Sync develop changes June 6 - July 2 to hdf5_1_14

.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: