Updating code for suggestions from clang-tidy

.clang-tidy

@@ -1,4 +1,14 @@
-Checks: 'cert-*,cppcoreguidelines-*,performance-*,clang-diagnostic-*,clang-analyzer-*,-clang-diagnostic-unqualified-std-cast-call,-clang-diagnostic-unknown-warning-option,-clang-analyzer-unix.BlockInCriticalSection'
+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-bounds-avoid-unchecked-container-access,
+"
 WarningsAsErrors: '*'
 HeaderFileExtensions:
   - ''
@@ -17,11 +27,13 @@ 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-err33-c.CheckedFunctions: '*'
   cert-oop54-cpp.WarnOnlyIfThisHasSuspiciousField: 'false'
   cert-str34-c.DiagnoseSignedUnsignedCharComparisons: 'false'
   cppcoreguidelines-non-private-member-variables-in-classes.IgnorePublicMemberVariables: 'true'
   cppcoreguidelines-rvalue-reference-param-not-moved.AllowPartialMove: 'true'
+  cppcoreguidelines-avoid-magic-numbers.IgnoredIntegerValues: '1;2;3;4;10'
+  cppcoreguidelines-avoid-magic-numbers.IgnoredFloatingPointValues: '1.0;2.0;10.0;100.0'
   google-readability-braces-around-statements.ShortStatementLines: '1'
   google-readability-function-size.StatementThreshold: '800'
   google-readability-namespace-comments.ShortNamespaceLines: '10'

src/duplication_results.cpp

@@ -25,6 +25,7 @@
 #include <limits>
 #include <numeric>
 #include <ranges>
+#include <span>
 #include <string>
 #include <tuple>
 #include <unordered_map>
@@ -35,7 +36,7 @@
 
 static constexpr auto n_bins = 16;
 
-static constexpr auto bin_breaks = std::array{
+static constexpr auto bin_breaks_impl = std::array{
   1,
   2,
   3,
@@ -54,11 +55,12 @@ static constexpr auto bin_breaks = std::array{
   10'000,
   std::numeric_limits<int>::max(),
 };
+static constexpr std::span bin_breaks = bin_breaks_impl;
 
 // clang-format off
 
 // ADS: previously for plots: std::array{"1", "2", ..., "5k+", "10k+"}
-static constexpr auto bin_labels = std::array{
+static constexpr auto bin_labels_impl = std::array{
   "0",
   "1",
   "2",
@@ -77,6 +79,7 @@ static constexpr auto bin_labels = std::array{
   ">5k",
   ">10k",
 };
+static constexpr std::span bin_labels = bin_labels_impl;
 
 // clang-format on
 
@@ -181,9 +184,7 @@ make_bins(const auto &breaks, const auto &hist) {
   std::vector<std::uint64_t> binned(std::size(breaks), 0);
   auto b_itr = std::cbegin(breaks);
   for (const auto [i, h] : falco::views::enumerate(hist)) {
-    // ADS: clang-tidy false positive?
-    // NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-pointer-arithmetic)
-    b_itr += (b_itr < std::cend(breaks) && i >= *b_itr);
+    b_itr += (b_itr != std::cend(breaks) && i >= *b_itr);
     binned[std::distance(std::cbegin(breaks), b_itr)] += h;
   }
   return binned;

src/falco.cpp

@@ -277,7 +277,7 @@ main(int argc, char *argv[]) {
     if (argc >= 2)
       app.footer(std::format(description, falco::get_share_dir()));
 
-    // NOLINTNEXTLINE (cppcoreguidelines-avoid-magic-numbers)
+    // NOLINTNEXTLINE(cppcoreguidelines-avoid-magic-numbers)
     app.get_formatter()->long_option_alignment_ratio(0.2);
     app.set_help_flag("-h,--help", "Print more detailed help");
     app.set_version_flag("--version", VERSION, "Print program version");

src/falco_config.cpp

@@ -95,11 +95,10 @@ load_config_and_set_graders(const std::string &filename,
         continue;
       const auto get_cutoff = [&](const std::string &label0) {
         const auto x = json_in[label][label0].get<std::string>();
-        const auto beg = std::data(x);
-        const auto end = beg + std::size(x);  // NOLINT(*-pointer-arithmetic)
         double val{};
-        const auto res = std::from_chars(beg, end, val);
-        if (res.ec != std::errc{})
+        // NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-pointer-arithmetic)
+        if (std::from_chars(std::data(x), std::data(x) + std::size(x), val)
+              .ec != std::errc{})
           throw std::runtime_error("error parsing cutoff: " + x);
         return val;
       };

