Update dependencies and fix warnings

Author: nicolaasuni

.github/workflows/check.yaml

@@ -9,8 +9,8 @@ on:
       - 'main'
 
 env:
-  NODE_VERSION: 22
-  PYTHON_VERSION: 3.12
+  NODE_VERSION: '22'
+  PYTHON_VERSION: '3.13'
 
 permissions:
   contents: read
@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: install dependencies
         run: sudo apt install -y lcov astyle
       - name: set RELEASE number
@@ -37,9 +37,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: setup go build environment
-        uses: actions/setup-go@v5
+        uses: actions/setup-go@v6
         with:
           go-version-file: 'go.mod'
           check-latest: true
@@ -52,9 +52,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: setup node build environment
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@v5
         with:
           node-version: ${{ env.NODE_VERSION }}
       - name: install dependencies
@@ -68,9 +68,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: setup python build environment
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Install dependencies
@@ -86,9 +86,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: setup python build environment
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Install dependencies
@@ -104,7 +104,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: setup R build environment
         uses: r-lib/actions/setup-r@v2
       - name: Install dependencies

VERSION

@@ -1 +1 @@
-5.7.9
+5.7.10

c/CMakeLists.txt

@@ -29,7 +29,7 @@ option(BUILD_SHARED_LIB "Build a shared library" ON)
 if(CMAKE_COMPILER_IS_GNUCC)
     message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
     execute_process(COMMAND ${CMAKE_C_COMPILER} -dumpversion OUTPUT_VARIABLE GCC_VERSION)
-    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D VERSION='\"${PROJECT_VERSION}\"' -s -pedantic -std=c17 -Wall -Wextra -Wno-strict-prototypes -Wcast-align -Wundef -Wformat -Wformat-security")
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D VERSION='\"${PROJECT_VERSION}\"' -s -pedantic -std=c2x -Wall -Wextra -Wno-strict-prototypes -Wcast-align -Wundef -Wformat -Wformat-security")
 
     if (GCC_VERSION VERSION_GREATER 4.8 OR GCC_VERSION VERSION_EQUAL 4.8)
         set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wshadow")

c/Makefile

@@ -58,7 +58,6 @@ help:
 	@echo "$(PROJECT) Makefile."
 	@echo "The following commands are available:"
 	@echo ""
-	@echo "  make qa        : Run all the tests and static analysis reports"
 	@echo "  make test      : Run the unit tests"
 	@echo "  make tidy      : Check the code using clang-tidy"
 	@echo "  make build     : Build the library"
@@ -77,7 +76,7 @@ all: clean version format test tidy build rpm deb package_vk doc
 # Test C code compatibility with C++
 .PHONY: testcpp
 testcpp:
-	find ./src/variantkey -type f -name '*.h' -exec gcc -c -pedantic -Werror -Wall -Wextra -Wcast-align -Wundef -Wformat-security -std=c++17 -x c++ -o /dev/null {} \;
+	find ./src/variantkey -type f -name '*.h' -exec gcc -c -pedantic -Werror -Wall -Wextra -Wcast-align -Wundef -Wformat-security -std=c++23 -x c++ -o /dev/null {} \;
 
 # Build and run the unit tests
 .PHONY: test

c/doc/Doxyfile

@@ -32,7 +32,7 @@ PROJECT_NAME           = "VariantKey"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER = 5.7.9
+PROJECT_NUMBER = 5.7.10
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -922,12 +922,6 @@ HTML_COLORSTYLE_SAT    = 100
 
 HTML_COLORSTYLE_GAMMA  = 80
 
-# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-# page will contain the date and time when the page was generated. Setting
-# this to NO can help when comparing the output of multiple runs.
-
-HTML_TIMESTAMP         = NO
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded.
@@ -1142,14 +1136,6 @@ EXT_LINKS_IN_WINDOW    = NO
 
