feat(fmt/cif): implement CIF 1.1 parser

.github/ubsanignore.txt

@@ -1,2 +1,5 @@
 implicit-signed-integer-truncation:ascii.cc
 implicit-signed-integer-truncation:raw_hash_set.h
+implicit-integer-sign-change:string_view
+implicit-integer-sign-change:predefined_ops.h
+implicit-integer-sign-change:cif.cpp

.github/workflows/_run-clang-tools.yaml

@@ -64,7 +64,7 @@ jobs:
           style: file
           tidy-checks: ""
           database: build
-          ignore: ".github|build|third-party|test"
+          ignore: ".github|build|third-party|test|fuzz"
         env:
           GITHUB_TOKEN: ${{ github.token }}
 

CMakeLists.txt

@@ -19,6 +19,7 @@ option(NURI_ENABLE_AVX2 "Use -mavx2 flag for optimization" OFF)
 option(NURI_ENABLE_ARCH_NATIVE "Use -march=native flag for optimization" OFF)
 
 option(NURI_ENABLE_SANITIZERS "Enable sanitizers for debug build" OFF)
+option(NURI_BUILD_FUZZING "Enable fuzzing build" OFF)
 option(NURI_PREBUILT_ABSL "Download prebuilt abseil binary" ON)
 
 option(NURI_TEST_COVERAGE "Enable coverage build" OFF)
@@ -89,6 +90,16 @@ elseif(NURI_ENABLE_IPO)
   set(CMAKE_INTERPROCEDURAL_OPTIMIZATION ON)
 endif()
 
+if(NURI_BUILD_FUZZING)
+  if(NOT CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+    message(FATAL_ERROR "Fuzzing build is only supported with Clang")
+  endif()
+
+  message("Fuzzing build: enabling sanitizers")
+  set(NURI_ENABLE_SANITIZERS ON)
+  add_compile_options(-fsanitize=fuzzer)
+endif()
+
 set_sanitizer_envs()
 
 if(NURI_ENABLE_SANITIZERS)
@@ -153,6 +164,7 @@ endif()
 
 include(CTest)
 add_subdirectory(test EXCLUDE_FROM_ALL)
+add_subdirectory(fuzz EXCLUDE_FROM_ALL)
 
 if(BUILD_TESTING AND NURI_POSTINSTALL_TEST)
   message(NOTICE "Running tests after post-installation step")

NOTICE.md

@@ -265,6 +265,11 @@ Spectra is under the MPLv2 license.
 ## pybind11
 
 - Project URL: <https://github.com/pybind/pybind11>
+- Files in this repository subject to the license:
+  - [include/nuri/meta.h](include/nuri/meta.h). The following functions are
+    imported from pybind11's implementation:
+    - `overload_cast`
+    - `overload_cast_impl`
 - Full license text:
 
   ```txt
@@ -570,3 +575,45 @@ Our implementation is based on the original TM-align software (version 20220412)
   ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
   DEALINGS IN THE SOFTWARE.
   ```
+
+## Misc
+
+### BioPython
+
+Some testcases were imported from BioPython.
+
+- Project URL: <https://github.com/biopython/biopython>
+- Full license text:
+
+  ```txt
+  BSD 3-Clause License
+  --------------------
+
+  Copyright (c) 1999-2024, The Biopython Contributors
+  All rights reserved.
+
+  Redistribution and use in source and binary forms, with or without
+  modification, are permitted provided that the following conditions are met:
+
+  1. Redistributions of source code must retain the above copyright notice,
+    this list of conditions and the following disclaimer.
+
+  2. 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.
+
+  3. Neither the name of the copyright holder 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 THE COPYRIGHT HOLDER OR CONTRIBUTORS 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.
+  ```

cmake-variants.json

@@ -37,6 +37,15 @@
         "settings": {
           "NURI_ENABLE_SANITIZERS": true
         }
+      },
+      "fuzzer": {
+        "buildType": "RelWithDebInfo",
+        "long": "Fuzzing build.",
+        "short": "Fuzz",
+        "settings": {
+          "NURI_ENABLE_SANITIZERS": true,
+          "NURI_BUILD_FUZZING": true
+        }
       }
     }
   }

cmake/NuriKitTest.cmake

@@ -18,26 +18,54 @@ if(NURI_ENABLE_SANITIZERS AND CMAKE_VERSION VERSION_GREATER_EQUAL 3.18)
   set(NURI_GTEST_EXTRA_ARGS DISCOVERY_MODE PRE_TEST)
 endif()
 
-function(nuri_add_test file)
+function(_nuri_generate_test_name root file)
   get_filename_component(test_dir ${file} DIRECTORY)
-  file(RELATIVE_PATH test_dir "${PROJECT_SOURCE_DIR}/test" "${test_dir}")
+  file(RELATIVE_PATH test_dir "${root}" "${test_dir}")
   string(REPLACE "/" "_" test_prefix ${test_dir})
 
   get_filename_component(test_name ${file} NAME_WE)
 
