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Merge pull request #202 from eseiler/fix/install
[INFRA] Add external_project tests
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‎.github/workflows/ci_cmake.yml

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name: CMake
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on:
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push:
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branches:
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- 'main'
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pull_request:
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types:
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- unlabeled
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workflow_dispatch:
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concurrency:
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group: cmake-${{ github.event.pull_request.number || github.ref }}
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cancel-in-progress: ${{ github.event_name != 'push' }}
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env:
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SHARG_NO_VERSION_CHECK: 1
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TZ: Europe/Berlin
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defaults:
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run:
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shell: bash -Eexuo pipefail {0}
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jobs:
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build:
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name: "External project"
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runs-on: ubuntu-22.04
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timeout-minutes: 120
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if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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with:
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path: sharg-parser
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fetch-depth: 1
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submodules: true
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- name: Install CMake
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uses: seqan/actions/setup-cmake@main
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with:
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cmake: 3.16.9
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- name: Setup toolchain
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uses: seqan/actions/setup-toolchain@main
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with:
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compiler: gcc-13
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use_actions_cache: false
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- name: Configure tests
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run: |
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mkdir sharg-build
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cd sharg-build
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cmake ../sharg-parser/test/external_project -DCMAKE_BUILD_TYPE=Debug
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make -j2 sharg_test_prerequisite
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- name: Build tests
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run: |
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cd sharg-build
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make -k -j2
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‎.github/workflows/lint.yml

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cancel-in-progress: true
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runs-on: ubuntu-22.04
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steps:
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- name: "Cancel Coverage"
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run: echo "Cancelling Coverage"
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- name: "Cancel Documentation"
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run: echo "Cancelling Documentation"
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cancel_cmake:
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name: Cancel running Workflows
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concurrency:
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group: cmake-${{ github.event.pull_request.number }}
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cancel-in-progress: true
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runs-on: ubuntu-22.04
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steps:
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- name: "Cancel CMake"
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run: echo "Cancelling CMake"
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lint:
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name: Lint
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concurrency:
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group: lint-${{ github.event.pull_request.number }}
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cancel-in-progress: true
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needs: [cancel_linux, cancel_macos, cancel_misc, cancel_coverage, cancel_documentation]
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needs: [cancel_linux, cancel_macos, cancel_misc, cancel_coverage, cancel_documentation, cancel_cmake]
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runs-on: ubuntu-22.04
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timeout-minutes: 15
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steps:

‎CHANGELOG.md

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@@ -18,16 +18,29 @@ The following API changes should be documented as such:
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If possible, provide tooling that performs the changes, e.g. a shell-script.
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-->
2020

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# Release 1.1.1
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## Bug fixes
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* Fixed installation of Sharg via `make install` ([#202](https://github.com/seqan/sharg-parser/pull/202)).
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## API changes
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#### Compiler
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* Dropped support for gcc-10 ([#199](https://github.com/seqan/sharg-parser/pull/199)).
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* Added support for gcc-13 ([#199](https://github.com/seqan/sharg-parser/pull/199)).
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* Added support for clang-17 ([#197](https://github.com/seqan/sharg-parser/pull/197),
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[#198](https://github.com/seqan/sharg-parser/pull/198)).
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# Release 1.1.0
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## Features
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* We support Gitpod. [Click here](https://gitpod.io/#https://github.com/seqan/sharg-parser/)
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to try it out.
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* **CWL support** (Common Workflow Language): An app using Sharg can now automatically export a CWL tool
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description file via `--export-help cwl` [#94](https://github.com/seqan/sharg-parser/pull/94).
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## API changes
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description file via `--export-help cwl` ([#94](https://github.com/seqan/sharg-parser/pull/94)).
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## Bug fixes
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‎build_system/sharg-config.cmake

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# ----------------------------------------------------------------------------
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# tool description lib (tdl) dependency
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# ----------------------------------------------------------------------------
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set (STORED_CMAKE_MESSAGE_LOG_LEVEL "${CMAKE_MESSAGE_LOG_LEVEL}")
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set (CMAKE_MESSAGE_LOG_LEVEL "ERROR")
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find_package (TDL QUIET HINTS ${SHARG_SUBMODULES_DIR}/submodules/tool_description_lib ${SHARG_HINT_TDL})
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set (CMAKE_MESSAGE_LOG_LEVEL "${STORED_CMAKE_MESSAGE_LOG_LEVEL}")
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unset (STORED_CMAKE_MESSAGE_LOG_LEVEL)
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if (TDL_FOUND)
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sharg_config_print ("Dependency: TDL found.")

