Merge branch 'develop' into feature/Navier-Stokes

cmake/PugsDoc.cmake

@@ -78,6 +78,8 @@ if (EMACS)
       DEPENDS
       "${PUGS_SOURCE_DIR}/doc/userdoc.org"
       "${PUGS_SOURCE_DIR}/doc/lisp/userdoc-pdf.el"
+      "${PUGS_SOURCE_DIR}/tools/pgs-pygments.sh"
+      "${PUGS_SOURCE_DIR}/tools/pgs-pygments.py"
       pugs
       pugsdoc-dir
       pugsdoc-download-elpa

doc/lisp/build-doc-config.el

@@ -43,8 +43,7 @@
 
 (custom-set-variables
  '(org-export-html-postamble nil)
- ;; By now pugs is not known by Pygments raw text is better
- '(org-latex-minted-langs '((pugs "Text") (pugs-error "Text")))
+ '(org-latex-minted-langs '((pugs "Pugs") (pugs-error "Pugs")))
  '(org-confirm-babel-evaluate nil)
  '(org-html-validation-link nil)
  '(org-src-fontify-natively t)

packages/CLI11/.appveyor.yml

-version: 2.1.2.{build}
+version: 2.2.0.{build}
 
 branches:
   only:
@@ -19,7 +19,9 @@ install:
 build_script:
   - mkdir build
   - cd build
-  - ps: cmake .. -DCLI11_WARNINGS_AS_ERRORS=ON -DCLI11_SINGLE_FILE_TESTS=ON -DCMAKE_BUILD_TYPE=Debug -DCMAKE_GENERATOR="Visual Studio 14 2015"
+  - ps:
+      cmake .. -DCLI11_WARNINGS_AS_ERRORS=ON -DCLI11_SINGLE_FILE_TESTS=ON
+      -DCMAKE_BUILD_TYPE=Debug -DCMAKE_GENERATOR="Visual Studio 14 2015"
   - ps: cmake --build .
   - cd ..
   - conan create . CLIUtils/CLI11

packages/CLI11/.ci/azure-build.yml

 steps:
+  # Needed on GCC 4.8 docker image for some reason
+  - script: mkdir build
+    displayName: "Make build directory"
 
   - task: CMake@1
     inputs:
-    cmakeArgs: .. -DCLI11_WARNINGS_AS_ERRORS=ON -DCLI11_SINGLE_FILE=$(cli11.single) -DCMAKE_CXX_STANDARD=$(cli11.std) -DCLI11_SINGLE_FILE_TESTS=$(cli11.single) -DCMAKE_BUILD_TYPE=$(cli11.build_type) $(cli11.options)
-  displayName: 'Configure'
+      cmakeArgs:
+        .. -DCLI11_WARNINGS_AS_ERRORS=ON -DCLI11_SINGLE_FILE=$(cli11.single)
+        -DCMAKE_CXX_STANDARD=$(cli11.std)
+        -DCLI11_SINGLE_FILE_TESTS=$(cli11.single)
+        -DCMAKE_BUILD_TYPE=$(cli11.build_type) $(cli11.options)
+    displayName: "Configure"
+
+  - script: cmake --build . -- -j2 --keep-going
+    displayName: "Build Unix"
+    workingDirectory: build
+    condition: ne( variables['Agent.OS'], 'Windows_NT' )
 
   - script: cmake --build .
-  displayName: 'Build'
+    displayName: "Build Windows"
     workingDirectory: build
+    condition: eq( variables['Agent.OS'], 'Windows_NT' )

packages/CLI11/.ci/azure-cmake.yml

 steps:
-
   # Note that silkeh/clang does not include ca-certificates, so check the shasum for verification
   - bash: |
       wget --no-check-certificate "https://cmake.org/files/v3.14/cmake-3.14.3-Linux-x86_64.tar.gz"
@@ -8,9 +7,11 @@ steps:
 
   - task: ExtractFiles@1
     inputs:
-    archiveFilePatterns: 'cmake*.tar.gz'
-    destinationFolder: 'cmake_program'
+      archiveFilePatterns: "cmake*.tar.gz"
+      destinationFolder: "cmake_program"
       displayName: Extract CMake
 
