Merge remote-tracking branch 'origin/develop' into threading_updates

qkoziol · Mar 26, 2024 · 4ab928b · 4ab928b
2 parents a74ef90 + c4d2891
commit 4ab928b
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diff --git a/.github/workflows/abi-report.yml b/.github/workflows/abi-report.yml
@@ -178,4 +178,4 @@ jobs:
         with:
           name: abi-reports
           path: |
-            ${{ runner.workspace }}/buildabi/${{ inputs.file_base }}.html.abi.reports
+            ${{ runner.workspace }}/buildabi/${{ inputs.file_base }}.html.abi.reports.tar.gz
diff --git a/.github/workflows/cmake-bintest.yml b/.github/workflows/cmake-bintest.yml
@@ -129,12 +129,6 @@ jobs:
         run: |
             ls -l ${{ github.workspace }}/HDF_Group/HDF5
 
-      - name: Set file base name (Linux)
-        id: set-file-base
-        run: |
-          FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
-          echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
-
       - name: List files for the space (Linux)
         run: |
               ls -l ${{ github.workspace }}
@@ -187,12 +181,6 @@ jobs:
         run: |
             ls -l ${{ github.workspace }}/HDF_Group/HDF5
 
-      - name: Set file base name (MacOS)
-        id: set-file-base
-        run: |
-          FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
-          echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
-
       - name: List files for the space (MacOS)
         run: |
               ls ${{ github.workspace }}

diff --git a/.github/workflows/cmake-ctest.yml b/.github/workflows/cmake-ctest.yml
@@ -4,6 +4,11 @@ name: hdf5 dev ctest runs
 on:
   workflow_call:
     inputs:
+      snap_name:
+        description: 'The name in the source tarballs'
+        type: string
+        required: false
+        default: hdfsrc
       file_base:
         description: "The common base name of the source tarballs"
         required: true
@@ -46,11 +51,11 @@ jobs:
         run: |
           FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
           echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
-          if [[ '${{ inputs.use_environ }}' == 'snapshots' ]]
+          if [[ '${{ inputs.use_environ }}' == 'release' ]]
           then
-            SOURCE_NAME_BASE=$(echo "hdfsrc")
+            SOURCE_NAME_BASE=$(echo "${{ inputs.snap_name }}")
           else
-            SOURCE_NAME_BASE=$(echo "$FILE_NAME_BASE")
+            SOURCE_NAME_BASE=$(echo "hdfsrc")
           fi
           echo "SOURCE_BASE=$SOURCE_NAME_BASE" >> $GITHUB_OUTPUT
         shell: bash
@@ -129,11 +134,11 @@ jobs:
         run: |
           FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
           echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
-          if [[ '${{ inputs.use_environ }}' == 'snapshots' ]]
+          if [[ '${{ inputs.use_environ }}' == 'release' ]]
           then
-            SOURCE_NAME_BASE=$(echo "hdfsrc")
+            SOURCE_NAME_BASE=$(echo "${{ inputs.snap_name }}")
           else
-            SOURCE_NAME_BASE=$(echo "$FILE_NAME_BASE")
+            SOURCE_NAME_BASE=$(echo "hdfsrc")
           fi
           echo "SOURCE_BASE=$SOURCE_NAME_BASE" >> $GITHUB_OUTPUT
 
@@ -253,11 +258,11 @@ jobs:
         run: |
           FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
           echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
-          if [[ '${{ inputs.use_environ }}' == 'snapshots' ]]
+          if [[ '${{ inputs.use_environ }}' == 'release' ]]
           then
-            SOURCE_NAME_BASE=$(echo "hdfsrc")
+            SOURCE_NAME_BASE=$(echo "${{ inputs.snap_name }}")
           else
-            SOURCE_NAME_BASE=$(echo "$FILE_NAME_BASE")
+            SOURCE_NAME_BASE=$(echo "hdfsrc")
           fi
           echo "SOURCE_BASE=$SOURCE_NAME_BASE" >> $GITHUB_OUTPUT
 
@@ -333,11 +338,11 @@ jobs:
         run: |
           FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
           echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
-          if [[ '${{ inputs.use_environ }}' == 'snapshots' ]]
+          if [[ '${{ inputs.use_environ }}' == 'release' ]]
           then
-            SOURCE_NAME_BASE=$(echo "hdfsrc")
+            SOURCE_NAME_BASE=$(echo "${{ inputs.snap_name }}")
           else
-            SOURCE_NAME_BASE=$(echo "$FILE_NAME_BASE")
+            SOURCE_NAME_BASE=$(echo "hdfsrc")
           fi
           echo "SOURCE_BASE=$SOURCE_NAME_BASE" >> $GITHUB_OUTPUT
 
