ablab · asl · Feb 25, 2026 · Feb 25, 2026 · Feb 25, 2026 · Mar 16, 2026
diff --git a/docs/installation.md b/docs/installation.md
@@ -58,7 +58,7 @@ Just as in Linux, SPAdes is ready to use and no further installation steps are r
 If you wish to compile SPAdes by yourself you will need the following libraries to be pre-installed:
 
 -   g++ (version 9 or higher)
--   cmake (version 3.16 or higher)
+-   cmake (version 3.18 or higher)
 -   zlib
 -   libbz2
 

diff --git a/ext/src/CMakeLists.txt b/ext/src/CMakeLists.txt
@@ -31,6 +31,7 @@ add_subdirectory(llvm)
 add_subdirectory(bwa)
 add_subdirectory(gqf)
 add_subdirectory(edlib)
+set(LEXY_ENABLE_INSTALL OFF)
 add_subdirectory(lexy)
 add_subdirectory(easel)
 add_subdirectory(hmmer)

diff --git a/ext/src/mimalloc/.gitignore b/ext/src/mimalloc/.gitignore
@@ -1,8 +1,13 @@
+build
 ide/vs20??/*.db
 ide/vs20??/*.opendb
 ide/vs20??/*.user
-ide/vs20??/*.vcxproj.filters
 ide/vs20??/.vs
+ide/vs20??/VTune*
 out/
 docs/
 *.zip
+*.tar
+*.gz
+.vscode
+.DS_STore
diff --git a/ext/src/mimalloc/CMakeLists.txt b/ext/src/mimalloc/CMakeLists.txt
diff --git a/ext/src/mimalloc/LICENSE b/ext/src/mimalloc/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018-2021 Microsoft Corporation, Daan Leijen
+Copyright (c) 2018-2025 Microsoft Corporation, Daan Leijen
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/ext/src/mimalloc/SECURITY.md b/ext/src/mimalloc/SECURITY.md
@@ -0,0 +1,41 @@
+<!-- BEGIN MICROSOFT SECURITY.MD V0.0.9 BLOCK -->
+
+## Security
+
+Microsoft takes the security of our software products and services seriously, which includes all source code repositories managed through our GitHub organizations, which include [Microsoft](https://github.com/Microsoft), [Azure](https://github.com/Azure), [DotNet](https://github.com/dotnet), [AspNet](https://github.com/aspnet) and [Xamarin](https://github.com/xamarin).
+
+If you believe you have found a security vulnerability in any Microsoft-owned repository that meets [Microsoft's definition of a security vulnerability](https://aka.ms/security.md/definition), please report it to us as described below.
+
+## Reporting Security Issues
+
+**Please do not report security vulnerabilities through public GitHub issues.**
+
+Instead, please report them to the Microsoft Security Response Center (MSRC) at [https://msrc.microsoft.com/create-report](https://aka.ms/security.md/msrc/create-report).
+
+If you prefer to submit without logging in, send email to [secure@microsoft.com](mailto:secure@microsoft.com).  If possible, encrypt your message with our PGP key; please download it from the [Microsoft Security Response Center PGP Key page](https://aka.ms/security.md/msrc/pgp).
+
+You should receive a response within 24 hours. If for some reason you do not, please follow up via email to ensure we received your original message. Additional information can be found at [microsoft.com/msrc](https://www.microsoft.com/msrc). 
+
+Please include the requested information listed below (as much as you can provide) to help us better understand the nature and scope of the possible issue:
+
+  * Type of issue (e.g. buffer overflow, SQL injection, cross-site scripting, etc.)
+  * Full paths of source file(s) related to the manifestation of the issue
+  * The location of the affected source code (tag/branch/commit or direct URL)
+  * Any special configuration required to reproduce the issue
+  * Step-by-step instructions to reproduce the issue
+  * Proof-of-concept or exploit code (if possible)
+  * Impact of the issue, including how an attacker might exploit the issue
+
+This information will help us triage your report more quickly.
+
+If you are reporting for a bug bounty, more complete reports can contribute to a higher bounty award. Please visit our [Microsoft Bug Bounty Program](https://aka.ms/security.md/msrc/bounty) page for more details about our active programs.
+
+## Preferred Languages
+
+We prefer all communications to be in English.
+
+## Policy
+
+Microsoft follows the principle of [Coordinated Vulnerability Disclosure](https://aka.ms/security.md/cvd).
+
+<!-- END MICROSOFT SECURITY.MD BLOCK -->
diff --git a/ext/src/mimalloc/azure-pipelines.yml b/ext/src/mimalloc/azure-pipelines.yml
@@ -6,16 +6,15 @@
 trigger:
   branches:
     include:
-    - master
-    - dev
-    - dev-slice
+    - main
+    - dev*
   tags:
     include:
     - v*
 
-jobs:  
+jobs:
 - job:
-  displayName: Windows
+  displayName: Windows 2022
   pool:
     vmImage:
       windows-2022
@@ -29,10 +28,30 @@ jobs:
         BuildType: release
         cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Release
         MSBuildConfiguration: Release
+      Release SIMD:
+        BuildType: release-simd
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Release -DMI_OPT_ARCH=ON -DMI_OPT_SIMD=ON -DMI_WIN_USE_FIXED_TLS=ON
+        MSBuildConfiguration: Release
       Secure:
         BuildType: secure
         cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Release -DMI_SECURE=ON
         MSBuildConfiguration: Release
+      Debug x86:
+        BuildType: debug
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Debug -DMI_DEBUG_FULL=ON -A Win32
+        MSBuildConfiguration: Debug
+      Release x86:
+        BuildType: release
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Release -A Win32
+        MSBuildConfiguration: Release
+      Debug Fixed TLS:
+        BuildType: debug
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Debug -DMI_DEBUG_FULL=ON -DMI_WIN_USE_FIXED_TLS=ON
+        MSBuildConfiguration: Debug
+      Release Fixed TLS:
+        BuildType: release
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Release -DMI_WIN_USE_FIXED_TLS=ON
+        MSBuildConfiguration: Release
   steps:
   - task: CMake@1
     inputs:
@@ -43,7 +62,7 @@ jobs:
       solution: $(BuildType)/libmimalloc.sln
       configuration: '$(MSBuildConfiguration)'
       msbuildArguments: -m
-  - script: ctest --verbose --timeout 120 -C $(MSBuildConfiguration)
+  - script: ctest --verbose --timeout 240 -C $(MSBuildConfiguration)
     workingDirectory: $(BuildType)
     displayName: CTest
   #- script: $(BuildType)\$(BuildType)\mimalloc-test-stress
@@ -52,10 +71,10 @@ jobs:
   #  artifact: mimalloc-windows-$(BuildType)
 
