neighbors[index][j]) == neighbors[index][j])
+        {
+          // This unions unlabeled points.
+          uf.Union(index, neighbors[index][j]);
+        }
+        else if (neighbors[neighbors[index][j]].size() >= (minPoints - 1))
+        {
+          // This unions core points of other clusters.
+          uf.Union(index, neighbors[index][j]);
+        }
+      }
+    }
   }
 }
 
diff --git a/src/mlpack/tests/dbscan_test.cpp b/src/mlpack/tests/dbscan_test.cpp
index a59f4a47f3..a775c1cf6f 100644
--- a/src/mlpack/tests/dbscan_test.cpp
+++ b/src/mlpack/tests/dbscan_test.cpp
@@ -302,3 +302,36 @@ TEST_CASE("RandomPointSelectionTest", "[DBSCANTest]")
   // The number of assignments returned should be the same as points.
   REQUIRE(assignments.n_elem == points.n_cols);
 }
+
+/**
+ * Check that noise points do not accidentally connect clusters.
+ * See issue #3339.  (Thanks @iad-ABDUL-RAOUF!)
+ */
+TEST_CASE("NoiseConnectionTest", "[DBSCANTest]")
+{
+  arma::mat dataset({
+      // cluster 1           cluster 2            noise
+      { 0.0, 0.5,  0.5, 1.0, 3.0, 3.5,  3.5, 4.0, 2.0 },
+      { 0.0, 0.5, -0.5, 0.0, 0.0, 0.5, -0.5, 0.0, 0.0 }});
+
+  // Now perform clustering.
+  const double epsilon = 1.1;
+  size_t minPts = 4;
+
+  DBSCAN<> dbscan(epsilon, minPts, false);
+
+  arma::Row<size_t> labels;
+  arma::mat centroids;
+
+  size_t numClusters = dbscan.Cluster(dataset, labels, centroids);
+
+  // The noisy element should not link the two clusters together, since it has
+  // less than minPts neighbors.
+  REQUIRE(numClusters == 2);
+
+  // Now make sure the same is true with batch clustering.
+  dbscan = DBSCAN<>(epsilon, minPts, true);
+  numClusters = dbscan.Cluster(dataset, labels, centroids);
+
+  REQUIRE(numClusters == 2);
+}