@@ -413,11 +418,11 @@ jobs:
         run: |
           FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
           echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
-          if [[ '${{ inputs.use_environ }}' == 'snapshots' ]]
+          if [[ '${{ inputs.use_environ }}' == 'release' ]]
           then
-            SOURCE_NAME_BASE=$(echo "hdfsrc")
+            SOURCE_NAME_BASE=$(echo "${{ inputs.snap_name }}")
           else
-            SOURCE_NAME_BASE=$(echo "$FILE_NAME_BASE")
+            SOURCE_NAME_BASE=$(echo "hdfsrc")
           fi
           echo "SOURCE_BASE=$SOURCE_NAME_BASE" >> $GITHUB_OUTPUT
         shell: bash
@@ -502,11 +507,11 @@ jobs:
         run: |
           FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
           echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
-          if [[ '${{ inputs.use_environ }}' == 'snapshots' ]]
+          if [[ '${{ inputs.use_environ }}' == 'release' ]]
           then
-            SOURCE_NAME_BASE=$(echo "hdfsrc")
+            SOURCE_NAME_BASE=$(echo "${{ inputs.snap_name }}")
           else
-            SOURCE_NAME_BASE=$(echo "$FILE_NAME_BASE")
+            SOURCE_NAME_BASE=$(echo "hdfsrc")
           fi
           echo "SOURCE_BASE=$SOURCE_NAME_BASE" >> $GITHUB_OUTPUT
 

diff --git a/.github/workflows/daily-build.yml b/.github/workflows/daily-build.yml
@@ -42,10 +42,10 @@ jobs:
     needs: call-workflow-tarball
     uses: ./.github/workflows/cmake-ctest.yml
     with:
-      file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
       preset_name: ci-StdShar
+      file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
+#      use_tag: snapshot
       use_environ: snapshots
-      #use_tag: snapshot
     if: ${{ needs.call-workflow-tarball.outputs.has_changes == 'true' }}
 
   call-workflow-abi:

diff --git a/.github/workflows/main-auto-spc.yml b/.github/workflows/main-auto-spc.yml
@@ -417,8 +417,10 @@ jobs:
           sh ./autogen.sh
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
-          CFLAGS=-Werror $GITHUB_WORKSPACE/configure \
+          CFLAGS=-Werror JAVACFLAGS=-Werror JNIFLAGS=-Werror \
+          $GITHUB_WORKSPACE/configure \
             --enable-build-mode=debug \
+            --enable-warnings-as-errors \
             --enable-deprecated-symbols \
             --with-default-api-version=v114 \
             --enable-shared \
@@ -478,8 +480,10 @@ jobs:
           sh ./autogen.sh
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
-          CFLAGS=-Werror $GITHUB_WORKSPACE/configure \
+          CFLAGS=-Werror JAVACFLAGS=-Werror JNIFLAGS=-Werror \
+          $GITHUB_WORKSPACE/configure \
             --enable-build-mode=production \
+            --enable-warnings-as-errors \
             --enable-deprecated-symbols \
             --with-default-api-version=v114 \
             --enable-shared \

diff --git a/.github/workflows/main-cmake.yml b/.github/workflows/main-cmake.yml
@@ -135,10 +135,6 @@ jobs:
 
       # CMake gets libaec from fetchcontent
 
-      - name: Install Dependencies (Windows)
-        run: choco install ninja
-        if: matrix.os == 'windows-latest'
-
       - name: Install Dependencies (macOS)
         run: brew install ninja
         if: matrix.os == 'macos-13'

diff --git a/.github/workflows/markdown-link-check.yml b/.github/workflows/markdown-link-check.yml
@@ -0,0 +1,14 @@
+name: Check Markdown links
+
+on:
+  workflow_dispatch:
+  push:
+  pull_request:
+    branches: [ develop ]
+
+jobs:
+  markdown-link-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1
diff --git a/.github/workflows/release-files.yml b/.github/workflows/release-files.yml
@@ -149,18 +149,18 @@ jobs:
 
       - name: Create sha256 sums for files
         run: |
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.doxygen.zip > sha256sums.txt
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.tar.gz >> sha256sums.txt
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.zip >> sha256sums.txt
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-osx12.tar.gz >> sha256sums.txt
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.tar.gz >> sha256sums.txt
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.deb >> sha256sums.txt
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.rpm >> sha256sums.txt
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc_s3.tar.gz >> sha256sums.txt
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-win-vs2022_cl.zip >> sha256sums.txt
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_intel.tar.gz >> sha256sums.txt
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-win-vs2022_intel.zip >> sha256sums.txt
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.html.abi.reports.tar.gz >> sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.doxygen.zip > ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.zip >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-osx12.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.deb >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.rpm >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc_s3.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-win-vs2022_cl.zip >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_intel.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-win-vs2022_intel.zip >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.html.abi.reports.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
 
