Add cron jobs

.github/config/codechecker.skip

@@ -0,0 +1,7 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+-${GITHUB_WORKSPACE}/include/fpgalign/contrib/*
++${GITHUB_WORKSPACE}/*
+-*

.github/config/codechecker.yml

@@ -0,0 +1,23 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+analyze:
+  - --enable=performance
+  - --enable=bugprone
+  - --enable=prefix:clang-diagnostic-shadow
+  - --disable=bugprone-easily-swappable-parameters
+  - --disable=clang-diagnostic-implicit-int-float-conversion
+  - --disable=clang-diagnostic-float-conversion
+  - --disable=clang-diagnostic-implicit-int-conversion
+  - --disable=bugprone-exception-escape
+  - --disable=bugprone-narrowing-conversions
+  - --disable=deadcode.DeadStores
+  - --skip=${GITHUB_WORKSPACE}/.github/config/codechecker.skip
+  - --clean
+
+parse:
+  - --export=html
+  - --output=./html
+  - --skip=${GITHUB_WORKSPACE}/.github/config/codechecker.skip
+  - --trim-path-prefix=${GITHUB_WORKSPACE}/

.github/config/custom.imp

@@ -0,0 +1,7 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+[
+  { "include": [ "<seqan3/contrib/std/detail/adaptor_base.hpp>", "public", "<hibf/contrib/std/detail/adaptor_base.hpp>", "public"] }
+]

.github/workflows/cron_codechecker.yml

@@ -0,0 +1,37 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: CodeChecker
+
+on:
+  schedule:
+    - cron: "0 4 * * MON"
+  workflow_dispatch:
+
+concurrency:
+  group: codechecker-actions
+  cancel-in-progress: true
+
+env:
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eexuo pipefail {0}
+
+jobs:
+  build:
+    name: CodeChecker
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
+    container:
+      image: ghcr.io/seqan/codechecker
+    steps:
+      - name: Run CodeChecker
+        uses: seqan/actions/codechecker@main
+        with:
+          deploy_host: ${{ secrets.DEPLOY_HOST }}
+          deploy_user: ${{ secrets.DEPLOY_USER }}
+          deploy_ssh_key: ${{ secrets.DEPLOY_SSH_KEY }}
+          deploy_path: ${{ secrets.DEPLOY_CODECHECKER_PATH }}

.github/workflows/cron_codeql.yml

@@ -0,0 +1,48 @@
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: CodeQL
+
+on:
+  schedule:
+    - cron: "0 6 * * SAT"
+  workflow_dispatch:
+
+concurrency:
+  group: codeql-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  CODEQL_EXTRACTOR_CPP_AUTOINSTALL_DEPENDENCIES: false
+  SHARG_NO_VERSION_CHECK: 1
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eeuxo pipefail {0}
+
+jobs:
+  codeql:
+    name: CodeQL
+    runs-on: ubuntu-latest
+    permissions:
+      security-events: write
+    container:
+      image: ghcr.io/seqan/gcc-second-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: cpp
+
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v3
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:cpp"

.github/workflows/cron_cpm.yml

@@ -0,0 +1,32 @@
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: Update CPM
+
+on:
+  schedule:
+    - cron: "0 12 * * SAT"
+  workflow_dispatch:
+
+env:
+  TZ: Europe/Berlin
+
+concurrency:
+  group: update-cpm-actions
+  cancel-in-progress: true
+
+jobs:
+  update_cpm:
+    name: Update CPM
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
+    steps:
+      - name: Run update CPM
+        uses: seqan/actions/update_cpm_package_lock@main
+        with:
+          token: ${{ secrets.SEQAN_ACTIONS_PAT }}
+          gpg_key: ${{ secrets.SEQAN_ACTIONS_GPG_KEY }}
+          gpg_passphrase: ${{ secrets.SEQAN_ACTIONS_GPG_PASSPHRASE }}
+          package_lock_file: cmake/package-lock.cmake

.github/workflows/cron_iwyu.yml

@@ -0,0 +1,37 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: IWYU
+
+on:
+  schedule:
+    - cron: "0 4 * * MON"
+  workflow_dispatch:
+
+concurrency:
+  group: iwyu-actions
+  cancel-in-progress: true
+
+env:
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eexuo pipefail {0}
+
+jobs:
+  build:
+    name: IWYU
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
+    container:
+      image: ghcr.io/seqan/iwyu
+    steps:
+      - name: Run IWYU
+        uses: seqan/actions/iwyu@main
+        with:
+          configure_path: .
+          token: ${{ secrets.SEQAN_ACTIONS_PAT }}
+          gpg_key: ${{ secrets.SEQAN_ACTIONS_GPG_KEY }}
+          gpg_passphrase: ${{ secrets.SEQAN_ACTIONS_GPG_PASSPHRASE }}

.github/workflows/cron_sanitizer.yml

@@ -0,0 +1,99 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: Sanitizer
+
+on:
+  schedule:
+    - cron: "0 4 * * SAT"
+  workflow_dispatch:
+
+concurrency:
+  group: sanitizer-actions
+  cancel-in-progress: true
+
+env:
+  TZ: Europe/Berlin
+  TSAN_OPTIONS: ignore_noninstrumented_modules=1
+  UBSAN_OPTIONS: print_stacktrace=1
+
+defaults:
+  run:
+    shell: bash -Eeuxo pipefail {0}
+
+jobs:
+  build:
+    name: ${{ matrix.name }} ${{ matrix.build_type }} ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
+    env:
+      ASAN_OPTIONS: strict_string_checks=1:detect_stack_use_after_return=1:check_initialization_order=1:strict_init_order=1:detect_leaks=${{ contains(matrix.os, 'macos') && '0' || '1' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        name: [ASan, TSan, UBSan]
+        os: [ubuntu-latest, macos-latest]
+        build_type: [Release, RelWithDebInfo, Debug]
+        exclude:
+          - name: "TSan"
+            os: macos-latest
+
+        include:
+          - name: "ASan"
+            cxx_flags: "-fno-omit-frame-pointer -fsanitize=address"
+
+          - name: "TSan"
+            cxx_flags: "-fno-omit-frame-pointer -fsanitize=thread"
+
+          - name: "UBSan"
+            os: macos-latest
+            cxx_flags: "-fno-omit-frame-pointer -fsanitize=undefined,float-divide-by-zero,implicit-conversion,local-bounds,nullability -Wno-pass-failed"
+
+          - name: "UBSan"
+            os: macos-latest
+            build_type: Release
+            ctest_excludes: "-E tmp_directory_snippet_cmp_output"
+
+          - name: "UBSan"
+            os: macos-latest
+            build_type: RelWithDebInfo
+            ctest_excludes: "-E tmp_directory_snippet_cmp_output"
+
+          - name: "UBSan"
+            os: ubuntu-latest
+            cxx_flags: "-fno-omit-frame-pointer -fsanitize=undefined,float-divide-by-zero"
+
+          - os: macos-latest
+            compiler: clang-latest
+
+          - os: ubuntu-latest
+            compiler: gcc-latest
+            image: ghcr.io/seqan/gcc-latest
+
+          - name: "TSan"
+            os: ubuntu-latest
+            compiler: clang-latest
+            image: ghcr.io/seqan/clang-latest
+    container:
+      image: ${{ matrix.image || '' }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup compiler
+        if: contains(matrix.os, 'macos')
+        uses: seqan/actions/setup-compiler@main
+        with:
+          compiler: ${{ matrix.compiler }}
+
+      - name: Configure tests
+        run: |
+          mkdir build && cd build
+          cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+          make gtest_main
+
+      - name: Build and run tests
+        working-directory: build
+        run: make -k check

cmake/package-lock.cmake

@@ -88,7 +88,7 @@ CPMDeclarePackage (use_ccache
 # thresholding
 CPMDeclarePackage (thresholding
                    NAME thresholding
-                   URL "${PROJECT_SOURCE_DIR}/contrib/threshold.tar.gz"
+                   URL "${PROJECT_SOURCE_DIR}/contrib/threshold.tar.gz" # main
                    URL_HASH SHA256=4990c7fb9778a2fb8a19794b966d57496ca77bcd708b4cee3c93eea6e5b67d80
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE

include/fpgalign/argument_parsing.hpp

@@ -4,10 +4,11 @@
 
 #pragma once
 
-#include <string>
-#include <vector>
+#include <cstdint> // for uint8_t
+#include <string>  // for string
+#include <vector>  // for vector
 
-#include <fpgalign/config.hpp>
+#include <fpgalign/config.hpp> // for config
 
 enum class subcommand : uint8_t
 {

include/fpgalign/config.hpp

@@ -4,7 +4,8 @@
 
 #pragma once
 
-#include <filesystem>
+#include <cstdint>    // for uint8_t, uint16_t, uint32_t
+#include <filesystem> // for path
 
 struct config
 {

include/fpgalign/contrib/minimiser_hash.hpp

@@ -9,7 +9,10 @@
 
 #include <seqan3/alphabet/nucleotide/dna4.hpp>
 
+// IWYU pragma: begin_exports
+#include <hibf/contrib/std/detail/adaptor_base.hpp>
 #include <hibf/contrib/std/detail/adaptor_from_functor.hpp>
+// IWYU pragma: end_exports
 
 // Same as seqan3::views::minimiser_hash, but optimized for dna4, with integrated adjust_seed
 

include/fpgalign/meta.hpp

@@ -4,14 +4,17 @@
 
 #pragma once
 
-#include <filesystem>
-#include <string>
-#include <vector>
+#include <cstddef> // for size_t
+#include <cstdint> // for uint8_t, uint32_t
+#include <string>  // for basic_string, string
+#include <vector>  // for vector
 
-#include <seqan3/io/sequence_file/input.hpp>
+#include <seqan3/alphabet/nucleotide/dna4.hpp> // for dna4
+#include <seqan3/io/detail/misc.hpp>           // for set_format
+#include <seqan3/io/record.hpp>                // for field, fields
+#include <seqan3/io/sequence_file/input.hpp>   // for sequence_file_input, sequence_file_input_default_traits_dna
 
-#include <cereal/types/string.hpp>
-#include <cereal/types/vector.hpp>
+#include <cereal/macros.hpp> // for CEREAL_SERIALIZE_FUNCTION_NAME
 
 struct dna4_traits : seqan3::sequence_file_input_default_traits_dna
 {

include/fpgalign/search/search.hpp

@@ -4,9 +4,11 @@
 
 #pragma once
 
-#include <fpgalign/config.hpp>
-#include <fpgalign/contrib/slotted_cart_queue.hpp>
-#include <fpgalign/meta.hpp>
+#include <cstddef> // for size_t
+
+#include <fpgalign/config.hpp>                     // for config
+#include <fpgalign/contrib/slotted_cart_queue.hpp> // for slotted_cart_queue
+#include <fpgalign/meta.hpp>                       // for meta
 
 namespace search
 {

include/fpgalign/utility/fmindex.hpp

@@ -4,9 +4,11 @@
 
 #pragma once
 
-#include <fmindex-collection/fmindex/BiFMIndex.h>
+#include <cstddef> // for size_t
 
-#include <fpgalign/config.hpp>
+#include <fmindex-collection/fmindex/BiFMIndex.h> // for BiFMIndex
+
+#include <fpgalign/config.hpp> // for config
 
 namespace utility
 {