1 12 minor merges from develop (#297)

* OESS-98 fix tools test for plugins

* sync fork

* Merge of changes from dev

* Move problem option to bottom of the list until fixed

* HDFFV-11106 - fix parsing optional args

* HDFFV-11106 add note

* grammer fix

* Whitespace after clang formatting

* Undo format version 11 changes

* Update check to working version

* Merge workflow and minor changes from develop

* Update supported platforms

2 files changed, 165 insertions, 8 deletions

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index c891bac..4d0d3bb 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -17,14 +17,19 @@ jobs:
     strategy:
 #      fail-fast: false
       matrix:
-        name: ["Windows Latest MSVC", "Ubuntu Latest GCC", "Ubuntu Debug GCC", "macOS Latest Clang", "Ubuntu Autotools GCC"]
+        name: ["Windows Latest MSVC", "Ubuntu Latest GCC", "Ubuntu Debug GCC", "macOS Latest Clang", "Ubuntu Autotools GCC", "Windows TS MSVC", "Ubuntu TS GCC", "TS Debug GCC", "macOS TS Clang", "TS Autotools GCC"]
         include:
           - name: "Windows Latest MSVC"
             artifact: "Windows-MSVC.tar.xz"
             os: windows-latest
             build_type: "Release"
             toolchain: ""
+            cpp: ON
             fortran: OFF
+            java: ON
+            ts: OFF
+            hl: ON
+            parallel: OFF
             generator: "-G \"Visual Studio 16 2019\" -A x64"
           - name: "Ubuntu Latest GCC"
             artifact: "Linux.tar.xz"
@@ -32,6 +37,9 @@ jobs:
             build_type: "Release"
             cpp: ON
             fortran: OFF
+            java: ON
+            ts: OFF
+            hl: ON
             parallel: OFF
             toolchain: "config/toolchain/GCC.cmake"
             generator: "-G Ninja"
@@ -41,6 +49,9 @@ jobs:
             build_type: "Release"
             cpp: ON
             fortran: OFF
+            java: ON
+            ts: OFF
+            hl: ON
             parallel: OFF
             toolchain: "config/toolchain/clang.cmake"
             generator: "-G Ninja"
@@ -50,15 +61,82 @@ jobs:
             build_type: "Debug"
             cpp: ON
             fortran: OFF
+            java: OFF
+            ts: OFF
+            hl: ON
             parallel: OFF
             toolchain: "config/toolchain/GCC.cmake"
             generator: "-G Ninja"
           - name: "Ubuntu Autotools GCC"
-            artifact: "Linux.tar.xz"
+            artifact: "LinuxA.tar.xz"
             os: ubuntu-latest
             build_type: "Release"
             cpp: enable
             fortran: enable
+            java: enable
+            ts: disable
+            hl: enable
+            parallel: disable
+            toolchain: ""
+            generator: "autogen"
+#  Threadsafe runs
+          - name: "Windows TS MSVC"
+            artifact: "Windows-MSVCTS.tar.xz"
+            os: windows-latest
+            build_type: "Release"
+            toolchain: ""
+            cpp: OFF
+            fortran: OFF
+            java: OFF
+            ts: ON
+            hl: OFF
+            parallel: OFF
+            generator: "-G \"Visual Studio 16 2019\" -A x64"
+          - name: "Ubuntu TS GCC"
+            artifact: "LinuxTS.tar.xz"
+            os: ubuntu-latest
+            build_type: "Release"
+            cpp: OFF
+            fortran: OFF
+            java: OFF
+            ts: ON
+            hl: OFF
+            parallel: OFF
+            toolchain: "config/toolchain/GCC.cmake"
+            generator: "-G Ninja"
+          - name: "macOS TS Clang"
+            artifact: "macOSTS.tar.xz"
+            os: macos-latest
+            build_type: "Release"
+            cpp: OFF
+            fortran: OFF
+            java: OFF
+            ts: ON
+            hl: OFF
+            parallel: OFF
+            toolchain: "config/toolchain/clang.cmake"
+            generator: "-G Ninja"
+          - name: "TS Debug GCC"
+            artifact: "LinuxTSDBG.tar.xz"
+            os: ubuntu-latest
+            build_type: "Debug"
+            cpp: OFF
+            fortran: OFF
+            java: OFF
+            ts: ON
+            hl: OFF
+            parallel: OFF
+            toolchain: "config/toolchain/GCC.cmake"
+            generator: "-G Ninja"
+          - name: "TS Autotools GCC"
+            artifact: "LinuxATS.tar.xz"
+            os: ubuntu-latest
+            build_type: "Release"
+            cpp: disable
+            fortran: disable
+            java: disable
+            ts: enable
+            hl: disable
             parallel: disable
             toolchain: ""
             generator: "autogen"
@@ -109,7 +187,7 @@ jobs:
         sh ./bin/chkmanifest
         mkdir "${{ runner.workspace }}/build"
         cd "${{ runner.workspace }}/build"
-        $GITHUB_WORKSPACE/configure --enable-shared --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --enable-java
+        $GITHUB_WORKSPACE/configure --enable-shared --${{ matrix.ts }}-threadsafe --${{ matrix.hl }}-hl --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --${{ matrix.java }}-java
       shell: bash
 
     - name: Configure
@@ -117,7 +195,7 @@ jobs:
       run: |
         mkdir "${{ runner.workspace }}/build"
         cd "${{ runner.workspace }}/build"
-        cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=ON $GITHUB_WORKSPACE
+        cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_THREADSAFE:BOOL=${{ matrix.ts }} -DHDF5_BUILD_HL_LIB:BOOL=${{ matrix.hl }} -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=${{ matrix.java }} $GITHUB_WORKSPACE
       shell: bash
 
     - name: Autotools Build
diff --git a/.github/workflows/pr-check.yml b/.github/workflows/pr-check.yml
index 47feb7a..8c3bb2c 100644
--- a/.github/workflows/pr-check.yml
+++ b/.github/workflows/pr-check.yml
@@ -12,14 +12,19 @@ jobs:
     strategy:
 #      fail-fast: false
       matrix:
-        name: ["Windows Latest MSVC", "Ubuntu Latest GCC", "Ubuntu Debug GCC", "macOS Latest Clang", "Ubuntu Autotools GCC"]
+        name: ["Windows Latest MSVC", "Ubuntu Latest GCC", "Ubuntu Debug GCC", "macOS Latest Clang", "Ubuntu Autotools GCC", "Windows TS MSVC", "Ubuntu TS GCC", "TS Debug GCC", "macOS TS Clang", "TS Autotools GCC"]
         include:
           - name: "Windows Latest MSVC"
             artifact: "Windows-MSVC.tar.xz"
             os: windows-latest
             build_type: "Release"
             toolchain: ""
+            cpp: ON
             fortran: OFF
+            java: ON
+            ts: OFF
+            hl: ON
+            parallel: OFF
             generator: "-G \"Visual Studio 16 2019\" -A x64"
           - name: "Ubuntu Latest GCC"
             artifact: "Linux.tar.xz"
@@ -27,6 +32,9 @@ jobs:
             build_type: "Release"
             cpp: ON
             fortran: OFF
+            java: ON
+            ts: OFF
+            hl: ON
             parallel: OFF
             toolchain: "config/toolchain/GCC.cmake"
             generator: "-G Ninja"
@@ -36,6 +44,9 @@ jobs:
             build_type: "Release"
             cpp: ON
             fortran: OFF
+            java: ON
+            ts: OFF
+            hl: ON
             parallel: OFF
             toolchain: "config/toolchain/clang.cmake"
             generator: "-G Ninja"
@@ -45,15 +56,82 @@ jobs:
             build_type: "Debug"
             cpp: ON
             fortran: OFF
+            java: OFF
+            ts: OFF
+            hl: ON
             parallel: OFF
             toolchain: "config/toolchain/GCC.cmake"
             generator: "-G Ninja"
           - name: "Ubuntu Autotools GCC"
-            artifact: "Linux.tar.xz"
+            artifact: "LinuxA.tar.xz"
             os: ubuntu-latest
             build_type: "Release"
             cpp: enable
             fortran: enable
+            java: enable
+            ts: disable
+            hl: enable
+            parallel: disable
+            toolchain: ""
+            generator: "autogen"
+#  Threadsafe runs
+          - name: "Windows TS MSVC"
+            artifact: "Windows-MSVCTS.tar.xz"
+            os: windows-latest
+            build_type: "Release"
+            toolchain: ""
+            cpp: OFF
+            fortran: OFF
+            java: OFF
+            ts: ON
+            hl: OFF
+            parallel: OFF
+            generator: "-G \"Visual Studio 16 2019\" -A x64"
+          - name: "Ubuntu TS GCC"
+            artifact: "LinuxTS.tar.xz"
+            os: ubuntu-latest
+            build_type: "Release"
+            cpp: OFF
+            fortran: OFF
+            java: OFF
+            ts: ON
+            hl: OFF
+            parallel: OFF
+            toolchain: "config/toolchain/GCC.cmake"
+            generator: "-G Ninja"
+          - name: "macOS TS Clang"
+            artifact: "macOSTS.tar.xz"
+            os: macos-latest
+            build_type: "Release"
+            cpp: OFF
+            fortran: OFF
+            java: OFF
+            ts: ON
+            hl: OFF
+            parallel: OFF
+            toolchain: "config/toolchain/clang.cmake"
+            generator: "-G Ninja"
+          - name: "TS Debug GCC"
+            artifact: "LinuxTSDBG.tar.xz"
+            os: ubuntu-latest
+            build_type: "Debug"
+            cpp: OFF
+            fortran: OFF
+            java: OFF
+            ts: ON
+            hl: OFF
+            parallel: OFF
+            toolchain: "config/toolchain/GCC.cmake"
+            generator: "-G Ninja"
+          - name: "TS Autotools GCC"
+            artifact: "LinuxATS.tar.xz"
+            os: ubuntu-latest
+            build_type: "Release"
+            cpp: disable
+            fortran: disable
+            java: disable
+            ts: enable
+            hl: disable
             parallel: disable
             toolchain: ""
             generator: "autogen"
@@ -70,6 +148,7 @@ jobs:
     name: ${{ matrix.name }}
     # The type of runner that the job will run on
     runs-on: ${{ matrix.os }}
+    if: "!contains(github.event.head_commit.message, 'skip-ci')"
           
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
@@ -103,7 +182,7 @@ jobs:
         sh ./bin/chkmanifest
         mkdir "${{ runner.workspace }}/build"
         cd "${{ runner.workspace }}/build"
-        $GITHUB_WORKSPACE/configure --enable-shared --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --enable-java
+        $GITHUB_WORKSPACE/configure --enable-shared --${{ matrix.ts }}-threadsafe --${{ matrix.hl }}-hl --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --${{ matrix.java }}-java
       shell: bash
 
     - name: Configure
@@ -111,7 +190,7 @@ jobs:
       run: |
         mkdir "${{ runner.workspace }}/build"
         cd "${{ runner.workspace }}/build"
-        cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=ON $GITHUB_WORKSPACE
+        cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_THREADSAFE:BOOL=${{ matrix.ts }} -DHDF5_BUILD_HL_LIB:BOOL=${{ matrix.hl }} -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=${{ matrix.java }} $GITHUB_WORKSPACE
       shell: bash
 
     - name: Autotools Build