Merge remote-tracking branch 'origin/master' into fix-macos-regex

2022-11-03 09:03:02 -04:00
parent 28be9dea83 79cb12eaef
commit 399dba77d0
3 changed files with 70 additions and 45 deletions
@@ -3,9 +3,11 @@ on:
  push:
    branches:
      - master
+      - main
  pull_request:
    branches:
      - master
+      - main
  release:
    types: [published, created, edited]
 permissions:
@@ -16,13 +18,13 @@ jobs:
  jobR:
    name: mlpack R tarball
    if: ${{ github.repository == 'mlpack/mlpack' }}
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest

    outputs:
      r_bindings: ${{ steps.mlpack_version.outputs.mlpack_r_package }}

    steps:
-        - uses: actions/checkout@v2
+        - uses: actions/checkout@v3

        - name: Extract mlpack version
          id: mlpack_version
@@ -33,9 +35,11 @@ jobs:
            MLPACK_VERSION_VALUE=${MLPACK_VERSION_MAJOR}.${MLPACK_VERSION_MINOR}.${MLPACK_VERSION_PATCH}
            echo ::set-output name=mlpack_r_package::$(echo mlpack_"$MLPACK_VERSION_VALUE".tar.gz)

-        - uses: r-lib/actions/setup-r@master
-          with:
-            r-version: release
+        # Setup Pandoc 
+        - uses: r-lib/actions/setup-pandoc@v2
+
+        # Setup R actions
+        - uses: r-lib/actions/setup-r@v2

        - name: Query dependencies
          run: |
@@ -44,7 +48,7 @@ jobs:

        - name: Cache R packages
          if: runner.os != 'Windows' && runner.os != 'macOS'
-          uses: actions/cache@v1
+          uses: actions/cache@v3
          with:
            path: ${{ env.R_LIBS_USER }}
            key: ${{ runner.os }}-r-release-${{ hashFiles('depends.Rds') }}
@@ -76,7 +80,7 @@ jobs:
            cd build && CTEST_OUTPUT_ON_FAILURE=1 ctest -T Test .

        - name: Upload R packages
-          uses: actions/upload-artifact@v2
+          uses: actions/upload-artifact@v3
          with:
              name: mlpack_r_tarball
              path: build/src/mlpack/bindings/R/${{ steps.mlpack_version.outputs.mlpack_r_package }}
@@ -92,10 +96,9 @@ jobs:
      fail-fast: false
      matrix:
        config:
-        - {os: windows-latest, r: '4.0', name: 'Windows R'}
-        - {os: macos-10.15, r: 'release', name: 'macOS R'}
-        - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", name: 'Linux R'}
-
+        - {os: windows-latest, r: 'release', name: 'Windows R'}
+        - {os: macOS-latest, r: 'release', name: 'macOS R'}
+        - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release', name: 'Linux R'}

    env:
      MAKEFLAGS: "-j 2"
@@ -103,20 +106,22 @@ jobs:
      R_CHECK_ARGS: "--no-build-vignettes"
      _R_CHECK_FORCE_SUGGESTS: 0
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes

    steps:
      - uses: actions/download-artifact@v2
        with:
          name: mlpack_r_tarball

-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@master
-
+          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')"

@@ -146,7 +151,7 @@ jobs:

      - name: Upload check results
        if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v3
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: |
@@ -7,7 +7,6 @@ src="https://cdn.rawgit.com/mlpack/mlpack.org/e7d36ed8/mlpack-black.svg" style="
 <h5 align="center">
  <a href="https://mlpack.org">Home</a> |
  <a href="https://www.mlpack.org/docs.html">Documentation</a> |
-  <a href="https://www.mlpack.org/doc/mlpack-git/doxygen/index.html">Doxygen</a> |
  <a href="https://www.mlpack.org/community.html">Community</a> |
  <a href="https://www.mlpack.org/questions.html">Help</a> |
  <a href="https://webchat.freenode.net/?channels=mlpack">IRC Chat</a>
@@ -47,7 +46,7 @@ programs, Python bindings, Julia bindings, Go bindings and R bindings.
 - [mlpack homepage](https://www.mlpack.org/)
 - [mlpack documentation](https://www.mlpack.org/docs.html)
 - [Examples repository](https://github.com/mlpack/examples/)
- - [Tutorials](https://www.mlpack.org/doc/mlpack-git/doxygen/tutorials.html)
+ - [Tutorials](doc/tutorials/README.md)
 - [Development Site (Github)](https://www.github.com/mlpack/mlpack/)

