2075 Commits

Author SHA1 Message Date
Allen Byrne
526f0769a3
Minor fixes for CMake code and install docs (#2623) 2023-04-03 14:38:10 -07:00
Allen Byrne
fa388e6ba4
Update java logger version (#2643) 2023-04-03 14:36:23 -07:00
Allen Byrne
2ca2a300ac
Change libaec URL to actively maintained repo GH#2552 (#2559) 2023-03-15 18:48:54 -05:00
Mark Kittisopikul
5d3d43b1ee
Fix new codespell issues (#2521)
* Fix new codespell issues

* Have codespell ignore ./config/sanitizer/sanitizers.cmake
2023-03-08 14:42:47 -06:00
Allen Byrne
7b833f04b5
Update cross compile checks and files (#2497) 2023-03-02 11:18:13 -06:00
Allen Byrne
d7128d144b
Add fetchcontent for compression libs and fix cmake config (#2487)
* Add fetchcontent for compression libs and fix cmake config

* MSDOS is a reserved define name

* Add release note and update install doc for FetchContent

* Add CI test for FetchContent

* Use LINK_COMP_LIBS instead of STATIC_LIBRARY for depends

* Use general link
2023-02-26 15:06:14 -08:00
Allen Byrne
7ff3eac667
Remove space from toolchain name (#2482)
* Remove space from toolchain name

* Another space removed
2023-02-21 06:24:53 -08:00
Allen Byrne
bfef9945a8
Develop toolchain lowercase names and updates (#2426)
* lowercase the toolchain filenames

* Change name of option define

* Update CI with changed toolchain name

* Correct Intel compiler names

* Account for Intels name for compiler based on clang

* Make icx default and rename classic to icc
2023-02-17 14:37:26 -08:00
Allen Byrne
32a54c0e2e
CMake generated pkg-config file is incorrect #2259 (#2476)
* CMake generated pkg-config file is incorrect #2259

* Fix fortran pc template

* hdf5.pc is incorrect for debug builds #1546

* Correct pkg name and lib name

* Fix typo

* Fix missing space
2023-02-17 14:17:17 -08:00
kwryankrattiger
509fe962d4
CMake: Find MPI in HDF5 CMake config (#2400) 2023-01-18 16:26:35 -06:00
Mark Kittisopikul
720e04e196
Include shlwapi.h explicitly on Windows (#2407)
* Include shlwapi.h explicitly

* Add shlwapi library to LINK_LIB when header is detected

Looking for StrStrIA in the shlwapi library is not reliable due
to stdcall on mingw32.
2023-01-17 07:27:25 -08:00
Dana Robinson
83f81a6422
Adds -Warray-temporaries to the developer warnings (#2385)
These generate a LOT of noise that we are not going to address anytime
soon.
2023-01-03 06:18:48 -08:00
Dana Robinson
cfd5059e77
HL GIF tools changes (#2360)
* Fixes the broken Autotools option
* Removes the "build HL tools" option
2022-12-23 16:05:31 -08:00
Allen Byrne
9f5cf0a457
H5F_LIBVER_LATEST changes for move to 1.15 (#2288)
* H5F_LIBVER_LATEST changes for move to 1.15

* Add new default api check

* Format fixes

* Fix default configure

* fix lib version tests

* Fix another version variable

* Add 1.14 doc link
2022-12-21 10:07:25 -08:00
Allen Byrne
96a4e10102
Add aarch64 toolchain and change dump test to long opt (#2271) 2022-12-01 14:32:34 -08:00
Egbert Eich
158dff6b50
Make sure testsuite can handle multiple dependent scripts (#2256)
Commit afc54d75a19 to the test suite to eliminate a separate
shell script did not take into account that there may be
multiple dependent test scripts which resulted in the
message:
`/bin/sh: line 7: [: too many arguments`.
when running the test suite.

Beware that this new version still makes use of non-posix GNU
extensions to `test`.

Signed-off-by: Egbert Eich <eich@suse.com>

Signed-off-by: Egbert Eich <eich@suse.com>
2022-11-28 13:19:31 -06:00
Scot Breitenfeld
03cc221016
moved quad precision checks (#2252)
* Only check quad sizes if fortran is enabled

* fixed if struct
2022-11-12 12:53:35 -06:00
Dana Robinson
d93c6fae43
Removes MPE instrumentation support. (#2245)
* Removes MPE instrumentation support.

The Autotools will no longer accept --with-mpe= and the logging commands
have been removed from the FUNC_ENTER macros. CMake has never supported
instrumenting for MPE.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-11-09 11:06:26 -08:00
Dana Robinson
0f30852242
Removes dmalloc support (#2239)
This has not been used to debug the library in a very long time. Most
developers use valgrind, -fsanitize=address, or some other memory checker
instead of this library.

