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nixpkgs/pkgs/by-name/mi/minia/no-bundle.patch
aleksana 571c71e6f7 treewide: migrate packages to pkgs/by-name, take 1 
We are migrating packages that meet below requirements:

1. using `callPackage`
2. called path is a directory
3. overriding set is empty (`{ }`)
4. not containing path expressions other than relative path (to
makenixpkgs-vet happy)
5. not referenced by nix files outside of the directory, other
than`pkgs/top-level/all-packages.nix`
6. not referencing nix files outside of the directory
7. not referencing `default.nix` (since it's changed to `package.nix`)
8. `outPath` doesn't change after migration

The tool is here: https://github.com/Aleksanaa/by-name-migrate.
2024-11-09 20:04:51 +08:00

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diff --git a/thirdparty/gatb-core/gatb-core/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/CMakeLists.txt
index f48a70b..0e11ece 100644
--- a/thirdparty/gatb-core/gatb-core/CMakeLists.txt
+++ b/thirdparty/gatb-core/gatb-core/CMakeLists.txt
@@ -257,7 +257,6 @@ ADD_SUBDIRECTORY(thirdparty)
# DEPENDENCIES
################################################################################
# we must be sure that hdf5 is built and installed before building gatb-core
-ADD_DEPENDENCIES (gatbcore-static hdf5 hdf5_postbuild)
################################################################################
# DOCUMENTATION GENERATION
@@ -288,7 +287,6 @@ IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt DESTINATION . OPTIONAL)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE DESTINATION . OPTIONAL)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md DESTINATION . OPTIONAL)
- INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include)
ENDIF()
################################################################################
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
index dfeee1c..d5553a2 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
@@ -35,7 +35,7 @@
#include <stdint.h>
#include <algorithm>
#include <iostream>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
#include <gatb/system/api/Exception.hpp>
#include <gatb/system/api/config.hpp>
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
index 60be5d5..25ae75e 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
@@ -33,7 +33,7 @@
/********************************************************************************/
#include <iostream>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
#include <gatb/system/api/types.hpp>
#include <gatb/tools/misc/api/Abundance.hpp>
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
index 6a71bb0..b9205df 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
@@ -31,7 +31,7 @@
#include <iostream>
#include <gatb/system/api/types.hpp>
#include <gatb/tools/misc/api/Abundance.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
/********************************************************************************/
namespace gatb {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
index c22b892..62e6586 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
@@ -31,7 +31,7 @@
#include <iostream>
#include <gatb/system/api/types.hpp>
#include <gatb/tools/misc/api/Abundance.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
/********************************************************************************/
namespace gatb {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
index c06aaab..e0befba 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
@@ -31,7 +31,7 @@
#include <iostream>
#include <gatb/system/api/types.hpp>
#include <gatb/tools/misc/api/Abundance.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
extern const unsigned char revcomp_4NT[];
extern const unsigned char comp_NT [];
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
index 9659874..0c79ff6 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
@@ -31,7 +31,7 @@
#include <iostream>
#include <gatb/system/api/types.hpp>
#include <gatb/tools/misc/api/Abundance.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
/********************************************************************************/
namespace gatb {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
index 3cb84f8..cd5d382 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
@@ -31,7 +31,7 @@
/********************************************************************************/
#include <sys/types.h>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
/********************************************************************************/
namespace gatb {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
index b8f6c79..a040832 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
@@ -28,7 +28,7 @@
#include <gatb/system/api/ISmartPointer.hpp>
#include <gatb/tools/storage/impl/Storage.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
/********************************************************************************/
namespace gatb {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
index 2645abd..fad48c0 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
@@ -40,7 +40,7 @@
#include <string>
#include <vector>
#include <stdarg.h>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
/********************************************************************************/
namespace gatb {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
index a92b729..66d552f 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
@@ -40,7 +40,7 @@
#include <string>
#include <vector>
#include <stdarg.h>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
/********************************************************************************/
namespace gatb {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
index 29e0949..0565cc4 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
@@ -33,7 +33,7 @@
#include <gatb/tools/storage/impl/CollectionHDF5.hpp>
#include <gatb/tools/storage/impl/CollectionHDF5Patch.hpp>
#include <gatb/system/impl/System.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
#include <sstream>
/********************************************************************************/
diff --git a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
index 6e0b5c4..34aef28 100644
--- a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
+++ b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
@@ -1,54 +1,3 @@
-################################################################################
-# HDF5 GENERATION
-################################################################################
-
-#SET (HDF5_ENABLE_THREADSAFE ON)
-#SET (H5_HAVE_THREADSAFE 1)
-
-########## MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED ##########
-SET (HDF5_BUILD_TOOLS ON CACHE BOOL "Build HDF5 Tools")
-#SET (CMAKE_EXE_LINKER_FLAGS "-lpthread -lz")
-
-SET (HDF5_EXTERNALLY_CONFIGURED ON)
-
-#SET (HDF5_INSTALL_BIN_DIR ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE})
-#SET (HDF5_INSTALL_LIB_DIR ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE})
-SET (HDF5_INSTALL_BIN_DIR bin)
-SET (HDF5_INSTALL_LIB_DIR lib)
-
-SET (HDF5_INSTALL_INCLUDE_DIR ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5)
-SET (HDF5_INSTALL_DATA_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
-SET (HDF5_INSTALL_CMAKE_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
-
-IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
- SET (HDF5_EXPORTED_TARGETS "gatb-hdf5")
-ENDIF()
-
-IF (NOT DEFINED GATB_CORE_EXCLUDE_HDF5_ZLIB)
- OPTION (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON)
-ENDIF()
-
-# We don't want warnings from HDF5 compilation
-set (COMPILE_DEFINITIONS "${COMPILE_DEFINITIONS} -w")
-add_definitions (${COMPILE_DEFINITIONS})
-
-# add HDF5 generation
-ADD_SUBDIRECTORY (hdf5)
-
-# We add a custom target for copying header files.
-add_custom_target (hdf5_postbuild ALL)
-
-# We build the output directory
-add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR})
-
-# We define all the header files to be copied
-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h)
-
-# We copy each header file
-foreach (header ${headerfiles})
- add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR} )
-endforeach()
-
# include other smaller libraries (json, Boophf)
add_custom_target (thirdparty_copy ALL)
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