Sync develop changes June 6 - July 2 to hdf5_1_14 (#4623)

* Fix typos in context/property documentation (#4550)

* Fix CI markdown link check http 500 errors (#4556)

Sites like GitLab can have internal problems that return http 500
errors while they fix their problems. Some sites also return http
200 OK, which is fine.

This PR adds a config file to the markdown link check so those
are considered "passing" and don't break the CI.

* Simplify property copying between lists internally (#4551)

* Add Python examples (#4546)

These examples are referred to from the replacement page of https://portal.hdfgroup.org/display/HDF5/Other+Examples.

* Correct property cb signatures in docs (#4554)

* Correct property cb signatures in docs
* Correct delete callback type name in docs
* add missing word to H5P__free_prop doc

* Move C++ and Fortran and examples to HDF5Examples folder (#4552)

* Document 'return-and-read' field in API context (#4560)

* Add compression includes to tests needing zlib support (#4561)

* Allow usage of page buffering for serial file access from parallel HDF5 builds (#4568)

* Remove old version of libaec (#4567)

* Add property names to context field docs (#4563)

* Document property shared name behavior (#4565)

* Clarify H5CX macro documentation (#4569)

* Document H5Punregister modifying default properties (#4570)

* Update NVHPC to 24.5 (#4171)

We don't test parallel in other GitHub actions, so this also converts the
NVHPC check to configure and build only while we discuss how we'll
test parallel HDF5 in GitHub.

There is a blocking GitHub issue to address the test failures for
HDF5 1.14.5 (#4571).

* Clean up comments in H5FDros3.c (#4572)

* Rename INSTALL_Auto.txt to INSTALL_Autotools.txt (#4575)

* Clean up ros3 VFD stats code (#4579)

* Removes printf debugging
* Simplifies and centralizes stats code
* Use #ifdef ROS3_STATS instead of #if
* Other misc tidying

* Turn off ros3 VFD stat collection by default (#4581)

Not a new change - an artifact from a previous check-in.

* Pause recording errors instead of clearing the error stack (#4475)

An internal capability that's similar to the H5E_BEGIN_TRY / H5E_END_TRY
macros in H5Epublic.h, but more efficient since we can avoid pushing errors on
the stack entirely (and those macros use public API routines).

This capability (and other techniques) can be used to remove use of
H5E_clear_stack() and H5E_BEGIN_TRY / H5E_END_TRY within library routines.

We want to remove H5E_clear_stack() because it can trigger calls to the H5I
interface from within the H5E code, which creates a great deal of complexity
for threadsafe code.  And we want to remove H5E_BEGIN_TRY / H5E_END_TRY's
because they make public API calls from within the library code.

Also some other minor tidying in routines related to removing the use of
H5E_clear_stack() and H5E_BEGIN_TRY / H5E_END_TRY from H5Fint.c

* Add page buffer cache command line option to tools (#4562)


Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Clarify documentation for H5CX_get_data_transform (#4580)

* Correct comment for H5CX_get_data_transform

* Document why data transform ctx field doesnt use macro

* Remove public API call from ros3 VFD (#4583)

* Remove printf debugging from H5FDs3comms.c (#4584)

* Cleanup of ros3 test (#4587)

* Removed JS* macro scheme (replaced w/ h5test.h macros)
* Moved curl setup/teardown to main()
* A lot of cleanup and simplification

* Removed unused code from H5FDs3comms.c (#4588)

* H5FD_s3comms_nlowercase()
* H5FD_s3comms_trim()
* H5FD_s3comms_uriencode()

* Remove magic fields from s3comms structs (#4589)

* Remove dead H5FD_s3comms_percent_encode_char() (#4591)

* Rework the TestExpress usage and refactor dead code (#4590)

* Skip examples if running sanitizers (#4592)

* Clean up s3comms test code (#4594)

* Remove JS* macros
* Remove dead code
* Bring in line with other test code

* Add publish to bucket workflow (#4566)

* Update abi report CI workflow for last release (#4596)

* Update abi report workflow to handle 1.14.4.3 release

* Update name of java report

* Document that ctx VOL property isn't drawn from the FAPL (#4597)

* Update macos workflow to 14 (keep 13 as alternate) (#4603)

* Removed unnecessary call to H5E_clear_stack (#4607)

H5FO_opened and H5SL_search don't push errors on the stack

* Bring subfiling VFD code closer to typical library code (#4595)

Remove API calls, use FUNC_ENTER/LEAVE macros, use the library's error macros,
rename functions to have more standardized names, etc.