‎submodules/tool_description_lib

‎test/external_project/CMakeLists.txt

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# --------------------------------------------------------------------------------------------------------
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# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
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# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
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# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
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# shipped with this file and also available at: https://github.com/seqan/sharg-parser/blob/main/LICENSE.md
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# --------------------------------------------------------------------------------------------------------
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cmake_minimum_required (VERSION 3.16)
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project (sharg_test_external_project CXX)
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include (../sharg-test.cmake) # for SHARG_EXTERNAL_PROJECT_CMAKE_ARGS, SHARG_VERSION
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include (ExternalProject)
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set (SHARG_ROOT "${CMAKE_CURRENT_LIST_DIR}/../../")
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include (install-sharg.cmake)
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option (SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE
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"Enable this option if you want to get a detailed list which paths were considered for find_package(...)" FALSE)
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# 1) This tests test/external_project/sharg_submodule_add_subdirectory/CMakeLists.txt
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# That means we use add_subdirectory directly on sharg's top level CMakeLists.txt.
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# This will automatically call find_package and expose our sharg::sharg target.
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# This is expected to work with CMake >= 3.4.
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# (ExternalProject_Add simulates a fresh and separate invocation of cmake ../)
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ExternalProject_Add (
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sharg_submodule_add_subdirectory
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PREFIX sharg_submodule_add_subdirectory
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SOURCE_DIR "${CMAKE_CURRENT_LIST_DIR}/sharg_submodule_add_subdirectory"
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CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS}
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"-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}" #
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"-DSHARG_ROOT=${SHARG_ROOT}")
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# 2) This tests test/external_project/sharg_submodule_find_package/CMakeLists.txt
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# We have a sharg checkout somewhere and we point CMAKE_PREFIX_PATH to <checkout>/sharg/build_system
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# and then use `find_package` to find `sharg-config.cmake` which exposes our `sharg::sharg` target.
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# This is expected to work with CMake >= 3.4.
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# (ExternalProject_Add simulates a fresh and separate invocation of cmake ../)
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ExternalProject_Add (
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sharg_submodule_find_package
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PREFIX sharg_submodule_find_package
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SOURCE_DIR "${CMAKE_CURRENT_LIST_DIR}/sharg_submodule_find_package"
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CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}"
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"-DCMAKE_PREFIX_PATH=${SHARG_ROOT}/build_system")
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# 3) This tests test/external_project/sharg_installed/CMakeLists.txt
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# This test assumes that sharg was installed by make install (e.g. system-wide).
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# This is the way most upstream packages, like debian, provide our library.
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# This test assumes that `sharg-config.cmake` can be found by cmake in some global paths like /usr/share/cmake/.
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#
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# We simulate this by using our `make package` release, e.g. the one we release under
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# https://github.com/seqan/sharg/releases, and unzipping it to some folder and making
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# that path globally accessible by CMAKE_SYSTEM_PREFIX_PATH.
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# (ExternalProject_Add simulates a fresh and separate invocation of cmake ../)
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ExternalProject_Add (
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sharg_installed
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PREFIX sharg_installed
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SOURCE_DIR "${CMAKE_CURRENT_LIST_DIR}/sharg_installed"
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CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}"
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"-DCMAKE_SYSTEM_PREFIX_PATH=${SHARG_SYSTEM_PREFIX}")
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add_dependencies (sharg_installed sharg_test_prerequisite)
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# 4) This tests test/external_project/sharg_fetch_content_zip/CMakeLists.txt
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# It uses fetch_content (a CMake 3.14 feature) to download our zip-release (e.g. zip, tar.xz) from
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# https://github.com/seqan/sharg/releases. fetch_content will automatically download, verify, extract it.
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# The user only needs to define CMAKE_PREFIX_PATH to be able to find our `sharg-config.cmake`.
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# Note that FetchContent is a CMake >= 3.14 feature.
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# This is expected to work with CMake >= 3.14.
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# (ExternalProject_Add simulates a fresh and separate invocation of cmake ../)
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ExternalProject_Add (
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sharg_fetch_content_zip
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PREFIX sharg_fetch_content_zip
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SOURCE_DIR "${CMAKE_CURRENT_LIST_DIR}/sharg_fetch_content_zip"
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CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}"
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"-DSHARG_PACKAGE_ZIP_URL=${SHARG_PACKAGE_ZIP_URL}")
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add_dependencies (sharg_fetch_content_zip sharg_test_prerequisite)
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# 5) This test is the same as 2) but emulates the settings within the setup tutorial.
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# This test is used as snippet in the setup tutorial.
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ExternalProject_Add (
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sharg_setup_tutorial
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PREFIX sharg_setup_tutorial
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SOURCE_DIR "${CMAKE_CURRENT_LIST_DIR}/sharg_setup_tutorial"
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CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}")