This removes:
    * dmalloc.h include from H5private.h
    * --with-dmalloc= Autotools configure option
    * HDF5_ENABLE_USING_DMALLOC CMake option
2022-11-09 09:22:14 -08:00
Dana Robinson
018f093c09
Removes the memory allocation sanity checks feature (#2218)
* Removes the memory allocation sanity checks feature

* Committing clang-format changes

* Removes zero size checks for H5MM_(c|m)alloc()

* Explicitly return NULL when size == 0 in H5allocate_memory()

* Committing clang-format changes

* Format fix

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-11-03 16:30:08 -07:00
Larry Knox
6924d590cc
Use ctest_test and APPEND to correctly report passed and failed test numbers in CDash (#2208)
* Change how HPC tests are executed

* Move ctest_test commands for serial and parallel tests into cmake files.

* Update checks for uploading Test.xml to CDash.

* Correct cmake scripots.

* Remove extraneous characters.

* Add ctest_start (APPEND).

* Add binary directories to scripts running ctest_test.

* Correct parameters for appending Test.xml.

* Set CTEST_SITE and CTEST_BUILD_NAME.

* Try to pass site and build_name to ctest_test sripts.

* Add site name and build name for ctest_test commands vi environment.

* Revert "Try to pass site and build_name to ctest_test sripts."

This reverts commit d364aaf0fa65ee7f9e222b2633ee916d50afbc42.

* Correct typo in src/CMakeLists.txt.

* Update batch scripts to run ctest_test scripts.

Co-authored-by: Allen Byrne <byrn@hdfgroup.org>
2022-11-02 09:02:47 -07:00
Allen Byrne
94119211a7
Correct the CMake link for MPI (#2198) 2022-11-01 16:03:13 -05:00
Larry Knox
11dfa25910
Update copyright headers (#2184)
* Updated source file copyright headers to remove "Copyright by the Board of Trustees
of the University of Illinois", which is kept in the top-level COPYING file.
2022-11-01 16:02:27 -05:00
Larry Knox
0173706826
Update develop branch version to 1.13.4-1 (#2189)
* Updated version to 1.13.4-1 after creating hdf5_1_13_3 branch for 1.13.3
release.
Added new version to exceptions in lines 74-5 of src/H5.c
2022-10-26 11:07:17 -05:00
Allen Byrne
ea902f9ace
Implement option for using CMake GNUInstallDirs (#2175)
* Implement option for using CMake GNUInstallDirs

* Add release notes
2022-10-25 08:50:43 -07:00
Pierce Brooks
a898cef6c2
make sure to match the debug library postfix with external cmake projects and allow for zlib link name to be manually overridden (#2166) 2022-10-19 09:06:51 -05:00
Allen Byrne
853a592d2d
Add missing windows include/lib configure for StrStrIA (#2114) 2022-09-22 13:52:31 -05:00
Frank Berghaus
100b22e6c2
Use case-insensitive comparison for headers fix #2100 (#2101)
* Use case-inseneitive comparison for headers

HTTP headers should be case-insensitive. Use case-insensitive string
comparisons when working with HTTP header responses to ensure
compatibility.

* Revert "Use case-inseneitive comparison for headers"

This reverts commit a02f591723506b62b7208449be6eef7122120398

* Ignore case when searching HTTP header responses

Looking up the Content-Length in the header returned by S3 storage
endpoints should ignore case. To guarantee portability implement a
function for case-insensitive string search, because it is non-standard.

* Add an _ after H5 for the strcasestr implementation

It is a private function and should sport that underscore.

* Remove author comment from the doc comment

* Use search function defined by system if available

Check whether the system provides a function implementing case
insensitive string searches. Only use the custom implementation if the
system does not provide the functionality.

* Add tests for case-insensitive search

Basic tests:
  - Search for empty string
  - Search with exact match
  - Search with case-insensitive match
  - search with no match

* Enforce clang-format style

Some variable definitions in the th5_system tests did not conform to
clang-format's expectations. Updated the offending lines.

