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Sync develop changes 8/27 - 9/11 to hdf5_1_14. (#4822)
* Remove dummy comments that repeat function names. (#4775) * Fix grammar in H5Odtype.c comment block (#4777) * Add subfiling checks to the gcc action (#4776) * Replace non-VOL calls with VOL calls - part 3 (#4771) This PR switches H5I_object() to H5VL_vol_object() in H5O and H5T APIs. H5M is the last one and left out of this PR because it needs more work in documentation and there is no test for the API functions. Fixes GH-4730 * Add subfiling to CI more places where we test parallel (#4778) * CMake: gcc,, AOCC * Autotools: AOCC (gcc was added in a previous commit) NVHPC generates a lot of tools errors for some reason * Convert Collective Calls html file to doxygen (#4779) * Fix grammar in H5Fint.c comment block (#4782) * Improve the consistency of configure help messages (#4783) Fix grammar in configure message * Fixes Fortran parallel build race condition for tests (#4789) * Update URL documentation links to support site (#4781) * Fix grammar and simplify comment in H5Fint.c (#4790) * Fix char-subscripts warnings in H5private.h (#4793) * Bump the github-actions group with 3 updates (#4798) Bumps the github-actions group with 3 updates: [actions/checkout](https://github.com/actions/checkout), [DoozyX/clang-format-lint-action](https://github.com/doozyx/clang-format-lint-action) and [github/codeql-action](https://github.com/github/codeql-action). Updates `actions/checkout` from 4.1.1 to 4.1.7 - [Release notes](https://github.com/actions/checkout/releases) - [Commits](actions/checkout@v4.1.1...v4.1.7) Updates `DoozyX/clang-format-lint-action` from 0.17 to 0.18 - [Release notes](https://github.com/doozyx/clang-format-lint-action/releases) - [Commits](DoozyX/clang-format-lint-action@v0.17...v0.18) Updates `github/codeql-action` from 3.25.15 to 3.26.6 - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@afb54ba...4dd1613) --- updated-dependencies: - dependency-name: actions/checkout 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: github/codeql-action dependency-type: direct:production update-type: version-update:semver-minor dependency-group: github-actions ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix typo argueably in H5Cprivate.h (#4795) * Fix typos in H5Cpkg.h (#4796) * Add bounds checking to avoid Out-of-bounds Write for gif2h5 (#4786) * Replace non-VOL calls with VOL calls - part 5 (#4788) This PR switches H5I_object() and H5I_object_verify() to H5VL_vol_object() and H5VL_vol_object_verify(), respectively, in the H5M APIs and H5Gdeprec (was left out by mistake). This completes the fixes of issue GH-4730. * Correct the URL paths (#4802) * Fix a few issues with error reporting during sec2 reads/writes (#4794) * Update windows and apple signing process (#4806) * Use latest clang format action (#4807) * Correct path to document (#4808) * Detect invalid ID to H5Gmove2 (#4765) User's application segfaulted because the returned value H5I_BADID wasn't detected when H5I_get_type() was called. This PR adds checks for invalid file/group identifiers passed into H5Gmove2. This defect occurs in many other places, hence, issue GH-4764. Fixes #4737 * Fix use of public API calls (#4809) Switch public API calls to private ones. Root cause of #4672, which it fixes. Also minor code cleanups * Remove call to H5E_clear_stack() (#4810) Remove call to H5E_clear_stack() in H5G_node_debug() Add