Merge remote-tracking branch 'canonical/develop' into aws_13m_securit…

…y_fixes
derobins · Mar 26, 2024 · b1f9707 · b1f9707
2 parents 636bf02 + 724eaaf
commit b1f9707
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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/CMakeLists.txt b/CMakeLists.txt
@@ -1072,8 +1072,6 @@ 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 (${HDF_RESOURCES_DIR}/HDF5UseFortran.cmake)
@@ -1147,16 +1145,6 @@ if (EXISTS "${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)?

diff --git a/HDF5Examples/C/H5T/CMakeLists.txt b/HDF5Examples/C/H5T/CMakeLists.txt
@@ -115,7 +115,7 @@ if (HDF5_BUILD_TOOLS)
     if (NOT ${example_name} STREQUAL "h5ex_t_convert")
         if (${example_name} STREQUAL "h5ex_t_vlen" OR ${example_name} STREQUAL "h5ex_t_vlenatt")
           if (HDF5_VERSION_STRING VERSION_GREATER_EQUAL "1.14.3")
-            if (${H5_LIBVER_DIR} EQUAL 16 AND ${example_name} STREQUAL "h5ex_t_vlenatt")
+            if ((${EXAMPLE_VARNAME}_USE_16_API OR ${H5_LIBVER_DIR} EQUAL 16) AND ${example_name} STREQUAL "h5ex_t_vlenatt")
               add_custom_command (
                   TARGET     ${EXAMPLE_VARNAME}_${example_name}
                   POST_BUILD
@@ -130,7 +130,7 @@ if (HDF5_BUILD_TOOLS)
                   ARGS       -E copy_if_different ${PROJECT_SOURCE_DIR}/tfiles/114/${example_name}.ddl ${PROJECT_BINARY_DIR}/${example_name}.ddl
               )
             endif ()
-          elseif (${H5_LIBVER_DIR} EQUAL 16)
+          elseif (${EXAMPLE_VARNAME}_USE_16_API OR ${H5_LIBVER_DIR} EQUAL 16)
             add_custom_command (
                 TARGET     ${EXAMPLE_VARNAME}_${example_name}
                 POST_BUILD
@@ -180,7 +180,7 @@ if (HDF5_BUILD_TOOLS)
                 )
               endif ()
             elseif (HDF5_VERSION_MAJOR VERSION_GREATER_EQUAL "1.12")
-              if (${H5_LIBVER_DIR} EQUAL 16)
+              if (${EXAMPLE_VARNAME}_USE_16_API OR ${H5_LIBVER_DIR} EQUAL 16)
                 add_custom_command (
                     TARGET     ${EXAMPLE_VARNAME}_${example_name}
                     POST_BUILD
@@ -196,12 +196,21 @@ if (HDF5_BUILD_TOOLS)
                 )
               endif ()
             else ()
-              add_custom_command (
-                  TARGET     ${EXAMPLE_VARNAME}_${example_name}
-                  POST_BUILD
-                  COMMAND    ${CMAKE_COMMAND}
-                  ARGS       -E copy_if_different ${PROJECT_SOURCE_DIR}/tfiles/18/${example_name}.ddl ${PROJECT_BINARY_DIR}/${example_name}.ddl
-              )
+              if (${EXAMPLE_VARNAME}_USE_16_API OR ${H5_LIBVER_DIR} EQUAL 16)
+                add_custom_command (
+                    TARGET     ${EXAMPLE_VARNAME}_${example_name}
+                    POST_BUILD
+                    COMMAND    ${CMAKE_COMMAND}
+                    ARGS       -E copy_if_different ${PROJECT_SOURCE_DIR}/tfiles/16/${example_name}.ddl ${PROJECT_BINARY_DIR}/${example_name}.ddl
+                )
+              else ()
+                add_custom_command (
+                    TARGET     ${EXAMPLE_VARNAME}_${example_name}
+                    POST_BUILD
+                    COMMAND    ${CMAKE_COMMAND}
+                    ARGS       -E copy_if_different ${PROJECT_SOURCE_DIR}/tfiles/18/${example_name}.ddl ${PROJECT_BINARY_DIR}/${example_name}.ddl
+                )
+              endif ()
             endif ()
           else ()
             if (HDF5_VERSION_MAJOR VERSION_EQUAL "1.8")
@@ -260,12 +269,21 @@ if (HDF5_BUILD_TOOLS)
               ARGS       -E copy_if_different ${PROJECT_SOURCE_DIR}/tfiles/16/${example_name}.ddl ${PROJECT_BINARY_DIR}/${example_name}.ddl
           )
         else ()
-          add_custom_command (
-              TARGET     ${EXAMPLE_VARNAME}_${example_name}
-              POST_BUILD
-              COMMAND    ${CMAKE_COMMAND}
-              ARGS       -E copy_if_different ${PROJECT_SOURCE_DIR}/tfiles/18/${example_name}.ddl ${PROJECT_BINARY_DIR}/${example_name}.ddl
-          )
+          if (${EXAMPLE_VARNAME}_USE_16_API)
+            add_custom_command (
+                TARGET     ${EXAMPLE_VARNAME}_${example_name}
+                POST_BUILD
+                COMMAND    ${CMAKE_COMMAND}
+                ARGS       -E copy_if_different ${PROJECT_SOURCE_DIR}/tfiles/16/${example_name}.ddl ${PROJECT_BINARY_DIR}/${example_name}.ddl
+            )
+          else ()
+            add_custom_command (
+                TARGET     ${EXAMPLE_VARNAME}_${example_name}
+                POST_BUILD
+                COMMAND    ${CMAKE_COMMAND}
+                ARGS       -E copy_if_different ${PROJECT_SOURCE_DIR}/tfiles/18/${example_name}.ddl ${PROJECT_BINARY_DIR}/${example_name}.ddl
+            )
+          endif ()
         endif ()
       endif ()
   endforeach ()

