seqan · eseiler · Jul 28, 2024 · Jul 28, 2024 · Jul 28, 2024 · Jul 28, 2024
diff --git a/.github/ISSUE_TEMPLATE/cron_comment_template.md b/.github/ISSUE_TEMPLATE/cron_comment_template.md
@@ -1,4 +1,4 @@
-Failure {{ build }} on gcc{{ compiler }}
+Failure {{ build }} on {{ compiler }}
 ---
 
 See {{ url }} for more information.
diff --git a/.github/workflows/cron_api.yml b/.github/workflows/cron_api.yml
@@ -18,76 +18,58 @@ concurrency:
 env:
   SEQAN3_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
-  ISSUE: 2746 # Issue number to use for reporting failures
+  ISSUE: 3280 # Issue number to use for reporting failures
 
 defaults:
   run:
-    shell: bash -Eexuo pipefail {0}
+    shell: bash -Eeuxo pipefail {0}
 
 jobs:
   build:
-    name: API-Stability gcc${{ matrix.compiler }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 300
+    name: API-Stability ${{ matrix.compiler }}
+    runs-on: ubuntu-latest
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
-        compiler: [11, 12, 13]
-
+        compiler: ["gcc-14", "gcc-13", "gcc-12", "gcc-11"]
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
-      - name: Checkout SeqAn3
+      - name: Checkout
         uses: actions/checkout@v4
         with:
-          path: seqan3
-          fetch-depth: 1
           submodules: true
 
       - name: Checkout SeqAn2
         uses: actions/checkout@v4
         with:
           repository: seqan/seqan
-          path: seqan3/submodules/seqan
-          fetch-depth: 1
-
-      - 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
+          path: submodules/seqan
 
       - name: Configure tests
         run: |
-          mkdir seqan3-build
-          cd seqan3-build
-          cmake ../seqan3/test/api_stability -DCMAKE_BUILD_TYPE=Release
+          mkdir build && cd build
+          cmake ../test/api_stability -DCMAKE_BUILD_TYPE=Release \
+                                      -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
 
       - name: Build tests
-        run: |
-          cd seqan3-build
-          CMAKE_BUILD_PARALLEL_LEVEL=2 cmake --build . -- -k 2>&1 | tee build.log
-
-      - name: Setup Python
-        if: ${{ failure() }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.x'
+        working-directory: build
+        run: make -k 2>&1 | tee build.log
 
       - name: Process Log
-        if: ${{ failure() }}
+        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: ${{ failure() }}
+        if: failure()
         id: comment-body
         run: |
-          FILE="seqan3/.github/ISSUE_TEMPLATE/cron_comment_template.md"
+          FILE=".github/ISSUE_TEMPLATE/cron_comment_template.md"
           URL="$GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
           sed -i "s@{{ build }}@${{ matrix.build }}@" $FILE
           sed -i "s@{{ compiler }}@${{ matrix.compiler }}@" $FILE
@@ -96,21 +78,31 @@ jobs:
           cat $FILE >> $GITHUB_OUTPUT
           echo "EOF" >> $GITHUB_OUTPUT
 
+      - name: Create comment body
+        if: success()
+        id: comment-body
+        run:  echo "body=Success ${{ matrix.build }} on ${{ matrix.compiler }}" >> $GITHUB_OUTPUT
+
       - name: Reopen issue
-        if: ${{ failure() }}
-        uses: octokit/[email protected]
-        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
+        uses: peter-evans/find-comment@v3
+        id: find_comment
+        with:
+          issue-number: ${{ env.ISSUE }}
+          body-includes: ${{ matrix.build }} on ${{ matrix.compiler }}
+
+      - name: Update comment
         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/scripts/process_compiler_error_log.py b/.github/workflows/scripts/process_compiler_error_log.py
@@ -11,8 +11,8 @@
 import re
 import sys
 
