[fix] view madness in seqan2

.github/workflows/ci_linux.yml

@@ -21,6 +21,12 @@ jobs:
       fail-fast: false
       matrix:
         include:
+          - name: "gcc12"
+            install: "g++-12"
+            cxx: "g++-12"
+            cc: "gcc-12"
+            build_type: Release
+
           - name: "gcc11"
             install: "g++-11"
             cxx: "g++-11"
@@ -88,7 +94,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake ../lambda -DLAMBDA_COMPILE_THREADS=2 -DLAMBDA_NATIVE_BUILD=ON -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_C_COMPILER_LAUNCHER=ccache
+          cmake ../lambda -DLAMBDA_COMPILE_THREADS=2 -DLAMBDA_NATIVE_BUILD=OFF -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_C_COMPILER_LAUNCHER=ccache
 
       - name: Build tests
         if: matrix.name != 'clang_format'

.github/workflows/ci_macos.yml

@@ -22,9 +22,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - name: "gcc11"
-            cxx: "g++-11"
-            cc: "gcc-11"
+          - name: "gcc12"
+            cxx: "g++-12"
+            cc: "gcc-12"
             build_type: Release
 
           - name: "gcc10"
@@ -75,7 +75,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake ../lambda -DLAMBDA_COMPILE_THREADS=3 -DLAMBDA_NATIVE_BUILD=ON -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_C_COMPILER_LAUNCHER=ccache
+          cmake ../lambda -DLAMBDA_COMPILE_THREADS=3 -DLAMBDA_NATIVE_BUILD=OFF -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_C_COMPILER_LAUNCHER=ccache
 
       - name: Build tests
         env:

src/CMakeLists.txt

@@ -40,6 +40,8 @@ if (LAMBDA_NATIVE_BUILD)
     if (CMAKE_CXX_COMPILER_ID MATCHES "Intel")
         set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHOST -ipo -no-prec-div -fp-model fast=2")
     endif (CMAKE_CXX_COMPILER_ID MATCHES "Intel")
+else (LAMBDA_NATIVE_BUILD)
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mmmx -msse -msse2 -msse3 -mssse3 -msse4 -mpopcnt")
 endif (LAMBDA_NATIVE_BUILD)
 
 if (LAMBDA_STATIC_BUILD)

src/holder_tristate_overload.h

@@ -0,0 +1,224 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Andreas Gogol-Döring <[email protected]>
+// ==========================================================================
+// Tristate Holder Implementation.
+// ==========================================================================
+
+#pragma once
+
+#include <seqan/basic.h>
+
+using overload_t = std::ranges::take_view<std::ranges::drop_view<seqan3::detail::view_translate_single<std::ranges::ref_view<std::vector<seqan3::dna5>>>>>;
+
+template <typename t>
+concept overload_c = std::same_as<std::remove_cvref_t<t>, overload_t>;
+
+namespace seqan
+{
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+template <overload_c TValue>
+struct Holder<TValue, Tristate>
+{
+    enum EHolderState
+    {
+        EMPTY = 0,
+        OWNER = 1,
+        DEPENDENT = 2
+    };
+
+    typedef std::optional<TValue> THostValue;
+
+    // ------------------------------------------------------------------------
+    // Members
+    // ------------------------------------------------------------------------
+
+    THostValue data_value;
+    EHolderState data_state;
+
+    // ------------------------------------------------------------------------
+    // Constructors; Destructor
+    // ------------------------------------------------------------------------
+
+    Holder() : data_value{}, data_state(EMPTY)
+    {
+    }
+
+    Holder(Holder const & source_) : data_value{}, data_state(EMPTY)
+    {
+        data_value = source_;
+    }
+
+    explicit
+    Holder(THostValue & value_) : data_value{}, data_state(EMPTY)
+    {
+        data_value = value_;
+    }
+
+    explicit
+    Holder(THostValue const & value_) : data_value{}, data_state(EMPTY)
+    {
+        data_value = value_;
+    }
+
+    ~Holder()
+    {
+        clear(*this);
+    }
+
+    // ------------------------------------------------------------------------
+    // Assignment Operators;  Must be defined in class.
+    // ------------------------------------------------------------------------
+
+    Holder & operator=(Holder const &) = default;
+
+    Holder & operator=(THostValue const & value_)
+    {
+        data_value = value_;
+        return *this;
+    }
+
+    // ------------------------------------------------------------------------
+    // Conversion Operators;  Must be defined in class.
+    // ------------------------------------------------------------------------
+
+    inline operator THostValue()
+    {
+        return data_value;
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+/// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <overload_c TValue>
+inline void
+clear(Holder<TValue, Tristate> & me)
+{
+    me.data_value.reset();
+    me.data_state = Holder<TValue, Tristate>::EMPTY;
+}
+
+// ----------------------------------------------------------------------------
+// Function setValue()
+// ----------------------------------------------------------------------------
+
+template <overload_c TValue>
+inline void
+setValue(Holder<TValue, Tristate> & me,
+         TValue const & value_)
+{
+    me.data_value = value_;
+    me.data_state = Holder<TValue, Tristate>::OWNER;
+}
+
+template <overload_c TValue>
+inline void
+setValue(Holder<TValue const, Tristate> & me,
+         TValue const & value_)
+{
+    me.data_value = value_;
+    me.data_state = Holder<TValue const, Tristate>::OWNER;
+}
+
+// ----------------------------------------------------------------------------
+// Function value()
+// ----------------------------------------------------------------------------
+
+template <overload_c TValue>
+auto & value(Holder<TValue, Tristate> & me)
+{
+    SEQAN_ASSERT_NOT(empty(me)); // HERE BE DRAGONS!!!
+    return * me.data_value;
+}
+
+template <overload_c TValue>
+auto & value(Holder<TValue, Tristate> const & me)
+{
+    SEQAN_ASSERT_NOT(empty(me));
+
+    return * me.data_value;
+}
+
+// ----------------------------------------------------------------------------
+// Function assignValue()
+// ----------------------------------------------------------------------------
+
+template <overload_c TValue, typename TSource>
+inline void
+assignValue(Holder<TValue, Tristate> & me,
+            TSource const & value_)
+{
+    setValue(me, value_);
+}
+
+// ----------------------------------------------------------------------------
+// Function moveValue()
+// ----------------------------------------------------------------------------
+
+template <overload_c TValue, typename TSource>
+inline void
+moveValue(Holder<TValue, Tristate> & me,
+          TSource const & value_)
+{
+    setValue(me, value_);
+}
+
+// ----------------------------------------------------------------------------
+// Function assign()
+// ----------------------------------------------------------------------------
+
+template <overload_c TValue>
+inline void
+assign(Holder<TValue, Tristate> & target_,
+       Holder<TValue, Tristate> const & source_)
+{
+    target_ = source_;
+}
+
+template <overload_c TValue>
+inline void
+assign(Holder<TValue const, Tristate> & target_,
+       Holder<TValue const, Tristate> const & source_)
+{
+    target_ = source_;
+}
+
+}  // namespace seqan