-- bash: echo "##vso[task.prependpath]$(Build.SourcesDirectory)/cmake_program/cmake-3.14.3-Linux-x86_64/bin"
+  - bash:
+      echo
+      "##vso[task.prependpath]$(Build.SourcesDirectory)/cmake_program/cmake-3.14.3-Linux-x86_64/bin"
     displayName: Add CMake to PATH

packages/CLI11/.ci/azure-test.yml

 steps:
-
   - script: ctest --output-on-failure -C $(cli11.build_type) -T test
-  displayName: 'Test'
+    displayName: "Test"
     workingDirectory: build
 
   - task: PublishTestResults@2
     inputs:
-    testResultsFormat: 'cTest'
-    testResultsFiles: '**/Test.xml'
+      testResultsFormat: "cTest"
+      testResultsFiles: "**/Test.xml"

packages/CLI11/.ci/build_doxygen.sh

-#!/bin/env sh
-# (Source me)
-
-set -evx
-
-#DOXYGEN_URL="http://doxygen.nl/files/doxygen-1.8.17.src.tar.gz"
-DOXYGEN_URL="https://github.com/doxygen/doxygen/archive/Release_1_8_15.tar.gz"
-cd "${DEPS_DIR}"
-
-if [[ ! -f "${DEPS_DIR}/doxygen/build/bin/doxygen" ]] ; then
-  echo "Downloading Doxygen"
-  mkdir -p doxygen
-  travis_retry wget --no-check-certificate --quiet -O - "${DOXYGEN_URL}" | tar --strip-components=1 -xz -C doxygen
-  cd doxygen
-  mkdir -p build
-  cd build
-  cmake ..
-  make -j2
-fi
-
-export PATH="${DEPS_DIR}/doxygen/build/bin:${PATH}"
-
-cd "${TRAVIS_BUILD_DIR}"
-
-set +evx

packages/CLI11/.ci/build_lcov.sh

-#!/bin/env sh
-# (Source me)
-set -evx
-
-LCOV_URL="http://ftp.de.debian.org/debian/pool/main/l/lcov/lcov_1.13.orig.tar.gz"
-cd "${DEPS_DIR}"
-
-if [[ ! -f "${DEPS_DIR}/lcov/bin/lcov" ]] ; then
-  echo "Downloading lcov"
-  mkdir -p lcov
-  travis_retry wget --no-check-certificate --quiet -O - "${LCOV_URL}" | tar --strip-components=1 -xz -C lcov
-fi
-
-export PATH="${DEPS_DIR}/lcov/bin:${PATH}"
-cd "${TRAVIS_BUILD_DIR}"
-
-set +evx

packages/CLI11/.ci/make_and_test.sh

-#!/usr/bin/env bash
-echo -en "travis_fold:start:script.build\\r"
-echo "Building..."
-STD="$1"
-shift
-set -evx
-
-
-mkdir -p build
-cd build
-cmake .. -DCLI11_WARNINGS_AS_ERRORS=ON -DCLI11_SINGLE_FILE=ON -DCMAKE_CXX_STANDARD="$STD" -DCLI11_SINGLE_FILE_TESTS=ON -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_COMPILER_LAUNCHER=ccache $@
-cmake --build . -- -j2
-
-set +evx
-echo -en "travis_fold:end:script.build\\r"
-echo -en "travis_fold:start:script.test\\r"
-echo "Testing..."
-set -evx
-
-ctest --output-on-failure
-
-set +evx
-echo -en "travis_fold:end:script.test\\r"

packages/CLI11/.ci/run_codecov.sh

-#!/usr/bin/env bash
-
-echo -en "travis_fold:start:script.build\\r"
-echo "Building..."
-set -evx
-
-cd "${TRAVIS_BUILD_DIR}"
-mkdir -p build
-cd build
-cmake .. -DCLI11_SINGLE_FILE_TESTS=OFF -DCLI11_EXAMPLES=OFF -DCMAKE_BUILD_TYPE=Coverage
-cmake --build . -- -j2
-cmake --build . --target CLI11_coverage
-
-set +evx
-echo -en "travis_fold:end:script.build\\r"
-echo -en "travis_fold:start:script.lcov\\r"
-echo "Capturing and uploading LCov..."
-set -evx
-
-lcov --directory . --capture --output-file coverage.info # capture coverage info
-lcov --remove coverage.info '*/tests/*' '*/examples/*' '*gtest*' '*gmock*' '/usr/*' --output-file coverage.info # filter out system
-lcov --list coverage.info #debug info
-# Uploading report to CodeCov
-bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports"
-
-set +evx
-echo -en "travis_fold:end:script.lcov\\r"