* Correct comment describing test case

* Added some spaces to please clang-format

* Ignore discarding const

Ask the compiler to ignore discarding the const when retunring a match from H5_strcasestr

Co-authored-by: Frank Berghaus <frank.berghaus@mpcdf.mpg.de>
2022-09-21 11:50:17 -05:00
Allen Byrne
d491c33a72
Update examples reference to single-source version 2.0.1 (#2107) 2022-09-20 17:21:15 -05:00
Allen Byrne
45178c87a3
develop Merge doxygen from 1.12 branch (#2095) 2022-09-14 15:44:24 -05:00
Allen Byrne
05a0411140
Remove bitbucket.hdfgroup.org dependency. #2082 (#2086)
*
2022-09-07 17:12:55 -05:00
Allen Byrne
c8fdd92cd4
Update CMake code to 3.18 minimum version (#2080)
* Update CMake code to 3.18 minimum version

* Updated release note
2022-09-02 17:31:29 -07:00
Dana Robinson
6e8aaab1b4
Minor changes to CMake comments, etc. (#2078) 2022-08-31 11:03:37 -05:00
Dana Robinson
5097ff016f
Tidying of configure check C code (#2077)
* Tidying of configure check C code

* Fixed missing endif removal
2022-08-29 08:59:15 -07:00
Dana Robinson
08aebb6d1a
Adds documentation for config directory (#2065)
* Adds documentation for config directory

* Fix spelling error
2022-08-24 23:05:28 -07:00
Dana Robinson
ee55dd777b
Fortran module directory improvements (#2060)
* Removes the module directory from the Automake flags as this
  generated a large number of "missing include directory" warnings
  and is unecessary
* Adds the module path to libhdf5.settings
2022-08-23 12:25:07 -07:00
Dana Robinson
f020d129b2
Corrects more Fortran warnings (#2059)
* Moves -Wunused-dummy-arguments to the developer warnings since this
  generates a lot of spurious, unfixable noise due to things like
  callback wrappers
* Changes the return cast in h5fget_fileno_c, fixes a comment, and comment
  on potential badness
* Initializes a variable in tH5L_F03.F90 to quiet a 'maybe
  uninitialized' warning
2022-08-23 08:48:14 -07:00
Dana Robinson
f24dff5157
Quiets Fortran Autotools builds (#2052) 2022-08-22 08:21:06 -07:00
jhendersonHDF
2b786ffe5a
[WIP] Add Developer build mode to CMake (#1659)
* Add Developer build mode to CMake

* Set a few CMake variables for Developer build modes

* Refactor enabling of debug and developer-level compile definitions

* Convert cache debugging macros to normal ifdef style

Normal ifdef-style instead of if-style allows build system to define macros
without warning about redefining macros with different values (0 vs. 1)

* Add HDF5 Developer compile definitions to testing files

* Temporarily disable -fanalyzer flag for GCC 12+ Developer builds
2022-08-19 17:18:30 -07:00
Dana Robinson
7f6261a677
Removes cmake_ext_mod (files moved to cmake) (#2041)
At one time this content was a git submodule shared between several
projects but that time has long passed.
2022-08-19 07:54:42 -07:00
Dana Robinson
afc54d75a1
Replaces bin/newer with -nt comparison in Makefiles (#2020) 2022-08-17 09:21:24 -07:00
Dana Robinson
d6927e49c0
Replaced bin/mkdirs w/ mkdir -p -m 755, which is POSIX (#2018) 2022-08-17 08:02:39 -07:00
Larry Knox
25ef534039
Update version to 1.13.3-1 after creating hdf5_1_13_2 branch for 1.13.2 (#2004)
release.
Added new version to exceptions in line 75 of src/H5.c.
2022-08-12 08:17:25 -05:00
Larry Knox
029cde6111 Revert "Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for release"
This reverts commit c58558e872d529da6eda327183ca2d14cfa91b95.

H5TEST-tcheck_version-release failed.
2022-08-11 22:45:43 -05:00
Larry Knox
c58558e872 Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for release
of HDF5 1.13.2.
2022-08-11 22:15:46 -05:00
Allen Byrne
8d5fcbcdce
Correct target name for szaec lib (#2000) 2022-08-11 15:35:14 -07:00
luzpaz
174505ca3c
Fix typos found in the rest of the hdf5 code-base (#1985)
* Fix typos found in the rest of the hdf5 code-base

* Typo in tool.cmake

* Revert "Typo in tool.cmake"

This reverts commit 06b8403d99757c7d20f1eed530cf317c3d84de4b.

* Fix clang-format styling
2022-08-10 13:57:26 -07:00
luzpaz
f04312a792
Fix bug in cppcheck in tool.cmake (#1988)
Ref: https://github.com/HDFGroup/hdf5/pull/1985#issuecomment-1211046328
2022-08-10 12:19:26 -07:00
Allen Byrne
b84241e57a
Remove stray files, incorrect vds and mpi clean files (#1979) 2022-08-09 08:29:58 -07:00
Allen Byrne
60ba2356de
Revert for older cmake versions (#1974)
* Revert for older cmake versions

* Remove unneeded clear/clean tests because of changes to test macro
2022-08-08 13:01:06 -07:00