diff --git a/HDF5Examples/FORTRAN/H5G/h5ex_g_traverse.F90 b/HDF5Examples/FORTRAN/H5G/h5ex_g_traverse.F90
@@ -84,7 +84,9 @@ RECURSIVE INTEGER(KIND=C_INT) FUNCTION op_func(loc_id, name, info, operator_data
     CHARACTER(LEN=10) :: space
     INTEGER :: spaces ! Number of whitespaces to prepend to output
     INTEGER :: len
+    INTEGER :: ret_val_func
 
+    ret_val_func = 0
     ret_val = 0
 
     name_string(1:10) = " "
@@ -140,8 +142,8 @@ RECURSIVE INTEGER(KIND=C_INT) FUNCTION op_func(loc_id, name, info, operator_data
           ptr2 = C_LOC(nextod%recurs)
           funptr = C_FUNLOC(op_func)
           CALL h5literate_by_name_f(loc_id, name_string, H5_INDEX_NAME_F, H5_ITER_NATIVE_F, idx, &
-               funptr, ptr2, ret_val, status)
-
+               funptr, ptr2, ret_val_func, status)
+          ret_val = INT(ret_val_func,C_INT)
        ENDIF
        WRITE(*,'(A)') space(1:spaces)//"}"
        RETURN

diff --git a/HDF5Examples/FORTRAN/H5PAR/ph5_f90_dataset.F90 b/HDF5Examples/FORTRAN/H5PAR/ph5_f90_dataset.F90
@@ -25,9 +25,10 @@ PROGRAM DATASET
      !
      ! MPI definitions and calls.
      !
-     INTEGER :: mpierror       ! MPI error flag
-     INTEGER :: comm, info
-     INTEGER :: mpi_size, mpi_rank
+     INTEGER(KIND=MPI_INTEGER_KIND) :: mpierror       ! MPI error flag
+     INTEGER(KIND=MPI_INTEGER_KIND) :: comm, info
+     INTEGER(KIND=MPI_INTEGER_KIND) :: mpi_size, mpi_rank
+
      comm = MPI_COMM_WORLD
      info = MPI_INFO_NULL
      CALL MPI_INIT(mpierror)

diff --git a/HDF5Examples/FORTRAN/H5PAR/ph5_f90_file_create.F90 b/HDF5Examples/FORTRAN/H5PAR/ph5_f90_file_create.F90
@@ -18,9 +18,9 @@ PROGRAM FILE_CREATE
      !
      ! MPI definitions and calls.
      !
-     INTEGER :: mpierror       ! MPI error flag
-     INTEGER :: comm, info
-     INTEGER :: mpi_size, mpi_rank
+     INTEGER(KIND=MPI_INTEGER_KIND) :: mpierror       ! MPI error flag
+     INTEGER(KIND=MPI_INTEGER_KIND) :: comm, info
+     INTEGER(KIND=MPI_INTEGER_KIND) :: mpi_size, mpi_rank
      comm = MPI_COMM_WORLD
      info = MPI_INFO_NULL
 

diff --git a/HDF5Examples/FORTRAN/H5PAR/ph5_f90_filtered_writes_no_sel.F90 b/HDF5Examples/FORTRAN/H5PAR/ph5_f90_filtered_writes_no_sel.F90
@@ -27,7 +27,7 @@ MODULE filter
   INTEGER          , PARAMETER :: PATH_MAX = 512
 
   ! Global variables 
-  INTEGER :: mpi_rank, mpi_size
+  INTEGER(KIND=MPI_INTEGER_KIND) :: mpi_rank, mpi_size
 
 CONTAINS
   !
@@ -91,10 +91,11 @@ SUBROUTINE cleanup(filename)
 
     LOGICAL :: do_cleanup
     INTEGER :: status
+    INTEGER(KIND=MPI_INTEGER_KIND) :: mpierror
 
     CALL get_environment_variable("HDF5_NOCLEANUP", STATUS=status)
     IF(status.EQ.0)THEN
-       CALL MPI_File_delete(filename, MPI_INFO_NULL, status)
+       CALL MPI_File_delete(filename, MPI_INFO_NULL, mpierror)
     ENDIF
 
   END SUBROUTINE cleanup
@@ -241,18 +242,19 @@ PROGRAM main
    USE filter
    IMPLICIT NONE
 