* Correct documentation for return-and-read fields (#4598)

* These two generators create strings without NUL for testing (#4608)

* Fix Fortran pkconfig to indicate full path of modules (#4593)

* Updated release schedule (#4615)

1.16 and 2.0 information

* Document VOL object wrapping context (#4611)

* Earray.c and farray.c in hdf5_1_14 still need time_t curr_time for HDsrandom.

* Remove line to use future 116_API from CMakeListat.txt files in HDF5
examples directories

.github/workflows/abi-report.yml

@@ -1,5 +1,6 @@
 name: hdf5 1.14 Check Application Binary Interface (ABI)
 
+# Triggers the workflow on a call from another workflow
 on:
   workflow_call:
     inputs:
@@ -40,8 +41,10 @@ jobs:
       - 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/")
+          FILE_DOTS=$(echo "${{ inputs.file_ref }}" | sed -r "s/([0-9]+)\.([0-9]+)\.([0-9]+)\.([0-9]+).*/\1\.\2\.\3-\4/")
           echo "HDF5R_DOTS=$FILE_DOTS" >> $GITHUB_OUTPUT
+          FILE_DOTSMAIN=$(echo "${{ inputs.file_ref }}" | sed -r "s/([0-9]+)\.([0-9]+)\.([0-9]+).*/\1\.\2\.\3/")
+          echo "HDF5R_DOTSMAIN=$FILE_DOTSMAIN" >> $GITHUB_OUTPUT
 
       - uses: actions/[email protected]
 
@@ -81,8 +84,8 @@ jobs:
         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-${{ inputs.file_ref }}-ubuntu-2204.tar.gz
+          wget -q https://github.com/HDFGroup/hdf5/releases/download/hdf5_${{ inputs.file_ref }}/hdf5-${{ steps.convert-hdf5lib-refname.outputs.HDF5R_DOTS }}-ubuntu-2204_gcc.tar.gz
+          tar zxf hdf5-${{ steps.convert-hdf5lib-refname.outputs.HDF5R_DOTS }}-ubuntu-2204_gcc.tar.gz
 
       - name: List files for the space (Linux)
         run: |
@@ -91,7 +94,7 @@ jobs:
       - 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
+          tar -zxvf ${{ github.workspace }}/hdf5R/hdf5/HDF5-${{ inputs.file_ref }}-Linux.tar.gz --strip-components 1
 
       - name: List files for the HDFR space (Linux)
         run: |
@@ -113,7 +116,7 @@ jobs:
 
       - 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
+          japi-compliance-checker ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib/jarhdf5-${{ steps.convert-hdf5lib-refname.outputs.HDF5R_DOTSMAIN }}.jar ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib/jarhdf5-${{ steps.set-hdf5lib-name.outputs.HDF5_VERS }}.jar
 
       - name: Run ABI report
         run: |
@@ -145,7 +148,7 @@ jobs:
 
       - 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 ${{ inputs.file_base }}-java_compat_report.html
+          cp compat_reports/jarhdf5-/${{ steps.convert-hdf5lib-refname.outputs.HDF5R_DOTSMAIN }}_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

.github/workflows/aocc-auto.yml

@@ -1,5 +1,6 @@
 name: hdf5 1.14 PAR autotools aocc ompi
 
+# Triggers the workflow on a call from another workflow
 on:
   workflow_call:
     inputs:

.github/workflows/aocc-cmake.yml

@@ -1,5 +1,6 @@
 name: hdf5 1.14 PAR CMake aocc ompi
 
+# Triggers the workflow on a call from another workflow
 on:
   workflow_call:
     inputs:

.github/workflows/autotools.yml

@@ -1,6 +1,6 @@
 name: hdf5 1.14 autools CI
 
-# Controls when the action will run. Triggers the workflow on push or pull request
+# Triggers the workflow on push or pull request or on demand
 on:
   workflow_dispatch:
   push:
@@ -23,9 +23,6 @@ concurrency:
 permissions:
   contents: read
 
-# A workflow run is made up of one or more jobs that can run sequentially or
-# in parallel. We just have one job, but the matrix items defined below will
-# run in parallel.
 jobs:
     call-workflow-special-autotools:
       name: "Autotools Special Workflows"

.github/workflows/cmake-bintest.yml

@@ -1,6 +1,6 @@
 name: hdf5 1.14 examples bintest runs
 
-# Controls when the action will run. Triggers the workflow on a schedule
+# Triggers the workflow on a call from another workflow
 on:
   workflow_call:
     inputs:
@@ -12,8 +12,6 @@ on:
 permissions:
   contents: read
 