-# https://regex101.com/r/aE0qX3/1
-tokenise_regex = re.compile(r"(\[\s*\d+%\](?:.(?!\[\s*\d+%\]))+(?:error:).*?(?=\[\s*\d+%\]|$))", re.DOTALL)
+# https://regex101.com/r/aE0qX3/2
+tokenise_regex = re.compile(r"(\[\s*\d+%\](?:.(?!\[\s*\d+%\]))+(?:: error:).*?(?=\[\s*\d+%\]|$))", re.DOTALL)
 # Match line containg 'error:', but stop at linebreak, semicolon or parenthesis.
 error_regex = re.compile(r"(error:[^(;\n]*)")
 

diff --git a/test/api_stability/3.3.0/0001-FIX-take_until_view_test.patch b/test/api_stability/3.3.0/0001-FIX-take_until_view_test.patch
@@ -1,7 +1,7 @@
-From e89261cd4f2dfdffe982e8c95af1666acf9cfc47 Mon Sep 17 00:00:00 2001
+From e3f24c7888ab68746b9beb7619a1dd6661a73d71 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Thu, 28 Sep 2023 21:28:37 +0200
-Subject: [PATCH 1/2] [FIX] take_until_view_test
+Subject: [PATCH 1/4] [FIX] take_until_view_test
 
 mutable refers to the capture
 ---
@@ -27,5 +27,5 @@ index 970a3a1b1..8f34f7014 100644
          });
      do_concepts(adapt2, false);
 -- 
-2.42.0
+2.43.0
 
diff --git a/test/api_stability/3.3.0/0002-FIX-Change-constexpr-test.patch b/test/api_stability/3.3.0/0002-FIX-Change-constexpr-test.patch
@@ -1,7 +1,7 @@
-From e3eaa3f826fbab51db415d0dd6cbf8a93ecad153 Mon Sep 17 00:00:00 2001
+From cb9c300606e3a4c1860f3195b98f5245f09474e5 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Thu, 28 Sep 2023 19:35:57 +0200
-Subject: [PATCH 2/2] [FIX] Change constexpr test
+Subject: [PATCH 2/4] [FIX] Change constexpr test
 
 gcc11 complains suddenly
 ---
@@ -21,5 +21,5 @@ index 54bcb640c..460fab223 100644
 +    [[maybe_unused]] static constinit auto combined = adaptor1 | adaptor2;
  }
 -- 
-2.42.0
+2.43.0
 
