Merge pull request #4019 from lrknox/1_14_dev_sync2_lrk

* Update upload- artifact to match download version (#3929)

* Reorg and update options for doc and cmake config (#3934)

* Add binary build for linux S3 (#3936)

* Clean up Doxygen for szip functions and constants (#3943)

* Replace off_t with HDoff_t internally (#3944)

off_t is a 32-bit signed value on Windows, so we should use HDoff_t
(which is __int64 on Windows) internally instead.

Also defines HDftell on Windows to be _ftelli64().

* Fix chid_t to hid_t (#3948)

* Fortran API work. (#3941)

* - Added Fortran APIs:
      H5FGET_INTENT_F, H5SSELECT_ITER_CREATE_F, H5SSEL_ITER_GET_SEQ_LIST_F,
      H5SSELECT_ITER_CLOSE_F, H5S_mp_H5SSELECT_ITER_RESET_F

    - Added Fortran Parameters:
      H5S_SEL_ITER_GET_SEQ_LIST_SORTED_F, H5S_SEL_ITER_SHARE_WITH_DATASPACE_F

    - Added tests for new APIs
    - Removed H5F C wrapper stubs
    - Documentation misc. cleanup.

* Add the user test program in HDFFV-9174 for committed types. (#3937)

Add the user test program for committed types in HDFFV-9174

* Remove cached datatype conversion path table entries on file close (#3942)

* fixed BIND name (#3957)

* update H5Ssel_iter_reset_f test

* Change 'extensible' to 'fixed' in H5FA code (#3964)

* RF: move codespell configuration into .codespellrc so could be used locally as well (#3958)

* Add RELEASE.txt note for the fix for issue #1256 (#3955)

* Fix doxygen errors (#3962)

* Add API support for Fortran MPI_F08 module definitions. (#3959)

* revert to using c-stub for _F08 MPI APIs

* use mpi compiler wrappers for cmake and nvhpc

* Added a GitHub Codespaces configuration. (#3966)

* Fixed XL and gfortran errors (#3968)

* h5 compiler wrappers now pass all arguments passed to it to the compile line (#3954)

* The issue was that the "allargs" variable was not being used in the final command of the compiler wrapper. Any entries containing an escaped quote (\", \') or other non-matching argument (*) would not be passed to the compile line. I have fixed this problem by ensuring all arguments passed to the compiler wrapper are now included in the compile line.

* Add binary testing to CI testing (#3971)

* Replace 'T2' with ' ' to avoid failure to match expected output due to (#3975)

* Clarify vlen string datatype message (#3950)

* append '-WF,' when passing C preprocessor directives to the xlf compiler (#3976)

* Create CITATION.cff (#3927)

Add citation source based on http://web.archive.org/web/20230610185232/https://portal.hdfgroup.org/display/knowledge/How+do+I+properly+cite+HDF5%The space difference in the Fortran examples must be fixed to match the expected output for compression filter examples.

* corrected warning: implicit conversion changes signedness (#3982)

* Skip mac bintest until more reliable (#3983)

* Make platform specific test presets for windows and macs (#3988)

* chore: fix typo (#3989)

* Add a missing left parenthesis in RELEASE.txt. (#3990)

* Remove ADB signature from RELEASE.txt. (#3986)

* Bump the github-actions group with 6 updates (#3981)

* Sync API tests with vol-tests (#3940)

* Fix for github issue #2414: segfault when copying dataset with attrib… (#3967)

* Fix for github issue #2414: segfault when copying dataset with attributes.
This also fixes github issue #3241: segfault when copying dataset.
Need to set the location via H5T_set_loc() of the src datatype
when copying dense attributes.
Otherwise the vlen callbacks are not set up therefore causing seg fault
when doing H5T_convert() -> H5T__conv_vlen().

* Fix broken links caused by examples relocation. (#3995)

* Add abi-complience check and upload to releases (#3996)

* Fix h5watch test failures to ignore system warnings on ppc64le. (#3997)

* Remove oneapi/clang compiler printf() type warning. (#3994)

* Updated information about obtaining the HDF5 source code to use the repos. (#3972)

* Fix overwritten preset names (#4000)

* Fix incompatible pointer type warnings in object reference examples (#3999)

* Fix build issue and some warnings in H5_api_dataset_test.c (#3998)

* Modern C++ dtor declarations (#1830)

* C++ dtor modernization

- Replaced a bunch of empty dtors with `= default`
- Removed deprecated `throw()`. In C++11, dtors are `noexcept` by default.

