Adding automation for tests and modernizing code with interface updates

.clang-format

@@ -1,23 +1,7 @@
-# This file is part of preseq
-#
-# Copyright (C) 2024: Andrew D. Smith
-#
-# Authors: Andrew D. Smith
-#
-# This is free software: you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This software is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# General Public License for more details.
-
 BasedOnStyle: LLVM
 ColumnLimit: 80
 IndentWidth: 2
-AlwaysBreakAfterReturnType: TopLevel
+AlwaysBreakAfterReturnType: All
 ContinuationIndentWidth: 2
 ConstructorInitializerIndentWidth: 2
 BraceWrapping:
@@ -26,3 +10,4 @@ BraceWrapping:
 BreakBeforeBraces: Custom
 BreakConstructorInitializers: AfterColon
 SpacesBeforeTrailingComments: 2
+ReflowComments: false

.clang-format-ignore

@@ -0,0 +1,2 @@
+src/CLI11/CLI11.hpp
+src/nlohmann/json.hpp

.clang-tidy

@@ -0,0 +1,31 @@
+Checks: 'cert-*,cppcoreguidelines-*,performance-*,clang-diagnostic-*,clang-analyzer-*,-clang-diagnostic-unqualified-std-cast-call,-clang-diagnostic-unknown-warning-option,-clang-analyzer-unix.BlockInCriticalSection,-cppcoreguidelines-pro-type-vararg'
+WarningsAsErrors: '*'
+HeaderFileExtensions:
+  - ''
+  - h
+  - hh
+  - hpp
+  - hxx
+ImplementationFileExtensions:
+  - c
+  - cc
+  - cpp
+  - cxx
+HeaderFilterRegex: ''
+ExcludeHeaderFilterRegex: 'OptionParser.hpp'
+FormatStyle: none
+CheckOptions:
+  cert-dcl16-c.NewSuffixes: 'L;LL;LU;LLU'
+  cert-err33-c.AllowCastToVoid: 'true'
+  cert-err33-c.CheckedFunctions: '::aligned_alloc;::asctime_s;::at_quick_exit;::atexit;::bsearch;::bsearch_s;::btowc;::c16rtomb;::c32rtomb;::calloc;::clock;::cnd_broadcast;::cnd_init;::cnd_signal;::cnd_timedwait;::cnd_wait;::ctime_s;::fclose;::fflush;::fgetc;::fgetpos;::fgets;::fgetwc;::fopen;::fopen_s;::fprintf;::fprintf_s;::fputc;::fputs;::fputwc;::fputws;::fread;::freopen;::freopen_s;::fscanf;::fscanf_s;::fseek;::fsetpos;::ftell;::fwprintf;::fwprintf_s;::fwrite;::fwscanf;::fwscanf_s;::getc;::getchar;::getenv;::getenv_s;::gets_s;::getwc;::getwchar;::gmtime;::gmtime_s;::localtime;::localtime_s;::malloc;::mbrtoc16;::mbrtoc32;::mbsrtowcs;::mbsrtowcs_s;::mbstowcs;::mbstowcs_s;::memchr;::mktime;::mtx_init;::mtx_lock;::mtx_timedlock;::mtx_trylock;::mtx_unlock;::printf_s;::putc;::putwc;::raise;::realloc;::remove;::rename;::scanf;::scanf_s;::setlocale;::setvbuf;::signal;::snprintf;::snprintf_s;::sprintf;::sprintf_s;::sscanf;::sscanf_s;::strchr;::strerror_s;::strftime;::strpbrk;::strrchr;::strstr;::strtod;::strtof;::strtoimax;::strtok;::strtok_s;::strtol;::strtold;::strtoll;::strtoul;::strtoull;::strtoumax;::strxfrm;::swprintf;::swprintf_s;::swscanf;::swscanf_s;::thrd_create;::thrd_detach;::thrd_join;::thrd_sleep;::time;::timespec_get;::tmpfile;::tmpfile_s;::tmpnam;::tmpnam_s;::tss_create;::tss_get;::tss_set;::ungetc;::ungetwc;::vfprintf;::vfprintf_s;::vfscanf;::vfscanf_s;::vfwprintf;::vfwprintf_s;::vfwscanf;::vfwscanf_s;::vprintf_s;::vscanf;::vscanf_s;::vsnprintf;::vsnprintf_s;::vsprintf;::vsprintf_s;::vsscanf;::vsscanf_s;::vswprintf;::vswprintf_s;::vswscanf;::vswscanf_s;::vwprintf_s;::vwscanf;::vwscanf_s;::wcrtomb;::wcschr;::wcsftime;::wcspbrk;::wcsrchr;::wcsrtombs;::wcsrtombs_s;::wcsstr;::wcstod;::wcstof;::wcstoimax;::wcstok;::wcstok_s;::wcstol;::wcstold;::wcstoll;::wcstombs;::wcstombs_s;::wcstoul;::wcstoull;::wcstoumax;::wcsxfrm;::wctob;::wctrans;::wctype;::wmemchr;::wprintf_s;::wscanf;::wscanf_s;'
+  cert-oop54-cpp.WarnOnlyIfThisHasSuspiciousField: 'false'
+  cert-str34-c.DiagnoseSignedUnsignedCharComparisons: 'false'
+  cppcoreguidelines-non-private-member-variables-in-classes.IgnorePublicMemberVariables: 'true'
+  google-readability-braces-around-statements.ShortStatementLines: '1'
+  google-readability-function-size.StatementThreshold: '800'
+  google-readability-namespace-comments.ShortNamespaceLines: '10'
+  google-readability-namespace-comments.SpacesBeforeComments: '2'
+  llvm-else-after-return.WarnOnConditionVariables: 'false'
+  llvm-else-after-return.WarnOnUnfixable: 'false'
+  llvm-qualified-auto.AddConstToQualified: 'false'
+SystemHeaders: 'false'