src/seqan2seqan3.hpp

@@ -57,6 +57,7 @@ inline seqan3::gapped<alph_t> gapValueImpl(seqan3::gapped<alph_t> const *)
 #include <seqan/score.h>
 #include <seqan/sequence.h>
 
+#include "holder_tristate_overload.h"
 #include "bisulfite_scoring.hpp"
 
 namespace seqan
@@ -214,6 +215,25 @@ struct GetValue<Iter<TContainer const, StdIteratorAdaptor>>
     using Type = std::ranges::range_reference_t<TContainer const>;
 };
 
+template <overload_c TSequence>
+decltype(auto) source(Gaps<TSequence, ArrayGaps> const & gaps)
+{
+    return value(gaps._source);
+}
+
+template <overload_c TSequence>
+decltype(auto) source(Gaps<TSequence, ArrayGaps> & gaps)
+{
+    return value(gaps._source);
+}
+
+template <overload_c TSequence>
+inline void assignSource(Gaps<TSequence, ArrayGaps> & gaps, TSequence const & source)
+{
+    setValue(gaps._source, source);
+    _reinitArrayGaps(gaps);
+}
+
 // –---------------------------------------------------------------------------
 // range stuff
 // –---------------------------------------------------------------------------

test/cli/index_test.cpp

@@ -5,6 +5,18 @@
 
 struct index_test : public cli_test
 {
+    std::string md5_cmd;
+
+    void determine_md5_cmd()
+    {
+        if (std::system("echo foo | md5sum > /dev/null 2>&1") == 0)
+            md5_cmd = "md5sum";
+        else if (std::system("echo foo | md5 > /dev/null 2>&1") == 0)
+            md5_cmd = "md5";
+
+        ASSERT_FALSE(md5_cmd.empty());
+    }
+
     void run_index_test(std::string const & index_command,
                         std::string const & db_file,
                         std::string const & index_file,
@@ -18,10 +30,15 @@ struct index_test : public cli_test
                                              "--db-index-type", index_type,
                                              "-r", reduction);
 
-        EXPECT_EQ(result.exit_code, 0);
+        ASSERT_EQ(result.exit_code, 0);
+
+        if (md5_cmd.empty())
+            determine_md5_cmd();
 
-        std::system(("md5sum " + index_file + " > md5sum_test.txt").c_str());
-        std::system(("md5sum " + (std::string) data(control_file) + " > md5sum_control.txt").c_str());
+        int ret = std::system((md5_cmd + " " + index_file + " > md5sum_test.txt").c_str());
+        ASSERT_TRUE(ret == 0);
+        ret = std::system((md5_cmd + " " + (std::string) data(control_file) + " > md5sum_control.txt").c_str());
+        ASSERT_TRUE(ret == 0);
 
         std::ifstream test_output ("md5sum_test.txt");
         std::ifstream control_output ("md5sum_control.txt");