‎test/external_project/find-package-diagnostics.cmake

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# --------------------------------------------------------------------------------------------------------
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# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
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# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
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# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
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# shipped with this file and also available at: https://github.com/seqan/sharg-parser/blob/main/LICENSE.md
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# --------------------------------------------------------------------------------------------------------
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# list all search places
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# NOTE: this can be enabled globally by -DSHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE=1 to help debug search paths
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# set (CMAKE_FIND_DEBUG_MODE ${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE})
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macro (sharg_print_diagnostics text)
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message (STATUS " ${text}")
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endmacro ()
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message (STATUS "=== SHARG find_package Diagnostics start ===")
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sharg_print_diagnostics ("CMAKE_COMMAND: ${CMAKE_COMMAND}")
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sharg_print_diagnostics ("CMAKE_VERSION: ${CMAKE_VERSION}")
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sharg_print_diagnostics ("CMAKE_SYSTEM_NAME: ${CMAKE_SYSTEM_NAME}")
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sharg_print_diagnostics (
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"Search paths (https://cmake.org/cmake/help/latest/command/find_package.html#config-mode-search-procedure)")
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sharg_print_diagnostics ("1) CMAKE_FIND_USE_PACKAGE_ROOT_PATH: ${CMAKE_FIND_USE_CMAKE_PATH}")
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sharg_print_diagnostics (" SHARG_ROOT: ${SHARG_ROOT}")
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sharg_print_diagnostics ("2) CMAKE_FIND_USE_CMAKE_PATH: ${CMAKE_FIND_USE_CMAKE_PATH}")
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sharg_print_diagnostics (" CMAKE_PREFIX_PATH: ${CMAKE_PREFIX_PATH}")
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sharg_print_diagnostics (" CMAKE_FRAMEWORK_PATH: ${CMAKE_FRAMEWORK_PATH}")
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sharg_print_diagnostics (" CMAKE_APPBUNDLE_PATH: ${CMAKE_APPBUNDLE_PATH}")
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sharg_print_diagnostics ("3) CMAKE_FIND_USE_CMAKE_ENVIRONMENT_PATH: ${CMAKE_FIND_USE_CMAKE_ENVIRONMENT_PATH}")
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sharg_print_diagnostics (" SHARG_DIR: ${SHARG_DIR}")
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# 4) Using the HINTS option.
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# See point 4 in https://cmake.org/cmake/help/latest/command/find_package.html#config-mode-search-procedure.
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# There is no output.
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sharg_print_diagnostics ("5) CMAKE_FIND_USE_SYSTEM_ENVIRONMENT_PATH: ${CMAKE_FIND_USE_SYSTEM_ENVIRONMENT_PATH}")
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sharg_print_diagnostics ("6) CMAKE_FIND_USE_PACKAGE_REGISTRY: ${CMAKE_FIND_USE_PACKAGE_REGISTRY}")
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sharg_print_diagnostics ("7) CMAKE_FIND_USE_CMAKE_SYSTEM_PATH: ${CMAKE_FIND_USE_CMAKE_SYSTEM_PATH}")
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sharg_print_diagnostics (" CMAKE_SYSTEM_PREFIX_PATH: ${CMAKE_SYSTEM_PREFIX_PATH}")
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sharg_print_diagnostics (" CMAKE_SYSTEM_FRAMEWORK_PATH: ${CMAKE_SYSTEM_FRAMEWORK_PATH}")
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sharg_print_diagnostics (" CMAKE_SYSTEM_APPBUNDLE_PATH: ${CMAKE_SYSTEM_APPBUNDLE_PATH}")
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sharg_print_diagnostics ("8) CMAKE_FIND_USE_SYSTEM_PACKAGE_REGISTRY: ${CMAKE_FIND_USE_SYSTEM_PACKAGE_REGISTRY}")
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message (STATUS "=== SHARG find_package Diagnostics end ===")

