seqan · eseiler · Oct 27, 2024 · Oct 27, 2024 · Oct 27, 2024 · Oct 27, 2024
diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml
@@ -48,7 +48,6 @@ jobs:
         uses: actions/cache@v4
         with:
           path: /home/runner/.ccache
-          save-always: true
           key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}-${{ github.run_id }}
           restore-keys: |
             ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}

diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
@@ -49,7 +49,6 @@ jobs:
         uses: actions/cache@v4
         with:
           path: /home/runner/.ccache
-          save-always: true
           key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}-${{ github.run_id }}
           restore-keys: |
             ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}

diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml
@@ -50,7 +50,6 @@ jobs:
         uses: actions/cache@v4
         with:
           path: /home/runner/.ccache
-          save-always: true
           key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.build }}-${{ matrix.compiler }}-${{ github.ref }}-${{ github.run_id }}
           restore-keys: |
             ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.build }}-${{ matrix.compiler }}-${{ github.ref }}

diff --git a/.github/workflows/cron_avx2.yml b/.github/workflows/cron_avx2.yml
@@ -26,39 +26,32 @@ defaults:
 
 jobs:
   build:
-    name: ${{ matrix.build }} gcc${{ matrix.compiler }}
+    name: ${{ matrix.build }} ${{ matrix.compiler }}
     runs-on: ubuntu-22.04
     timeout-minutes: 300
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
-        compiler: [11, 12, 13]
+        compiler: ["clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "gcc-11", "intel"]
         build: [unit, snippet, performance, header]
-
+        include:
+          - compiler: "intel"
+            cxx_flags: "-fp-model=strict -Wno-overriding-option"
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
-      - name: Checkout SeqAn3
+      - name: Checkout
         uses: actions/checkout@v4
-        with:
-          path: seqan3
-
-      - name: Setup compiler
-        uses: seqan/actions/setup-compiler@main
-        with:
-          compiler: gcc-${{ matrix.compiler }}
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.16.9
 
       - name: Configure tests
         run: |
-          mkdir seqan3-build
-          cd seqan3-build
-          cmake ../seqan3/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=Release \
-                                                   -DSEQAN3_BENCHMARK_MIN_TIME=0.01 \
-                                                   -DCMAKE_CXX_FLAGS="-mavx2"
+          mkdir build && cd build
+          cmake ../test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=Release \
+                                            -DCMAKE_CXX_FLAGS="-mavx2 ${{ matrix.cxx_flags }}" \
+                                            -DSEQAN3_BENCHMARK_MIN_TIME=0.01
           case "${{ matrix.build }}" in
             unit) make gtest_main;;
             snippet) make gtest_main;;
@@ -67,8 +60,8 @@ jobs:
           esac
 
       - name: Build tests
+        working-directory: build
         run: |
-          cd seqan3-build
           make -k 2>&1 | tee build.log
 
       - name: Setup Python
@@ -80,38 +73,47 @@ jobs:
       - name: Process Log
         if: ${{ failure() }}
         run: |
-          FILE="seqan3/.github/ISSUE_TEMPLATE/cron_comment_template.md"
-          python3 seqan3/.github/workflows/scripts/process_compiler_error_log.py seqan3-build/build.log >> $FILE
+          FILE=".github/ISSUE_TEMPLATE/cron_comment_template.md"
+          python3 .github/workflows/scripts/process_compiler_error_log.py build/build.log >> $FILE
 
       - name: Create comment body
         if: ${{ failure() }}
         id: comment-body
         run: |
-          FILE="seqan3/.github/ISSUE_TEMPLATE/cron_comment_template.md"
-          URL="$GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
-          sed -i "s@{{ build }}@${{ matrix.build }}@" $FILE
-          sed -i "s@{{ compiler }}@${{ matrix.compiler }}@" $FILE
-          sed -i "s@{{ url }}@$URL@" $FILE
-          echo "body<<EOF" >> $GITHUB_OUTPUT
-          cat $FILE >> $GITHUB_OUTPUT
-          echo "EOF" >> $GITHUB_OUTPUT
+          if [[ "${{ job.status }}" == "success" ]]; then
+            echo "body=Success ${{ matrix.build }} on ${{ matrix.compiler }}" >> $GITHUB_OUTPUT
+          else
+            FILE=".github/ISSUE_TEMPLATE/cron_comment_template.md"
+            URL="$GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
+            sed -i "s@{{ build }}@${{ matrix.build }}@" $FILE
+            sed -i "s@{{ compiler }}@${{ matrix.compiler }}@" $FILE
+            sed -i "s@{{ url }}@$URL@" $FILE
+            echo "body<<EOF" >> $GITHUB_OUTPUT
+            cat $FILE >> $GITHUB_OUTPUT
+            echo "EOF" >> $GITHUB_OUTPUT
+          fi
 
