minimap2 0.2.25.1 → 0.2.26.0

data/ext/minimap2/lib/simde/test/arm/test-arm-internal.h

@@ -1,18 +0,0 @@
-#if !defined(SIMDE_TESTS_ARM_INTERNAL_H)
-#define SIMDE_TESTS_CURRENT_ARCH arm
-
-#include "../run-tests.h"
-
-HEDLEY_BEGIN_C_DECLS
-
-#define SIMDE_TESTS_ARM_GENERATE_SUITE_GETTERS(isax) \
-  MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, native, c)(void); \
-  MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, native, cpp)(void); \
-  MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, emul,   c)(void); \
-  MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, emul,   cpp)(void)
-
-SIMDE_TESTS_ARM_GENERATE_SUITE_GETTERS(neon);
-
-HEDLEY_END_C_DECLS
-
-#endif /* !defined(SIMDE_TESTS_ARM_INTERNAL_H) */

data/ext/minimap2/lib/simde/test/arm/test-arm.c

@@ -1,20 +0,0 @@
-#include "test-arm.h"
-#include "test-arm-internal.h"
-#include "neon/test-neon.h"
-
-#include <stdio.h>
-
-MunitSuite*
-simde_tests_arm_get_suite(void) {
-  static MunitSuite children[] = {
-    { NULL, NULL, NULL, 1, MUNIT_SUITE_OPTION_NONE },
-    { NULL, NULL, NULL, 1, MUNIT_SUITE_OPTION_NONE }
-  };
-  static MunitSuite suite = { HEDLEY_STATIC_CAST(char*, "/arm"), NULL, NULL, 1, MUNIT_SUITE_OPTION_NONE };
-
-  children[0] = *simde_tests_arm_neon_get_suite();
-
-  suite.suites = children;
-
-  return &suite;
-}

data/ext/minimap2/lib/simde/test/arm/test-arm.h

@@ -1,8 +0,0 @@
-#include "../../simde/hedley.h"
-#include "../munit/munit.h"
-
-HEDLEY_BEGIN_C_DECLS
-
-MunitSuite* simde_tests_arm_get_suite(void);
-
-HEDLEY_END_C_DECLS