‎test/external_project/install-sharg.cmake

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# --------------------------------------------------------------------------------------------------------
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# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
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# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
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# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
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# shipped with this file and also available at: https://github.com/seqan/sharg-parser/blob/main/LICENSE.md
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# --------------------------------------------------------------------------------------------------------
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cmake_minimum_required (VERSION 3.14)
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# install and package sharg library
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ExternalProject_Add (
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sharg_test_prerequisite
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PREFIX sharg_test_prerequisite
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SOURCE_DIR "${SHARG_ROOT}"
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CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} #
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"-DCMAKE_INSTALL_PREFIX=<BINARY_DIR>/usr"
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STEP_TARGETS configure install
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BUILD_BYPRODUCTS "<BINARY_DIR>/include")
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set (SHARG_PACKAGE_ZIP_URL "${PROJECT_BINARY_DIR}/sharg-${SHARG_VERSION}-${CMAKE_SYSTEM_NAME}.zip")
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ExternalProject_Add_Step (
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sharg_test_prerequisite package
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COMMAND ${CMAKE_CPACK_COMMAND} -G ZIP -B "${PROJECT_BINARY_DIR}"
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DEPENDEES configure install
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WORKING_DIRECTORY "<BINARY_DIR>"
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BYPRODUCTS ${SHARG_PACKAGE_ZIP_URL} #
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"${SHARG_PACKAGE_ZIP_URL}.sha256")
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ExternalProject_Get_Property (sharg_test_prerequisite BINARY_DIR)
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set (SHARG_SYSTEM_PREFIX "${BINARY_DIR}/usr")

‎test/external_project/sharg_fetch_content_zip/CMakeLists.txt

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# --------------------------------------------------------------------------------------------------------
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# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
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# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
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# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
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# shipped with this file and also available at: https://github.com/seqan/sharg-parser/blob/main/LICENSE.md
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# --------------------------------------------------------------------------------------------------------
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cmake_minimum_required (VERSION 3.14)
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project (sharg_app CXX)
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# --- helper scripts
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include (../find-package-diagnostics.cmake)
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file (SHA256 "${SHARG_PACKAGE_ZIP_URL}" SHARG_PACKAGE_ZIP_HASH)
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message (STATUS "SHARG_PACKAGE_ZIP_URL: ${SHARG_PACKAGE_ZIP_URL}")
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message (STATUS "SHARG_PACKAGE_ZIP_HASH: SHA256=${SHARG_PACKAGE_ZIP_HASH}")
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# ---
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# fetch sharg sources (requires >= cmake 3.14)
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include (FetchContent)
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FetchContent_Declare (
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sharg
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URL "${SHARG_PACKAGE_ZIP_URL}" # change these values
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URL_HASH "SHA256=${SHARG_PACKAGE_ZIP_HASH}" # change these values
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)
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FetchContent_MakeAvailable (sharg)
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# add sharg to search path
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list (APPEND CMAKE_PREFIX_PATH "${sharg_SOURCE_DIR}")
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# require sharg with a version between >=1.0.0 and <2.0.0
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find_package (sharg 1.0 REQUIRED)
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# build app with sharg
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add_executable (hello_world ../src/hello_world.cpp)
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target_link_libraries (hello_world sharg::sharg)
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install (TARGETS hello_world)

‎test/external_project/sharg_installed/CMakeLists.txt

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# --------------------------------------------------------------------------------------------------------
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# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
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# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
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# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
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# shipped with this file and also available at: https://github.com/seqan/sharg-parser/blob/main/LICENSE.md
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# --------------------------------------------------------------------------------------------------------
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cmake_minimum_required (VERSION 3.4)
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project (sharg_app CXX)
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# --- helper scripts
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include (../find-package-diagnostics.cmake)
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# ---
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# require sharg with a version between >=1.0.0 and <2.0.0
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find_package (sharg 1.0 REQUIRED)
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# build app with sharg
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add_executable (hello_world ../src/hello_world.cpp)
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target_link_libraries (hello_world sharg::sharg)
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if (CMAKE_VERSION VERSION_LESS 3.14)
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install (TARGETS hello_world RUNTIME DESTINATION bin)
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else ()
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install (TARGETS hello_world) # RUNTIME DESTINATION not needed anymore since cmake 3.14
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endif ()

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