diff --git a/test/api_stability/3.3.0/0003-API-hamming-scoring-scheme.patch b/test/api_stability/3.3.0/0003-API-hamming-scoring-scheme.patch
@@ -0,0 +1,81 @@
+From 9f061adb903403ee7e039f6480c87d7d1c577c14 Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <[email protected]>
+Date: Sun, 28 Jul 2024 15:17:28 +0200
+Subject: [PATCH 3/4] [API] hamming scoring scheme
+
+---
+ .../08_pairwise_alignment/pa_assignment_3_solution.cpp    | 6 ++++--
+ .../alignment/configuration/align_cfg_method_global.cpp   | 6 ++++--
+ .../alignment/configuration/minimal_alignment_config.err  | 2 +-
+ .../alignment/configuration/align_config_edit_test.cpp    | 8 ++++++--
+ 4 files changed, 15 insertions(+), 7 deletions(-)
+
+diff --git a/doc/tutorial/08_pairwise_alignment/pa_assignment_3_solution.cpp b/doc/tutorial/08_pairwise_alignment/pa_assignment_3_solution.cpp
+index d9790afca..b761ca884 100644
+--- a/doc/tutorial/08_pairwise_alignment/pa_assignment_3_solution.cpp
++++ b/doc/tutorial/08_pairwise_alignment/pa_assignment_3_solution.cpp
+@@ -28,8 +28,10 @@ int main()
+                                                    seqan3::align_cfg::free_end_gaps_sequence2_leading{true},
+                                                    seqan3::align_cfg::free_end_gaps_sequence1_trailing{false},
+                                                    seqan3::align_cfg::free_end_gaps_sequence2_trailing{true}}
+-                | seqan3::align_cfg::scoring_scheme{
+-                    seqan3::aminoacid_scoring_scheme{seqan3::aminoacid_similarity_matrix::blosum62}};
++                | seqan3::align_cfg::scoring_scheme{seqan3::aminoacid_scoring_scheme{
++                    seqan3::aminoacid_similarity_matrix::blosum62}}
++                | seqan3::align_cfg::gap_cost_affine{seqan3::align_cfg::open_score{-10},
++                                                     seqan3::align_cfg::extension_score{-1}};
+
+     for (auto const & res : seqan3::align_pairwise(source, config))
+         seqan3::debug_stream << "Score: " << res.score() << '\n';
+diff --git a/test/snippet/alignment/configuration/align_cfg_method_global.cpp b/test/snippet/alignment/configuration/align_cfg_method_global.cpp
+index 0e1f92757..46e74c3dd 100644
+--- a/test/snippet/alignment/configuration/align_cfg_method_global.cpp
++++ b/test/snippet/alignment/configuration/align_cfg_method_global.cpp
+@@ -11,8 +11,10 @@ int main()
+ {
+     // configure a global alignment for DNA sequences
+     auto min_cfg = seqan3::align_cfg::method_global{}
+-                 | seqan3::align_cfg::scoring_scheme{
+-                     seqan3::nucleotide_scoring_scheme{seqan3::match_score{4}, seqan3::mismatch_score{-5}}};
++                 | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
++                                                                                       seqan3::mismatch_score{-5}}}
++                 | seqan3::align_cfg::gap_cost_affine{seqan3::align_cfg::open_score{-10},
++                                                      seqan3::align_cfg::extension_score{-1}};
+
+     auto seq1 = "TCGT"_dna4;
+     auto seq2 = "ACGA"_dna4;
+diff --git a/test/snippet/alignment/configuration/minimal_alignment_config.err b/test/snippet/alignment/configuration/minimal_alignment_config.err
+index 7f8f011eb..f599e28b8 100644
+--- a/test/snippet/alignment/configuration/minimal_alignment_config.err
++++ b/test/snippet/alignment/configuration/minimal_alignment_config.err
+@@ -1 +1 @@
+-7
++10
+diff --git a/test/unit/alignment/configuration/align_config_edit_test.cpp b/test/unit/alignment/configuration/align_config_edit_test.cpp
+index 7ec211537..ee2e501a8 100644
+--- a/test/unit/alignment/configuration/align_config_edit_test.cpp
++++ b/test/unit/alignment/configuration/align_config_edit_test.cpp
+@@ -9,14 +9,18 @@
+
+ #include <seqan3/alignment/configuration/align_config_edit.hpp>
+ #include <seqan3/alignment/configuration/align_config_method.hpp>
++#include <seqan3/alphabet/concept.hpp>
++#include <seqan3/alphabet/nucleotide/dna15.hpp>
+
+ TEST(align_cfg_edit, is_hamming)
+ {
+     auto scheme = seqan3::get<seqan3::align_cfg::scoring_scheme>(seqan3::align_cfg::edit_scheme).scheme;
+
+-    for (unsigned i = 0; i < decltype(scheme)::matrix_size; ++i)
++    constexpr uint32_t dna15_size_v = seqan3::alphabet_size<seqan3::dna15>;
++
++    for (uint32_t i = 0; i < dna15_size_v; ++i)
+     {
+-        for (unsigned j = 0; j < decltype(scheme)::matrix_size; ++j)
++        for (uint32_t j = 0; j < dna15_size_v; ++j)
+         {