-# A workflow run is made up of one or more jobs that can run sequentially or
-# in parallel
 jobs:
   test_binary_win:
   # Windows w/ MSVC + CMake
@@ -149,7 +147,7 @@ jobs:
   # MacOS w/ Clang + CMake
   #
     name: "MacOS Clang Binary Test"
-    runs-on: macos-13
+    runs-on: macos-latest
     steps:
       - name: Install Dependencies (MacOS)
         run: brew install ninja doxygen
@@ -189,12 +187,12 @@ jobs:
               ls ${{ runner.workspace }}
 
       # symlinks the compiler executables to a common location 
-      # - name: Setup GNU Fortran
-      #   uses: fortran-lang/setup-fortran@v1
-      #   id: setup-fortran
-      #   with:
-      #     compiler: gcc
-      #     version: 12
+      - name: Setup GNU Fortran
+        uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: gcc
+          version: 12
 
       - name: Run ctest (MacOS)
         id: run-ctest

.github/workflows/cmake-ctest.yml

@@ -1,6 +1,6 @@
 name: hdf5 1.14 ctest runs
 
-# Controls when the action will run. Triggers the workflow on a call
+# Triggers the workflow on a call from another workflow
 on:
   workflow_call:
     inputs:
@@ -26,8 +26,6 @@ on:
 permissions:
   contents: read
 
-# A workflow run is made up of one or more jobs that can run sequentially or
-# in parallel
 jobs:
   build_and_test_win:
   # Windows w/ MSVC + CMake

.github/workflows/cmake.yml

@@ -1,6 +1,6 @@
 name: hdf5 1.14 cmake CI
 
-# Controls when the action will run. Triggers the workflow on push or pull request
+# Triggers the workflow on push or pull request or on demand
 on:
   workflow_dispatch:
   push:
@@ -23,9 +23,6 @@ concurrency:
 permissions:
   contents: read
 
-# A workflow run is made up of one or more jobs that can run sequentially or
-# in parallel. We just have one job, but the matrix items defined below will
-# run in parallel.
 jobs:
     call-workflow-special-cmake:
       name: "CMake Special Workflows"

.github/workflows/cve.yml

@@ -1,5 +1,6 @@
 name: cve 1.14
 
+# Triggers the workflow on push or pull request or on demand
 on:
   workflow_dispatch:
   push:

.github/workflows/cygwin-auto.yml

@@ -1,5 +1,6 @@
 name: hdf5 1.14 autotools cygwin
 
+# Triggers the workflow on a call from another workflow
 on:
   workflow_call:
     inputs:

.github/workflows/cygwin-cmake.yml

@@ -1,5 +1,6 @@
 name: hdf5 1.14 CMake cygwin
 
+# Triggers the workflow on a call from another workflow
 on:
   workflow_call:
     inputs:

.github/workflows/daily-build.yml

@@ -1,6 +1,6 @@
 name: hdf5 1.14 daily build
 
-# Controls when the action will run. Triggers the workflow on a schedule
+# Triggers the workflow on a schedule or on demand
 on:
   workflow_dispatch:
   schedule:
@@ -9,8 +9,6 @@ on:
 permissions:
   contents: read
 
-# A workflow run is made up of one or more jobs that can run sequentially or
-# in parallel.
 jobs:
   get-old-names:
     runs-on: ubuntu-latest
@@ -52,7 +50,7 @@ jobs:
     needs: [call-workflow-tarball, call-workflow-ctest]
     uses: ./.github/workflows/abi-report.yml
     with:
-      file_ref: '1_14_3'
+      file_ref: '1.14.4.3'
       file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
       use_tag: snapshot-1.14
       use_environ: snapshots

.github/workflows/hdfeos5.yml

@@ -1,5 +1,6 @@
 name: hdfeos5 1.14
 
+# Triggers the workflow on push or pull request or on demand
 on:
   workflow_dispatch:
   push:

.github/workflows/intel-auto.yml

@@ -1,5 +1,6 @@
 name: hdf5 1.14 autotools icx CI
 
+# Triggers the workflow on a call from another workflow
 on:
   workflow_call:
     inputs:

.github/workflows/intel-cmake.yml

@@ -1,5 +1,6 @@
 name: hdf5 1.14 CMake icx CI
 
+# Triggers the workflow on a call from another workflow
 on:
   workflow_call:
     inputs:

.github/workflows/main-auto.yml

@@ -1,6 +1,6 @@
 name: hdf5 1.14 autotools CI
 
-# Controls when the action will run. Triggers the workflow on a call
+# Triggers the workflow on a call from another workflow
 on:
   workflow_call:
     inputs:
@@ -16,9 +16,6 @@ on:
 permissions:
   contents: read
 
-# A workflow run is made up of one or more jobs that can run sequentially or
-# in parallel. We just have one job, but the matrix items defined below will
-# run in parallel.
 jobs:
 
   # A workflow that builds the library and runs all the tests

.github/workflows/main-cmake.yml

@@ -1,6 +1,6 @@
 name: hdf5 1.14 CMake CI
 
-# Controls when the action will run. Triggers the workflow on a call
+# Triggers the workflow on a call from another workflow
 on:
   workflow_call:
     inputs:
@@ -17,9 +17,6 @@ on:
 permissions:
   contents: read
 
-# A workflow run is made up of one or more jobs that can run sequentially or
-# in parallel. We just have one job, but the matrix items defined below will
-# run in parallel.
 jobs:
 
   # A workflow that builds the library and runs all the tests
@@ -36,6 +33,7 @@ jobs:
         name:
           - "Windows MSVC"
           - "Ubuntu gcc"
+          - "MacOS-13 Clang"
           - "MacOS Clang"
 
         # This is where we list the bulk of the options for each configuration.
@@ -85,15 +83,35 @@ jobs:
             generator: "-G Ninja"
             run_tests: true
 
+            # MacOS w/ Clang + CMake
+            #
+            # We could also build with the Autotools via brew installing them,
+            # but that seems unnecessary
+          - name: "MacOS-13 Clang"
+            os: macos-13
+            cpp: OFF
+            fortran: ON
+            java: ON
+            docs: ON
+            libaecfc: ON
+            localaec: OFF
+            zlibfc: ON
+            localzlib: OFF
+            parallel: OFF
+            mirror_vfd: ON
+            direct_vfd: OFF
+            ros3_vfd: OFF
+            generator: "-G Ninja"
+            run_tests: true
 
           # MacOS w/ Clang + CMake
           #
           # We could also build with the Autotools via brew installing them,
           # but that seems unnecessary
           - name: "MacOS Clang"
-            os: macos-13
-            cpp: ON
-            fortran: OFF
+            os: macos-latest
+            cpp: OFF
+            fortran: ON
             java: ON
             docs: ON
             libaecfc: ON
@@ -137,7 +155,16 @@ jobs:
 
       - name: Install Dependencies (macOS)
         run: brew install ninja
-        if: matrix.os == 'macos-13'
+        if: ${{ matrix.os == 'macos-13' || matrix.os == 'macos-latest' }}
+
+        # symlinks the compiler executables to a common location 
+      - name: Install GNU Fortran (macOS)
+        uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+            compiler: gcc
+            version: 12
+        if: ${{ matrix.os == 'macos-13' || matrix.os == 'macos-latest' }}
 
       - name: Install Dependencies
         uses: ssciwr/doxygen-install@v1
@@ -264,4 +291,4 @@ jobs:
               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-13') && (inputs.thread_safety != 'TS') }}
+        if: ${{ (matrix.os == 'macos-latest') && (inputs.thread_safety != 'TS') }}

.github/workflows/markdown-link-check.yml

@@ -1,14 +1,19 @@
 name: Check Markdown links
 
+# Triggers the workflow on push or pull request or on demand
 on:
   workflow_dispatch:
   push:
   pull_request:
     branches: [ hdf5_1_14 ]
 
+# The config file handles things like http 500 errors from sites like GitLab
+# and http 200 responses
 jobs:
   markdown-link-check:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@master
     - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        config-file: '.github/workflows/markdown_config.json'

.github/workflows/markdown_config.json

@@ -0,0 +1,3 @@
+{
+    "aliveStatusCodes": [200, 500]
+}

.github/workflows/msys2-auto.yml

@@ -1,5 +1,6 @@
 name: hdf5 1.14 Autotools MSys2
 
+# Triggers the workflow on a call from another workflow
 on:
   workflow_call:
     inputs:

.github/workflows/netcdf.yml

@@ -1,5 +1,6 @@
 name: netCDF 1.14
 
+# Triggers the workflow on push or pull request or on demand
 on:
   workflow_dispatch:
   push: