Fix/update to newest cpm

.github/dependabot.yml

@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+#
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/ci_on_pr.yml

@@ -0,0 +1,56 @@
+# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+name: "CI"
+
+on:
+  push:
+    branches:
+      - 'main'
+  pull_request:
+
+env:
+  NANOBENCH_SUPPRESS_WARNINGS: 1
+  TZ: Europe/Berlin
+
+concurrency:
+  group: ${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: ${{ matrix.os }}-${{ matrix.compiler }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 120
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - {os: ubuntu-22.04, compiler: spdx_license_lint}
+          - {os: ubuntu-22.04, compiler: gcc14-cpp20-release}
+          - {os: ubuntu-22.04, compiler: gcc14-cpp20-debug-sanitize_address}
+          - {os: ubuntu-22.04, compiler: gcc14-cpp20-debug-sanitize_undefined}
+          - {os: ubuntu-22.04, compiler: gcc14-cpp20-debug-sanitize_thread}
+
+
+    steps:
+      - name: Standard IV-project testing
+        uses: iv-project/[email protected]
+        with:
+          compiler: ${{ matrix.compiler }}
+          threads: 2
+          cmake_flags: ${{ matrix.cmake_flags }}
+          cmake_c_flags: ${{ matrix.cmake_c_flags }}
+          cmake_cxx_flags: ${{ matrix.cmake_cxx_flags }}
+  final:
+    runs-on: ubuntu-22.04
+    name: final-pass
+    needs: build
+    if: always()
+    steps:
+      - name: Succeeded
+        if: ${{ !(contains(needs.*.result, 'failure')) }}
+        run: exit 0
+      - name: CI failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1

.github/workflows/cron_daily_check_tag.yml

@@ -0,0 +1,34 @@
+# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+name: "Daily CI - check main has tag"
+
+on:
+  schedule:
+    - cron: '0 8 * * *'
+  workflow_dispatch:
+env:
+  TZ: Europe/Berlin
+
+concurrency:
+  group: daily_check_tag
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: ${{ matrix.os }}-${{ matrix.compiler }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 120
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - {os: ubuntu-22.04, compiler: check_tag-open_issue}
+    steps:
+      - name: Standard IV-project testing
+        uses: iv-project/[email protected]
+        with:
+          compiler: ${{ matrix.compiler }}
+          threads: 2
+          cmake_flags: ${{ matrix.cmake_flags }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/cron_daily_cpm_version.yml

@@ -0,0 +1,34 @@
+# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+name: "Daily CI - check CPM versions"
+
+on:
+  schedule:
+    - cron: '0 8 * * *'
+  workflow_dispatch:
+env:
+  TZ: Europe/Berlin
+
+concurrency:
+  group: daily
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: ${{ matrix.os }}-${{ matrix.compiler }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 120
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - {os: ubuntu-22.04, compiler: cpm_update_version}
+    steps:
+      - name: Standard IV-project testing
+        uses: iv-project/[email protected]
+        with:
+          compiler: ${{ matrix.compiler }}
+          threads: 2
+          cmake_flags: ${{ matrix.cmake_flags }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/cron_weekly.yml

@@ -0,0 +1,34 @@
+# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+name: "Weekly CI"
+
+on:
+  schedule:
+    - cron: '0 5 * * Mon'
+  workflow_dispatch:
+env:
+  TZ: Europe/Berlin
+
+concurrency:
+  group: weekly
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: ${{ matrix.os }}-${{ matrix.compiler }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 120
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - {os: ubuntu-22.04, compiler: gcc14-cpp20-release-open_issue}
+    steps:
+      - name: Standard IV-project testing
+        uses: iv-project/[email protected]
+        with:
+          compiler: ${{ matrix.compiler }}
+          threads: 2
+          cmake_flags: ${{ matrix.cmake_flags }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

CMakeLists.txt

@@ -1,9 +1,7 @@
-# -----------------------------------------------------------------------------------------------------
-# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
-# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
-# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
-# shipped with this file.
-# -----------------------------------------------------------------------------------------------------
+# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: BSD-3-Clause
+
 cmake_minimum_required (VERSION 3.16)
 
 project (sahara VERSION 1.0.0)
@@ -13,13 +11,10 @@ set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
-find_package(fmt REQUIRED)
-find_package(cereal REQUIRED PATHS lib/fmindex-collection/lib)
-find_package(fmindex_collection REQUIRED PATHS lib/fmindex-collection)
-find_package(clice REQUIRED PATHS lib/clice)
-find_package(ivio REQUIRED PATHS lib/ivio)
-find_package(ivsigma REQUIRED PATHS lib/ivsigma)
-find_package(xxHash REQUIRED PATHS lib/cmake)
 
+find_package(OpenMP QUIET)
+include(cmake/CPM.cmake)
+CPMAddPackage("gh:SGSSGene/[email protected]")
+CPMLoadDependenciesFile("${CMAKE_CURRENT_SOURCE_DIR}/cpm.dependencies")
 
 add_subdirectory(src/sahara)

LICENSES/BSD-3-Clause.txt

@@ -0,0 +1,11 @@
+Copyright (c) <year> <owner>. 
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.