* remove incorrect check for environ (#4002)

* Add a missing file into Makefile.am for MinGW Autotools build error. (#4004)

* Issue #1824: Replaced most remaining sprintf with safer snprint (#4003)

* Add hl and cpp ABI reports to daily build (#4006)

* Don't add files and directories with names that begin with ., or that match *autom4te* to release tar & zip files. (#4009)

* Fix some output issues with ph5diff (#4008)

* Update install texts (#4010)

* Add C in project line for CMake to fix #4012. (#4014)

* separate out individual checks for string removal (#4015)

* Add compound subset ops on attributes to API tests (#4005)

---------

.codespellrc

@@ -0,0 +1,6 @@
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+[codespell]
+skip = .git,*.svg,.codespellrc,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c,./config/sanitizer/LICENSE,./config/sanitizer/sanitizers.cmake,./tools/test/h5repack/testfiles/*.dat,./test/API/driver,./configure,./bin/ltmain.sh,./bin/depcomp,./bin/config.guess,./bin/config.sub,./autom4te.cache,./m4/libtool.m4,./c++/src/*.html,./HDF5Examples/depcomp
+check-hidden = true
+# ignore-regex = 
+ignore-words-list = ot,isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,ake,gord,numer,ro,oce,msdos

.devcontainer/Dockerfile

@@ -0,0 +1,5 @@
+FROM mcr.microsoft.com/devcontainers/base:debian
+
+RUN apt-get update && apt-get -y install --no-install-recommends \
+  build-essential cmake cmake-curses-gui doxygen git graphviz \
+  less libtool-bin libyajl-dev mpi-default-dev valgrind wget

.devcontainer/devcontainer.json

@@ -0,0 +1,26 @@
+{
+  "name": "HDF5 Developer",
+  "build": {
+    "context": "..",
+    "dockerfile": "Dockerfile"
+  },
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "ms-python.python",
+        "ms-toolsai.jupyter",
+        "ms-vscode.cpptools",
+        "ms-vscode.live-server",
+        "ms-vscode-remote.remote-containers",
+        "ms-azuretools.vscode-docker",
+        "h5web.vscode-h5web",
+        "davidanson.vscode-markdownlint"
+      ],
+      "settings": {
+        "C_Cpp.default.cppStandard": "c++17",
+        "C_Cpp.default.cStandard": "c99",
+        "terminal.integrated.shell.linux": "/bin/bash"
+      }
+    }
+  }
+}

.devcontainer/noop.txt

@@ -0,0 +1,3 @@
+This file is copied into the container along with environment.yml* from the
+parent folder. This file prevents the Dockerfile COPY instruction from failing
+if no environment.yml is found.