misc. minor cleanups * Enable win Intel signing (#4812) * Remove unneeded file name part (#4814) * Update NVHPC optimization settings (#4815) * Use -gopt in Autotools/CMake instead of -g * Autotools uses -O3 for release, -O1 for debug * Remove CMake optimization flag removal hack * Add mirror VFD to serial -Werror CI action (#4753) * Add mirror VFD to serial -Werror CI action * NUL terminate mirror_vfd.c strings * Add THREADS check to configuration file (#4746) * Cleanup threads package checks * Check first if package was found * Remove unnecessary dependent checks * Remove Unused options and fix names of option prefix * Rework RFC url in aliases (#4813) * Update config/cmake/hdf5-config.cmake.in _ENABLE_THREADS doesn't belong in hdf5_1_14
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@@ -1,17 +1,20 @@ | ||
name: clang-format Check | ||
on: | ||
pull_request: | ||
|
||
permissions: | ||
contents: read | ||
|
||
jobs: | ||
formatting-check: | ||
name: Formatting Check | ||
runs-on: ubuntu-latest | ||
if: "!contains(github.event.head_commit.message, 'skip-ci')" | ||
steps: | ||
- uses: actions/[email protected] | ||
|
||
- 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 | ||
with: | ||
source: '.' | ||
extensions: 'c,h,cpp,hpp,java' | ||
|
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|
@@ -11,8 +11,10 @@ name: clang-format Commit Changes | |
on: | ||
workflow_dispatch: | ||
push: | ||
|
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permissions: | ||
contents: read | ||
|
||
jobs: | ||
formatting-check: | ||
name: Commit Format Changes | ||
|
@@ -21,16 +23,18 @@ jobs: | |
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] | ||
|
||
- 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 | ||
with: | ||
source: '.' | ||
extensions: 'c,h,cpp,hpp,java' | ||
clangFormatVersion: 13 | ||
inplace: True | ||
style: file | ||
exclude: './config ./hl/src/H5LTanalyze.c ./hl/src/H5LTparse.c ./hl/src/H5LTparse.h ./src/H5Epubgen.h ./src/H5Einit.h ./src/H5Eterm.h ./src/H5Edefin.h ./src/H5version.h ./src/H5overflow.h' | ||
|
||
- uses: EndBug/add-and-commit@a94899bca583c204427a224a7af87c02f9b325d5 # v9.1.4 | ||
with: | ||
author_name: github-actions | ||
|
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|
@@ -23,6 +23,12 @@ on: | |
required: true | ||
default: snapshots | ||
secrets: | ||
APPLE_CERTS_BASE64: | ||
required: true | ||
APPLE_CERTS_BASE64_PASSWD: | ||
required: true | ||
KEYCHAIN_PASSWD: | ||
required: true | ||
AZURE_TENANT_ID: | ||
required: true | ||
AZURE_CLIENT_ID: | ||
|
@@ -53,13 +59,15 @@ jobs: | |
run: | | ||
if [[ '${{ env.signing_secret }}' == '' ]] | ||
then | ||
SIGN_VAL=$(echo "false") | ||
SIGN_VAL=$(echo 'notexists') | ||
else | ||
SIGN_VAL=$(echo "true") | ||
SIGN_VAL=$(echo 'exists') | ||
fi | ||
echo "BINSIGN=$SIGN_VAL" >> $GITHUB_OUTPUT | ||
shell: bash | ||
|
||
- run: echo "signing is ${{ steps.set-signing-state.outputs.BINSIGN }}." | ||
|
||
build_and_test_win: | ||
# Windows w/ MSVC + CMake | ||
# | ||
|
@@ -114,7 +122,27 @@ jobs: | |
run: 7z x ${{ steps.set-file-base.outputs.FILE_BASE }}.zip | ||
shell: bash | ||
|
||
- name: Install TrustedSigning (Windows) | ||
run: | | ||
Invoke-WebRequest -Uri https://dist.nuget.org/win-x86-commandline/latest/nuget.exe -OutFile .\nuget.exe | ||
.\nuget.exe install Microsoft.Windows.SDK.BuildTools -Version 10.0.22621.3233 -x | ||
.\nuget.exe install Microsoft.Trusted.Signing.Client -Version 1.0.53 -x | ||