 FORMULA_FONTSIZE       = 10
 
-# Use the FORMULA_TRANPARENT tag to determine whether or not the images
-# generated for formulas are transparent PNGs. Transparent PNGs are
-# not supported properly for IE 6.0, but are supported on all modern browsers.
-# Note that when changing this option you need to delete any form_*.png files
-# in the HTML output before the changes have effect.
-
-FORMULA_TRANSPARENT    = YES
-
 # Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
 # (see http://www.mathjax.org) which uses client side Javascript for the
 # rendering instead of using prerendered bitmaps. Use this if you do not
@@ -1567,20 +1553,6 @@ HAVE_DOT               = NO
 
 DOT_NUM_THREADS        = 0
 
-# By default doxygen will use the Helvetica font for all dot files that
-# doxygen generates. When you want a differently looking font you can specify
-# the font name using DOT_FONTNAME. You need to make sure dot is able to find
-# the font, which can be done by putting it in a standard location or by setting
-# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
-# directory containing the font.
-
-DOT_FONTNAME           = Helvetica
-
-# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
-# The default size is 10pt.
-
-DOT_FONTSIZE           = 10
-
 # By default doxygen will tell dot to use the Helvetica font.
 # If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
 # set the path where dot can find it.
@@ -1722,14 +1694,6 @@ DOT_GRAPH_MAX_NODES    = 50
 
 MAX_DOT_GRAPH_DEPTH    = 0
 
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, because dot on Windows does not
-# seem to support this out of the box. Warning: Depending on the platform used,
-# enabling this option may lead to badly anti-aliased labels on the edges of
-# a graph (i.e. they become hard to read).
-
-DOT_TRANSPARENT        = NO
-
 # Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
 # files in one run (i.e. multiple -o and -T options on the command line). This
 # makes dot run faster, but since only newer versions of dot (>1.8.10)

c/src/variantkey/binsearch.h

@@ -44,6 +44,7 @@
 #include <inttypes.h>
 #include <fcntl.h>
 #include <stdbool.h>
+#include <stdint.h>
 #include <unistd.h>
 #include <sys/mman.h>
 #include <sys/stat.h>
@@ -989,7 +990,8 @@ static inline void mmap_binfile(const char *file, mmfile_t *mf)
     mf->dlength = 0;
     mf->nrows = 0;
     struct stat statbuf;
-    if (((mf->fd = open(file, O_RDONLY)) < 0) || (fstat(mf->fd, &statbuf) < 0))
+    mf->fd = open(file, O_RDONLY);
+    if ((mf->fd < 0) || (fstat(mf->fd, &statbuf) < 0))
     {
         return;
     }

c/src/variantkey/esid.h

@@ -18,6 +18,7 @@
 #define VARIANTKEY_ESID_H
 
 #include <inttypes.h>
+#include <stdint.h>
 #include <stdio.h>
 
 #define ESID_MAXLEN   10 //!< Maximum number of characters that can be encoded
@@ -333,6 +334,9 @@ static inline uint64_t hash_string_id(const char *str, size_t size)
     // fall through
     case 1:
         v ^= (uint64_t)tail[0];
+        break;
+    default:
+        break;
     }
     if (v > 0)
     {

c/src/variantkey/genoref.h

@@ -21,6 +21,8 @@
 #ifndef VARIANTKEY_GENOREF_H
 #define VARIANTKEY_GENOREF_H
 
+#include <inttypes.h>
+#include <stdint.h>
 #include <stdio.h>
 #include <string.h>
 #include "binsearch.h"

c/src/variantkey/hex.h

@@ -18,6 +18,7 @@
 #define VARIANTKEY_HEX_H
 
 #include <inttypes.h>
+#include <stdint.h>
 #include <stdio.h>
 
 /** @brief Returns uint64_t hexadecimal string (16 characters).

c/src/variantkey/nrvk.h

@@ -30,6 +30,8 @@
 #ifndef VARIANTKEY_NRVK_H
 #define VARIANTKEY_NRVK_H
 
+#include <inttypes.h>
+#include <stdint.h>
 #include <stdio.h>
 #include <string.h>
 #include "binsearch.h"