       - name: Reopen issue
-        if: ${{ failure() }}
-        uses: octokit/request-action@v2.x
-        with:
-          route: PATCH /repos/{owner}/{repo}/issues/{issue_number}
-          owner: ${{ github.repository_owner }}
-          repo: seqan3
-          issue_number: ${{ env.ISSUE }}
-          state: "open"
+        if: failure()
+        run: gh issue reopen ${{ env.ISSUE }}
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_TOKEN: ${{ secrets.SEQAN_ACTIONS_PAT }}
+          GH_REPO: ${{ github.repository }}
 
-      - name: Create comment
-        if: ${{ failure() }}
+      - name: Find Comment
+        if: always()
+        uses: peter-evans/find-comment@v3
+        id: find_comment
+        with:
+          issue-number: ${{ env.ISSUE }}
+          body-includes: ${{ matrix.build }} on ${{ matrix.compiler }}
+
+      - name: Update comment
+        if: always()
         uses: peter-evans/create-or-update-comment@v4
         with:
+          comment-id: ${{ steps.find_comment.outputs.comment-id }}
           issue-number: ${{ env.ISSUE }}
           body: ${{ steps.comment-body.outputs.body }}
-
+          edit-mode: replace
+          token: ${{ secrets.SEQAN_ACTIONS_PAT }}
diff --git a/.github/workflows/cron_latest_libraries.yml b/.github/workflows/cron_latest_libraries.yml
@@ -5,6 +5,9 @@
 name: Latest Libraries
 
 on:
+  # Will always run on the default branch
+  schedule:
+    - cron: "0 4 * * SUN"
   # Enables a manual trigger, may run on any branch
   workflow_dispatch:
 
@@ -23,7 +26,7 @@ defaults:
 
 jobs:
   build:
-    name: ${{ matrix.build }} gcc${{ matrix.compiler }}
+    name: ${{ matrix.build }} ${{ matrix.compiler }}
     runs-on: ubuntu-22.04
     timeout-minutes: 300
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
@@ -54,9 +57,9 @@ jobs:
       - name: Configure tests
         run: |
           mkdir build && cd build
-          cmake ../seqan3/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=Release \
-                                                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
-                                                   -DSEQAN3_BENCHMARK_MIN_TIME=0.01
+          cmake ../test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=Release \
+                                            -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
+                                            -DSEQAN3_BENCHMARK_MIN_TIME=0.01
           case "${{ matrix.build }}" in
             unit) make gtest_main;;
             snippet) make gtest_main;;

diff --git a/test/performance/range/container_push_back_benchmark.cpp b/test/performance/range/container_push_back_benchmark.cpp
@@ -20,21 +20,21 @@ template <typename t>
 using sdsl_int_vec = sdsl::int_vector<sizeof(t) * 8>;
 
 template <typename t>
-using small_vec = seqan3::small_vector<t, 10'000>;
+using small_vec = seqan3::small_vector<t, 10000>;
 
 // ============================================================================
 //  push_back
 // ============================================================================
 
-template <template <typename, typename...> typename container_t, typename alphabet_t, typename... args>
+template <template <typename...> typename container_t, typename alphabet_t, typename... args>
 void push_back(benchmark::State & state)
 {
     alphabet_t letter{};
 
     for (auto _ : state)
     {
         container_t<alphabet_t, args...> container;
-        for (size_t i = 0; i < 10'000; ++i)
+        for (size_t i = 0; i < 10000; ++i)
             container.push_back(letter);
         benchmark::DoNotOptimize(letter = container.back());
     }
@@ -119,7 +119,7 @@ void push_back2(benchmark::State & state)
     for (auto _ : state)
     {
         container_t<alphabet_t, spec_t> container;
-        for (size_t i = 0; i < 10'000; ++i)
+        for (size_t i = 0; i < 10000; ++i)
             seqan2::appendValue(container, letter);
         benchmark::DoNotOptimize(letter = seqan2::back(container));
     }
@@ -159,11 +159,11 @@ BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Packed<>, seqan2::Iupac);
 BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Packed<>, seqan2::AminoAcid);
 // BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Packed<>, seqan2::Dna5Q); // broken in SeqAn2
 
-BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Array<10'000>, seqan2::Dna);
-BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Array<10'000>, seqan2::Dna5);
-BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Array<10'000>, seqan2::Iupac);
-BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Array<10'000>, seqan2::AminoAcid);
-BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Array<10'000>, seqan2::Dna5Q);
+BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Array<10000>, seqan2::Dna);
+BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Array<10000>, seqan2::Dna5);
+BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Array<10000>, seqan2::Iupac);
+BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Array<10000>, seqan2::AminoAcid);
+BENCHMARK_TEMPLATE(push_back2, seqan2::String, seqan2::Array<10000>, seqan2::Dna5Q);
 