.github/workflows/abi-report.yml

@@ -0,0 +1,171 @@
+name: hdf5 1.14 Check Application Binary Interface (ABI)
+
+on:
+  workflow_call:
+    inputs:
+      use_tag:
+        description: 'Release version tag'
+        type: string
+        required: false
+        default: snapshot
+      use_environ:
+        description: 'Environment to locate files'
+        type: string
+        required: true
+        default: snapshots
+      file_base:
+        description: "The common base name of the binary"
+        required: true
+        type: string
+      file_ref:
+        description: "The reference name for the release binary"
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+
+    steps:
+      - name: Install System dependencies
+        run: |
+          sudo apt update
+          sudo apt install -q -y abi-compliance-checker abi-dumper
+          sudo apt install -q -y japi-compliance-checker
+
+      - name: Convert hdf5 reference name (Linux)
+        id: convert-hdf5lib-refname
+        run:  |
+          FILE_DOTS=$(echo "${{ inputs.file_ref }}" | sed -r "s/([0-9]+)\_([0-9]+)\_([0-9]+).*/\1\.\2\.\3/")
+          echo "HDF5R_DOTS=$FILE_DOTS" >> $GITHUB_OUTPUT
+
+      - uses: actions/checkout@v4.1.1
+
+      - name: Get published binary (Linux)
+        uses: actions/download-artifact@f44cd7b40bfd40b6aa1cc1b9b5b7bf03d3c67110 # v4.1.0
+        with:
+            name: tgz-ubuntu-2204_gcc-binary
+            path: ${{ github.workspace }}
+
+      - name: List files for the space (Linux)
+        run: |
+          ls -l ${{ github.workspace }}
+
+      - name: Uncompress gh binary (Linux)
+        run: tar -zxvf ${{ github.workspace }}/${{ inputs.file_base }}-ubuntu-2204_gcc.tar.gz
+
+      - name: Uncompress hdf5 binary (Linux)
+        run:  |
+          cd "${{ github.workspace }}/hdf5"
+          tar -zxvf ${{ github.workspace }}/hdf5/HDF5-*-Linux.tar.gz --strip-components 1
+
+      - name: List files for the HDF space (Linux)
+        run: |
+          ls -l ${{ github.workspace }}/hdf5
+          ls -l ${{ github.workspace }}/hdf5/HDF_Group/HDF5
+
+      - name: set hdf5lib name
+        id: set-hdf5lib-name
+        run: |
+          HDF5DIR=${{ github.workspace }}/hdf5/HDF_Group/HDF5/
+          FILE_NAME_HDF5=$(ls ${{ github.workspace }}/hdf5/HDF_Group/HDF5)
+          FILE_VERS=$(echo "$FILE_NAME_HDF5" | sed -r "s/([0-9]+\.[0-9]+\.[0-9]+)\..*/\1/")
+          echo "HDF5_ROOT=$HDF5DIR$FILE_NAME_HDF5" >> $GITHUB_OUTPUT
+          echo "HDF5_VERS=$FILE_VERS" >> $GITHUB_OUTPUT
+
+      - name: Download reference version
+        run: |
+          mkdir "${{ github.workspace }}/hdf5R"
+          cd "${{ github.workspace }}/hdf5R"
+          wget -q https://github.com/HDFGroup/hdf5/releases/download/hdf5-${{ inputs.file_ref }}/hdf5-${{ inputs.file_ref }}-ubuntu-2204.tar.gz
+          tar zxf hdf5-${{ inputs.file_ref }}-ubuntu-2204.tar.gz
+
+      - name: List files for the space (Linux)
+        run: |
+          ls -l ${{ github.workspace }}/hdf5R
+
+      - name: Uncompress hdf5 reference binary (Linux)
+        run:  |
+          cd "${{ github.workspace }}/hdf5R"
+          tar -zxvf ${{ github.workspace }}/hdf5R/hdf5/HDF5-${{ steps.convert-hdf5lib-refname.outputs.HDF5R_DOTS }}-Linux.tar.gz --strip-components 1
+
+      - name: List files for the HDFR space (Linux)
+        run: |
+          ls -l ${{ github.workspace }}/hdf5R
+          ls -l ${{ github.workspace }}/hdf5R/HDF_Group/HDF5
+
+      - name: set hdf5lib reference name
+        id: set-hdf5lib-refname
+        run: |
+          HDF5RDIR=${{ github.workspace }}/hdf5R/HDF_Group/HDF5/
+          FILE_NAME_HDF5R=$(ls ${{ github.workspace }}/hdf5R/HDF_Group/HDF5)
+          echo "HDF5R_ROOT=$HDF5RDIR$FILE_NAME_HDF5R" >> $GITHUB_OUTPUT
+          echo "HDF5R_VERS=$FILE_NAME_HDF5R" >> $GITHUB_OUTPUT
+
+      - name: List files for the lib spaces (Linux)
+        run: |
+          ls -l ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib
+          ls -l ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib
+
+      - name: Run Java API report
+        run: |
+          japi-compliance-checker ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib/jarhdf5-${{ steps.convert-hdf5lib-refname.outputs.HDF5R_DOTS }}.jar ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib/jarhdf5-${{ steps.set-hdf5lib-name.outputs.HDF5_VERS }}.jar
+
+      - name: Run ABI report
+        run: |
+          abi-dumper ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib/libhdf5.so -o ABI-0.dump -public-headers ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/include
+          abi-dumper ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib/libhdf5.so -o ABI-1.dump -public-headers ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/include
+          abi-compliance-checker -l ${{ inputs.file_base }} -old ABI-0.dump -new ABI-1.dump
+        continue-on-error: true
+
+      - name: Run hl ABI report
+        run: |
+          abi-dumper ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib/libhdf5_hl.so -o ABI-2.dump -public-headers ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/include
+          abi-dumper ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib/libhdf5_hl.so -o ABI-3.dump -public-headers ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/include
+          abi-compliance-checker -l ${{ inputs.file_base }}_hl -old ABI-2.dump -new ABI-3.dump
+        continue-on-error: true
+
+      - name: Run cpp ABI report
+        run: |
+          abi-dumper ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib/libhdf5_cpp.so -o ABI-4.dump -public-headers ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/include
+          abi-dumper ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib/libhdf5_cpp.so -o ABI-5.dump -public-headers ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/include
+          abi-compliance-checker -l ${{ inputs.file_base }}_cpp -old ABI-4.dump -new ABI-5.dump
+        continue-on-error: true
+
+      - name: Run hl_cpp ABI report
+        run: |
+          abi-dumper ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib/libhdf5_hl_cpp.so -o ABI-6.dump -public-headers ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/include
+          abi-dumper ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib/libhdf5_hl_cpp.so -o ABI-7.dump -public-headers ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/include
+          abi-compliance-checker -l ${{ inputs.file_base }}_hl_cpp -old ABI-6.dump -new ABI-7.dump
+        continue-on-error: true
+
+      - name: Copy ABI reports
+        run: |
+          cp compat_reports/jarhdf5-/${{ steps.set-hdf5lib-refname.outputs.HDF5R_VERS }}_to_${{ steps.set-hdf5lib-name.outputs.HDF5_VERS }}/compat_report.html ${{ inputs.file_base }}-java_compat_report.html
+          ls -l compat_reports/${{ inputs.file_base }}/X_to_Y
+          cp compat_reports/${{ inputs.file_base }}/X_to_Y/compat_report.html ${{ inputs.file_base }}-hdf5_compat_report.html
+          ls -l compat_reports/${{ inputs.file_base }}_hl/X_to_Y
+          cp compat_reports/${{ inputs.file_base }}_hl/X_to_Y/compat_report.html ${{ inputs.file_base }}-hdf5_hl_compat_report.html
+          ls -l compat_reports/${{ inputs.file_base }}_cpp/X_to_Y
+          cp compat_reports/${{ inputs.file_base }}_cpp/X_to_Y/compat_report.html ${{ inputs.file_base }}-hdf5_cpp_compat_report.html
+#          ls -l compat_reports/${{ inputs.file_base }}_hl_cpp/X_to_Y
+#          cp compat_reports/${{ inputs.file_base }}_hl_cpp/X_to_Y/compat_report.html ${{ inputs.file_base }}-hdf5_hl_cpp_compat_report.html
+
+      - name: List files for the report spaces (Linux)
+        run: |
+          ls -l compat_reports
+          ls -l *.html
+
+      - name: Save output as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: abi-reports
+          path: |
+            ${{ inputs.file_base }}-hdf5_compat_report.html
+            ${{ inputs.file_base }}-hdf5_hl_compat_report.html
+            ${{ inputs.file_base }}-hdf5_cpp_compat_report.html
+            ${{ inputs.file_base }}-java_compat_report.html

.github/workflows/autotools.yml

@@ -17,7 +17,19 @@ jobs:
 
     call-parallel-special-autotools:
       name: "Autotools Parallel Special Workflows"
+      uses: ./.github/workflows/main-auto-par-spc.yml
+
+    call-debug-parallel-autotools:
+      name: "Autotools Parallel Workflows"
       uses: ./.github/workflows/main-auto-par.yml
+      with:
+            build_mode: "debug"
+
+    call-release-parallel-autotools:
+      name: "Autotools Parallel Workflows"
+      uses: ./.github/workflows/main-auto-par.yml
+      with:
+            build_mode: "production"
 
     call-debug-thread-autotools:
       name: "Autotools Debug Thread-Safety Workflows"

.github/workflows/clang-format-fix.yml

@@ -31,7 +31,7 @@ jobs:
         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@1bad3abcf0d6ec49a5857d124b0bfb52dc7bb081 # v9.1.3
+    - uses: EndBug/add-and-commit@a94899bca583c204427a224a7af87c02f9b325d5 # v9.1.4
       with:
           author_name: github-actions
           author_email: 41898282+github-actions[bot]@users.noreply.github.com