 - job:
-  displayName: Linux
+  displayName: Ubuntu 22.04
   pool:
     vmImage:
-     ubuntu-18.04
+     ubuntu-22.04
   strategy:
     matrix:
       Debug:
@@ -88,6 +107,11 @@ jobs:
         CXX: clang++
         BuildType: release-clang
         cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Release
+      Release SIMD Clang:
+        CC: clang
+        CXX: clang++
+        BuildType: release-simd-clang
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Release -DMI_OPT_ARCH=ON -DMI_OPT_SIMD=ON
       Secure Clang:
         CC: clang
         CXX: clang++
@@ -98,24 +122,47 @@ jobs:
         CXX: clang++
         BuildType: debug-clang-cxx
         cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Debug -DMI_DEBUG_FULL=ON -DMI_USE_CXX=ON
+      Debug ASAN Clang:
+        CC: clang
+        CXX: clang++
+        BuildType: debug-asan-clang
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Debug -DMI_DEBUG_FULL=ON -DMI_TRACK_ASAN=ON
+      Debug UBSAN Clang:
+        CC: clang
+        CXX: clang++
+        BuildType: debug-ubsan-clang
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Debug -DMI_DEBUG_FULL=ON -DMI_DEBUG_UBSAN=ON
+      Debug TSAN Clang++:
+        CC: clang
+        CXX: clang++
+        BuildType: debug-tsan-clang-cxx
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=RelWithDebInfo -DMI_USE_CXX=ON -DMI_DEBUG_TSAN=ON
+      Debug Guarded Clang:
+        CC: clang
+        CXX: clang
+        BuildType: debug-guarded-clang
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=RelWithDebInfo -DMI_DEBUG_FULL=ON -DMI_GUARDED=ON
+
   steps:
   - task: CMake@1
     inputs:
       workingDirectory: $(BuildType)
       cmakeArgs: .. $(cmakeExtraArgs)
   - script: make -j$(nproc) -C $(BuildType)
     displayName: Make
-  - script: ctest --verbose --timeout 120
+  - script: ctest --verbose --timeout 240
     workingDirectory: $(BuildType)
     displayName: CTest
+    env:
+      MIMALLOC_GUARDED_SAMPLE_RATE: 1000
 #  - upload: $(Build.SourcesDirectory)/$(BuildType)
 #    artifact: mimalloc-ubuntu-$(BuildType)
 
 - job:
-  displayName: macOS
+  displayName: macOS 14 (Sonoma)
   pool:
     vmImage:
-      macOS-latest
+      macOS-14
   strategy:
     matrix:
       Debug:
@@ -124,6 +171,9 @@ jobs:
       Release:
         BuildType: release
         cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Release
+      Release SIMD:
+        BuildType: release-simd
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Release -DMI_OPT_ARCH=ON -DMI_OPT_SIMD=ON
       Secure:
         BuildType: secure
         cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Release -DMI_SECURE=ON
@@ -134,48 +184,79 @@ jobs:
       cmakeArgs: .. $(cmakeExtraArgs)
   - script: make -j$(sysctl -n hw.ncpu) -C $(BuildType)
     displayName: Make
-  # - script: MIMALLOC_VERBOSE=1 ./mimalloc-test-api
-  #   workingDirectory: $(BuildType)
-  #   displayName: TestAPI
-  # - script: MIMALLOC_VERBOSE=1 ./mimalloc-test-stress
-  #   workingDirectory: $(BuildType)
-  #   displayName: TestStress    
-  - script: ctest --verbose --timeout 120
+  - script: ctest --verbose --timeout 240
     workingDirectory: $(BuildType)
     displayName: CTest
-
 #  - upload: $(Build.SourcesDirectory)/$(BuildType)
 #    artifact: mimalloc-macos-$(BuildType)
 
