Adding setup for static analysis through cmake

.clang-tidy

@@ -0,0 +1,5 @@
+---
+Checks: '-*'
+WarningsAsErrors: ''
+HeaderFilterRegex: '.*'
+FormatStyle: none

.cppcheck_suppress

@@ -0,0 +1,5 @@
+unmatchedSuppression
+checkersReport
+# Exclude all for now
+*:*.hpp
+*:*.cpp

CMakeLists.txt

@@ -32,6 +32,18 @@ set(CMAKE_EXPORT_COMPILE_COMMANDS on)
 
 include(GNUInstallDirs)
 
+if(STATIC_ANALYSIS)
+  include(cmake/static_analysis.cmake)
+endif()
+
+add_compile_options(
+  -Wall
+  -Wextra
+  -Wpedantic
+  -Werror
+  -Wfatal-errors
+)
+
 file(GLOB cpp_files "*.cpp")
 
 set(LIBRARY_OBJECTS "")
@@ -42,5 +54,9 @@ foreach(cpp_file ${cpp_files})
 endforeach()
 
 add_library(smithlab_cpp)
-target_include_directories(smithlab_cpp PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
-target_link_libraries(smithlab_cpp PUBLIC ${LIBRARY_OBJECTS})
+target_include_directories(smithlab_cpp PUBLIC
+  ${CMAKE_CURRENT_SOURCE_DIR}
+)
+target_link_libraries(smithlab_cpp PUBLIC
+  ${LIBRARY_OBJECTS}
+)

CPPLINT.cfg

@@ -0,0 +1 @@
+exclude_files=.*\.*pp

GenomicRegion.cpp

@@ -21,11 +21,15 @@
  */
 
 #include "GenomicRegion.hpp"
-
-#include <exception>
+#include "smithlab_os.hpp"
 
 #include <cassert>
+#include <cctype>
+#include <cstdlib>
 #include <fstream>
+#include <limits>
+#include <sstream>
+#include <stdexcept>
 #include <unordered_map>
 
 using std::ostringstream;
@@ -136,8 +140,6 @@ bool SimpleGenomicRegion::operator!=(const SimpleGenomicRegion &rhs) const {
   return (chrom != rhs.chrom || start != rhs.start || end != rhs.end);
 }
 
-#include <iostream>
-
 unordered_map<string, chrom_id_type> GenomicRegion::fw_table_in;
 unordered_map<chrom_id_type, string> GenomicRegion::fw_table_out;
 

GenomicRegion.hpp

@@ -24,19 +24,20 @@
 #ifndef GENOMIC_REGION_HPP
 #define GENOMIC_REGION_HPP
 
-#include "smithlab_os.hpp"
 #include "smithlab_utils.hpp"
 
+#include <algorithm>
 #include <fstream>
-#include <limits>
+#include <iterator>
+#include <stdio.h>
 #include <string>
 #include <unordered_map>
+#include <utility>
 #include <vector>
+class GenomicRegion;
 
 typedef unsigned chrom_id_type;
 
-class GenomicRegion;
-
 class SimpleGenomicRegion {
 public:
   SimpleGenomicRegion() : chrom(assign_chrom("(null)")), start(0), end(0) {}

MappedRead.cpp

@@ -21,11 +21,11 @@
  */
 
 #include "MappedRead.hpp"
-#include "smithlab_utils.hpp"
 
 #include <algorithm>
-#include <fstream>
+#include <cctype>
 #include <sstream>
+#include <stdexcept>
 #include <string>
 
 using std::runtime_error;

MappedRead.hpp

@@ -24,6 +24,8 @@
 #define MAPPED_READ_HPP
 
 #include "GenomicRegion.hpp"
+#include <cstdio>
+#include <string>
 
 struct MappedRead {
   MappedRead() {}

OptionParser.cpp

@@ -22,20 +22,18 @@
  */
 
 #include "OptionParser.hpp"
+#include "smithlab_utils.hpp"
 
