Merge pull request #89 from eseiler/infra/tag_deps

[INFRA] pin dependencies
xxsds · Oct 28, 2021 · cf9ff4a · cf9ff4a
2 parents 47250ca + d999596
commit cf9ff4a
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Showing 16 changed files with 92 additions and 40 deletions.
diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
@@ -48,8 +48,8 @@ jobs:
             build_threads: 2
             test_threads: 2
             cxx_flags: "-std=c++20 -fsanitize=address"
-            ctest_exclude: "faust|moby"
-            ctest_include: "-im"
+            ctest_exclude: "-E 'faust|moby'"
+            ctest_include: "-R '-im'"
 
           - name: "cereal gcc11"
             cxx: "g++-11"
@@ -107,8 +107,8 @@ jobs:
             build_threads: 2
             test_threads: 2
             cxx_flags: "-std=c++20 -fsanitize=address"
-            ctest_exclude: "faust|moby"
-            ctest_include: "-im"
+            ctest_exclude: "-E 'faust|moby'"
+            ctest_include: "-R '-im'"
 
           - name: "cereal clang12"
             cxx: "clang++-12"
@@ -118,6 +118,7 @@ jobs:
             test_threads: 2
             cxx_flags: "-std=c++20"
             has_cereal: "1"
+            ctest_exclude: "-E 'k2-treap-test_k2-0.1.0.0'"
 
           - name: "clang11"
             cxx: "clang++-11"
@@ -196,7 +197,12 @@ jobs:
         run: |
           mkdir sdsl-build
           cd sdsl-build
-          cmake ../sdsl -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_FLAGS="-pedantic -Wall -Wextra -Werror ${{ matrix.cxx_flags }}" -DSDSL_CEREAL=${{ matrix.has_cereal }} -DSDSL_HEADER_TEST=${{ matrix.header_test }}
+          cmake ../sdsl -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                        -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \
+                        -DCMAKE_C_COMPILER_LAUNCHER=ccache \
+                        -DCMAKE_CXX_FLAGS="-pedantic -Wall -Wextra -Werror ${{ matrix.cxx_flags }}" \
+                        -DSDSL_CEREAL=${{ matrix.has_cereal }} \
+                        -DSDSL_HEADER_TEST=${{ matrix.header_test }}
           make -j${{ matrix.build_threads }} gtest_build
 
       - name: Build tests
@@ -220,4 +226,9 @@ jobs:
       - name: Run tests
         run: |
           cd sdsl-build
-          ctest . -j${{ matrix.test_threads }} --output-on-failure -E "${{ matrix.ctest_exclude }}" -R "${{ matrix.ctest_include }}"
+          ctest . -j${{ matrix.test_threads }} \
+                  ${{ matrix.ctest_exclude }} \
+                  ${{ matrix.ctest_include }} \
+            || ctest . -j${{ matrix.test_threads }} \
+                       --output-on-failure \
+                       --rerun-failed
diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml
@@ -39,8 +39,8 @@ jobs:
             build_threads: 3
             test_threads: 3
             cxx_flags: "-std=c++20 -fsanitize=address"
-            ctest_exclude: "faust|moby"
-            ctest_include: "-im"
+            ctest_exclude: "-E 'faust|moby'"
+            ctest_include: "-R '-im'"
 
           - name: "cereal clang12"
             cxx: "clang++-12"
@@ -79,7 +79,7 @@ jobs:
         uses: actions/checkout@v2
         with:
           repository: seqan/seqan3
-          ref: 79d2ba35359f7efd795853262280630a0aa9fd7e
+          ref: 141677c2ca0d24771d53bf2c6bc784c1e10eff90
           path: seqan3
           fetch-depth: 2
           submodules: false
@@ -95,12 +95,8 @@ jobs:
 
       - name: Install compiler ${{ matrix.cxx }}
         env:
-          CXX: ${{ matrix.cxx }}
-        run: |
-          bash ./seqan3/.github/workflows/scripts/install_via_brew.sh llvm ${CXX/clang++-/}
-          install_prefix=$(brew --prefix llvm@${CXX/clang++-/})/bin
-          ln -s ${install_prefix}/clang++ ${install_prefix}/"${{ matrix.cxx }}" || true
-          echo "${install_prefix}/" >> $GITHUB_PATH
+          CC: ${{ matrix.cc }}
+        run: bash ./seqan3/.github/workflows/scripts/install_via_brew.sh $(echo ${CC/clang/llvm} | awk -F '-' '{print $1, $2}')
 
       - name: Load ccache
         uses: actions/cache@v2
@@ -125,7 +121,12 @@ jobs:
         run: |
           mkdir sdsl-build
           cd sdsl-build
-          cmake ../sdsl -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_FLAGS="-pedantic -Wall -Wextra -Werror ${{ matrix.cxx_flags }}" -DSDSL_CEREAL=${{ matrix.has_cereal }} -DSDSL_HEADER_TEST=${{ matrix.header_test }}
+          cmake ../sdsl -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                        -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \
+                        -DCMAKE_C_COMPILER_LAUNCHER=ccache \
+                        -DCMAKE_CXX_FLAGS="-pedantic -Wall -Wextra -Werror ${{ matrix.cxx_flags }}" \
+                        -DSDSL_CEREAL=${{ matrix.has_cereal }} \
+                        -DSDSL_HEADER_TEST=${{ matrix.header_test }}
           make -j${{ matrix.build_threads }} gtest_build
 
       - name: Build tests
@@ -149,4 +150,9 @@ jobs:
       - name: Run tests
         run: |
           cd sdsl-build
-          ctest . -j${{ matrix.test_threads }} --output-on-failure -E "${{ matrix.ctest_exclude }}" -R "${{ matrix.ctest_include }}"
+          ctest . -j${{ matrix.test_threads }} \
+                  ${{ matrix.ctest_exclude }} \
+                  ${{ matrix.ctest_include }} \
+            || ctest . -j${{ matrix.test_threads }} \
+                       --output-on-failure \
+                       --rerun-failed
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -22,12 +22,12 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Run clang-format
-        uses: DoozyX/clang-format-lint-action@v0.11
+        uses: DoozyX/clang-format-lint-action@v0.13
         with:
           source: '.'
           exclude: './external'
           extensions: 'h,hpp,hpp.cmake,cpp'
-          clangFormatVersion: 11
+          clangFormatVersion: 12
           inplace: True
       - name: Create Pull Request
         uses: peter-evans/create-pull-request@v3

diff --git a/README.md b/README.md
@@ -1 +1,33 @@
-Development repository for SDSL Version 3
+# SDSL v3 - Succinct Data Structure Library
+
+[![linux status][1]][2]
+[![macos status][3]][4]
+
+[1]: https://img.shields.io/github/workflow/status/xxsds/sdsl-lite/SDSL%20CI%20on%20Linux/master?style=flat&logo=github&label=Linux%20CI "Open GitHub actions page"
+[2]: https://github.com/xxsds/sdsl-lite/actions?query=branch%3Amaster
+[3]: https://img.shields.io/github/workflow/status/xxsds/sdsl-lite/SDSL%20CI%20on%20macOS/master?style=flat&logo=github&label=macOS%20CI "Open GitHub actions page"
+[4]: https://github.com/xxsds/sdsl-lite/actions?query=branch%3Amaster
+
+## Main differences to [v2](https://github.com/simongog/sdsl-lite)
+
+* header-only library
+* support for serialisation via [cereal](https://github.com/USCiLab/cereal)
+* compatible with C++17 and C++20
+
+## Supported compilers
+
+Other compiler may work, but are not tested within the continuous integration. In general, the latest minor release of each
+listed major compiler version is supported.
+
+* GCC 8, 9, 10, 11
+* clang 9, 10, 11, 12
+
+## Dependencies
+
+As SDSL v3 is header-only, dependencies marked as `required` only apply to building tests/examples.
+
+* required: [CMake >= 3.2](https://github.com/Kitware/CMake)
+* required: [googletest 1.11.0](https://github.com/google/googletest/releases/tag/release-1.11.0)
+* optional: [cereal 1.3.0](https://github.com/USCiLab/cereal)
+
+cereal can be activated by passing `-DSDSL_CEREAL=1` to CMake.
diff --git a/external/CMakeLists.txt b/external/CMakeLists.txt
@@ -8,10 +8,13 @@ endif()
 macro (add_gtest)
 	set (SDSL_EXTERNAL_PROJECT_CMAKE_ARGS "")
 	list (APPEND SDSL_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}")
+	list (APPEND SDSL_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}")
 	list (APPEND SDSL_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_CXX_COMPILER_LAUNCHER=${CMAKE_CXX_COMPILER_LAUNCHER}")
+	list (APPEND SDSL_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_C_COMPILER_LAUNCHER=${CMAKE_C_COMPILER_LAUNCHER}")
 	list (APPEND SDSL_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}")
 	list (APPEND SDSL_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR}")
 	list (APPEND SDSL_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_VERBOSE_MAKEFILE=${CMAKE_VERBOSE_MAKEFILE}")
+	list (APPEND SDSL_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_POLICY_DEFAULT_CMP0025=NEW")
 
 	set (gtest_project_args ${SDSL_EXTERNAL_PROJECT_CMAKE_ARGS})
 	list (APPEND gtest_project_args "-DBUILD_GMOCK=0")

diff --git a/external/cereal b/external/cereal
diff --git a/external/googletest b/external/googletest
diff --git a/test/bit_vector_test.cpp b/test/bit_vector_test.cpp
@@ -228,13 +228,13 @@ void do_serialisation(TypeParam const & l)
         oarchive(l);
     }
 
+    TypeParam in_l{};
     {
-        TypeParam in_l{};
         std::ifstream is{ temp_file, std::ios::binary };
         in_archive_t iarchive{ is };
         iarchive(in_l);
-        EXPECT_EQ(l, in_l);
     }
+    EXPECT_EQ(l, in_l);
 }
 
 TYPED_TEST(bit_vector_test, cereal)

diff --git a/test/csa_byte_test.cpp b/test/csa_byte_test.cpp
@@ -297,13 +297,13 @@ void do_serialisation(TypeParam const & l)
         oarchive(l);
     }
 
+    TypeParam in_l{};
     {
-        TypeParam in_l{};
         std::ifstream is{ temp_file, std::ios::binary };
         in_archive_t iarchive{ is };
         iarchive(in_l);
-        EXPECT_EQ(l, in_l);
     }
+    EXPECT_EQ(l, in_l);
 }
 
 TYPED_TEST(csa_byte_test, cereal)

diff --git a/test/csa_int_test.cpp b/test/csa_int_test.cpp
@@ -223,13 +223,13 @@ void do_serialisation(TypeParam const & l)
         oarchive(l);
     }
 
+    TypeParam in_l{};
     {
-        TypeParam in_l{};
         std::ifstream is{ temp_file, std::ios::binary };
         in_archive_t iarchive{ is };
         iarchive(in_l);
-        EXPECT_EQ(l, in_l);
     }
+    EXPECT_EQ(l, in_l);
 }
 
 TYPED_TEST(csa_int_test, cereal)

diff --git a/test/cst_byte_test.cpp b/test/cst_byte_test.cpp
@@ -500,13 +500,13 @@ void do_serialisation(TypeParam const & l)
         oarchive(l);
     }
 
+    TypeParam in_l{};
     {
-        TypeParam in_l{};
         std::ifstream is{ temp_file, std::ios::binary };
         in_archive_t iarchive{ is };
         iarchive(in_l);
-        EXPECT_EQ(l, in_l);
     }
+    EXPECT_EQ(l, in_l);
 }
 
 TYPED_TEST(cst_byte_test, cereal)

diff --git a/test/cst_int_test.cpp b/test/cst_int_test.cpp
@@ -483,13 +483,13 @@ void do_serialisation(TypeParam const & l)
         oarchive(l);
     }
 
+    TypeParam in_l{};
     {
-        TypeParam in_l{};
         std::ifstream is{ temp_file, std::ios::binary };
         in_archive_t iarchive{ is };
         iarchive(in_l);
-        EXPECT_EQ(l, in_l);
     }
+    EXPECT_EQ(l, in_l);
 }
 
 TYPED_TEST(cst_int_test, cereal)

diff --git a/test/k2_treap_test.cpp b/test/k2_treap_test.cpp
@@ -254,13 +254,13 @@ void do_serialisation(TypeParam const & l)
         oarchive(l);
     }
 
+    TypeParam in_l{};
     {
-        TypeParam in_l{};
         std::ifstream is{ temp_file, std::ios::binary };
         in_archive_t iarchive{ is };
         iarchive(in_l);
-        EXPECT_EQ(l, in_l);
     }
+    EXPECT_EQ(l, in_l);
 }
 
 TYPED_TEST(k2_treap_test, cereal)

diff --git a/test/rmq_test.cpp b/test/rmq_test.cpp
@@ -149,13 +149,13 @@ void do_serialisation(TypeParam const & l)
         oarchive(l);
     }
 
+    TypeParam in_l{};
     {
-        TypeParam in_l{};
         std::ifstream is{ temp_file, std::ios::binary };
         in_archive_t iarchive{ is };
         iarchive(in_l);
-        EXPECT_EQ(l, in_l);
     }
+    EXPECT_EQ(l, in_l);
 }
 
 TYPED_TEST(rmq_test, cereal)

diff --git a/test/wt_byte_test.cpp b/test/wt_byte_test.cpp
@@ -563,13 +563,13 @@ void do_serialisation(TypeParam const & l)
         oarchive(l);
     }
 
+    TypeParam in_l{};
     {
-        TypeParam in_l{};
         std::ifstream is{ temp_file, std::ios::binary };
         in_archive_t iarchive{ is };
         iarchive(in_l);
-        EXPECT_EQ(l, in_l);
     }
+    EXPECT_EQ(l, in_l);
 }
 
 TYPED_TEST(wt_byte_test, cereal)

diff --git a/test/wt_int_test.cpp b/test/wt_int_test.cpp
@@ -842,13 +842,13 @@ void do_serialisation(TypeParam const & l)
         oarchive(l);
     }
 
+    TypeParam in_l{};
     {
-        TypeParam in_l{};
         std::ifstream is{ temp_file, std::ios::binary };
         in_archive_t iarchive{ is };
         iarchive(in_l);
-        EXPECT_EQ(l, in_l);
     }
+    EXPECT_EQ(l, in_l);
 }
 
 TYPED_TEST(wt_int_test, cereal)