data/ext/minimap2/lib/simde/test/cmake/AddCompilerFlags.cmake

@@ -1,171 +0,0 @@
-# This module provides a convenient way to add C/C++ compiler flags if
-# the compiler supports them.
-
-include (CheckCCompilerFlag)
-include (CheckCXXCompilerFlag)
-
-cmake_policy(SET CMP0054 NEW)
-
-# Depending on the settings, some compilers will accept unknown flags.
-# We try to disable this behavior by also passing these flags when we
-# check if a flag is supported.
-set (ADD_COMPILER_FLAGS_PREPEND "")
-
-if (CMAKE_C_COMPILER_ID STREQUAL "GNU")
-  set (ADD_COMPILER_FLAGS_PREPEND "-Wall -Wextra -Werror")
-elseif (CMAKE_C_COMPILER_ID STREQUAL "Clang")
-  set (ADD_COMPILER_FLAGS_PREPEND "-Werror=unknown-warning-option")
-endif ()
-
-##
-# Set a variable to different flags, depending on which compiler is in
-# use.
-#
-# Example:
-#   set_compiler_specific_flags(VARIABLE varname MSVC /wd666 INTEL /wd1729)
-#
-#   This will set varname to /wd666 if the compiler is MSVC, and /wd1729
-#   if it is Intel.
-#
-# Possible compilers:
-#  - GCC: GNU C Compiler
-#  - GCCISH: A compiler that (tries to) be GCC-compatible on the CLI
-#    (i.e., anything but MSVC).
-#  - CLANG: clang
-#  - MSVC: Microsoft Visual C++ compiler
-#  - INTEL: Intel C Compiler
-#  - PGI: PGI C Compiler
-#
-# Note: the compiler is determined based on the value of the
-# CMAKE_C_COMPILER_ID variable, not CMAKE_CXX_COMPILER_ID.
-##
-function (set_compiler_specific_flags)
-  set (oneValueArgs VARIABLE)
-  set (multiValueArgs GCC GCCISH INTEL CLANG MSVC PGI)
-  cmake_parse_arguments(COMPILER_SPECIFIC_FLAGS "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-  unset (options)
-  unset (oneValueArgs)
-  unset (multiValueArgs)
-
-  set (compiler_flags)
-
-  if (CMAKE_C_COMPILER_ID STREQUAL "GNU")
-    list (APPEND compiler_flags ${COMPILER_SPECIFIC_FLAGS_GCC})
-  elseif(CMAKE_C_COMPILER_ID STREQUAL "Clang")
-    list (APPEND compiler_flags ${COMPILER_SPECIFIC_FLAGS_CLANG})
-  elseif(CMAKE_C_COMPILER_ID STREQUAL "Intel")
-    list (APPEND compiler_flags ${COMPILER_SPECIFIC_FLAGS_INTEL})
-  elseif(CMAKE_C_COMPILER_ID STREQUAL "MSVC")
-    list (APPEND compiler_flags ${COMPILER_SPECIFIC_FLAGS_MSVC})
-  elseif(CMAKE_C_COMPILER_ID STREQUAL "PGI")
-    list (APPEND compiler_flags ${COMPILER_SPECIFIC_FLAGS_PGI})
-  endif()
-
-  set(GCCISH_COMPILERS GNU Clang Intel)
-  list(FIND GCCISH_COMPILERS "${CMAKE_C_COMPILER_ID}" IS_GCCISH)
-  if (IS_GCCISH GREATER -1)
-    list (APPEND compiler_flags ${COMPILER_SPECIFIC_FLAGS_GCCISH})
-  endif ()
-
-  set (${COMPILER_SPECIFIC_FLAGS_VARIABLE} "${compiler_flags}" PARENT_SCOPE)
-endfunction ()
-
-function (source_file_add_compiler_flags_unchecked file)
-  set (flags ${ARGV})
-  list (REMOVE_AT flags 0)
-  get_source_file_property (sources ${file} SOURCES)
-
-  foreach (flag ${flags})
-    get_source_file_property (existing ${file} COMPILE_FLAGS)
-    if ("${existing}" STREQUAL "NOTFOUND")
-      set_source_files_properties (${file}
-        PROPERTIES COMPILE_FLAGS "${flag}")
-    else ()
-      set_source_files_properties (${file}
-        PROPERTIES COMPILE_FLAGS "${existing} ${flag}")
-    endif ()
-  endforeach (flag)
-endfunction ()
-
-function (source_file_add_compiler_flags file)
-  set (flags ${ARGV})
-  list (REMOVE_AT flags 0)
-  get_source_file_property (sources ${file} SOURCES)
-
-  foreach (flag ${flags})
-    if (CMAKE_C_COMPILER_ID STREQUAL "GNU")
-      # Because https://gcc.gnu.org/wiki/FAQ#wnowarning
-      string (REGEX REPLACE "\\-Wno\\-(.+)" "-W\\1" flag_to_test "${flag}")
-    else ()
-      set (flag_to_test ${flag})
-    endif ()
-
-    if (file MATCHES "\\.c$")
-      string (REGEX REPLACE "[^a-zA-Z0-9]+" "_" test_name "CFLAG_${flag_to_test}")
-      CHECK_C_COMPILER_FLAG ("${ADD_COMPILER_FLAGS_PREPEND} ${flag_to_test}" ${test_name})
-    elseif (file MATCHES "\\.(cpp|cc|cxx)$")
-      string (REGEX REPLACE "[^a-zA-Z0-9]+" "_" test_name "CXXFLAG_${flag_to_test}")
-      CHECK_CXX_COMPILER_FLAG ("${ADD_COMPILER_FLAGS_PREPEND} ${flag_to_test}" ${test_name})
-    endif ()
-
-    if (${test_name})
-      source_file_add_compiler_flags_unchecked (${file} ${flag})
-    endif ()
-
-    unset (test_name)
-    unset (flag_to_test)
-  endforeach (flag)
-
-  unset (flags)
-endfunction ()
-
-function (target_add_compiler_flags target)
-  set (flags ${ARGV})
-  list (REMOVE_AT flags 0)
-  get_target_property (sources ${target} SOURCES)
-
-  foreach (source ${sources})
-    source_file_add_compiler_flags (${source} ${flags})
-  endforeach (source)
-
-  unset (flags)
-  unset (sources)
-endfunction (target_add_compiler_flags)
-
-# global_add_compiler_flags (flag1 [flag2 [flag3 ...]]):
-#
-# This just adds the requested compiler flags to
-# CMAKE_C/CXX_FLAGS variable if they work with the compiler.
-function (global_add_compiler_flags)
-  set (flags ${ARGV})
-
-  foreach (flag ${flags})
-    if ("GNU" STREQUAL "${CMAKE_C_COMPILER_ID}")
-      # Because https://gcc.gnu.org/wiki/FAQ#wnowarning
-      string (REGEX REPLACE "\\-Wno\\-(.+)" "-W\\1" flag_to_test "${flag}")
-    else ()
-      set (flag_to_test "${flag}")
-    endif ()
-
-    string (REGEX REPLACE "[^a-zA-Z0-9]+" "_" c_test_name "CFLAG_${flag_to_test}")
-    CHECK_C_COMPILER_FLAG ("${ADD_COMPILER_FLAGS_PREPEND} ${flag_to_test}" ${c_test_name})
-    if (${c_test_name})
-      set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${flag}")
-    endif ()
-    unset (c_test_name)
-
-    string (REGEX REPLACE "[^a-zA-Z0-9]+" "_" cxx_test_name "CFLAG_${flag_to_test}")
-    CHECK_CXX_COMPILER_FLAG ("${ADD_COMPILER_FLAGS_PREPEND} ${flag_to_test}" ${cxx_test_name})
-    if (${cxx_test_name})
-      set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${flag}")
-    endif ()
-    unset (cxx_test_name)
-
-    unset (flag_to_test)
-  endforeach (flag)
-
-  unset (flags)
-
-  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS}" PARENT_SCOPE)
-  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}" PARENT_SCOPE)
-endfunction (global_add_compiler_flags)

