Merge branch 'master' into fix/bgzf_thread_count_variable

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,68 @@
+name: 🐞 Bug report
+description: Create a report to help us improve SeqAn3.
+labels: [bug]
+body:
+- type: checkboxes
+  attributes:
+    label: Does this problem persist on the current master?
+    description: Update to the latest master branch of SeqAn and see if the issue persists.
+    options:
+    - label: I have verified the issue on the current master
+      required: true
+- type: checkboxes
+  attributes:
+    label: Is there an existing issue for this?
+    description: Please search to see if an issue already exists for the bug you encountered.
+    options:
+    - label: I have searched the existing issues
+      required: true
+- type: textarea
+  attributes:
+    label: Current Behavior
+    description: A concise description of what you're experiencing.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Expected Behavior
+    description: A concise description of what you expected to happen.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Steps To Reproduce
+    description: Steps to reproduce the behavior.
+    placeholder: |
+      1. In this environment...
+      2. With this code...
+      3. Run '...'
+      4. See error...
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Environment
+    description: |
+      examples:
+        - **Operating system**: Ubuntu 20.04
+        - **SeqAn version**: 3.1.0 or 8a4f31cb7 (provide tag or commit as applicable)
+        - **Compiler**: gcc 11.2
+    value: |
+        - Operating system:
+        - SeqAn version:
+        - Compiler:
+    render: markdown
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Anything else?
+    description: |
+      Links? References? Anything that will give us more context about the issue you are encountering!
+
+      If you already know how to fix the issue, you can directly create a pull-request instead of an issue.
+      See the [contributor guide](https://docs.seqan.de/seqan/3-master-user/about_contributing.html) for more details.
+
+      Tip: You can attach images or log files by clicking this area to highlight it and then dragging files in.
+  validations:
+    required: false

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: true
+contact_links:
+  - name: Questions and Answers
+    url: https://github.com/seqan/seqan3/discussions
+    about: Ask us about installing and using SeqAn3 in our GitHub Discussions forum!
+  - name: Documentation
+    url: https://docs.seqan.de/
+    about: See our extensive documentation for usage examples and more!

.github/ISSUE_TEMPLATE/question.md

@@ -1,5 +1,5 @@
 ---
-name: Question
+name: Question (alternative to Discussions)
 about: Ask us about anything SeqAn-related that you would like to know.
 title: ''
 labels: 'question'

.github/workflows/README.md

@@ -6,6 +6,14 @@ Runs the [API-Stability](https://github.com/seqan/seqan3/blob/master/test/api_st
 
 In case of failure, creates an issue containing error logs.
 
+## avx2.yml
+
+Will run all test suites on all compiler with AVX2 enabled:
+  * Every Sunday on master
+  * Manually on any branch
+
+In case of failure, creates an issue containing error logs.
+
 ## cancel.yml
 
 Cancels ongoing and queued runs for a branch if a new push is made:

.github/workflows/avx2.yml

@@ -0,0 +1,127 @@
+name: SeqAn3 AVX2 CI
+
+on:
+  # Will always run on the default branch
+  schedule:
+    - cron: "0 6 * * SUN"
+  # Enables a manual trigger, may run on any branch
+  workflow_dispatch:
+
+concurrency:
+  group: avx2-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  CMAKE_VERSION: 3.10.3
+  SEQAN3_NO_VERSION_CHECK: 1
+  TZ: Europe/Berlin
+  ISSUE: 2905 # Issue number to use for reporting failures
+
+defaults:
+  run:
+    shell: bash -exo pipefail {0}
+
+jobs:
+  build:
+    name: ${{ matrix.build }} gcc${{ matrix.compiler }}
+    runs-on: ubuntu-20.04
+    timeout-minutes: 300
+    strategy:
+      fail-fast: false
+      matrix:
+        compiler: [9, 10, 11]
+        build: [unit, snippet, performance, header]
+
+    steps:
+      - name: Checkout SeqAn3
+        uses: actions/checkout@v2
+        with:
+          path: seqan3
+          submodules: true
+
+      - name: Checkout SeqAn2
+        uses: actions/checkout@v2
+        with:
+          repository: seqan/seqan
+          ref: develop
+          path: seqan3/submodules/seqan
+
+      - name: Configure APT
+        continue-on-error: true
+        run: bash ./seqan3/.github/workflows/scripts/configure_apt.sh
+
+      - name: Install CMake
+        run: bash ./seqan3/.github/workflows/scripts/install_cmake.sh
+
+      - name: Install compiler g++-${{ matrix.compiler }}
+        run: sudo apt-get install --yes g++-${{ matrix.compiler }}
+
+      - name: Configure tests
+        env:
+          CXX: g++-${{ matrix.compiler }}
+          CC: gcc-${{ matrix.compiler }}
+        run: |
+          mkdir seqan3-build
+          cd seqan3-build
+          cmake ../seqan3/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=Release \
+                                                   -DSEQAN3_VERBOSE_TESTS=OFF \
+                                                   -DSEQAN3_BENCHMARK_MIN_TIME=0.01 \
+                                                   -DCMAKE_CXX_FLAGS="-mavx2"
+          case "${{ matrix.build }}" in
+            unit) make -j2 gtest_build;;
+            snippet) make -j2 gtest_build;;
+            performance) make -j2 gbenchmark_build;;
+            header) make -j2 gtest_build gbenchmark_build;;
+          esac
+
+      - name: Build tests
+        run: |
+          cd seqan3-build
+          make -k -j2 2>&1 | tee build.log
+
+      - name: Setup Python
+        if: ${{ failure() }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      - 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
+
+      - 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@" $FILE
+          body=$(cat $FILE)
+          body="${body//'%'/'%25'}"
+          body="${body//$'\n'/'%0A'}"
+          body="${body//$'\r'/'%0D'}"
+          echo ::set-output name=body::$body
+
+      - 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"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Create comment
+        if: ${{ failure() }}
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          issue-number: ${{ env.ISSUE }}
+          body: ${{ steps.comment-body.outputs.body }}
+

include/seqan3/alignment/pairwise/edit_distance_algorithm.hpp

@@ -82,8 +82,6 @@ class edit_distance_algorithm
      * \param[in] callback The callback function to be invoked with the alignment result; must model
      *                     std::invocable with the respective seqan3::alignment_result type.
      *
-     * \returns A std::vector over seqan3::alignment_result.
-     *
      * \details
      *
      * Computes for each contained sequence pair the respective alignment and invokes the given callback for each

include/seqan3/alignment/pairwise/policy/affine_gap_policy.hpp

@@ -171,7 +171,6 @@ class affine_gap_policy
     /*!\brief Initialise the alignment state for affine gap computation.
      * \tparam alignment_configuration_t The type of alignment configuration.
      * \param[in] config The alignment configuration.
-     * \returns The initialised seqan3::detail::alignment_algorithm_state.
      *
      * \details
      *

include/seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp

@@ -149,7 +149,6 @@ class simd_affine_gap_policy
     /*!\brief Initialise the alignment state for affine gap computation.
      * \tparam alignment_configuration_t The type of alignment configuration.
      * \param[in] config The alignment configuration.
-     * \returns The initialised seqan3::detail::alignment_algorithm_state.
      *
      * \details
      *

include/seqan3/alphabet/aminoacid/aminoacid_base.hpp

@@ -81,7 +81,7 @@ class aminoacid_base : public alphabet_base<derived_type, size, char>, public am
                       detail::writable_constexpr_alphabet<other_aa_type>)
         {
             static_cast<derived_type &>(*this) =
-                detail::convert_through_char_representation<derived_type, other_aa_type>[seqan3::to_rank(other)];
+                detail::convert_through_char_representation<other_aa_type, derived_type>[seqan3::to_rank(other)];
         }
         else
         {

include/seqan3/alphabet/container/bitpacked_sequence.hpp

@@ -730,7 +730,6 @@ class bitpacked_sequence
      * \{
      */
     /*!\brief Removes all elements from the container.
-     * \returns The number of elements in the container.
      *
      * ### Complexity
      *

include/seqan3/alphabet/container/concatenated_sequences.hpp

@@ -1001,7 +1001,6 @@ class concatenated_sequences
      * \{
      */
     /*!\brief Removes all elements from the container.
-     * \returns The number of elements in the container.
      *
      * ### Complexity
      *

