Commit Graph

22646 Commits

Author SHA1 Message Date
Scot Breitenfeld
94ea835bbb
speed-up building HDF5 (#3087)
Disables building the tests when building the netCDF, etc.
2023-06-20 16:58:50 -07:00
Larry Knox
7e3c100755
Fix #1978 h5vers usage message. (#3162)
Update Platforms Tested in RELEASE.txt.
2023-06-20 16:57:43 -07:00
Diogo Teles Sant'Anna
b0404e7f9c
Create Security Policy (#3152) 2023-06-18 22:14:56 -07:00
Sean McBride
65d8c93470
Many fixes to various compiler warnings (#3124)
* Fixed various -Wmissing-variable-declarations by adding static keyword
* In a few cases, renamed the variable suffix from _g to _s.
* Fixed some -Wmissing-variable-declarations by using different declaration macros
* Fixed various -Wconditional-uninitialized warnings by just initializing variable to zero
* Fixed various -Wcomma warnings
* Fixed clang -Wstrict-prototypes warnings
* Fixed various -Wunused-variable warnings
* Updated some casts to fix the only 3 -Wcast-qual warnings
* Fixed the only -Wsometimes-uninitialized warning
2023-06-18 22:13:38 -07:00
Allen Byrne
1f20354ee6
Correct the zip usage (#3153) 2023-06-18 21:56:24 -07:00
Dana Robinson
560110dbc7
Removes the HD prefix from java C99 calls (#3149)
POSIX calls (HDstrndup, etc.) are unchanged
2023-06-18 21:55:57 -07:00
H. Joe Lee
a37795d8b9
chore: fix grammar (#3150)
* chore: fix grammar
2023-06-16 12:43:26 -07:00
Allen Byrne
0f2cb0fd91
Fix the snapshots workflow (#3148)
* Add upload url as artifact
* Change doxygen path and comment log-url upload
* zip doxygen files for upload
* add workspace var
2023-06-16 11:34:24 -07:00
mattjala
cef648eb14
Track s3 i/o when S3COMMS_DEBUG enabled (#3139)
* Track s3 i/o when S3COMMS_DEBUG enabled
2023-06-16 09:04:44 -07:00
Diogo Teles Sant'Anna
5e8a230619
Define minimal permissions for new GitHub workflows (#3147) 2023-06-16 07:57:14 -07:00
Jan-Willem Blokland
8135cc280c
CMake: (feature) ROS3 and cmake config file. (#3146)
- Added a cmake variable to the hdf5-config.cmake file which
  indicate if the library has been build with or without the
  read-only S3 functionality.
2023-06-16 07:34:06 -07:00
Dana Robinson
41b474bf4a
Remove hbool_t/TRUE/FALSE from java (#3145)
Replaces with bool/true/false
2023-06-16 07:30:56 -07:00
Dana Robinson
546d79dad7
Remove HD prefix from network calls (#3142)
HDsocket(), etc. Only affects the mirror VFD and its test code.
2023-06-16 00:16:29 -07:00
Sean McBride
68eba3da69
Many clang -Wextra-semi-stmt fixes (#2537)
* Adds semicolons to function-like macros
* Adds a do..while(0) loop to some macros
* Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END
2023-06-15 21:49:02 -07:00
H. Joe Lee
10093f7c43
Fix path to libhdf5.settings in cmakehdf5 (#3140) 2023-06-15 21:46:33 -07:00
Dana Robinson
de2cbcf891
Removed .lnt linter files (#3143)
These were last usefully modified in 2004
2023-06-15 21:36:57 -07:00
mattjala
966d7e1055
Add java options to build scripts (#3127)
* Add java options to build scripts

Previously, cmakehdf5 turned on compiling of the java interface
by default due to a value set in cacheinit.cmake.

Now, consistent with how Fortran and CPP interfaces are handled,
the script overwrites this default value to disable the libraries,
fixing #2958.

I also implemented the --enable-java/--disable java options for
cmakehdf5, and -java for buildhdf5.