       - name: Store snapshot name
         run: |
@@ -198,7 +198,7 @@ jobs:
               ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_intel.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}-win-vs2022_intel.zip
               ${{ steps.get-file-base.outputs.FILE_BASE }}.html.abi.reports.tar.gz
-              sha256sums.txt
+              ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
               if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
 
       - name: Release tag
@@ -222,7 +222,7 @@ jobs:
               ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_intel.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}-win-vs2022_intel.zip
               ${{ steps.get-file-base.outputs.FILE_BASE }}.html.abi.reports.tar.gz
-              sha256sums.txt
+              ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
               if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
 
       - name: List files for the space (Linux)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -31,15 +31,16 @@ jobs:
     needs: log-the-inputs
     uses: ./.github/workflows/tarball.yml
     with:
-      use_tag: ${{ inputs.use_tag }}
+      use_tag: ${{ needs.log-the-inputs.outputs.rel_tag }}
       use_environ: release
 
   call-workflow-ctest:
     needs: call-workflow-tarball
     uses: ./.github/workflows/cmake-ctest.yml
     with:
-      file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
       preset_name: ci-StdShar
+      file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
+      snap_name: hdf5-${{ needs.call-workflow-tarball.outputs.source_base }}
       use_environ: release
 
   call-workflow-abi:
@@ -58,8 +59,8 @@ jobs:
     uses: ./.github/workflows/release-files.yml
     with:
       file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
-      file_branch: ${{ needs.log-the-inputs.outputs.rel_tag }}
-      file_sha: ${{ needs.log-the-inputs.outputs.rel_tag }}
+      file_branch: ${{ needs.call-workflow-tarball.outputs.file_branch }}
+      file_sha: ${{ needs.call-workflow-tarball.outputs.file_sha }}
       use_tag: ${{ needs.log-the-inputs.outputs.rel_tag }}
       use_environ: release
 
diff --git a/.github/workflows/remove-files.yml b/.github/workflows/remove-files.yml
@@ -45,6 +45,7 @@ jobs:
           token: ${{ github.token }}
           tag: "${{ inputs.use_tag }}"
           assets: |
+              ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
               ${{ steps.get-file-base.outputs.FILE_BASE }}.html.abi.reports.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}.doxygen.zip
               ${{ steps.get-file-base.outputs.FILE_BASE }}.tar.gz

diff --git a/.github/workflows/tarball.yml b/.github/workflows/tarball.yml
@@ -18,6 +18,9 @@ on:
       has_changes:
         description: "Whether there were changes the previous day"
         value: ${{ jobs.check_commits.outputs.has_changes }}
+      source_base:
+        description: "The common base name of the source tarballs"
+        value: ${{ jobs.create_tarball.outputs.source_base }}
       file_base:
         description: "The common base name of the source tarballs"
         value: ${{ jobs.create_tarball.outputs.file_base }}
@@ -80,6 +83,7 @@ jobs:
     if: ${{ ((inputs.use_environ == 'snapshots') && (needs.check_commits.outputs.has_changes == 'true')) || (inputs.use_environ  == 'release') }}
     outputs:
       file_base: ${{ steps.set-file-base.outputs.FILE_BASE }}
+      source_base: ${{ steps.version.outputs.SOURCE_TAG }}
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
@@ -96,47 +100,47 @@ jobs:
         id: version
         run: |
           cd "$GITHUB_WORKSPACE/hdfsrc"
-          echo "TAG_VERSION=$(bin/h5vers)" >> $GITHUB_OUTPUT
+          echo "SOURCE_TAG=$(bin/h5vers)" >> $GITHUB_OUTPUT
 
       - name: Set file base name
         id: set-file-base
         run: |
-          if [[ '${{ inputs.use_environ }}' == 'snapshots' && '${{ needs.check_commits.outputs.has_changes }}' == 'true' ]]
+          if [[ '${{ inputs.use_environ }}' == 'snapshots' ]]
           then
             FILE_NAME_BASE=$(echo "hdf5-${{ needs.check_commits.outputs.branch_ref }}-${{ needs.check_commits.outputs.branch_sha }}")
           else
             if [[ '${{ inputs.use_tag }}' == 'snapshot' ]]
             then
-              FILE_NAME_BASE=$(echo "${{ inputs.use_tag }}")
+              FILE_NAME_BASE=$(echo "snapshot")
             else
-              FILE_NAME_BASE=$(echo "hdf5-${{ steps.version.outputs.TAG_VERSION }}")
+              FILE_NAME_BASE=$(echo "hdf5-${{ steps.version.outputs.SOURCE_TAG }}")
             fi
           fi
           echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
         shell: bash
 
