Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Conversation

vchoi-hdfgroup
Copy link
Contributor

No description provided.

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 <quincey@koziol.cc>
@byrnHDF
Add windows extra options (#4854)
3307ff1
@fortnern
RELEASE.txt entry for PR #4843 (#4860)
b382a8e
@byrnHDF
Add binary testing steps (#4851)
417ae79
@github-advanced-security
Copy link

This pull request sets up GitHub code scanning for this repository. Once the scans have completed and the checks have passed, the analysis results for this pull request branch will appear on this overview. Once you merge this pull request, the 'Security' tab will show more code scanning analysis results (for example, for the default branch). Depending on your configuration and choice of analysis tool, future pull requests will be annotated with code scanning analysis results. For more information about GitHub code scanning, check out the documentation.

github-advanced-security[bot]
github-advanced-security bot found potential problems Sep 20, 2024
View reviewed changes
.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

Check warning

Code scanning / Scorecard

Pinned-Dependencies Medium

score is 1: third-party GitHubAction not pinned by hash
Remediation tip: update your workflow using https://app.stepsecurity.io
Click Remediation section below for further remediation help
.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/checkout@v4.1.7

Check warning

Code scanning / Scorecard

Pinned-Dependencies Medium

score is 1: GitHub-owned GitHubAction not pinned by hash
Remediation tip: update your workflow using https://app.stepsecurity.io
Click Remediation section below for further remediation help
.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

Check warning

Code scanning / Scorecard

Pinned-Dependencies Medium

score is 1: third-party GitHubAction not pinned by hash
Remediation tip: update your workflow using https://app.stepsecurity.io
Click Remediation section below for further remediation help
.github/workflows/cmake-ctest.yml

- name: create-json
id: create-json
uses: jsdaniell/create-json@v1.2.3

Check warning

Code scanning / Scorecard

Pinned-Dependencies Medium

score is 1: third-party GitHubAction not pinned by hash
Remediation tip: update your workflow using https://app.stepsecurity.io
Click Remediation section below for further remediation help
.github/workflows/cmake-ctest.yml

- name: create-json
id: create-json
uses: jsdaniell/create-json@v1.2.3

Check warning

Code scanning / Scorecard

Pinned-Dependencies Medium

score is 1: third-party GitHubAction not pinned by hash
Remediation tip: update your workflow using https://app.stepsecurity.io
Click Remediation section below for further remediation help
.github/workflows/julia-cmake.yml
runs-on: ubuntu-latest
steps:
- name: Get Sources
uses: actions/checkout@v4.1.7

Check warning

Code scanning / Scorecard

Pinned-Dependencies Medium

score is 1: GitHub-owned GitHubAction not pinned by hash
Remediation tip: update your workflow using https://app.stepsecurity.io
Click Remediation section below for further remediation help
.github/workflows/julia-cmake.yml
working-directory: ${{ runner.workspace }}/build

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

Check warning

Code scanning / Scorecard

Pinned-Dependencies Medium

score is 1: third-party GitHubAction not pinned by hash
Remediation tip: update your workflow using https://app.stepsecurity.io
Click Remediation section below for further remediation help
.github/workflows/julia-cmake.yml
arch: 'x64'

- name: Get julia hdf5 source
uses: actions/checkout@v4.1.7

Check warning

Code scanning / Scorecard

Pinned-Dependencies Medium

score is 1: GitHub-owned GitHubAction not pinned by hash
Remediation tip: update your workflow using https://app.stepsecurity.io
Click Remediation section below for further remediation help
.github/workflows/julia-cmake.yml
echo 'libhdf5 = "/tmp/lib/libhdf5.so"' >> LocalPreferences.toml
echo 'libhdf5_hl = "/tmp/lib/libhdf5_hl.so"' >> LocalPreferences.toml

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

Check warning

Code scanning / Scorecard

Pinned-Dependencies Medium

score is 1: third-party GitHubAction not pinned by hash
Remediation tip: update your workflow using https://app.stepsecurity.io
Click Remediation section below for further remediation help
.github/workflows/julia-cmake.yml
- uses: julia-actions/julia-buildpkg@latest

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

Check warning

Code scanning / Scorecard

Pinned-Dependencies Medium

score is 1: third-party GitHubAction not pinned by hash
Remediation tip: update your workflow using https://app.stepsecurity.io
Click Remediation section below for further remediation help
@vchoi-hdfgroup vchoi-hdfgroup merged commit 7429cef into feature/sparse_data Sep 20, 2024
60 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jhendersonHDF jhendersonHDF Awaiting requested review from jhendersonHDF jhendersonHDF is a code owner

@byrnHDF byrnHDF Awaiting requested review from byrnHDF byrnHDF is a code owner

@derobins derobins Awaiting requested review from derobins derobins is a code owner

@brtnfld brtnfld Awaiting requested review from brtnfld brtnfld is a code owner

@epourmal epourmal Awaiting requested review from epourmal epourmal is a code owner

@lrknox lrknox Awaiting requested review from lrknox lrknox is a code owner

@fortnern fortnern Awaiting requested review from fortnern fortnern is a code owner

@qkoziol qkoziol Awaiting requested review from qkoziol qkoziol is a code owner

@bmribler bmribler Awaiting requested review from bmribler bmribler is a code owner

@glennsong09 glennsong09 Awaiting requested review from glennsong09 glennsong09 is a code owner

@mattjala mattjala Awaiting requested review from mattjala mattjala is a code owner

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.