packages/CLI11/.clang-tidy

 # Checks that will be implemented in future PRs:
 # performance-unnecessary-value-param, hints to ~110 issues. Be careful with implementing the suggested changes of this one, as auto-fixes may break the code
+# bugprone-forwarding-reference-overload probably should be enabled and fixed.
+# clang-diagnostic-float-equal can be fixed by using _a from Catch::literals
+# bugprone-exception-escape due to main being a bit simple in examples
+# modernize-avoid-c-arrays trips up in TEMPLATE_TEST_CASE catch macro
+# modernize-return-braced-init-list triggers on lambdas ?
+# modernize-make-unique requires C++14
+# readability-avoid-const-params-in-decls Affected by the pre-compile split
 
-FormatStyle: file
-
-Checks: '
--*,
+Checks: |
+  *bugprone*,
+  -bugprone-easily-swappable-parameters,
+  -bugprone-forwarding-reference-overload,
+  -bugprone-exception-escape,
+  clang-analyzer-optin.cplusplus.VirtualCall,
+  clang-analyzer-optin.performance.Padding,
+  -clang-diagnostic-float-equal,
+  cppcoreguidelines-init-variables,
+  cppcoreguidelines-prefer-member-initializer,
+  cppcoreguidelines-pro-type-static-cast-downcast,
+  cppcoreguidelines-slicing,
   google-*,
   -google-runtime-references,
   llvm-include-order,
   llvm-namespace-comment,
+  misc-definitions-in-headers,
+  misc-misplaced-const,
+  misc-non-copyable-objects,
+  misc-static-assert,
   misc-throw-by-value-catch-by-reference,
+  misc-throw-by-value-catch-by-reference,
+  misc-uniqueptr-reset-release,
+  misc-unused-parameters,
   modernize*,
   -modernize-use-trailing-return-type,
+  -modernize-concat-nested-namespaces,
+  -modernize-return-braced-init-list,
+  -modernize-make-unique,
+  *performance*,
+  -performance-unnecessary-value-param,
+  -performance-inefficient-string-concatenation,
+  readability-const-return-type,
   readability-container-size-empty,
-'
-
-WarningsAsErrors: '*'
-
-HeaderFilterRegex: '.*hpp'
+  readability-delete-null-pointer,
+  readability-else-after-return,
+  readability-implicit-bool-conversion,
+  readability-inconsistent-declaration-parameter-name,
+  readability-make-member-function-const,
+  readability-misplaced-array-index,
+  readability-non-const-parameter,
+  readability-qualified-auto,
+  readability-redundant-function-ptr-dereference,
+  readability-redundant-smartptr-get,
+  readability-redundant-string-cstr,
+  readability-simplify-subscript-expr,
+  readability-static-accessed-through-instance,
+  readability-static-definition-in-anonymous-namespace,
+  readability-string-compare,
+  readability-suspicious-call-argument,
+  readability-uniqueptr-delete-release,
 
 CheckOptions:
   - key: google-readability-braces-around-statements.ShortStatementLines
-  value:           '3'
+    value: "3"
+  - key: performance-for-range-copy.WarnOnAllAutoCopies
+    value: true
+  - key: performance-inefficient-string-concatenation.StrictMode
+    value: true
+  - key: performance-unnecessary-value-param.AllowedTypes
+    value: "exception_ptr$;"
+  - key: readability-implicit-bool-conversion.AllowPointerConditions
+    value: true
+  - key: modernize-use-nodiscard.ReplacementString
+    value: "CLI11_NODISCARD"
+
+HeaderFilterRegex: "CLI.*hpp"
+
+FormatStyle: file
+# WarningsAsErrors: "*"

packages/CLI11/.codecov.yml

-
 ignore:
   - "tests"
   - "examples"

packages/CLI11/.editorconfig

@@ -2,10 +2,12 @@ root = true
 
 [*]
 indent_style = space
-indent_size = 4
 insert_final_newline = true
 end_of_line = lf
 trim_trailing_whitespace = true
 