shell: pwsh | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
|
||
- name: create-json | ||
id: create-json | ||
uses: jsdaniell/[email protected] | ||
with: | ||
name: "credentials.json" | ||
dir: '${{ steps.set-file-base.outputs.SOURCE_BASE }}' | ||
json: '{"Endpoint": "${{ secrets.AZURE_ENDPOINT }}","CodeSigningAccountName": "${{ secrets.AZURE_CODE_SIGNING_NAME }}","CertificateProfileName": "${{ secrets.AZURE_CERT_PROFILE_NAME }}"}' | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
|
||
- name: Run ctest (Windows) | ||
env: | ||
BINSIGN: ${{ needs.check-secret.outputs.sign-state }} | ||
SIGNTOOLDIR: ${{ github.workspace }}/Microsoft.Windows.SDK.BuildTools/bin/10.0.22621.0/x64 | ||
run: | | ||
cd "${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}" | ||
cmake --workflow --preset=${{ inputs.preset_name }}-MSVC --fresh | ||
|
@@ -134,7 +162,7 @@ jobs: | |
file-digest: SHA256 | ||
timestamp-rfc3161: http://timestamp.acs.microsoft.com | ||
timestamp-digest: SHA256 | ||
if: ${{ needs.check-secret.outputs.sign-state == 'true' }} | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
|
||
- name: Publish binary (Windows) | ||
id: publish-ctest-binary | ||
|
@@ -323,6 +351,28 @@ jobs: | |
with: | ||
version: "1.9.7" | ||
|
||
- name: Install the Apple certificate and provisioning profile | ||
shell: bash | ||
env: | ||
BUILD_CERTIFICATE_BASE64: ${{ secrets.APPLE_CERTS_BASE64 }} | ||
P12_PASSWORD: ${{ secrets.APPLE_CERTS_BASE64_PASSWD }} | ||
KEYCHAIN_PASSWD: ${{ secrets.KEYCHAIN_PASSWD }} | ||
run: | | ||
# create variables | ||
CERTIFICATE_PATH=$RUNNER_TEMP/build_certificate.p12 | ||
KEYCHAIN_FILE=${{ vars.KEYCHAIN_NAME }}.keychain | ||
# import certificate from secrets | ||
echo $BUILD_CERTIFICATE_BASE64 | base64 --decode > $CERTIFICATE_PATH | ||
security -v create-keychain -p $KEYCHAIN_PASSWD $KEYCHAIN_FILE | ||
security -v list-keychain -d user -s $KEYCHAIN_FILE | ||
security -v list-keychains | ||
security -v set-keychain-settings -lut 21600 $KEYCHAIN_FILE | ||
security -v unlock-keychain -p $KEYCHAIN_PASSWD $KEYCHAIN_FILE | ||
# import certificate to keychain | ||
security -v import $CERTIFICATE_PATH -P $P12_PASSWORD -A -t cert -f pkcs12 -k $KEYCHAIN_FILE | ||
security -v set-key-partition-list -S apple-tool:,codesign:,apple: -k $KEYCHAIN_PASSWD $KEYCHAIN_FILE | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
|
||
- name: Set up JDK 19 | ||
uses: actions/setup-java@v4 | ||
with: | ||
|
@@ -367,11 +417,100 @@ jobs: | |
|
||
- name: Run ctest (MacOS_latest) | ||
id: run-ctest | ||
env: | ||
BINSIGN: ${{ needs.check-secret.outputs.sign-state }} | ||
SIGNER: ${{ vars.SIGNER }} | ||
run: | | ||
cd "${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}" | ||
cmake --workflow --preset=${{ inputs.preset_name }}-MACOS-Clang --fresh | ||
cmake --workflow --preset=${{ inputs.preset_name }}-macos-Clang --fresh | ||
shell: bash | ||
|
||
- name: Sign dmg (MacOS_latest) | ||
id: sign-dmg | ||
env: | ||
KEYCHAIN_PASSWD: ${{ secrets.KEYCHAIN_PASSWD }} | ||
KEYCHAIN_NAME: ${{ vars.KEYCHAIN_NAME }} | ||
SIGNER: ${{ vars.SIGNER }} | ||
NOTARY_USER: ${{ vars.NOTARY_USER }} | ||
NOTARY_KEY: ${{ vars.NOTARY_KEY }} | ||
run: | | ||
/usr/bin/codesign --force --timestamp --options runtime --entitlements ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/config/cmake/distribution.entitlements --verbose=4 --strict --sign ${{ env.SIGNER }} --deep ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-macos-Clang/*.dmg | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
shell: bash | ||
|
||
- name: Check dmg timestamp (MacOS_latest) | ||
run: | | ||
/usr/bin/codesign -dvv ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-macos-Clang/*.dmg | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
shell: bash | ||
|
||
- name: Verify dmg (MacOS_latest) | ||
run: | | ||
/usr/bin/hdiutil verify ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-macos-Clang/*.dmg | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
shell: bash | ||
|
||
- name: Notarize dmg (MacOS_latest) | ||
id: notarize-dmg | ||
env: | ||
KEYCHAIN_PASSWD: ${{ secrets.KEYCHAIN_PASSWD }} | ||
KEYCHAIN_NAME: ${{ vars.KEYCHAIN_NAME }} | ||
SIGNER: ${{ vars.SIGNER }} | ||
NOTARY_USER: ${{ vars.NOTARY_USER }} | ||
NOTARY_KEY: ${{ vars.NOTARY_KEY }} | ||
run: | | ||
jsonout=$(/usr/bin/xcrun notarytool submit --wait --output-format json --apple-id ${{ env.NOTARY_USER }} --password ${{ env.NOTARY_KEY }} --team-id ${{ env.SIGNER }} ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-macos-Clang/*.dmg) | ||
echo "JSONOUT=$jsonout" >> $GITHUB_OUTPUT | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
shell: bash | ||
|
||
- name: Get ID token (MacOS_latest) | ||
id: get-id-token | ||
run: | | ||
echo "notary result is ${{ fromJson(steps.notarize-dmg.outputs.JSONOUT) }}" | ||
token=${{ fromJson(steps.notarize-dmg.outputs.JSONOUT).id }} | ||
echo "ID_TOKEN=$token" >> "$GITHUB_OUTPUT" | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
shell: bash | ||
|
||
- name: post notary check (MacOS_latest) | ||
id: post-notary | ||
env: | ||
KEYCHAIN_PASSWD: ${{ secrets.KEYCHAIN_PASSWD }} | ||
KEYCHAIN_NAME: ${{ vars.KEYCHAIN_NAME }} | ||
SIGNER: ${{ vars.SIGNER }} | ||
NOTARY_USER: ${{ vars.NOTARY_USER }} | ||
NOTARY_KEY: ${{ vars.NOTARY_KEY }} | ||
run: | | ||
{ | ||
echo 'NOTARYOUT<<EOF' | ||
/usr/bin/xcrun notarytool info --apple-id ${{ env.NOTARY_USER }} --password ${{ env.NOTARY_KEY }} --team-id ${{ env.SIGNER }} ${{ steps.get-id-token.outputs.ID_TOKEN }} | ||
echo EOF | ||
} >> $GITHUB_OUTPUT | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
shell: bash | ||
|
||
- name: Get notary info (MacOS_latest) | ||
id: get-notary-info | ||
run: | | ||
echo "notary info is ${{ steps.post-notary.outputs.NOTARYOUT }}." | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
shell: bash | ||
|
||
- name: Staple dmg (MacOS_latest) | ||
id: staple-dmg | ||
env: | ||
KEYCHAIN_PASSWD: ${{ secrets.KEYCHAIN_PASSWD }} | ||
KEYCHAIN_NAME: ${{ vars.KEYCHAIN_NAME }} | ||
SIGNER: ${{ vars.SIGNER }} | ||
NOTARY_USER: ${{ vars.NOTARY_USER }} | ||
NOTARY_KEY: ${{ vars.NOTARY_KEY }} | ||
run: | | ||
/usr/bin/xcrun stapler staple ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-macos-Clang/*.dmg | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
shell: bash | ||
continue-on-error: true | ||
|
||
- name: Publish binary (MacOS_latest) | ||
id: publish-ctest-binary | ||
run: | | ||
|
@@ -395,7 +534,7 @@ jobs: | |
cp ${{ runner.workspace }}/hdf5/build114/${{ inputs.preset_name }}-Clang/README.md ${{ runner.workspace }}/builddmg/hdf5 | ||
cp ${{ runner.workspace }}/hdf5/build114/${{ inputs.preset_name }}-Clang/*.dmg ${{ runner.workspace }}/builddmg/hdf5 | ||
cd "${{ runner.workspace }}/builddmg" | ||
tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-macos14_clang.arm64.dmg.tar.gz hdf5 | ||
tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-macos14_clang.dmg.tar.gz hdf5 | ||