src/falco_utils.cpp

@@ -4,6 +4,7 @@
 
 #include <array>
 #include <cmath>
+#include <compare>
 #include <cstdint>
 #include <ctime>  // for std::localtime
 #include <format>
@@ -17,7 +18,6 @@
 [[nodiscard]] auto
 size_to_units(const std::int64_t s, const std::string &suffix) -> std::string {
   const auto as_frac_2 = [](const auto a, const auto b) {
-    // NOLINTNEXTLINE(cppcoreguidelines-avoid-magic-numbers)
     return std::floor(10 * as_frac(a, b)) / 10;
   };
   if (s >= gigabytes)
@@ -63,10 +63,9 @@ get_theoretical_distribution(const std::vector<double> &gc,
   const auto sd = std::sqrt(as_frac(
     std::reduce(std::cbegin(id_gc), std::cend(id_gc)), total_count - 1));
   const auto to_normal = [&](const auto val) {
-    // NOLINTNEXTLINE(cppcoreguidelines-avoid-magic-numbers)
     return std::exp(-cntr_sq(val) / (2.0 * sd * sd));
   };
-  auto normed = std::views::iota(0u, n_bins) |
+  auto normed = std::views::iota(0U, n_bins) |
                 std::views::transform(to_normal) |
                 std::ranges::to<std::vector>();
   const auto denom = std::reduce(std::cbegin(normed), std::cend(normed));
@@ -103,52 +102,51 @@ smooth_gc_content(const std::vector<double> &data,
       std::ranges::subrange(std::cbegin(data), std::cbegin(data) + w)));
 #if __cpp_lib_ranges_slide
   for (const auto &window : data | std::views::slide(window_size))
-    // cppcheck-suppress useStlAlgorithm
     smoothed.push_back(get_mean(window));
 #else
-  for (auto i = 0LU; i < std::size(data); ++i)
-    // cppcheck-suppress useStlAlgorithm
-    smoothed.push_back(get_mean(std::ranges::subrange(
-      std::cbegin(data) + i, std::cbegin(data) + i + window_size)));
+  const auto lim = std::cend(data) - window_size;
+  for (auto itr = std::cbegin(data); itr != lim; ++itr)
+    smoothed.push_back(get_mean(std::ranges::subrange(itr, itr + window_size)));
 #endif
+  const auto d_end = std::cend(data);
   for (auto w = (window_size + 1) / 2; w > 1; --w)
-    smoothed.push_back(get_mean(
-      std::ranges::subrange(std::cend(data) - w + 1, std::cend(data))));
+    smoothed.push_back(get_mean(std::ranges::subrange(d_end - w + 1, d_end)));
   return smoothed;
 }
 
 [[nodiscard]] auto
-combine_gc_content_for_lengths(const std::vector<falco::gc_content_array> &gcs)
+combine_gc_content_for_lengths(const std::vector<falco::gc_content_t> &gcs)
   -> std::vector<double> {
   static constexpr auto histogram_size = 101;
   std::vector<double> hist(histogram_size);
-  for (auto i = 0U; i < std::size(gcs); ++i) {
-    if (std::reduce(std::cbegin(gcs[i]), std::cend(gcs[i])) == 0)
+  for (const auto &gc : gcs) {
+    if (std::ranges::none_of(gc, [](const auto x) { return x > 0.0; }))
       continue;
-    const auto increm = as_frac(histogram_size, std::size(gcs[i]));
-    for (auto gc_idx = 0U; gc_idx < std::size(gcs[i]); ++gc_idx) {
-      const auto curr_percent = gc_idx * increm;
-      const auto next_percent = (gc_idx + 1) * increm;
+    const auto increment = as_frac(histogram_size, std::size(gc));
+    for (auto gc_idx = 0U; gc_idx < std::size(gc); ++gc_idx) {
+      const auto curr_percent = gc_idx * increment;
+      const auto next_percent = (gc_idx + 1) * increment;
       const auto start_in_hist =
-        static_cast<std::uint64_t>(std::floor(curr_percent));
+        static_cast<std::int64_t>(std::floor(curr_percent));
       // ADS: below, not sure best way to do this for all edge cases
       const auto stop_in_hist =
-        static_cast<std::uint64_t>(std::min(static_cast<double>(histogram_size),
-                                            std::ceil(next_percent))) -
+        static_cast<std::int64_t>(std::min(static_cast<double>(histogram_size),
+                                           std::ceil(next_percent))) -
         1;
       assert(stop_in_hist < histogram_size);
       const auto splits = start_in_hist != stop_in_hist;
       const auto frac_left =
         splits ? static_cast<double>(start_in_hist) + 1.0 - curr_percent
-               : increm;
+               : increment;
       const auto frac_right =
-        splits ? next_percent - static_cast<double>(stop_in_hist) : increm;
-      for (auto h_idx = start_in_hist; h_idx <= stop_in_hist; ++h_idx) {
-        const auto contrib = (h_idx == start_in_hist)  ? frac_left
-                             : (h_idx == stop_in_hist) ? frac_right
-                                                       : 1.0;
-        hist[h_idx] += contrib * as_frac(gcs[i][gc_idx], increm);
-      }
+        splits ? next_percent - static_cast<double>(stop_in_hist) : increment;
+      const auto hist_begin = std::begin(hist) + start_in_hist;
+      const auto hist_end = std::cbegin(hist) + stop_in_hist;
+      const auto gc_val = as_frac(gc[gc_idx], increment);
+      for (auto hist_itr = hist_begin; hist_itr <= hist_end; ++hist_itr)
+        *hist_itr += gc_val * ((hist_itr == hist_begin) ? frac_left
+                               : (hist_itr == hist_end) ? frac_right
+                                                        : 1.0);
     }
   }
   return hist;