+[*.cpp,*.hpp,*.py]
+indent_size = 4
+
 [*.yml]
 indent_size = 2

packages/CLI11/.github/CONTRIBUTING.md

 # Contributing
 
-Thanks for considering to write a Pull Request (PR) for CLI11! Here are a few guidelines to get you started:
+Thanks for considering to write a Pull Request (PR) for CLI11! Here are a few
+guidelines to get you started:
 
-Make sure you are comfortable with the license; all contributions are licensed under the original license.
+Make sure you are comfortable with the license; all contributions are licensed
+under the original license.
 
 ## Adding functionality
 
 Make sure any new functions you add are are:
 
-* Documented by `///` documentation for Doxygen
-* Mentioned in the instructions in the README, though brief mentions are okay
-* Explained in your PR (or previously explained in an Issue mentioned in the PR)
-* Completely covered by tests
+- Documented by `///` documentation for Doxygen
+- Mentioned in the instructions in the README, though brief mentions are okay
+- Explained in your PR (or previously explained in an Issue mentioned in the PR)
+- Completely covered by tests
 
-In general, make sure the addition is well thought out and does not increase the complexity of CLI11 needlessly.
+In general, make sure the addition is well thought out and does not increase the
+complexity of CLI11 needlessly.
 
 ## Things you should know
 
-* Once you make the PR, tests will run to make sure your code works on all supported platforms
-* The test coverage is also measured, and that should remain 100%
-* Formatting should be done with pre-commit, otherwise the format check will not pass. However, it is trivial to apply this to your PR, so don't worry about this check. If you do want to run it, see below.
-* Everything must pass clang-tidy as well, run with `-DCLI11_CLANG_TIDY=ON` (if you set `-DCLI11_CLANG_TIDY_OPTIONS="-fix"`, make sure you use a single threaded build process, or just build one example target).
-* Your changes must also conform to most of the [Google C++ Style Guide](https://google.github.io/styleguide/cppguide.html) rules checked by [cpplint](https://github.com/cpplint/cpplint). For unused cpplint filters and justifications, see [CPPLINT.cfg](/CPPLINT.cfg).
+- Once you make the PR, tests will run to make sure your code works on all
+  supported platforms
+- The test coverage is also measured, and that should remain 100%
+- Formatting should be done with pre-commit, otherwise the format check will not
+  pass. However, it is trivial to apply this to your PR, so don't worry about
+  this check. If you do want to run it, see below.
+- Everything must pass clang-tidy as well, run with
+  `-DCMAKE_CXX_CLANG_TIDY="$(which clang-tidy)"` (if you set
+  `"$(which clang-tidy) -fix"`, make sure you use a single threaded build
+  process, or just build one example target).
+- Your changes must also conform to most of the
+  [Google C++ Style Guide](https://google.github.io/styleguide/cppguide.html)
+  rules checked by [cpplint](https://github.com/cpplint/cpplint). For unused
+  cpplint filters and justifications, see [CPPLINT.cfg](/CPPLINT.cfg).
 
 ## Pre-commit
 
-Format is handled by pre-commit. You should install it (or use [pipx](https://pypa.github.io/pipx/)):
+Format is handled by pre-commit. You should install it (or use
+[pipx](https://pypa.github.io/pipx/)):
 
 ```bash
 python3 -m pip install pre-commit
 ```
 
-Then, you can run it on the items you've added to your staging area, or all files:
+Then, you can run it on the items you've added to your staging area, or all
+files:
 
 ```bash
 pre-commit run
@@ -39,7 +53,8 @@ pre-commit run
 pre-commit run --all-files
 ```
 
-And, if you want to always use it, you can install it as a git hook (hence the name, pre-commit):
+And, if you want to always use it, you can install it as a git hook (hence the
+name, pre-commit):
 
 ```bash
 pre-commit install
@@ -47,7 +62,8 @@ pre-commit install
 
 ## For developers releasing to Conan.io
 
-This is now done by the CI system on tagged releases. Previously, the steps to make a Conan.io release were:
+This is now done by the CI system on tagged releases. Previously, the steps to
+make a Conan.io release were:
 
 ```bash
 conan remove '*' # optional, I like to be clean
@@ -59,7 +75,10 @@ Here I've assumed that the remote is `cli11`.
 