include/seqan3/alphabet/detail/convert.hpp

@@ -27,11 +27,11 @@ namespace seqan3::detail
 
 /*!\brief A precomputed conversion table for two alphabets based on their char representations.
  * \ingroup alphabet
- * \tparam out_t The type of the output, must satisfy seqan3::alphabet.
  * \tparam in_t The type of the input, must satisfy seqan3::alphabet.
+ * \tparam out_t The type of the output, must satisfy seqan3::alphabet.
  * \hideinitializer
  */
-template <alphabet out_t, alphabet in_t>
+template <alphabet in_t, alphabet out_t>
 constexpr std::array<out_t, alphabet_size<in_t>> convert_through_char_representation
 {
     [] () constexpr

include/seqan3/alphabet/nucleotide/nucleotide_base.hpp

@@ -86,7 +86,7 @@ class nucleotide_base : public alphabet_base<derived_type, size, char>
     explicit constexpr nucleotide_base(other_nucl_type const & other) noexcept
     {
         static_cast<derived_type &>(*this) =
-            detail::convert_through_char_representation<derived_type, other_nucl_type>[seqan3::to_rank(other)];
+            detail::convert_through_char_representation<other_nucl_type, derived_type>[seqan3::to_rank(other)];
     }
     //!\}
 

include/seqan3/argument_parser/validators.hpp

@@ -408,7 +408,6 @@ class file_validator_base
 
     /*!\brief Checks if the given path is readable.
      * \param path The path to check.
-     * \returns `true` if readable, otherwise `false`.
      * \throws seqan3::validation_error if the path is not readable, or
      *         std::filesystem::filesystem_error on underlying OS API errors.
      */
@@ -436,7 +435,6 @@ class file_validator_base
 
     /*!\brief Checks if the given path is writable.
      * \param path The path to check.
-     * \returns `true` if writable, otherwise `false`.
      * \throws seqan3::validation_error if the file could not be opened for writing, or
      *         std::filesystem::filesystem_error on underlying OS API errors.
      */

include/seqan3/contrib/stream/bgzf_stream_util.hpp

@@ -35,10 +35,9 @@
 namespace seqan3::contrib
 {
 
-/*!\brief A global variable indicating the number of threads to use for the bgzf-streams.
- *       Defaults to std::thread::hardware_concurrency.
+/*!\brief A static variable indicating the number of threads to use for the bgzf-streams. Defaults to 4.
  */
-inline uint64_t bgzf_thread_count = std::thread::hardware_concurrency();
+[[maybe_unused]] inline uint64_t bgzf_thread_count = 4;
 
 // ============================================================================
 // Forwards

include/seqan3/io/sam_file/format_bam.hpp

@@ -457,7 +457,7 @@ inline void format_bam::read_alignment_record(stream_type & stream,
                 {
                     assert(core.l_seq == (seq_length + offset_tmp + soft_clipping_end)); // sanity check
                     using alph_t = std::ranges::range_value_t<decltype(get<1>(align))>;
-                    constexpr auto from_dna16 = detail::convert_through_char_representation<alph_t, dna16sam>;
+                    constexpr auto from_dna16 = detail::convert_through_char_representation<dna16sam, alph_t>;
 
                     get<1>(align).reserve(seq_length);
 
@@ -501,7 +501,7 @@ inline void format_bam::read_alignment_record(stream_type & stream,
         else
         {
             using alph_t = std::ranges::range_value_t<decltype(seq)>;
-            constexpr auto from_dna16 = detail::convert_through_char_representation<alph_t, dna16sam>;
+            constexpr auto from_dna16 = detail::convert_through_char_representation<dna16sam, alph_t>;
 
             for (auto [d1, d2] : seq_stream)
             {
@@ -891,7 +891,7 @@ inline void format_bam::write_alignment_record([[maybe_unused]] stream_type &  s
 
         // write seq (bit-compressed: dna16sam characters go into one byte)
         using alph_t = std::ranges::range_value_t<seq_type>;
-        constexpr auto to_dna16 = detail::convert_through_char_representation<dna16sam, alph_t>;
+        constexpr auto to_dna16 = detail::convert_through_char_representation<alph_t, dna16sam>;
 
         auto sit = std::ranges::begin(seq);
         for (int32_t sidx = 0; sidx < ((core.l_seq & 1) ? core.l_seq - 1 : core.l_seq); ++sidx, ++sit)