+             if (i == j)
+                 EXPECT_EQ((scheme.score(seqan3::assign_rank_to(i, seqan3::dna15{}),
+-- 
+2.43.0
+
diff --git a/test/api_stability/3.3.0/0003-API-hamming-scoring-scheme.patch.license b/test/api_stability/3.3.0/0003-API-hamming-scoring-scheme.patch.license
@@ -0,0 +1,3 @@
+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
diff --git a/test/api_stability/3.3.0/0004-FIX-Unsupported-SAM-header.patch b/test/api_stability/3.3.0/0004-FIX-Unsupported-SAM-header.patch
@@ -0,0 +1,43 @@
+From 72f044049983ad3f2e72ea4342f9573102088479 Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <[email protected]>
+Date: Sun, 28 Jul 2024 16:06:27 +0200
+Subject: [PATCH 4/4] [FIX] Unsupported SAM header
+
+---
+ test/unit/io/sam_file/format_sam_test.cpp | 20 ++++++++++----------
+ 1 file changed, 10 insertions(+), 10 deletions(-)
+
+diff --git a/test/unit/io/sam_file/format_sam_test.cpp b/test/unit/io/sam_file/format_sam_test.cpp
+index 66683ce3b..3cdba0078 100644
+--- a/test/unit/io/sam_file/format_sam_test.cpp
++++ b/test/unit/io/sam_file/format_sam_test.cpp
+@@ -174,16 +174,16 @@ TEST_F(sam_format, header_errors)
+             "@SQ\tSN:ref2\tLN:243199373\tSB:user_tag\tLB:user_tag\tpb:user_tag\n"
+             "@RG\tID:U0a_A2_L1\tIB:user_tag\tpb:user_tag\n"
+             "@PG\tID:qc\tIB:user_tag\tPB:user_tag\tCB:user_tag\tDB:user_tag\tVB:user_tag\tpb:user_tag\n"};
+-        std::string expected_cerr{"Unsupported SAM header tag in @HD: VB\n"
+-                                  "Unsupported SAM header tag in @HD: SB\n"
+-                                  "Unsupported SAM header tag in @HD: GB\n"
+-                                  "Unsupported SAM header tag in @HD: pb\n"
+-                                  "Unsupported SAM header tag in @PG: IB\n"
+-                                  "Unsupported SAM header tag in @PG: PB\n"
+-                                  "Unsupported SAM header tag in @PG: CB\n"
+-                                  "Unsupported SAM header tag in @PG: DB\n"
+-                                  "Unsupported SAM header tag in @PG: VB\n"
+-                                  "Unsupported SAM header tag in @PG: pb\n"};
++        std::string expected_cerr{"Unsupported tag found in SAM header @HD: \"VB:user_tag\"\n"
++                                  "Unsupported tag found in SAM header @HD: \"SB:user_tag\"\n"
++                                  "Unsupported tag found in SAM header @HD: \"GB:user_tag\"\n"
++                                  "Unsupported tag found in SAM header @HD: \"pb:user_tag\"\n"
++                                  "Unsupported tag found in SAM header @PG: \"IB:user_tag\"\n"
++                                  "Unsupported tag found in SAM header @PG: \"PB:user_tag\"\n"
++                                  "Unsupported tag found in SAM header @PG: \"CB:user_tag\"\n"
++                                  "Unsupported tag found in SAM header @PG: \"DB:user_tag\"\n"
++                                  "Unsupported tag found in SAM header @PG: \"VB:user_tag\"\n"
++                                  "Unsupported tag found in SAM header @PG: \"pb:user_tag\"\n"};
+         std::istringstream istream(header_str);
+         seqan3::sam_file_input fin{istream, seqan3::format_sam{}};
+
+-- 
+2.43.0
+
diff --git a/test/api_stability/3.3.0/0004-FIX-Unsupported-SAM-header.patch.license b/test/api_stability/3.3.0/0004-FIX-Unsupported-SAM-header.patch.license
@@ -0,0 +1,3 @@
+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
diff --git a/test/api_stability/CMakeLists.txt b/test/api_stability/CMakeLists.txt
@@ -37,13 +37,14 @@ macro (seqan3_api_stability_test test_suite git_apply)
         COMMAND ${CMAKE_COMMAND} -E remove_directory "<SOURCE_DIR>/build_system"
         COMMAND sh -c "${git_apply}"
         TEST_BEFORE_INSTALL TRUE
-        TEST_COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -j2
+        TEST_COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -j
         INSTALL_COMMAND "")
 endmacro ()
 
 if (EXISTS "${CMAKE_CURRENT_LIST_DIR}/${SEQAN3_LAST_STABLE_VERSION}")
     set (SEQAN3_GIT_APPLY
-         "${GIT_EXECUTABLE} apply --verbose ${CMAKE_CURRENT_LIST_DIR}/${SEQAN3_LAST_STABLE_VERSION}/*.patch")
+         "${GIT_EXECUTABLE} init . && ${GIT_EXECUTABLE} apply --verbose ${CMAKE_CURRENT_LIST_DIR}/${SEQAN3_LAST_STABLE_VERSION}/*.patch"
+    )
 else ()
     set (SEQAN3_GIT_APPLY "true")
     message (STATUS "No patches found in ${CMAKE_CURRENT_LIST_DIR}/${SEQAN3_LAST_STABLE_VERSION}.")