-  set(target "nuri_${test_prefix}_${test_name}")
-  add_executable("${target}" "${file}")
-  target_link_libraries("${target}" PRIVATE
+  set(NURI_TEST_TARGET "nuri_${test_prefix}_${test_name}" PARENT_SCOPE)
+endfunction()
+
+function(nuri_add_test file)
+  _nuri_generate_test_name("${PROJECT_SOURCE_DIR}/test" "${file}")
+
+  add_executable("${NURI_TEST_TARGET}" "${file}")
+  target_link_libraries("${NURI_TEST_TARGET}" PRIVATE
     GTest::gtest GTest::gmock GTest::gtest_main
     absl::absl_log absl::absl_check)
 
   if(TARGET nuri_lib)
-    target_link_libraries("${target}" PRIVATE nuri_lib)
+    target_link_libraries("${NURI_TEST_TARGET}" PRIVATE nuri_lib)
   endif()
 
-  gtest_discover_tests("${target}"
+  gtest_discover_tests("${NURI_TEST_TARGET}"
     WORKING_DIRECTORY "${PROJECT_SOURCE_DIR}"
     ${NURI_GTEST_EXTRA_ARGS})
 
-  add_dependencies(nuri_all_test "${target}")
+  add_dependencies(nuri_all_test "${NURI_TEST_TARGET}")
+endfunction()
+
+if(NOT TARGET nuri_all_fuzz)
+  add_custom_target(nuri_all_fuzz)
+  clear_coverage_data(nuri_all_fuzz)
+
+  if(NURI_BUILD_FUZZING AND BUILD_TESTING)
+    set_target_properties(nuri_all_fuzz PROPERTIES EXCLUDE_FROM_ALL OFF)
+  endif()
+endif()
+
+function(nuri_add_fuzz file)
+  _nuri_generate_test_name("${PROJECT_SOURCE_DIR}/fuzz" "${file}")
+
+  add_executable("${NURI_TEST_TARGET}" "${file}")
+  target_link_options("${NURI_TEST_TARGET}" PRIVATE -fsanitize=fuzzer)
+  target_link_libraries("${NURI_TEST_TARGET}" PRIVATE absl::log_initialize)
+
+  if(TARGET nuri_lib)
+    target_link_libraries("${NURI_TEST_TARGET}" PRIVATE nuri_lib)
+  endif()
+
+  add_dependencies(nuri_all_fuzz "${NURI_TEST_TARGET}")
 endfunction()

cmake/NuriKitUtils.cmake

@@ -268,11 +268,11 @@ function(handle_boost_dependency target)
   target_system_include_directories(
     "${target}"
     Boost::spirit Boost::fusion Boost::mpl Boost::optional
-    Boost::iterator Boost::config
+    Boost::iterator Boost::config Boost::range
   )
   target_link_libraries(
     "${target}"
-    PUBLIC Boost::iterator Boost::config
+    PUBLIC Boost::iterator Boost::config Boost::range
     PRIVATE Boost::spirit Boost::fusion Boost::mpl Boost::optional
   )
 endfunction()

fuzz/CMakeLists.txt

@@ -0,0 +1,15 @@
+#
+# Project NuriKit - Copyright 2024 SNU Compbio Lab.
+# SPDX-License-Identifier: Apache-2.0
+#
+
+include(NuriKitTest)
+
+add_compile_options(-Wno-error)
+
+include_directories("${CMAKE_CURRENT_LIST_DIR}/include")
+file(GLOB_RECURSE NURI_FUZZ_SRCS *.cpp)
+
+foreach(nuri_test_src IN LISTS NURI_FUZZ_SRCS)
+  nuri_add_fuzz("${nuri_test_src}")
+endforeach()

fuzz/fmt/cif_fuzz.cpp

@@ -0,0 +1,34 @@
+//
+// Project NuriKit - Copyright 2024 SNU Compbio Lab.
+// SPDX-License-Identifier: Apache-2.0
+//
+
+#include <sstream>
+
+#include <absl/base/call_once.h>
+#include <absl/base/log_severity.h>
+#include <absl/log/globals.h>
+#include <absl/log/initialize.h>
+
+#include "fuzz_utils.h"
+#include "nuri/fmt/cif.h"
+
+NURI_FUZZ_MAIN(data, size) {
+  static absl::once_flag flag;
+  absl::call_once(flag, []() {
+    absl::InitializeLog();
+    absl::SetStderrThreshold(absl::LogSeverity::kFatal);
+  });
+
+  std::istringstream iss(
+      std::string { reinterpret_cast<const char *>(data), size });
+  nuri::CifParser parser(iss);
+
+  while (true) {
+    auto block = parser.next();
+    if (!block)
+      break;
+  }
+
+  return 0;
+}

fuzz/include/fuzz_utils.h

@@ -0,0 +1,14 @@
+//
+// Project NuriKit - Copyright 2024 SNU Compbio Lab.
+// SPDX-License-Identifier: Apache-2.0
+//
+
+#ifndef NURI_FUZZ_FUZZ_UTILS_H_
+#define NURI_FUZZ_FUZZ_UTILS_H_
+
+#define NURI_FUZZ_MAIN(data, size)                                             \
+  extern "C" int LLVMFuzzerTestOneInput(const uint8_t *data, size_t size)
+
+NURI_FUZZ_MAIN(/* data */, /* size */);
+
+#endif /* NURI_FUZZ_FUZZ_UTILS_H_ */