 [//]: # (numfocus-fiscal-sponsor-attribution)
@@ -129,6 +128,14 @@ cmake ../
 sudo make install
 ```

+Note: 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
+sudo cmake --build build --target install
+```
+
 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:
@@ -1,11 +1,11 @@
-// CLI11: Version 2.3.0
+// CLI11: Version 2.3.1
 // Originally designed by Henry Schreiner
 // https://github.com/CLIUtils/CLI11
 //
 // This is a standalone header file generated by MakeSingleHeader.py in CLI11/scripts
-// from: v2.3.0
+// from: v2.3.1
 //
-// CLI11 2.3.0 Copyright (c) 2017-2022 University of Cincinnati, developed by Henry
+// CLI11 2.3.1 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 <iterator>
-#include <fstream>
-#include <tuple>
-#include <iostream>
-#include <cstdint>
-#include <algorithm>
-#include <stdexcept>
-#include <map>
-#include <iomanip>
-#include <utility>
-#include <vector>
 #include <functional>
 #include <locale>
-#include <string>
-#include <cmath>
-#include <numeric>
+#include <cstdint>
+#include <iomanip>
 #include <memory>
-#include <sstream>
 #include <exception>
+#include <stdexcept>
+#include <string>
+#include <vector>
+#include <iterator>
+#include <algorithm>
+#include <sstream>
+#include <cmath>
 #include <type_traits>
-#include <set>
 #include <limits>
+#include <set>
+#include <utility>
+#include <map>
+#include <iostream>
+#include <numeric>
+#include <fstream>
+#include <tuple>


 #define CLI11_VERSION_MAJOR 2
 #define CLI11_VERSION_MINOR 3
-#define CLI11_VERSION_PATCH 0
-#define CLI11_VERSION "2.3.0"
+#define CLI11_VERSION_PATCH 1
+#define CLI11_VERSION "2.3.1"



@@ -2671,7 +2671,7 @@ class Config {
        if(item.inputs.empty()) {
            return "{}";
        }
-        throw ConversionError::TooManyInputsFlag(item.fullname());
+        throw ConversionError::TooManyInputsFlag(item.fullname());  // LCOV_EXCL_LINE
    }

    /// Parse a config file, throw an error (ParseError:ConfigParseError or FileError) on failure
@@ -3478,7 +3478,7 @@ class AsNumberWithUnit : public Validator {

        // transform function
        func_ = [mapping, opts](std::string &input) -> std::string {
-            Number num;
+            Number num{};

            detail::rtrim(input);
            if(input.empty()) {
@@ -3742,7 +3742,7 @@ CLI11_INLINE path_type check_path(const char *file) noexcept {
        return path_type::nonexistent;
    }
    switch(stat.type()) {
-    case std::filesystem::file_type::none:
+    case std::filesystem::file_type::none:  // LCOV_EXCL_LINE
    case std::filesystem::file_type::not_found:
        return path_type::nonexistent;
    case std::filesystem::file_type::directory:
@@ -3993,6 +3993,8 @@ class FormatterBase {
    FormatterBase() = default;
    FormatterBase(const FormatterBase &) = default;
    FormatterBase(FormatterBase &&) = default;
+    FormatterBase &operator=(const FormatterBase &) = default;
+    FormatterBase &operator=(FormatterBase &&) = default;

    /// Adding a destructor in this form to work around bug in GCC 4.7
    virtual ~FormatterBase() noexcept {}  // NOLINT(modernize-use-equals-default)
@@ -4054,6 +4056,8 @@ class Formatter : public FormatterBase {
    Formatter() = default;
    Formatter(const Formatter &) = default;
    Formatter(Formatter &&) = default;
+    Formatter &operator=(const Formatter &) = default;
+    Formatter &operator=(Formatter &&) = default;

    /// @name Overridables
    ///@{
@@ -7307,6 +7311,15 @@ CLI11_NODISCARD CLI11_INLINE CLI::App_p App::get_subcommand_ptr(int index) const
    throw OptionNotFound(std::to_string(index));
 }

+CLI11_NODISCARD CLI11_INLINE CLI::App *App::get_option_group(std::string group_name) const {
+    for(const App_p &app : subcommands_) {
+        if(app->name_.empty() && app->group_ == group_name) {
+            return app.get();
+        }
+    }
+    throw OptionNotFound(group_name);
+}
+
 CLI11_NODISCARD CLI11_INLINE std::size_t App::count_all() const {
    std::size_t cnt{0};
    for(const auto &opt : options_) {
@@ -9469,7 +9482,7 @@ CLI11_INLINE std::string Formatter::make_footer(const App *app) const {
    if(footer.empty()) {
        return std::string{};
    }
-    return footer + "\n";
+    return "\n" + footer + "\n";
 }

 CLI11_INLINE std::string Formatter::make_help(const App *app, std::string name, AppFormatMode mode) const {
@@ -9491,7 +9504,7 @@ CLI11_INLINE std::string Formatter::make_help(const App *app, std::string name,
    out << make_positionals(app);
    out << make_groups(app, mode);
    out << make_subcommands(app, mode);
-    out << '\n' << make_footer(app);
+    out << make_footer(app);

    return out.str();
 }