Allen said these scripts should mention that
compilers are to be specified in environment variables, but missing
compilers causes errors at the CMake level, and
CMake's error messages are already pretty informative (See the one
in #2958 about JAVA_COMPILER).
2023-06-15 10:20:10 -07:00
Dana Robinson
fcdd0ab9dc
Revert long double checks (#3133)
* Revert "Remove long double conversion work-arounds (#3097)"

This reverts commit 1e1dac1dac.

* Update comments to reflect newer systems
2023-06-15 09:13:22 -07:00
H. Joe Lee
9a8c5810ed
Fix function name in comment in ros3 VFD (#3131) 2023-06-15 07:29:35 -07:00
H. Joe Lee
fcadfca992
Add Python for HDF-EOS zoo description (#3129) 2023-06-14 19:03:26 -07:00
H. Joe Lee
3c122474d0
Make autogen.sh output message consistent (#3128) 2023-06-14 19:01:48 -07:00
Dana Robinson
b571da18fc
Fix spelling issues flagged by codespell (#3130) 2023-06-14 18:59:09 -07:00
Dana Robinson
69e8c8f58d
Clean up mirror VFD code in utils dir (#3121)
* Remove dead code
* Replace mybzero with memset
* Replace hbool_t/TRUE/FALSE with bool/true/false
2023-06-14 08:01:04 -07:00
Dana Robinson
61d43eb867
Adds an optional version arg to bin/format_source (#3119) 2023-06-14 08:00:46 -07:00
Dana Robinson
d1ef48e708
Remove unused HD macros (#3120)
* Remove unused HD macros
The library prefixes most C and POSIX API calls with 'HD'. We are
going to start removing these so the code looks like normal C.

This PR removes most of the unused HD markup macros.

* Replace ntohl/ntohs
2023-06-14 08:00:26 -07:00
Dana Robinson
ce794d6a88
Remove the checkposix script (#3122)
This script was used to ensure that all non-HDF5 calls were prefixed
with 'HD'. We are removing this scheme so this script is no longer
needed.
2023-06-14 07:59:49 -07:00
Allen Byrne
340c37629c
Use 1.14 toolchain (#3116) 2023-06-13 16:12:49 -07:00
Allen Byrne
75bcd68e7c
Add note for issue 3056 (#3117) 2023-06-13 16:12:14 -07:00
Allen Byrne
4462f73058
clang-tidy clang-analyzer-core issues addressed (#3113)
src/H5system.c:1293:13: warning: Dereference of null pointer
[clang-analyzer-core.NullDereference]
src/H5trace.c:4048:17: warning: Passed-by-value struct argument contains
uninitialized data (e.g., via the field chain: 'initial.user')
[clang-analyzer-core.CallAndMessage]
2023-06-13 09:33:35 -07:00
Dana Robinson
d4605919f9
Remove H5detect and H5make_libsettings (#3104)
Removes H5detect and H5make_libsettings from the build and replaces
their functionality with things that don't affect cross-compiling.

H5detect --> floating-point types are now detected on library load
H5make_libsettings --> Moved functionality to a new H5build_settings.c template file
2023-06-13 08:16:41 -07:00
Dana Robinson
9e7e2f8b8e
Fix a misc warning in test/vol.c (#3112)
The compiler complains about using integers instead of size_t
for some sizes.
2023-06-13 07:56:39 -07:00
Allen Byrne
281dbf49dc
Fix gh pages so that the doxygen files are uploaded (#3102)
* Add workspace path
* add debug
* Make one job so workspace files are available
* Put doxygen docs under docs folder in gh-pages
2023-06-12 20:43:06 -07:00
Allen Byrne
1891387ccb
Rework tools.cmake and add C flags (#3110) 2023-06-12 20:05:26 -07:00
Allen Byrne
8265bf31c9
Fix the default for API_VERSION to only allow one default (#3107) 2023-06-12 20:01:34 -07:00
Dana Robinson
b9f988ed63
Add Mark Kittisopikul to CODEOWNERS (#3111) 2023-06-12 18:03:21 -07:00
Dana Robinson
1e1dac1dac
Remove long double conversion work-arounds (#3097)
Several options and public symbols that were provided to paper
      over non-standard long double conversions between signed/unsigned
      long and long long values were removed from the Autotools and
      CMake. These were added twenty years ago, when C99 and 64-bit
      platforms were less common and are no longer needed.