 #endif // SEQAN3_HAS_SEQAN2
 

diff --git a/test/performance/range/container_seq_read_benchmark.cpp b/test/performance/range/container_seq_read_benchmark.cpp
@@ -21,21 +21,21 @@ template <typename t>
 using sdsl_int_vec = sdsl::int_vector<sizeof(t) * 8>;
 
 template <typename t>
-using small_vec = seqan3::small_vector<t, 10'000>;
+using small_vec = seqan3::small_vector<t, 10000>;
 
 // ============================================================================
 //  sequential_read
 // ============================================================================
 
-template <template <typename, typename...> typename container_t,
+template <template <typename...> typename container_t,
           typename alphabet_t,
           bool const_qualified = false,
           typename... args>
 void sequential_read(benchmark::State & state)
 {
     container_t<alphabet_t, args...> container = []()
     {
-        auto container = seqan3::test::generate_sequence<alphabet_t>(10'000, 0, 0);
+        auto container = seqan3::test::generate_sequence<alphabet_t>(10000, 0, 0);
         return container_t<alphabet_t, args...>(container.begin(), container.end());
     }();
 
@@ -178,7 +178,7 @@ template <template <typename...> typename container_t,
           bool const_qualified = false>
 void sequential_read2(benchmark::State & state)
 {
-    container_t<alphabet_t, spec_t> container{seqan3::test::generate_sequence_seqan2<alphabet_t>(10'000, 0, 0)};
+    container_t<alphabet_t, spec_t> container{seqan3::test::generate_sequence_seqan2<alphabet_t>(10000, 0, 0)};
 
     using container_reference_t =
         std::conditional_t<const_qualified, container_t<alphabet_t, spec_t> const &, container_t<alphabet_t, spec_t> &>;
@@ -213,11 +213,11 @@ BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::I
 BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::AminoAcid);
 // BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Packed<>, seqan2::Dna5Q); // broken in SeqAn2
 
-BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10'000>, seqan2::Dna);
-BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10'000>, seqan2::Dna5);
-BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10'000>, seqan2::Iupac);
-BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10'000>, seqan2::AminoAcid);
-BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10'000>, seqan2::Dna5Q);
+BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10000>, seqan2::Dna);
+BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10000>, seqan2::Dna5);
+BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10000>, seqan2::Iupac);
+BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10000>, seqan2::AminoAcid);
+BENCHMARK_TEMPLATE(sequential_read2, seqan2::String, seqan2::Array<10000>, seqan2::Dna5Q);
 
 // ============================================================================
 //  sequential_read (const)

diff --git a/test/performance/range/container_seq_write_benchmark.cpp b/test/performance/range/container_seq_write_benchmark.cpp
@@ -21,18 +21,18 @@ template <typename t>
 using sdsl_int_vec = sdsl::int_vector<sizeof(t) * 8>;
 
 template <typename t>
-using small_vec = seqan3::small_vector<t, 10'000>;
+using small_vec = seqan3::small_vector<t, 10000>;
 
 // ============================================================================
 //  sequential_write
 // ============================================================================
 
-template <template <typename, typename...> typename container_t, typename alphabet_t, typename... args>
+template <template <typename...> typename container_t, typename alphabet_t, typename... args>
 void sequential_write(benchmark::State & state)
 {
     container_t<alphabet_t, args...> container = []()
     {
-        auto container = seqan3::test::generate_sequence<alphabet_t>(10'000, 0, 0);
+        auto container = seqan3::test::generate_sequence<alphabet_t>(10000, 0, 0);
         return container_t<alphabet_t, args...>(container.begin(), container.end());
     }();
 
@@ -116,7 +116,7 @@ BENCHMARK_TEMPLATE(sequential_write, small_vec, seqan3::alphabet_variant<char, s
 template <template <typename...> typename container_t, typename spec_t, typename alphabet_t>
 void sequential_write2(benchmark::State & state)
 {
-    container_t<alphabet_t, spec_t> container{seqan3::test::generate_sequence_seqan2<alphabet_t>(10'000, 0, 0)};
+    container_t<alphabet_t, spec_t> container{seqan3::test::generate_sequence_seqan2<alphabet_t>(10000, 0, 0)};
 
     alphabet_t letter{};
     for (auto _ : state)
@@ -145,11 +145,11 @@ BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Packed<>, seqan2::
 BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Packed<>, seqan2::AminoAcid);
 // BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Packed<>, seqan2::Dna5Q); // broken in SeqAn2
 
-BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Array<10'000>, seqan2::Dna);
-BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Array<10'000>, seqan2::Dna5);
-BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Array<10'000>, seqan2::Iupac);
-BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Array<10'000>, seqan2::AminoAcid);
-BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Array<10'000>, seqan2::Dna5Q);
+BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Array<10000>, seqan2::Dna);
+BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Array<10000>, seqan2::Dna5);
+BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Array<10000>, seqan2::Iupac);
+BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Array<10000>, seqan2::AminoAcid);
+BENCHMARK_TEMPLATE(sequential_write2, seqan2::String, seqan2::Array<10000>, seqan2::Dna5Q);
 
 #endif // SEQAN3_HAS_SEQAN2