data/ext/minimap2/lib/simde/test/cmake/ExtraWarningFlags.cmake

@@ -1,68 +0,0 @@
-# This is basically supposed to be the CMake equivalent of
-# https://git.gnome.org/browse/gnome-common/tree/macros2/gnome-compiler-flags.m4
-
-include (AddCompilerFlags)
-
-if (MSVC)
-  set (EXTRA_WARNING_FLAGS
-    /W4
-    /analyze)
-else ()
-  set (EXTRA_WARNING_FLAGS
-    -Wall
-    -Wcast-align
-    -Wclobbered
-    -Wempty-body
-    -Werror=format=2
-    -Werror=format-security
-    -Werror=implicit-function-declaration
-    -Werror=init-self
-    -Werror=missing-include-dirs
-    -Werror=missing-prototypes
-    -Werror=pointer-arith
-    -Wextra
-    -Wformat-nonliteral
-    -Wformat-security
-    -Wignored-qualifiers
-    -Winit-self
-    -Winvalid-pch
-    -Wlogical-op
-    -Wmissing-declarations
-    -Wmissing-format-attribute
-    -Wmissing-include-dirs
-    -Wmissing-noreturn
-    -Wmissing-parameter-type
-    -Wmissing-prototypes
-    -Wnested-externs
-    -Wno-missing-field-initializers
-    -Wno-strict-aliasing
-    -Wno-uninitialized
-    -Wno-unused-parameter
-    -Wold-style-definition
-    -Woverride-init
-    -Wpacked
-    -Wpointer-arith
-    -Wredundant-decls
-    -Wreturn-type
-    -Wshadow
-    -Wsign-compare
-    -Wstrict-prototypes
-    -Wswitch-enum
-    -Wsync-nand
-    -Wtype-limits
-    -Wundef
-    -Wuninitialized
-    -WUnsafe-loop-optimizations
-    -Wwrite-strings
-    -Wsuggest-attribute=format)
-endif ()
-
-mark_as_advanced (EXTRA_WARNING_FLAGS)
-
-function (target_add_extra_warning_flags target)
-  target_add_compiler_flags (${target} ${EXTRA_WARNING_FLAGS})
-endfunction (target_add_extra_warning_flags)
-
-function (source_file_add_extra_warning_flags file)
-  source_file_add_compiler_flags (${file} ${EXTRA_WARNING_FLAGS})
-endfunction (source_file_add_extra_warning_flags)

data/ext/minimap2/lib/simde/test/meson.build

@@ -1,64 +0,0 @@
-munit_deps = []
-munit_defs = []
-if cc.get_id() == 'pgi'
-  munit_deps += dependency('openmp')
-endif
-if cc.has_function('clock_gettime')
-  librt_dep = cc.find_library('rt', required: false)
-  if not librt_dep.found()
-    munit_defs += '-DPSNIP_CLOCK_NO_LIBRT'
-  endif
-  munit_deps += librt_dep
-endif
-munit = static_library('munit', 'munit/munit.c', dependencies: munit_deps)
-
-simde_c_defs = []
-simde_cxx_defs = []
-simde_c_args = []
-simde_cxx_args = []
-simde_deps = []
-
-c_openmp_simd = false
-cxx_openmp_simd = false
-foreach omp_arg : ['-fopenmp-simd', '-qopenmp-simd']
-  if (not c_openmp_simd) and cc.has_argument(omp_arg)
-    simde_c_args += omp_arg
-    simde_c_defs += '-DSIMDE_ENABLE_OPENMP'
-    c_openmp_simd = true
-  endif
-
-  if (not cxx_openmp_simd) and cxx.has_argument(omp_arg)
-    simde_cxx_args += omp_arg
-    simde_cxx_defs += '-DSIMDE_ENABLE_OPENMP'
-    cxx_openmp_simd = true
-  endif
-endforeach
-
-simde_native_c_flags = []
-# if cc.has_argument('-march=native+simd')
-#   simde_native_c_flags += '-march=native+simd'
-# elif cc.has_argument('-march=native')
-#   simde_native_c_flags += '-march=native'
-# endif
-
-simde_native_cxx_flags = []
-# if cxx.has_argument('-march=native+simd')
-#   simde_native_cxx_flags += '-march=native+simd'
-# elif cxx.has_argument('-march=native')
-#   simde_native_cxx_flags += '-march=native'
-# endif
-
-if not c_openmp_simd
-  simde_deps += dependency('openmp', required: false)
-endif
-
-simde_include_dir = include_directories('..')
-
-subdir('x86')
-subdir('arm')
-
-executable('run-tests', 'run-tests.c',
-           link_with: [munit, simde_tests_x86, simde_tests_arm],
-           dependencies: simde_deps,
-           c_args: simde_c_args + simde_c_defs + simde_native_c_flags,
-           cpp_args: simde_cxx_args + simde_cxx_defs + simde_native_cxx_flags)