       - name: Create snapshot file base name
         id: create-file-base
-        if: ${{ (inputs.use_environ == 'snapshots') && (needs.check_commits.outputs.has_changes == 'true') }}
+        if: ${{ (inputs.use_environ == 'snapshots') }}
         run: |
           cd "$GITHUB_WORKSPACE/hdfsrc"
           bin/release -d $GITHUB_WORKSPACE --branch ${{ needs.check_commits.outputs.branch_ref }} --revision gzip zip
         shell: bash
 
       - name: Create release file base name
         id: create-rel-base
-        if: ${{ (inputs.use_environ == 'release') && (inputs.use_tag != 'snapshot') }}
+        if: ${{ (inputs.use_environ == 'release') }}
         run: |
           cd "$GITHUB_WORKSPACE/hdfsrc"
           bin/release -d $GITHUB_WORKSPACE gzip zip 
         shell: bash
 
-      - name: Create snapshot file base name
-        id: create-snap-base
-        if: ${{ (inputs.use_tag == 'snapshot') && (inputs.use_environ == 'release') }}
+      - name: Rename release file base name
+        id: ren-basename
+        if: ${{ (inputs.use_environ == 'release') && (inputs.use_tag  == 'snapshot') }}
         run: |
-          cd "$GITHUB_WORKSPACE/hdfsrc"
-          bin/release -d $GITHUB_WORKSPACE --branch ${{ inputs.use_tag }} gzip zip
+          mv hdf5-${{ steps.version.outputs.SOURCE_TAG }}.tar.gz ${{ inputs.use_tag }}.tar.gz
+          mv hdf5-${{ steps.version.outputs.SOURCE_TAG }}.zip ${{ inputs.use_tag }}.zip
         shell: bash
 
       - name: List files in the repository

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1055,8 +1055,6 @@ set (H5_FC_FUNC_ "H5_FC_FUNC_(name,NAME) name ## _")
 if (EXISTS "${HDF5_SOURCE_DIR}/fortran" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/fortran")
   option (HDF5_BUILD_FORTRAN "Build FORTRAN support" OFF)
   if (HDF5_BUILD_FORTRAN)
-    include (${HDF_RESOURCES_DIR}/HDFUseFortran.cmake)
-
     message (VERBOSE "Fortran compiler ID is ${CMAKE_Fortran_COMPILER_ID}")
     include (${HDF_RESOURCES_DIR}/HDFFortranCompilerFlags.cmake)
     include (${HDF_RESOURCES_DIR}/HDF5UseFortran.cmake)
@@ -1130,16 +1128,6 @@ if (EXISTS "${HDF5_SOURCE_DIR}/c++" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/c++")
   endif ()
 endif ()
 
-#-----------------------------------------------------------------------------
-# Check if Fortran's default real is double precision. If it is and HL is
-# being built then configure should fail due to bug HDFFV-889.
-#-----------------------------------------------------------------------------
-if (HDF5_BUILD_FORTRAN AND HDF5_BUILD_HL_LIB)
-  if (NOT H5_FORTRAN_DEFAULT_REAL_NOT_DOUBLE)
-    message (FATAL_ERROR " **** Fortran high-level routines are not supported when the default REAL is DOUBLE PRECISION, use HDF5_BUILD_HL_LIB:BOOL=OFF **** ")
-  endif ()
-endif ()
-
 #-----------------------------------------------------------------------------
 # Option to build HDF5 Java Library
 #-----------------------------------------------------------------------------

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -122,7 +122,7 @@ Please make sure that you check the items applicable to your pull request:
   * [ ] If changes were done to Autotools build, were they added to CMake and vice versa?
   * [ ] Is the pull request applicable to any other branches? If yes, which ones? Please document it in the GitHub issue.
   * [ ] Is the new code sufficiently documented for future maintenance?
-  * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://portal.hdfgroup.org/display/HDF5/API+Compatibility+Macros)
+  * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://docs.hdfgroup.org/hdf5/develop/api-compat-macros.html)
 * Documentation
   * [ ] Was the change described in the release_docs/RELEASE.txt file?
   * [ ] Was the new function documented in the corresponding public header file using [Doxygen](https://hdfgroup.github.io/hdf5/develop/_r_m_t.html)?