+#include <algorithm>
 #include <cassert>
 #include <cctype>
 #include <cstdlib>
-#include <cstring>
-#include <exception>
 #include <fstream>
-#include <functional>
 #include <iomanip>
 #include <iterator>
 #include <regex>
 #include <sstream>
-
-#include "smithlab_utils.hpp"
+#include <stdexcept>
 
 using std::begin;
 using std::end;

OptionParser.hpp

@@ -19,6 +19,7 @@
 #ifndef OPTION_PARSER_HPP
 #define OPTION_PARSER_HPP
 
+#include <cstddef>
 #include <limits>
 #include <string>
 #include <vector>

QualityScore.cpp

@@ -22,8 +22,9 @@
 
 #include "QualityScore.hpp"
 
-#include "smithlab_utils.hpp"
+#include <cctype>
 #include <fstream>
+#include <stdexcept>
 
 using std::runtime_error;
 using std::string;

QualityScore.hpp

@@ -25,6 +25,7 @@
 
 #include <algorithm>
 #include <cmath>
+#include <cstddef>
 #include <string>
 
 ////////////////////////////////////////////////////////////////////////

bisulfite_utils.cpp

@@ -22,14 +22,12 @@
  */
 
 #include "bisulfite_utils.hpp"
+#include <cctype>
 #include <cstdlib>
-#include <iostream>
 #include <random>
 
-using std::string;
-
-void bisulfite_treatment(std::mt19937 &generator, string &seq, double bs_rate,
-                         double meth_rate) {
+void bisulfite_treatment(std::mt19937 &generator, std::string &seq,
+                         double bs_rate, double meth_rate) {
 
   std::uniform_real_distribution<double> unif(0.0, 1.0);
 

chromosome_utils.cpp

@@ -21,8 +21,16 @@
  */
 
 #include "chromosome_utils.hpp"
+#include "GenomicRegion.hpp"
+#include "smithlab_os.hpp"
 
+#include <algorithm>
+#include <cassert>
 #include <cctype>
+#include <cmath>
+#include <cstdlib>
+#include <fstream>
+#include <iterator>
 #include <stdexcept>
 #include <string>
 #include <unordered_map>

chromosome_utils.hpp

@@ -23,18 +23,13 @@
 #ifndef CHROMOSOME_UTILS_HPP
 #define CHROMOSOME_UTILS_HPP
 
-#include <algorithm>
-#include <cassert>
-#include <cmath>
-#include <iostream>
-#include <iterator>
-#include <limits>
-#include <ostream>
-#include <sstream>
+#include <cstddef>
 #include <string>
+#include <unordered_map>
 #include <vector>
 
-#include "GenomicRegion.hpp"
+class GenomicRegion;
+class SimpleGenomicRegion;
 
 void parse_region_name(std::string region_name, std::string &chrom,
                        size_t &start, size_t &end);

cigar_utils.cpp

@@ -15,8 +15,8 @@
 
 #include "cigar_utils.hpp"
 
-#include <exception>
 #include <sstream>
+#include <stdexcept>
 #include <string>
 
 using std::runtime_error;

cigar_utils.hpp

@@ -17,7 +17,10 @@
 #define CIGAR_UTILS_HPP
 
 #include <algorithm>
-#include <cctype> // isdigit
+#include <cctype>
+#include <cstdio>
+#include <initializer_list>
+#include <iterator>
 #include <string>
 
