Engineering

CHANGES.md

@@ -1,7 +1,84 @@
 # NCBI External Developer Release:
 
 
-## SRA Toolkit 3.0.0
+## NCBI NGS Toolkit 3.3.0
+**November 18, 2025**
+
+  **ngs-tools**: fixed deprecation  
+
+
+## NCBI NGS Toolkit 3.2.0
+**January 14, 2025**
+
+  **sra-tools, ngs-tools**: SRA Tools were moved from _ngs-tools_ to _sra-tools_  
+
+
+## NCBI NGS Toolkit 3.1.1
+**May 21, 2024**
+
+  **ngs-tools**: changed version to match that of _sra-tools_  
+
+
+## NCBI NGS Toolkit 3.1.0
+**March 5, 2024**
+
+  **cloud, kns, ngs-tools, sra-tools**: don't change global network timeouts when checking cloud location  
+  **kns, ngs-tools, sra-tools**: fixed hanging on Mac and BSD when data access is unreliable  
+
+
+## NCBI NGS Toolkit 3.0.10
+**December 19, 2023**
+
+  **cloud, ngs-tools, sra-tools**: accept AWS credentials in CSV format; warn when credentials file cannot be loaded; don't load credentials if user doesn't agree to pay  
+  **cloud, ngs-tools, sra-tools**: fixed support of IMDSv2 to allow instance identity on Amazon Linux 2023  
+  **kns, ngs-tools, sra-tools, vfs**: print NCBI_PHID after error in names resolving to simplify troubleshooting  
+  **ncbi-vdb, ngs-tools, sra-tools**: added support for Arm64  
+  **ngs-tools, sra-tools, vdb, vfs**: avoids multiple calls to resolve the same accession  
+
+
+## NCBI NGS Toolkit 3.0.8
+**September 19, 2023**
+
+  **ngs-tools**: changed version to match that of _sra-tools_
+
+
+## NCBI NGS Toolkit 3.0.7
+**August 29, 2023**
+
+  **cloud, kns, ngs-tools, sra-tools**: added support of IMDSv2 to allow to use instance identity on new AWS machines  
+  **cloud, ngs-tools, sra-tools, vdb-config**: fixed use of AWS credentials  
+  **kns, ngs, ngs-tools, sra-tools**: fixed a bug that caused failure during accession resolution while reading HTTP stream  
+
+
+## NCBI NGS Toolkit 3.0.6
+**July 10, 2023**
+
+  **ngs-tools**: changed version to match that of _sra-tools_
+
+
+## NCBI NGS Toolkit 3.0.5
+**May 9, 2023**
+
+  **kfg, ngs-tools, sra-tools, vfs**: stopped using old names resolver cgi  
+  **ngs-tools**: updated aligns_to to use the latest libraries  
+
+
+## NCBI NGS Toolkit 3.0.2
+**December 12, 2022**
+
+  **ngs-tools**: changed version to match that of _sra-tools_
+
+
+## NCBI NGS Toolkit 3.0.1
+**November 15, 2022**
+
+  **build**: added support for overriding cmake and ctest commands  
+  **build**: will use a system-provided libmbedtls, otherwise the copy included in the source code will be used  
+  **ngs-tools**: fixed configure script  
+  **ref-variation**: added libraries and tools: ngs-vdb, general-writer, ref-variation, sra-search, general-loader, pileup-stats  
+
+
+## NCBI NGS Toolkit 3.0.0
 **February 10, 2022**
 
   **ngs-tools**: updated for _sra-tools 3.0.0_

CMakeLists.txt

@@ -1,8 +1,4 @@
-cmake_minimum_required (VERSION 2.8.12)
-
-message(CMAKE_VERSION = ${CMAKE_VERSION})
-
-set ( CMAKE_OSX_DEPLOYMENT_TARGET 10.10 )
+cmake_minimum_required (VERSION 2.8.12...3.28)
 
 set ( CMAKE_CXX_EXTENSIONS OFF )
 if (CMAKE_VERSION VERSION_LESS "3.1")
@@ -13,20 +9,20 @@ else ()
    message(CMAKE_CXX_STANDARD = ${CMAKE_CXX_STANDARD})
 endif ()
 
-
-set(CMAKE_VERBOSE_MAKEFILE ON)
-
 # best to use at the top
 project ( ngs-tools )
+if( PROJECT_SOURCE_DIR STREQUAL PROJECT_BINARY_DIR )
+    message(FATAL_ERROR "In-source builds are not supported")
+endif()
+
 
 # this has to follow the project() command!
 set(CMAKE_MODULE_PATH
     ${CMAKE_MODULE_PATH}
     "${CMAKE_CURRENT_SOURCE_DIR}/build"
 )
-include ( env )
+include ( env NO_POLICY_SCOPE )
 
-add_subdirectory(libs)
 add_subdirectory(tools)
 add_subdirectory(test)
 

build/.gitignore

@@ -1,6 +1,2 @@
-.cvsignore
-RHOST* ARCH* BUILD* COMP* OUTDIR*
-STATIC
 ld.linux.exe_cmd.sh
-LNKG.*
 Makefile.config*