.cppcheck_suppress

@@ -1,6 +1,6 @@
 # This file is part of preseq
 #
-# Copyright (C) 2024: Andrew D. Smith
+# Copyright (C) 2024-2025 Andrew D. Smith
 #
 # Authors: Andrew D. Smith
 #
@@ -17,7 +17,18 @@
 missingIncludeSystem
 constVariablePointer
 checkersReport
-unusedFunction:src/bam_record_utils.hpp
-unusedFunction:src/bam_record_utils.cpp
-*:src/smithlab_cpp*
-unusedStructMember:src/*.hpp
+unknownMacro
+unmatchedSuppression
+# Ignore unused function because it's too hard to get right
+unusedFunction
+# Ignore unused struct member because this won't go unnoticed anyway
+unusedStructMember
+# Ignore missing includes because if they are real things won't build
+missingInclude
+# Exclude external files
+*:*CLI11.hpp
+*:*json.hpp
+# Problem caused by external files
+toomanyconfigs
+# More problems caused by external files -- with too many ifdefs
+normalCheckLevelMaxBranches

.github/workflows/linux-system-tests.yml

@@ -0,0 +1,31 @@
+name: System tests (Linux)
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+  workflow_dispatch:
+
+jobs:
+  ubuntu-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      # - name: Dependencies
+      #   run: |
+      #     sudo apt-get update
+      #     sudo apt-get install -y zlib1g-dev libdeflate-dev libhts-dev samtools
+      - name: Configure
+        run: |
+          cmake -B build \
+          -DCMAKE_CXX_COMPILER=g++ \
+          -DCMAKE_BUILD_TYPE=Release
+      - name: Build
+        run: |
+          cmake --build build -j4
+      - name: Test
+        run: |
+          ctest --test-dir build --output-on-failure

.gitmodules

@@ -1,9 +1,6 @@
 [submodule "preseqR"]
-	path = preseqR
-	url = ../preseqR.git
-[submodule "src/smithlab_cpp"]
-	path = src/smithlab_cpp
-	url = ../smithlab_cpp.git
+        path = preseqR
+        url = ../preseqR.git
 [submodule "src/bamxx"]
-	path = src/bamxx
-	url = ../bamxx.git
+        path = src/bamxx
+        url = ../bamxx.git