      Autotools:
        --enable-dconv-accuracy

      CMake:
        HDF5_WANT_DATA_ACCURACY

      H5pubconf.h symbols:
        H5_WANT_DATA_ACCURACY
        H5_LDOUBLE_TO_LONG_SPECIAL
        H5_LONG_TO_LDOUBLE_SPECIAL
        H5_LDOUBLE_TO_LLONG_ACCURATE
        H5_LLONG_TO_LDOUBLE_CORRECT
        H5_DISABLE_SOME_LDOUBLE_CONV
2023-06-12 14:12:57 -07:00
Dana Robinson
d1d6a2187d
Remove code paths where long long < 8 bytes (#3098)
The C99 standard says that a long long is 8+ bytes. This change
removes a few parts of the code where we assume that a long long
could be less than that.
2023-06-12 12:18:23 -07:00
Dana Robinson
cedbc2eae0
Remove variable dereferences in CMake (#3080) 2023-06-12 12:15:40 -07:00
Dana Robinson
a1a9526b14
Address memory issues when copying empty enums (#3088)
When copying an empty enum type (including implicitly, as when an enum
is contained in a compound type), the library would allocate 0-size
blocks of memory and attempt to memcpy 0 bytes from NULL pointers, which
are undefined behavior. In debug mode, the library would raise an
assert in H5MM.

The library now avoid undefined memory operations when copying empty
enum types and a test that copies empty enums has been added.
2023-06-12 12:14:25 -07:00
Dana Robinson
37990e63c4
Make some changes to configure.ac to suppor MinGW (#3096)
Adds some H5pubconf.h entries and cpp flags for building on MinGW
using the Autotools.

Also updates the Windows-related H5pubconf.h comments to be more
accurate in CMake.
2023-06-11 17:39:15 -07:00
bmribler
a64d3a989a
Fixed typo: hdf5-examples should be hdf5_examples in a link (#3101) 2023-06-11 07:08:39 -07:00
Dana Robinson
03bd3e0840
Fix misc warnings on Windows (#3094)
* Debug functionality where pointers were munged into longs
  (which are only 32-bits on Windows)
* Fix a missing cast in Wstrcasestr_wrap()
2023-06-10 17:01:46 -07:00
Dana Robinson
4bda5eb33c
Add cross-compile defaults to Autotools (#3095)
Most instances of AC_RUN_IFELSE do not have an action set for
cross-compiling, even though there is an obvious 'reasonable'
value.
2023-06-10 12:24:33 -07:00
Dana Robinson
087d35a5b7
Build the ros3 VFD in GitHub actions (#3090)
* Build the ros3 VFD in GitHub actions
* Add curl to list of packages to install
* Disable CMake while we figure out the curl path issues
2023-06-10 12:23:11 -07:00
Dana Robinson
95b75de836
Remove template title text ([BUG], etc.) (#3093)
We use labels for this now
2023-06-09 17:48:59 -07:00
Dana Robinson
53ae53905d
Minor cleanup of H5detect.c (#3081)
* Clean up H5detect.c
* Whitespace cleanup
* Align things a bit better
* Comment changes
2023-06-09 08:12:03 -07:00
Lori Cooper
ee84868c56
Added new HDF5 logo and minor text and link changes to README.md (#3085) 2023-06-08 12:57:18 -07:00
H. Joe Lee
74f1a6e5b4
ci: add h5py action (#2986) (#3028) 2023-06-08 08:47:35 -07:00
Dana Robinson
44dccb5b15
Don't use -fstdarg-opt with clang-tidy (#3079)
* HDFCompilerFlags: mask -fstdarg-opt with clang-tidy

`clang-tidy` doesn't understand this `-f` flag and errors out.

* Add helpful comment

---------

Co-authored-by: Sean McBride <sean@rogue-research.com>
2023-06-07 16:40:57 -07:00
Dana Robinson
76bc845a2f
Removes old header/library checks (#3078)
In both CMake and the Autotools, remove checks for:
* lstat
* srandom

In CMake, remove checks for:
* string.h
* strings.h
* stdlib.h
We assume these exist. Configure will always check for them (we don't
add any special code to do this), but there's no reason to duplicate
that nonsense in CMake.
2023-06-07 16:40:31 -07:00