data/ext/minimap2/lib/simde/test/munit/COPYING

@@ -1,21 +0,0 @@
-µnit Testing Framework
-Copyright (c) 2013-2016 Evan Nemerson <evan@nemerson.com>
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/ext/minimap2/lib/simde/test/munit/Makefile

@@ -1,55 +0,0 @@
-# Using µnit is very simple; just include the header and add the C
-# file to your sources.  That said, here is a simple Makefile to build
-# the example.
-
-CSTD:=99
-OPENMP:=n
-ASAN:=n
-UBSAN:=n
-EXTENSION:=
-TEST_ENV:=
-CFLAGS:=
-AGGRESSIVE_WARNINGS=n
-
-ifeq ($(CC),pgcc)
-        CFLAGS+=-c$(CSTD)
-else
-        CFLAGS+=-std=c$(CSTD)
-endif
-
-ifeq ($(OPENMP),y)
-        ifeq ($(CC),pgcc)
-                CFLAGS+=-mp
-        else
-                CFLAGS+=-fopenmp
-        endif
-endif
-
-ifneq ($(SANITIZER),)
-        CFLAGS+=-fsanitize=$(SANITIZER)
-endif
-
-ifneq ($(CC),pgcc)
-        ifeq ($(EXTRA_WARNINGS),y)
-                CFLAGS+=-Wall -Wextra -Werror
-        endif
-
-        ifeq ($(ASAN),y)
-                CFLAGS+=-fsanitize=address
-        endif
-
-        ifeq ($(UBSAN),y)
-                CFLAGS+=-fsanitize=undefined
-        endif
-endif
-
-example$(EXTENSION): munit.h munit.c example.c
-	$(CC) $(CFLAGS) -o $@ munit.c example.c
-
-test:
-	$(TEST_ENV) ./example$(EXTENSION)
-
-clean:
-	rm -f example$(EXTENSION)
-
-all: example$(EXTENSION)

data/ext/minimap2/lib/simde/test/munit/README.md

@@ -1,54 +0,0 @@
-# µnit
-
-µnit is a small but full-featured unit testing framework for C.  It has
-no dependencies (beyond libc), is permissively licensed (MIT), and is
-easy to include into any project.
-
-For more information, see
-[the µnit web site](https://nemequ.github.io/munit).
-
-[![Build status](https://travis-ci.org/nemequ/munit.svg?branch=master)](https://travis-ci.org/nemequ/munit)
-[![Windows build status](https://ci.appveyor.com/api/projects/status/db515g5ifcwjohq7/branch/master?svg=true)](https://ci.appveyor.com/project/quixdb/munit/branch/master)
-
-## Features
-
-Features µnit currently includes include:
-
- * Handy assertion macros which make for nice error messages.
- * Reproducible cross-platform random number generation, including
-   support for supplying a seed via CLI.
- * Timing of both wall-clock and CPU time.
- * Parameterized tests.
- * Nested test suites.
- * Flexible CLI.
- * Forking
-   ([except on Windows](https://github.com/nemequ/munit/issues/2)).
- * Hiding output of successful tests.
-
-Features µnit does not currently include, but some day may include
-(a.k.a., if you file a PR…), include:
-
- * [TAP](http://testanything.org/) support; feel free to discuss in
-   [issue #1](https://github.com/nemequ/munit/issues/1)
-
-### Include into your project with meson
-
-In your `subprojects` folder put a `munit.wrap` file containing:
-
-```
-[wrap-git]
-directory=munit
-url=https://github.com/nemequ/munit/
-revision=head
-```
-
-Then you can use a subproject fallback when you include munit as a
-dependency to your project: `dependency('munit', fallback: ['munit', 'munit_dep'])`
-
-## Documentation
-
-See [the µnit web site](https://nemequ.github.io/munit).
-
-Additionally, there is a heavily-commented
-[example.c](https://github.com/nemequ/munit/blob/master/example.c) in
-the repository.