-# - job:
-#   displayName: Windows-2017
-#   pool:
-#     vmImage:
-#       vs2017-win2016
-#   strategy:
-#     matrix:
-#       Debug:
-#         BuildType: debug
-#         cmakeExtraArgs: -A x64 -DCMAKE_BUILD_TYPE=Debug -DMI_DEBUG_FULL=ON
-#         MSBuildConfiguration: Debug
-#       Release:
-#         BuildType: release
-#         cmakeExtraArgs: -A x64 -DCMAKE_BUILD_TYPE=Release
-#         MSBuildConfiguration: Release
-#       Secure:
-#         BuildType: secure
-#         cmakeExtraArgs: -A x64 -DCMAKE_BUILD_TYPE=Release -DMI_SECURE=ON
-#         MSBuildConfiguration: Release
-#   steps:
-#   - task: CMake@1
-#     inputs:
-#       workingDirectory: $(BuildType)
-#       cmakeArgs: .. $(cmakeExtraArgs)
-#   - task: MSBuild@1
-#     inputs:
-#       solution: $(BuildType)/libmimalloc.sln
-#       configuration: '$(MSBuildConfiguration)'
-#   - script: |
-#       cd $(BuildType)
-#       ctest --verbose --timeout 120
-#     displayName: CTest
+# ----------------------------------------------------------
+# Other OS versions (just debug mode)
+# ----------------------------------------------------------
+
+- job:
+  displayName: Ubuntu 24.04
+  pool:
+    vmImage:
+      ubuntu-24.04
+  strategy:
+    matrix:
+      Debug:
+        CC: gcc
+        CXX: g++
+        BuildType: debug
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Debug -DMI_DEBUG_FULL=ON
+      Debug++:
+        CC: gcc
+        CXX: g++
+        BuildType: debug-cxx
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Debug -DMI_DEBUG_FULL=ON -DMI_USE_CXX=ON
+      Debug Clang:
+        CC: clang
+        CXX: clang++
+        BuildType: debug-clang
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Debug -DMI_DEBUG_FULL=ON
+      Debug++ Clang:
+        CC: clang
+        CXX: clang++
+        BuildType: debug-clang-cxx
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Debug -DMI_DEBUG_FULL=ON -DMI_USE_CXX=ON
+      Release Clang:
+        CC: clang
+        CXX: clang++
+        BuildType: release-clang
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Release
+  steps:
+  - task: CMake@1
+    inputs:
+      workingDirectory: $(BuildType)
+      cmakeArgs: .. $(cmakeExtraArgs)
+  - script: make -j$(nproc) -C $(BuildType)
+    displayName: Make
+  - script: ctest --verbose --timeout 240
+    workingDirectory: $(BuildType)
+    displayName: CTest
+
+- job:
+  displayName: macOS 15 (Sequoia)
+  pool:
+    vmImage:
+      macOS-15
+  strategy:
+    matrix:
+      Debug:
+        BuildType: debug
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Debug -DMI_DEBUG_FULL=ON
+      Release:
+        BuildType: release
+        cmakeExtraArgs: -DCMAKE_BUILD_TYPE=Release
+  steps:
+  - task: CMake@1
+    inputs:
+      workingDirectory: $(BuildType)
+      cmakeArgs: .. $(cmakeExtraArgs)
+  - script: make -j$(sysctl -n hw.ncpu) -C $(BuildType)
+    displayName: Make
+  - script: ctest --verbose --timeout 240
+    workingDirectory: $(BuildType)
+    displayName: CTest
diff --git a/ext/src/mimalloc/cmake/JoinPaths.cmake b/ext/src/mimalloc/cmake/JoinPaths.cmake
@@ -0,0 +1,23 @@
+# This module provides function for joining paths
+# known from most languages
+#
+# SPDX-License-Identifier: (MIT OR CC0-1.0)
+# Copyright 2020 Jan Tojnar
+# https://github.com/jtojnar/cmake-snips
+#
+# Modelled after Python’s os.path.join
+# https://docs.python.org/3.7/library/os.path.html#os.path.join
+# Windows not supported
+function(join_paths joined_path first_path_segment)
+    set(temp_path "${first_path_segment}")
+    foreach(current_segment IN LISTS ARGN)
+        if(NOT ("${current_segment}" STREQUAL ""))
+            if(IS_ABSOLUTE "${current_segment}")
+                set(temp_path "${current_segment}")
+            else()
+                set(temp_path "${temp_path}/${current_segment}")
+            endif()
+        endif()
+    endforeach()
+    set(${joined_path} "${temp_path}" PARENT_SCOPE)
+endfunction()
diff --git a/ext/src/mimalloc/cmake/mimalloc-config-version.cmake b/ext/src/mimalloc/cmake/mimalloc-config-version.cmake
@@ -1,6 +1,6 @@
-set(mi_version_major 2)
-set(mi_version_minor 0)
-set(mi_version_patch 6)
+set(mi_version_major 3)
+set(mi_version_minor 2)
+set(mi_version_patch 8)
 set(mi_version ${mi_version_major}.${mi_version_minor})
 
 set(PACKAGE_VERSION ${mi_version})