Update branch with latest from develop #4708

vchoi-hdfgroup · 2024-08-12T18:52:32Z

No description provided.

Complete overhaul of the concurrency-related aspects of the library (threading, atomics, locking, etc.), adding private routines in the H5TS package to allow internal algorithms to use all of these capabilities. Adds many new features & components in the H5TS package that are equivalent to common concurrency data structures and capabilities: "regular" and recursive mutices, condition variables, semaphores, thread barriers, 'once' support, thread pools, atomic variables, thread-local keys, and spawning & joining internal threads. Now supports C11, pthreads, and Windows threading for all H5TS capabilities, except the recursive readers/writers lock, which is not supported on Windows (because Windows threads don't provide a callback on thread-local variable deletion). The "global" API lock is switched to use a recursive mutex from the H5TS package, instead of its own variant. API context code (H5CX package) and error stacks (H5E package) now use the common thread-local info, instead of their own variants. Subfiling code is switched from using Mercury threading features to the new internal H5TS features. Removes the mercury threading code. Adds a configure option (--enable-threads / HDF5_ENABLE_THREADS), enabled by default, to control whether threading is enabled within the library.

* warning fix * warning fix

Bumps the github-actions group with 5 updates: | Package | From | To | | --- | --- | --- | | [actions/download-artifact](https://github.com/actions/download-artifact) | `4.1.7` | `4.1.8` | | [DoozyX/clang-format-lint-action](https://github.com/doozyx/clang-format-lint-action) | `0.13` | `0.17` | | [softprops/action-gh-release](https://github.com/softprops/action-gh-release) | `2.0.6` | `2.0.8` | | [ossf/scorecard-action](https://github.com/ossf/scorecard-action) | `2.3.3` | `2.4.0` | | [github/codeql-action](https://github.com/github/codeql-action) | `3.25.11` | `3.25.15` | Updates `actions/download-artifact` from 4.1.7 to 4.1.8 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@65a9edc...fa0a91b) Updates `DoozyX/clang-format-lint-action` from 0.13 to 0.17 - [Release notes](https://github.com/doozyx/clang-format-lint-action/releases) - [Commits](DoozyX/clang-format-lint-action@v0.13...v0.17) Updates `softprops/action-gh-release` from 2.0.6 to 2.0.8 - [Release notes](https://github.com/softprops/action-gh-release/releases) - [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md) - [Commits](softprops/action-gh-release@a74c6b7...c062e08) Updates `ossf/scorecard-action` from 2.3.3 to 2.4.0 - [Release notes](https://github.com/ossf/scorecard-action/releases) - [Changelog](https://github.com/ossf/scorecard-action/blob/main/RELEASE.md) - [Commits](ossf/scorecard-action@dc50aa9...62b2cac) Updates `github/codeql-action` from 3.25.11 to 3.25.15 - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@b611370...afb54ba) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions - dependency-name: DoozyX/clang-format-lint-action dependency-type: direct:production update-type: version-update:semver-minor dependency-group: github-actions - dependency-name: softprops/action-gh-release dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions - dependency-name: ossf/scorecard-action dependency-type: direct:production update-type: version-update:semver-minor dependency-group: github-actions - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ...

Signed-off-by: Quincey Koziol <[email protected]>

* Ignore predetermined failing test and check pointer before use * Rework Analysis process

* Update logic for (deprecated) H5Gget_objinfo() call to eliminate H5E_BEGIN_TRY * Handle case for '.' at the end of a path

…_types() (#4694) Original case that the change in commit 2dc738a no longer applies.

These were found while investigating GH-4672, but they were not related to GH-4672.

* Correct logic * Technically, level 1 Express could skip tests

Added functionality tests for the following APIs: H5Rget_file_name H5Rget_obj_name H5Rget_attr_name Also removed "+1" when returning a name length in H5R__get_attr_name(). The exter "+1" gave an incorrect value for the length of the referenced object's attribute name. Fixed GH-4447 * Fix Fortran test The C API H5Rget_attr_name incorrectly added 1 to the length of the referenced object's attribute name, so the Fortran API h5rget_attr_name_f removed 1 from the returned value to accommodate the incorrectness. This PR fixes H5Rget_attr_name so this workaround in h5rget_attr_name_f is no longer needed. * Add test H5Aget_name against H5Rget_attr_name

github-advanced-security · 2024-08-12T18:52:33Z

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/workflows/clang-format-check.yml

@@ -11,7 +11,7 @@
    steps:
    - uses: actions/[email protected]
    - name: Run clang-format style check for C and Java code
-      uses: DoozyX/clang-format-lint-action@v0.13
+      uses: DoozyX/clang-format-lint-action@v0.17


.github/workflows/cmake-ctest.yml

@@ -86,6 +113,22 @@
          cmake --workflow --preset=${{ inputs.preset_name }}-MSVC --fresh
        shell: bash

+      - name: Sign files with Trusted Signing
+        uses: azure/[email protected]


.github/workflows/cmake-ctest.yml

        run: brew install ninja

      - name: Install Dependencies
        uses: ssciwr/doxygen-install@v1
        with:
          version: "1.9.7"

-      - name: Set file base name (MacOS)
+      - name: Set up JDK 19
+        uses: actions/setup-java@v4


.github/workflows/cmake-ctest.yml

        uses: actions/upload-artifact@v4
        with:
              name: tgz-osx-binary
              path: ${{ runner.workspace }}/build/${{ steps.set-file-base.outputs.FILE_BASE }}-osx.tar.gz
              if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`

+      - name: Save published dmg binary (MacOS_latest)
+        uses: actions/upload-artifact@v4


.github/workflows/cmake-ctest.yml

@@ -477,6 +558,22 @@
          cmake --workflow --preset=${{ inputs.preset_name }}-win-Intel --fresh
        shell: pwsh

+      - name: Sign files with Trusted Signing (Windows_intel)
+        uses: azure/[email protected]


.github/workflows/main-cmake.yml

        uses: actions/upload-artifact@v4
        with:
              name: tgz-osx-${{ inputs.build_mode }}-binary
              path: ${{ runner.workspace }}/build/HDF5-*-Darwin.tar.gz
              if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
        if: ${{ (matrix.os == 'macos-latest') && (inputs.thread_safety != 'TS') }}
+
+      - name: Save published dmg binary (Mac_latest)
+        uses: actions/upload-artifact@v4


lrknox and others added 22 commits July 29, 2024 12:57

Remove outdated line from Copyright header in new files. (#4676)

f54abf7

Fix binary examples process (#4666)

d309a40

Warning fix (#4682)

26f052c

* warning fix * warning fix

Add file name argument to publish workflow (#4686)

9dad0f9

CMake link line needs to use new HDF5_ENABLE_THREADS (#4685)

0f620e9

Correct the properties for using THREADS library (#4690)

1be198d

doxygen file is a zipfile (#4687)

f8e8256

Use filename in directory sync (#4691)

42095e3

Fix segfault when closing datatype during failure in H5Topen2 (#4683)

573c8bd

unzip does not create extra dir (#4692)

ac11d66

Remove racey condition for starting threads (#4693)

6061296

Signed-off-by: Quincey Koziol <[email protected]>

Rework Dynamic Analysis and sanitize testing (#4681)

f77b708

* Ignore predetermined failing test and check pointer before use * Rework Analysis process

Remove another H5E_BEGIN/END_TRY within the library (#4675)

eede36f

* Update logic for (deprecated) H5Gget_objinfo() call to eliminate H5E_BEGIN_TRY * Handle case for '.' at the end of a path

Drop H5E_BEGIN/END_TRY and just check the error return from H5I_clear…

3967f2a

…_types() (#4694) Original case that the change in commit 2dc738a no longer applies.

Add check of returned value from API calls. (#4702)

5c39fdd

These were found while investigating GH-4672, but they were not related to GH-4672.

Add mac dmg binary and remove old macos-13 workflows (#4699)

3355a5e

Add Windows SHLWAPI lib to public interface (#4701)

46a3a20

Use local variable in btree2 and print value (#4679)

695c0f2

* Correct logic * Technically, level 1 Express could skip tests

Add windows signing (#4703)

48aaf0c

vchoi-hdfgroup requested review from brtnfld, derobins, epourmal, lrknox, byrnHDF, fortnern and jhendersonHDF as code owners August 12, 2024 18:52

vchoi-hdfgroup requested review from qkoziol, bmribler, glennsong09 and mattjala as code owners August 12, 2024 18:52

github-advanced-security bot found potential problems Aug 12, 2024

View reviewed changes

vchoi-hdfgroup merged commit 9077ba6 into feature/sparse_data Aug 12, 2024
59 checks passed

lrknox temporarily deployed to snapshots August 13, 2024 00:56 — with GitHub Actions Inactive

lrknox temporarily deployed to snapshots August 13, 2024 00:57 — with GitHub Actions Inactive

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Update branch with latest from develop #4708

Update branch with latest from develop #4708

vchoi-hdfgroup commented Aug 12, 2024

github-advanced-security bot commented Aug 12, 2024

Update branch with latest from develop #4708

Update branch with latest from develop #4708

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vchoi-hdfgroup commented Aug 12, 2024

github-advanced-security bot commented Aug 12, 2024