Merge pull request #46 from SGSSGene/feat/improved_ci

Feat/improved ci

.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/tests.yml → .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

.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_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/[email protected]
+        with:
+          compiler: ${{ matrix.compiler }}
+          threads: 2
+          cmake_flags: ${{ matrix.cmake_flags }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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/[email protected].2")
+CPMAddPackage("gh:IlyaGrebnov/[email protected].4")
 
 if (FMC_USE_SDSL)
     CPMAddPackage(