Squashed 'modules/rmf/dependency/RMF/' changes from 29a9724967..e812c…

…e3e2a e812ce3e2a Fix broken links to HDF5 API docs 223a03c634 Use FindBoost module rather than BoostConfig.cmake d2d63e476d Skip gcov step for now e276a31a14 Use latest codecov with token git-subtree-dir: modules/rmf/dependency/RMF git-subtree-split: e812ce3e2a9b23e8ba575a5af5e85cb513638876
salilab · Aug 30, 2024 · 379b5a2 · 379b5a2
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diff --git a/modules/rmf/dependency/RMF/.github/workflows/build.yml b/modules/rmf/dependency/RMF/.github/workflows/build.yml
@@ -63,5 +63,7 @@ jobs:
     - name: Combine coverage
       run: |
         cd build/coverage
-        coverage combine && mv .coverage ../..
-    - uses: codecov/codecov-action@v1
+        coverage combine && coverage xml && mv coverage.xml ../..
+    - uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/modules/rmf/dependency/RMF/CMakeLists.txt b/modules/rmf/dependency/RMF/CMakeLists.txt
@@ -48,6 +48,12 @@ if(POLICY CMP0086)
   cmake_policy(SET CMP0086 NEW)
 endif(POLICY CMP0086)
 
+# Use FindBoost module rather than BoostConfig.cmake (which requires
+# Boost 1.70 or later)
+if(POLICY CMP0167)
+  cmake_policy(SET CMP0167 OLD)
+endif(POLICY CMP0167)
+
 # C++11 can use the boost version
 set(Boost_NO_BOOST_CMAKE ON)
 find_package(Boost COMPONENTS system filesystem thread program_options iostreams

diff --git a/modules/rmf/dependency/RMF/doc/FileFormat.md b/modules/rmf/dependency/RMF/doc/FileFormat.md
@@ -207,7 +207,7 @@ There are several ways that the files can be made more compact
 (without breaking forwards compatibility of existing files). They can be investigated
 further if there is sufficient demand.
 
-If [HDF5](https://support.hdfgroup.org/HDF5/) is available when RMF is built,
+If [HDF5](https://www.hdfgroup.org/solutions/hdf5/) is available when RMF is built,
 wrappers for it
 will be built and support for older HDF5-based RMF formats will be compiled.
 

diff --git a/modules/rmf/dependency/RMF/doc/HDF5.md b/modules/rmf/dependency/RMF/doc/HDF5.md
@@ -4,7 +4,7 @@ HDF5 {#hdf5}
 We provide a simple set of classes for accessing core HDF5 functionality from C++. This was needed since
 - The HDF5 C interface is not trivial to use properly, particularly in regards to data type conversions and resource management.
 - It is very easy to use the C interface incorrectly without knowing it.
-- The [standard HDF5 C++ interface](https://support.hdfgroup.org/HDF5/) doesn't really simplify use of the HDF5 library and doesn't make use of the features of C++.
+- The [standard HDF5 C++ interface](https://www.hdfgroup.org/solutions/hdf5/) doesn't really simplify use of the HDF5 library and doesn't make use of the features of C++.
 
 The main classes provide access to:
 - HDF5 files through RMF::HDF5::File and RMF::HDF5::ConstFile

diff --git a/modules/rmf/dependency/RMF/doc/Installation.md b/modules/rmf/dependency/RMF/doc/Installation.md
@@ -42,7 +42,7 @@ In order to build from source, you will need:
 
 If you want to be able to read older format RMF files, you will also need:
 
-- [HDF5](https://support.hdfgroup.org/HDF5/) (1.8 or later; 1.10 or 1.12
+- [HDF5](https://www.hdfgroup.org/solutions/hdf5/) (1.8 or later; 1.10 or 1.12
   should also work)
 
 ## Download {#installation_download}

diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstDataSetD.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstDataSetD.h
@@ -35,7 +35,7 @@ typedef std::vector<ConstDataSetAttributes> ConstDataSetAttributesList;
    named as
     RMF::HDF5IndexDataSet2D (or RMF.HDF5IndexDataSet2).
    See
-   \external{https://support.hdfgroup.org/HDF5/doc/RM/RM_H5D.html,
+   \external{https://docs.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/documentation/doxygen/group___h5_d.html,
    the HDF5 manual} for more information.
  */
 template <class TypeTraits, unsigned int D>

diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstFile.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstFile.h
@@ -18,7 +18,7 @@ namespace RMF {
 namespace HDF5 {
 
 /** Store a handle to a non-writable HDF5 file. See
-   \external{https://support.hdfgroup.org/HDF5/doc/RM/RM_H5F.html,
+   \external{https://docs.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/documentation/doxygen/group___h5_f.html,
    the HDF5 manual} for more information.
 