 ## For maintainers: remember to add contributions
 
-In a commit to a PR, just add "`@all-contributors please add <username> for <contributions>`" or similar (see <https://allcontributors.org>). Use `code` for code, `bug` if an issue was submitted, `platform` for packaging stuff, and `doc` for documentation updates.
+In a commit to a PR, just add
+"`@all-contributors please add <username> for <contributions>`" or similar (see
+<https://allcontributors.org>). Use `code` for code, `bug` if an issue was
+submitted, `platform` for packaging stuff, and `doc` for documentation updates.
 
 To run locally, do:
 
@@ -70,14 +89,15 @@ yarn all-contributors add username code,bug
 
 ## For maintainers: Making a release
 
-Remember to replace the emoji in the readme, being careful not to replace the ones in all-contributors if any overlap.
+Remember to replace the emoji in the readme, being careful not to replace the
+ones in all-contributors if any overlap.
 
 Steps:
 
-* Update changelog if needed
-* Update the version in `.appveyor.yml` and `include/CLI/Version.hpp`.
-* Find and replace in README (new minor/major release only):
-  * Replace " 🆕" and "🆕 " with "" (ignores the description line)
-  * Check for `\/\/$` (vi syntax) to catch leftover `// 🆕`
-  * Replace "🚧" with "🆕" (manually ignore the description line)
-* Make a release in the GitHub UI, use a name such as "Version X.Y(.Z): Title"
+- Update changelog if needed
+- Update the version in `.appveyor.yml` and `include/CLI/Version.hpp`.
+- Find and replace in README (new minor/major release only):
+  - Replace " 🆕" and "🆕 " with "" (ignores the description line)
+  - Check for `\/\/$` (vi syntax) to catch leftover `// 🆕`
+  - Replace "🚧" with "🆕" (manually ignore the description line)
+- Make a release in the GitHub UI, use a name such as "Version X.Y(.Z): Title"

packages/CLI11/.github/actions/quick_cmake/action.yml

 name: Quick CMake config
-description: 'Runs CMake 3.4+ (if already setup)'
+description: "Runs CMake 3.4+ (if already setup)"
 inputs:
   args:
-    description: 'Other arguments'
+    description: "Other arguments"
     required: false
-    default: ''
+    default: ""
   cmake-version:
-    description: 'The CMake version to run'
+    description: "The CMake version to run"
     required: true
 
 runs:
   using: composite
   steps:
     - name: CMake ${{ inputs.cmake-version }}
-      uses: jwlawson/actions-setup-cmake@v1.11
+      uses: jwlawson/actions-setup-cmake@v1.12
       with:
         cmake-version: "${{ inputs.cmake-version }}"
     - run: |

packages/CLI11/.github/codecov.yml

+codecov:
+  notify:
+    after_n_builds: 4
+coverage:
+  status:
+    project:
+      informational: true

packages/CLI11/.github/dependabot.yml

@@ -5,12 +5,3 @@ updates:
     directory: "/"
     schedule:
       interval: "daily"
-    ignore:
-      # Official actions have moving tags like v1
-      # that are used, so they don't need updates here
-      - dependency-name: "actions/checkout"
-      - dependency-name: "actions/setup-python"
-      - dependency-name: "actions/cache"
-      - dependency-name: "actions/upload-artifact"
-      - dependency-name: "actions/download-artifact"
-      - dependency-name: "actions/labeler"

packages/CLI11/.github/labeler_merged.yml

 needs changelog:
-  - all: ['!CHANGELOG.md']
+  - all: ["!CHANGELOG.md"]
 needs README:
-  - all: ['!README.md']
+  - all: ["!README.md"]