 inline bool consumes_query(const char op) {

cmake/static_analysis.cmake

@@ -0,0 +1,119 @@
+# Copyright (C) 2025 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/>.
+
+# StaticAnalysis
+message(STATUS "Enabling static analysis")
+# If no specific static analysis is requested, do them all
+if(NOT RUN_CPPCHECK AND NOT RUN_IWYU AND
+    NOT RUN_CPPLINT  AND NOT RUN_CLANG_TIDY)
+  set(RUN_CPPCHECK on)
+  set(RUN_IWYU on)
+  set(RUN_CPPLINT on)
+  set(RUN_CLANG_TIDY on)
+endif()
+
+set(STATIC_ANALYSIS_CHECKS "")
+if(RUN_CPPCHECK)
+  list(APPEND STATIC_ANALYSIS_CHECKS "cppcheck")
+endif()
+if(RUN_CPPLINT)
+  list(APPEND STATIC_ANALYSIS_CHECKS "cpplint")
+endif()
+if(RUN_IWYU)
+  list(APPEND STATIC_ANALYSIS_CHECKS "iwyu")
+endif()
+if(RUN_CLANG_TIDY)
+  list(APPEND STATIC_ANALYSIS_CHECKS "clang-tidy")
+endif()
+
+message(STATUS "Requested static analysis: ${STATIC_ANALYSIS_CHECKS}")
+
+# cpplint: all options are in the config file
+if ("cpplint" IN_LIST STATIC_ANALYSIS_CHECKS)
+  find_program(FOUND_CPPLINT cpplint)
+  if(FOUND_CPPLINT)
+    message(STATUS "Enabling cpplint analysis")
+    set(CMAKE_CXX_CPPLINT cpplint --quiet)
+  else()
+    message(STATUS "Could not find cpplint; disabling cpplint")
+  endif()
+endif()
+
+# include-what-you-use: config is a mappings file
+if ("iwyu" IN_LIST STATIC_ANALYSIS_CHECKS)
+  find_program(FOUND_IWYU include-what-you-use)
+  if(FOUND_IWYU)
+    message(STATUS "Enabling include-what-you-use analysis")
+    set(CMAKE_CXX_INCLUDE_WHAT_YOU_USE
+      include-what-you-use
+      -Xiwyu
+      --comment_style=none
+      -Xiwyu
+      --quoted_includes_first
+      -Xiwyu
+      --mapping_file=${PROJECT_SOURCE_DIR}/iwyu.json
+    )
+  else()
+    message(STATUS "Could not find iwyu; disabling iwyu")
+  endif()
+endif()
+
+# cppcheck: options on the command line as there is no config file
+if ("cppcheck" IN_LIST STATIC_ANALYSIS_CHECKS)
+  find_program(FOUND_CPPCHECK cppcheck)
+  if(FOUND_CPPCHECK)
+    message(STATUS "Enabling cppcheck analysis")
+    set(CMAKE_CXX_CPPCHECK
+      cppcheck
+      --quiet
+      --enable=all
+      --inline-suppr
+      --max-configs=1
+      --suppressions-list=${PROJECT_SOURCE_DIR}/.cppcheck_suppress
+    )
+  else()
+    message(STATUS "Could not find cppcheck; disabling cppcheck")
+  endif()
+endif()
+
+# clang-tidy: need to make sure version is at least 20
+if ("clang-tidy" IN_LIST STATIC_ANALYSIS_CHECKS)
+  find_program(CLANG_TIDY_EXECUTABLE NAMES clang-tidy)
+  # Minimum required version
+  set(MIN_CLANG_TIDY_VERSION "20.0.0")
+  if(CLANG_TIDY_EXECUTABLE)
+    execute_process(
+      COMMAND
+      bash -c
+      "${CLANG_TIDY_EXECUTABLE} --version | grep version | tr -cd '0-9.\n'"
+      OUTPUT_VARIABLE CLANG_TIDY_VERSION
+      OUTPUT_STRIP_TRAILING_WHITESPACE
+    )
+    # Compare the version numbers
+    if(CLANG_TIDY_VERSION VERSION_GREATER_EQUAL MIN_CLANG_TIDY_VERSION)
+      message(STATUS "Enabling clang-tidy (version: ${CLANG_TIDY_VERSION})")
+      set(CMAKE_CXX_CLANG_TIDY
+        clang-tidy
+        --quiet
+        --allow-no-checks
+        -p ${PROJECT_BINARY_DIR}
+      )
+    else()
+      message(STATUS "Not enabling clang-tidy (min version not found")
+    endif()
+  else()
+    message(STATUS "Could not find clang-tidy; disabling clang-tidy")
+  endif()
+endif()

dna_four_bit.hpp

@@ -17,8 +17,10 @@
 #ifndef DNA_FOUR_BIT_HPP
 #define DNA_FOUR_BIT_HPP
 
+#include <cstddef>
 #include <cstdint>
-#include <iterator>
+#include <iterator> // IWYU pragma: keep
+#include <utility>
 #include <vector>
 
 enum base_in_byte { left, right };