    \note At the moment, a given file can only be opened once within a

diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstGroup.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstGroup.h
@@ -24,7 +24,7 @@ RMF_ENABLE_WARNINGS namespace RMF {
 #endif
 
   /** Wrap an HDF5 Group. See
-      \external{https://support.hdfgroup.org/HDF5/doc/RM/RM_H5G.html,
+      \external{https://docs.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/documentation/doxygen/group___h5_g.html,
       the HDF5 manual} for more information.
    */
   class RMFEXPORT ConstGroup : public ConstAttributes<Object> {

diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetAccessPropertiesD.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetAccessPropertiesD.h
@@ -28,7 +28,7 @@ RMF_ENABLE_WARNINGS namespace RMF {
    public:
     hid_t get_handle() const { return *h_; }
     /* Set the chunk cache to a certain size. See
-       \external{https://support.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetChunkCache,H5Pset_chunk_cache}.
+       \external{https://docs.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/documentation/doxygen/group___d_a_p_l.html#ga104d00442c31714ee073dee518f661f1,H5Pset_chunk_cache}.
      */
     void set_chunk_cache_size(unsigned int entries, unsigned int size_bytes,
                               double policy = .75) {

diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetCreationPropertiesD.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetCreationPropertiesD.h
@@ -36,7 +36,7 @@ RMF_ENABLE_WARNINGS namespace RMF {
       }
     }
     /** See
-       \external{https://support.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetChunk,
+       \external{https://docs.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/documentation/doxygen/group___d_c_p_l.html#ga3584d592e377da3604b7604e266dcf5b,
        H5Pset_chunk}
      */
     void set_chunk_size(DataSetIndexD<D> chunk_size) {

diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetD.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetD.h
@@ -26,7 +26,7 @@ namespace HDF5 {
    named as
     RMF::HDF5::IndexDataSet2D (or RMF.HDF5.IndexDataSet2).
    See
-   \external{https://support.hdfgroup.org/HDF5/doc/RM/RM_H5D.html,
+   \external{https://docs.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/documentation/doxygen/group___h5_d.html,
    the HDF5 manual} for more information.
  */
 template <class TypeTraits, unsigned int D>

diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/File.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/File.h
@@ -20,7 +20,7 @@ RMF_ENABLE_WARNINGS namespace RMF {
       regards to data type conversions and resource management
       - It is very easy to use the C interface incorrectly without knowing it.
       - The
-      \external{https://support.hdfgroup.org/HDF5/, standard HDF5 C++ interface}
+      \external{https://www.hdfgroup.org/solutions/hdf5/, standard HDF5 C++ interface}
       doesn't really simplify use of the HDF5 library and doesn't make use
       of the features of C++.
 
@@ -50,7 +50,7 @@ RMF_ENABLE_WARNINGS namespace RMF {
   namespace HDF5 {
 
   /** Store a handle to an HDF5 file. See
-     \external{https://support.hdfgroup.org/HDF5/doc/RM/RM_H5F.html,
+     \external{https://docs.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/documentation/doxygen/group___h5_f.html,
      the HDF5 manual} for more information.*/
   class RMFEXPORT File : public Group {
    public:

diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/Group.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/Group.h
@@ -24,7 +24,7 @@ typedef std::vector<GroupAttributes> GroupAttributesList;
 #endif
 
 /** Wrap an HDF5 Group. See
-    \external{https://support.hdfgroup.org/HDF5/doc/RM/RM_H5G.html,
+    \external{https://docs.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/documentation/doxygen/group___h5_g.html,
     the HDF5 manual} for more information.
  */
 class RMFEXPORT Group : public MutableAttributes<ConstGroup> {

diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/MutableAttributes.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/MutableAttributes.h
@@ -18,7 +18,7 @@ RMF_ENABLE_WARNINGS
 namespace RMF {
 namespace HDF5 {
 /** Wrap a set of HDF5 Attributes. See
-    \external{https://support.hdfgroup.org/HDF5/doc/RM/RM_H5A.html,
+    \external{https://docs.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/documentation/doxygen/group___h5_a.html,
     the HDF5 manual} for more information.
  */
 template <class Base>

diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/Object.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/Object.h
@@ -24,7 +24,7 @@ namespace HDF5 {
 class File;
 
 /** Wrap an HDF5 Object. See
-    \external{https://support.hdfgroup.org/HDF5/doc/RM/RM_H5O.html,
+    \external{https://docs.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/documentation/doxygen/group___h5_o.html,
     the HDF5 manual} for more information.
  */
 class RMFEXPORT Object {