CMakeLists.txt

@@ -0,0 +1,103 @@
+# Copyright (C) 2026 Andrew D Smith
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <https://www.gnu.org/licenses/>.
+
+# to find the version of cmake do
+# $ cmake --version
+cmake_minimum_required(VERSION 3.30)
+project(
+  preseq
+  VERSION 3.2.0
+  DESCRIPTION
+  "predict properties of genomic sequencing libraries"
+  HOMEPAGE_URL https://github.com/smithlabcode/preseq
+  LANGUAGES CXX)
+
+# Set language version used
+set(CMAKE_CXX_STANDARD 23)
+set(CMAKE_CXX_STANDARD_REQUIRED yes)
+set(CMAKE_CXX_EXTENSIONS off)  # prevents std=gnu++23
+set(CMAKE_EXPORT_COMPILE_COMMANDS on)
+
+include(CheckIncludeFileCXX)
+include(CheckFunctionExists)
+include(CheckCXXCompilerFlag)
+
+include(GNUInstallDirs)
+
+configure_file(data/config.h.in config.h)
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
+
+add_compile_options(
+  -Wall
+  -Wextra
+  -Wpedantic
+  -Werror
+  -Wfatal-errors
+)
+
+if(STATIC_ANALYSIS)
+  include(cmake/static_analysis.cmake)
+endif()
+
+option(PRESEQ_TESTS "Enable testing (ctest or make test)" on)
+if(PRESEQ_TESTS)
+  include(cmake/tests.cmake)
+endif()
+
+find_package(Threads REQUIRED)
+find_package(spdlog REQUIRED)
+
+if(USE_HTSLIB)
+  find_package(HTSLIB 1.20 REQUIRED)
+  add_compile_definitions(HAVE_HTSLIB)
+  add_subdirectory(src/bamxx)
+endif()
+
+add_library(common OBJECT src/common.cpp)
+add_library(Interval6 OBJECT src/Interval6.cpp)
+add_library(lc_extrap OBJECT src/lc_extrap.cpp)
+add_library(gc_extrap OBJECT src/gc_extrap.cpp)
+add_library(c_curve OBJECT src/c_curve.cpp)
+add_library(bound_pop OBJECT src/bound_pop.cpp)
+add_library(pop_size OBJECT src/pop_size.cpp)
+add_library(continued_fraction OBJECT src/continued_fraction.cpp)
+add_library(moment_sequence OBJECT src/moment_sequence.cpp)
+add_library(load_data_for_complexity OBJECT src/load_data_for_complexity.cpp)
+
+add_executable(preseq src/preseq.cpp)
+
+# ADS: below, for config.h
+target_include_directories(preseq PUBLIC ${CMAKE_BINARY_DIR})
+
+target_link_libraries(preseq PRIVATE
+  common
+  continued_fraction
+  moment_sequence
+  Interval6
+  load_data_for_complexity
+  lc_extrap
+  gc_extrap
+  c_curve
+  bound_pop
+  pop_size
+)
+target_link_libraries(preseq PRIVATE spdlog::spdlog_header_only)
+
+if(USE_HTSLIB)
+  target_link_libraries(preseq PRIVATE
+    bamxx
+    HTSLIB::HTSLIB
+  )
+endif()

CPPLINT.cfg

@@ -1,19 +1,16 @@
 # This file is part of preseq
 #
-# Copyright (C) 2024: Andrew D. Smith
+# Copyright (C) 2023-2025 Andrew D. Smith
 #
-# Authors: Andrew D. Smith
+# This is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
 #
-# This is free software: you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This software is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# General Public License for more details.
-
+# This software is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details.
 set noparent
 filter=-runtime/references
 filter=-build/include_subdir
@@ -26,3 +23,6 @@ filter=-whitespace/newline
 filter=-readability/braces
 filter=-whitespace/semicolon
 filter=-whitespace/indent
+filter=-whitespace/braces
+filter=-whitespace/parens
+filter=-readability/nolint

Makefile.am

@@ -1,30 +1,28 @@
 # This file is part of preseq
 #
-# Copyright (C) 2018-2024: Andrew D. Smith
+# Copyright (C) 2018-2025: Andrew D. Smith
 #
 # Authors: Andrew D. Smith
 #
-# This is free software: you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
+# This is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
 #
-# This software is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# General Public License for more details.
+# This software is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details.
 
 ACLOCAL_AMFLAGS = -I m4
 
-SUBDIRS := src/smithlab_cpp
-install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp, $(SUBDIRS))
-AM_CPPFLAGS = -I $(top_srcdir)/src/smithlab_cpp
-if ENABLE_HTS
+AM_CPPFLAGS =
+if ENABLE_HTSLIB
 AM_CPPFLAGS += -I $(top_srcdir)/src/bamxx
 endif
 
 AM_CPPFLAGS += -Wall -Wextra -Wpedantic -Wno-unknown-attributes
-if ENABLE_HTS
+if ENABLE_HTSLIB
 AM_CPPFLAGS += -DHAVE_HTSLIB
 endif
 
@@ -36,7 +34,7 @@ EXTRA_DIST = \
 	docs \
 	tests/md5sum.txt \
 	tests/data/lc_extrap_input.vals \
-	tests/data/gc_extrap_input.mr \
+	tests/data/gc_extrap_input.bed \
 	tests/data/c_curve_input.hist \
 	tests/scripts/test_c_curve.test \
 	tests/scripts/test_gc_extrap.test \
@@ -49,8 +47,6 @@ TESTS = \
 
 TEST_EXTENSIONS = .test
 
-LDADD = src/smithlab_cpp/libsmithlab_cpp.a
-
 bin_PROGRAMS = preseq
 
 preseq_SOURCES = \
@@ -71,10 +67,12 @@ preseq_SOURCES = \
         src/continued_fraction.cpp \
         src/load_data_for_complexity.hpp \
         src/load_data_for_complexity.cpp \
+        src/Interval6.hpp \
+        src/Interval6.cpp \
         src/moment_sequence.hpp \
         src/moment_sequence.cpp
 
-if ENABLE_HTS
+if ENABLE_HTSLIB
 preseq_SOURCES += \
 	src/bamxx/bamxx.hpp \
 	src/bam_record_utils.hpp \