diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 00000000..b0755ab5 --- /dev/null +++ b/.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" diff --git a/.github/workflows/tests.yml b/.github/workflows/ci_on_pr.yml similarity index 88% rename from .github/workflows/tests.yml rename to .github/workflows/ci_on_pr.yml index 32899530..da402998 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/ci_on_pr.yml @@ -53,3 +53,15 @@ jobs: 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 diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/ci_onmerge_publish_docs.yml similarity index 100% rename from .github/workflows/publish_docs.yml rename to .github/workflows/ci_onmerge_publish_docs.yml diff --git a/.github/workflows/cron_daily_check_tag.yml b/.github/workflows/cron_daily_check_tag.yml new file mode 100644 index 00000000..886d4e56 --- /dev/null +++ b/.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/IVaction@v9.15 + with: + compiler: ${{ matrix.compiler }} + threads: 2 + cmake_flags: ${{ matrix.cmake_flags }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/cron_weekly.yml b/.github/workflows/cron_weekly.yml new file mode 100644 index 00000000..0c738a5b --- /dev/null +++ b/.github/workflows/cron_weekly.yml @@ -0,0 +1,36 @@ +# 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: + NANOBENCH_SUPPRESS_WARNINGS: 1 + 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/IVaction@v9.15 + with: + compiler: ${{ matrix.compiler }} + threads: 2 + cmake_flags: ${{ matrix.cmake_flags }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/fmindex_collection-config.cmake b/fmindex_collection-config.cmake index f87d2e7a..a748f224 100644 --- a/fmindex_collection-config.cmake +++ b/fmindex_collection-config.cmake @@ -8,7 +8,7 @@ endif() set(LIBSAIS_USE_OPENMP ${OpenMP_C_FOUND}) set(LIBSAIS_BUILD_SHARED_LIB OFF) -CPMAddPackage("gh:IlyaGrebnov/libsais@2.8.2") +CPMAddPackage("gh:IlyaGrebnov/libsais@2.8.4") if (FMC_USE_SDSL) CPMAddPackage(