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update feature/sparse_data with develop #4865

Merged
merged 94 commits into from
Sep 20, 2024
Merged

update feature/sparse_data with develop #4865

merged 94 commits into from
Sep 20, 2024

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hyoklee and others added 30 commits August 13, 2024 07:42
@hyoklee
Replace Visual Studio ???? with 2022 in MSI README file (#4709)
67ff153
@byrnHDF
Change logic for checking secrets exists (#4711)
9824e7f
@byrnHDF
Change osx refs to macos (#4707)
d7e0ad5
@bmribler
Replace alias \Code with \TText (#4714)
70c6a7a 
Fixed GH-2151
@byrnHDF
Correct signing names and variables (#4713)
819e00d
@byrnHDF
Add secrets to release workflow (#4719)
78fb239
@byrnHDF
Add missing blosc2 info (#4717)
32ee132
@derobins
Fix error return types in H5Rdeprec.c (#4722)
89f62a9 
Copy-pasted code from elsewhere used FAIL instead of H5G_UNKNOWN
and H5I_INVALID_HID.
@byrnHDF
Fix the release reference name (#4721)
6896bf4
@mattjala
Test creating unseekable file (#4720)
d25cc7d
@bmribler
Cleanup up tests (#4724)
b4731e4
@qkoziol
Fix semaphore test (#4725)
adc3a37 
* Make counter in semaphore test an atomic variable

* Revert using atomic counter and fix counter access outside of semaphore
@hyoklee
Add arch name to dmg file name (#4732)
b54cc5b 
The binaries in snapshot dmg file do not work on x86_64.
@hyoklee
Fix snapshot CI failure by adding arch name to dmg file (#4734)
b11f2d0 
See also #4732.
@bmribler
Fix incorrect VOL vs. non-VOL calls partially (#4733)
aea4c53 
* Fix incorrect VOL vs. non-VOL calls

H5Lget_info2() called H5I_object() instead of H5VL_vol_object() crashed
user application.
This is a wide-spread issue (GH-4730) but this PR only addresses GH-4705.

* Remove an incorrect change
@mattjala
Fix segfault in ROS3 credential parsing (#4736)
4791d34 
* Fix segfault in s3 credential parsing

* Fix AWS cred parsing when >1 profile provided
@hyoklee
Revert gh-pages action hash to fix daily build (#4735)
eed772e 
* Revert gh-pages action hash to fix daily build

See also #4734

* Revert gh-pages action hash to fix daily build
@qkoziol
Eliminate another use of H5E_clear_stack() within the library (#4726)
679b017 
* Remove call to H5E_clear_stack()

Also clean up a bunch of error macros and the return value from H5B_valid()
@hyoklee
Use gfortran 14 for cmake-ctest.yml on mac (#4739)
c1cbba6 
* Use gfortran 14 for cmake-test on mac

* Remove notarization step

* Address @byrnHDF review
@hyoklee
Fix enum type mismatch warning (#4741)
17123cd
@hyoklee
Fix macro redefined warnings (#4744)
8b3041f 
Removes a duplicated HDopen macro from the performance testing programs
@hyoklee
Update nvhpc CI version to 24.7 (#4740)
7a17a98
@ajelenak
Return basic HTTP range GET logging to ROS3 (#4738)
8a8ac85 
* Add minimal amount of S3 request logging to ROS3

* Fix ROS3 logging ifdef conditions
@bmribler
Replace non-VOL calls with VOL calls - part 1 (#4745)
a03203a 
This PR is part of the incremental switching H5I_object() and H5I_object_verify()
to their VOL counterpart, H5VL_object() and H5VL_vol_object_verify(), a newly addedinternal function.

Fixes GH-4730 partially.
@bmribler
Fix inconsistent documentation of get_name functions (#4715)
379a5ba 
- Verified that the listed functions do not include null terminator in the returned length
- Improved some of the tests
- Corrected documentation

Fixes GH-4704

* Casted a positive int to size_t
@derobins
Remove HDF-EOS5 CI action (#4750)
7cf3963 
The code can't be downloaded due to changes that put it behind an
EarthData login. We'll disable this while we figure out a work-around.
@bmribler
Replace non-VOL calls with VOL calls - part 2 (#4748)
9adacb5 
This PR switches H5I_object_verify() to H5VL_vol_object_verify() in the H5F API
and fixes documentation of H5Fmount and H5Funmount.

* More on H5F API
@derobins
Restore rand_r in a few parallel tests (#4749)
5c5b727 
The t_pmulti_dset and t_select_io_dset tests rely on the behavior
of the previous private rand_r-like implementation to get the
correct sequence of random numbers to pass. This has been restored
using a fully private rand_r-like implementation that doesn't
rely on rand_r and will work on Windows and other platforms
where rand_r doesn't exist.
@derobins
Don't run AOCC parallel tests with -j2 (#4752)
7c4b501 
Don't run parallel tests in both Autotools and CMake with multiple
processes. ph5diff still runs with -j2 w/ Autotools since the test
script is in the tools/test/h5diff directory.

* Split off AOCC CMake parallel tests

* Remove unnecessary NPROCS env vars

* Put NPROCS back in serial tests

We run ph5diff tests there
@qkoziol
Another try at correcting the ping pong semaphore test (#4754)
c38064b 
* Add ifdef around prototype

* Add casts to make MSVC happy

* Fix missing atomic load
byrnHDF and others added 14 commits September 12, 2024 22:46
@byrnHDF
Correct URLs in documentation (#4823)
0737d0d
@byrnHDF
Add release note for signed binaries (#4826)
6313814
@byrnHDF
Cleanup errors detected during merge compare (#4827)
1e9a8ef
@lrknox
Draw attention to 3rd step in process to update so numbers for releas…
19d3691 
…e. (#4825)
@byrnHDF
correct path for deb binary (#4835)
e2154c9
@lrknox
Update h5fc.in missed line for libhdf5hl_fortran filename change to l…
405d1b9 
…ibhdf5_hl_fortran. (#4831)

* Change name of libhdf5hl_fortran installed by autotools to libhdf5_hl_fortran to be
consistent with CMake install and with other hl lib files.  Switched
corresponding symlink to libhdf5hl_fortran.
Fixes issue #4684.

* Update h5fc.in to use renamed libhdf5_hl_fortran.
Fix typo in code to create link to libhdf5_hl_fortran.a.

* Removed code to create symlink for previous name of renamed lib
libhdf5hl_fortran.
Add RELEASE.txt entry about changeing name libhdf5hl_fortran to
libhdf5_hl_fortran.

* Update missed line in h5fc.in for libhdf5hl_fortran name change to
libhdf5_hl_fortran.  Fixes check-install failure.
@mattjala
Document usage for H5TSmutex_release/acquire() (#4836)
ca217e2
@jhendersonHDF
Print error stream when cmake greptest fails to match error ref. (#4841)
eeb94a8
@fortnern
Fix issues with large external data files (#4843)
3b65223
@mattjala
Fix memory leaks in ttsafe tests (#4842)
d1cfe52
@qkoziol
Reduce test iterations, etc. to keep time down on sower systems (#4853)
52d42fd 
Signed-off-by: Quincey Koziol <[email protected]>
@byrnHDF
Add windows extra options (#4854)
3307ff1
@fortnern
RELEASE.txt entry for PR #4843 (#4860)
b382a8e
@byrnHDF
Add binary testing steps (#4851)
417ae79
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github-advanced-security[bot]
github-advanced-security bot found potential problems Sep 20, 2024
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.github/workflows/clang-format-check.yml
- name: Run clang-format style check for C and Java code
uses: DoozyX/clang-format-lint-action@v0.17
uses: DoozyX/clang-format-lint-action@v0.18.2

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.github/workflows/clang-format-fix.yml
@@ -21,16 +23,18 @@
permissions:
contents: write # In order to allow EndBug/add-and-commit to commit changes
steps:
- uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
- uses: actions/[email protected]

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.github/workflows/clang-format-fix.yml
- name: Fix C and Java formatting issues detected by clang-format
uses: DoozyX/clang-format-lint-action@d3c7f85989e3b6416265a0d12f8b4a8aa8b0c4ff # v0.13
uses: DoozyX/clang-format-lint-action@v0.18.2

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.github/workflows/cmake-ctest.yml

- name: create-json
id: create-json
uses: jsdaniell/[email protected]

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- name: create-json
id: create-json
uses: jsdaniell/[email protected]

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runs-on: ubuntu-latest
steps:
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.github/workflows/julia-cmake.yml
working-directory: ${{ runner.workspace }}/build

- name: Install julia
uses: julia-actions/setup-julia@latest

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.github/workflows/julia-cmake.yml
arch: 'x64'

- name: Get julia hdf5 source
uses: actions/[email protected]

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echo 'libhdf5 = "/tmp/lib/libhdf5.so"' >> LocalPreferences.toml
echo 'libhdf5_hl = "/tmp/lib/libhdf5_hl.so"' >> LocalPreferences.toml

- uses: julia-actions/julia-buildpkg@latest

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- uses: julia-actions/julia-buildpkg@latest

- name: Julia Run Tests
uses: julia-actions/julia-runtest@latest

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@vchoi-hdfgroup vchoi-hdfgroup merged commit 7429cef into feature/sparse_data Sep 20, 2024
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