-   INTEGER :: comm = MPI_COMM_WORLD
-   INTEGER :: info = MPI_INFO_NULL
+   INTEGER(KIND=MPI_INTEGER_KIND) :: comm = MPI_COMM_WORLD
+   INTEGER(KIND=MPI_INTEGER_KIND) :: info = MPI_INFO_NULL
    INTEGER(hid_t) :: file_id
    INTEGER(hid_t) :: fapl_id
    INTEGER(hid_t) :: dxpl_id
    CHARACTER(LEN=PATH_MAX) :: par_prefix
    CHARACTER(LEN=PATH_MAX) :: filename
    INTEGER :: status
+   INTEGER(KIND=MPI_INTEGER_KIND) :: mpierror
 
-   CALL MPI_Init(status)
-   CALL MPI_Comm_size(comm, mpi_size, status)
-   CALL MPI_Comm_rank(comm, mpi_rank, status)
+   CALL MPI_Init(mpierror)
+   CALL MPI_Comm_size(comm, mpi_size, mpierror)
+   CALL MPI_Comm_rank(comm, mpi_rank, mpierror)
 
   !
   ! Initialize HDF5 library and Fortran interfaces.
@@ -349,6 +351,6 @@ PROGRAM main
   ! ------------------------------------
   CALL cleanup(filename)
 
-  CALL MPI_Finalize(status)
+  CALL MPI_Finalize(mpierror)
 
 END PROGRAM main
diff --git a/HDF5Examples/FORTRAN/H5PAR/ph5_f90_hyperslab_by_chunk.F90 b/HDF5Examples/FORTRAN/H5PAR/ph5_f90_hyperslab_by_chunk.F90
@@ -34,9 +34,9 @@ PROGRAM DATASET_BY_CHUNK
      !
      ! MPI definitions and calls.
      !
-     INTEGER :: mpierror       ! MPI error flag
-     INTEGER :: comm, info
-     INTEGER :: mpi_size, mpi_rank
+     INTEGER(KIND=MPI_INTEGER_KIND) :: mpierror       ! MPI error flag
+     INTEGER(KIND=MPI_INTEGER_KIND) :: comm, info
+     INTEGER(KIND=MPI_INTEGER_KIND) :: mpi_size, mpi_rank
 
      comm = MPI_COMM_WORLD
      info = MPI_INFO_NULL

diff --git a/HDF5Examples/FORTRAN/H5PAR/ph5_f90_hyperslab_by_col.F90 b/HDF5Examples/FORTRAN/H5PAR/ph5_f90_hyperslab_by_col.F90
@@ -30,9 +30,9 @@ PROGRAM DATASET_BY_COL
      !
      ! MPI definitions and calls.
      !
-     INTEGER :: mpierror       ! MPI error flag
-     INTEGER :: comm, info
-     INTEGER :: mpi_size, mpi_rank
+     INTEGER(KIND=MPI_INTEGER_KIND) :: mpierror       ! MPI error flag
+     INTEGER(KIND=MPI_INTEGER_KIND) :: comm, info
+     INTEGER(KIND=MPI_INTEGER_KIND) :: mpi_size, mpi_rank
      comm = MPI_COMM_WORLD
      info = MPI_INFO_NULL
      CALL MPI_INIT(mpierror)

diff --git a/HDF5Examples/FORTRAN/H5PAR/ph5_f90_hyperslab_by_pattern.F90 b/HDF5Examples/FORTRAN/H5PAR/ph5_f90_hyperslab_by_pattern.F90
@@ -36,9 +36,9 @@ PROGRAM DATASET_BY_PATTERN
      !
      ! MPI definitions and calls.
      !
-     INTEGER :: mpierror       ! MPI error flag
-     INTEGER :: comm, info
-     INTEGER :: mpi_size, mpi_rank
+     INTEGER(KIND=MPI_INTEGER_KIND) :: mpierror       ! MPI error flag
+     INTEGER(KIND=MPI_INTEGER_KIND) :: comm, info
+     INTEGER(KIND=MPI_INTEGER_KIND) :: mpi_size, mpi_rank
 
      comm = MPI_COMM_WORLD
      info = MPI_INFO_NULL

diff --git a/HDF5Examples/FORTRAN/H5PAR/ph5_f90_hyperslab_by_row.F90 b/HDF5Examples/FORTRAN/H5PAR/ph5_f90_hyperslab_by_row.F90
@@ -35,9 +35,9 @@ PROGRAM DATASET_BY_ROW
      !
      ! MPI definitions and calls.
      !
-     INTEGER :: mpierror       ! MPI error flag
-     INTEGER :: comm, info
-     INTEGER :: mpi_size, mpi_rank
+     INTEGER(KIND=MPI_INTEGER_KIND) :: mpierror       ! MPI error flag
+     INTEGER(KIND=MPI_INTEGER_KIND) :: comm, info
+     INTEGER(KIND=MPI_INTEGER_KIND) :: mpi_size, mpi_rank
 
      comm = MPI_COMM_WORLD
      info = MPI_INFO_NULL