shell: bash | ||
|
||
- name: List files in the space (MacOS_latest) | ||
|
@@ -415,7 +554,7 @@ jobs: | |
uses: actions/upload-artifact@v4 | ||
with: | ||
name: tgz-macos14_clang-dmg-binary | ||
path: ${{ runner.workspace }}/builddmg/${{ steps.set-file-base.outputs.FILE_BASE }}-macos14_clang.arm64.dmg.tar.gz | ||
path: ${{ runner.workspace }}/builddmg/${{ steps.set-file-base.outputs.FILE_BASE }}-macos14_clang.dmg.tar.gz | ||
if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn` | ||
|
||
build_and_test_S3_linux: | ||
|
@@ -544,11 +683,30 @@ jobs: | |
run: 7z x ${{ steps.set-file-base.outputs.FILE_BASE }}.zip | ||
shell: bash | ||
|
||
- name: Install TrustedSigning (Windows) | ||
run: | | ||
Invoke-WebRequest -Uri https://dist.nuget.org/win-x86-commandline/latest/nuget.exe -OutFile .\nuget.exe | ||
.\nuget.exe install Microsoft.Windows.SDK.BuildTools -Version 10.0.22621.3233 -x | ||
.\nuget.exe install Microsoft.Trusted.Signing.Client -Version 1.0.53 -x | ||
shell: pwsh | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
|
||
- name: create-json | ||
id: create-json | ||
uses: jsdaniell/[email protected] | ||
with: | ||
name: "credentials.json" | ||
dir: '${{ steps.set-file-base.outputs.SOURCE_BASE }}' | ||
json: '{"Endpoint": "${{ secrets.AZURE_ENDPOINT }}","CodeSigningAccountName": "${{ secrets.AZURE_CODE_SIGNING_NAME }}","CertificateProfileName": "${{ secrets.AZURE_CERT_PROFILE_NAME }}"}' | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
|
||
- name: Run ctest (Windows_intel) with oneapi | ||
env: | ||
FC: ${{ steps.setup-fortran.outputs.fc }} | ||
CC: ${{ steps.setup-fortran.outputs.cc }} | ||
CXX: ${{ steps.setup-fortran.outputs.cxx }} | ||
BINSIGN: ${{ needs.check-secret.outputs.sign-state }} | ||
SIGNTOOLDIR: ${{ github.workspace }}/Microsoft.Windows.SDK.BuildTools/bin/10.0.22621.0/x64 | ||
run: | | ||
cd "${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}" | ||
cmake --workflow --preset=${{ inputs.preset_name }}-win-Intel --fresh | ||
|
@@ -568,7 +726,7 @@ jobs: | |
file-digest: SHA256 | ||
timestamp-rfc3161: http://timestamp.acs.microsoft.com | ||
timestamp-digest: SHA256 | ||
if: ${{ needs.check-secret.outputs.sign-state == 'true' }} | ||
if: ${{ needs.check-secret.outputs.sign-state == 'exists' }} | ||
|
||
- name: Publish binary (Windows_intel) | ||
id: publish-ctest-binary | ||
|
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---|---|---|
|
@@ -17,7 +17,7 @@ jobs: | |
runs-on: ubuntu-latest | ||
steps: | ||
- name: Get Sources | ||
uses: actions/[email protected].1 | ||
uses: actions/[email protected].7 | ||
|
||
- name: Install Dependencies | ||
shell: bash | ||
|
@@ -60,7 +60,7 @@ jobs: | |
arch: 'x64' | ||
|
||
- name: Get julia hdf5 source | ||
uses: actions/[email protected].1 | ||
uses: actions/[email protected].7 | ||
with: | ||
repository: JuliaIO/HDF5.jl | ||
path: . | ||
|
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---|---|---|
|
@@ -17,7 +17,7 @@ jobs: | |
runs-on: ubuntu-latest | ||
steps: | ||
- name: Get Sources | ||
uses: actions/[email protected].1 | ||
uses: actions/[email protected].7 | ||
|
||
- name: Install Dependencies | ||
shell: bash | ||
|
@@ -63,7 +63,7 @@ jobs: | |
arch: 'x64' | ||
|
||
- name: Get julia hdf5 source | ||
uses: actions/[email protected].1 | ||
uses: actions/[email protected].7 | ||
with: | ||
repository: JuliaIO/HDF5.jl | ||
path: . | ||
|
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