PY: Add support for Python 3.12 with HDF5 1.14. (#861)

Signed-off-by: Michael Jackson <[email protected]>

conda/conda_build_config.yaml

@@ -8,6 +8,7 @@ cxx_compiler_version:
   - 10.4.0 # [linux]
 
 python:
+    - 3.12
     - 3.11
     - 3.10
     - 3.9

conda/meta.yaml

@@ -40,7 +40,7 @@ build:
 requirements:
   build:
     - {{ compiler('cxx') }}
-    - cmake >=3.26
+    - cmake =3.26
     - ninja
     - git
   host:
@@ -50,7 +50,8 @@ requirements:
     - boost_mp11
     - eigen
     - fmt =10
-    - hdf5 =1.12
+    - hdf5 >=1.14.3 # [py>=312]
+    - hdf5 =1.12 # [py<=311]
     - nlohmann_json
     - pybind11 >=2.10
     - reproc-cpp
@@ -66,7 +67,8 @@ requirements:
     - python
     - numpy
     - fmt =10
-    - hdf5 =1.12
+    - hdf5 >=1.14.3 # [py>=312]
+    - hdf5 =1.12 # [py<=311]
     - reproc-cpp
     - tbb
     - zlib

conda/recipe.yaml

@@ -51,7 +51,10 @@ requirements:
     - boost_mp11
     - eigen
     - fmt =10
-    - hdf5 =1.12
+    - sel(py>=312):
+      - hdf5 >=1.14.3
+    - sel(py>=39 and py<312):
+      - hdf5 >=1.12
     - nlohmann_json
     - pybind11 >=2.10
     - reproc-cpp
@@ -66,7 +69,10 @@ requirements:
     - python
     - numpy
     - fmt =10
-    - hdf5 =1.12
+    - sel(py>=312):
+      - hdf5 >=1.14.3
+    - sel(py>=39 and py<312):
+      - hdf5 >=1.12
     - reproc-cpp
     - tbb
     - zlib

src/simplnx/DataStructure/IO/HDF5/DataStoreIO.hpp

@@ -18,7 +18,7 @@ namespace Chunks
 constexpr int32 k_DimensionMismatchError = -2654;
 
 template <typename T>
-inline Result<> WriteDataStoreChunk(nx::core::HDF5::DatasetWriter& datasetWriter, const AbstractDataStore<T>& store, const std::vector<hsize_t>& h5dims,
+inline Result<> WriteDataStoreChunk(nx::core::HDF5::DatasetWriter& datasetWriter, const AbstractDataStore<T>& store, const nx::core::HDF5::DatasetWriter::DimsType& h5dims,
                                     const nx::core::HDF5::DatasetWriter::DimsType& chunkDims, const IDataStore::ShapeType& index)
 {
   auto rank = chunkDims.size();
@@ -53,7 +53,7 @@ inline Result<> WriteDataStoreChunk(nx::core::HDF5::DatasetWriter& datasetWriter
 }
 
 template <>
-inline Result<> WriteDataStoreChunk<bool>(nx::core::HDF5::DatasetWriter& datasetWriter, const AbstractDataStore<bool>& store, const std::vector<hsize_t>& h5dims,
+inline Result<> WriteDataStoreChunk<bool>(nx::core::HDF5::DatasetWriter& datasetWriter, const AbstractDataStore<bool>& store, const nx::core::HDF5::DatasetWriter::DimsType& h5dims,
                                           const nx::core::HDF5::DatasetWriter::DimsType& chunkDims, const IDataStore::ShapeType& index)
 {
   auto rank = chunkDims.size();
@@ -83,8 +83,8 @@ inline Result<> WriteDataStoreChunk<bool>(nx::core::HDF5::DatasetWriter& dataset
 }
 
 template <typename T>
-inline Result<> RecursivelyWriteChunks(nx::core::HDF5::DatasetWriter& datasetWriter, const AbstractDataStore<T>& store, const std::vector<hsize_t>& h5dims,
-                                       const nx::core::HDF5::DatasetWriter::DimsType& chunkDims, IDataStore::ShapeType index, const std::vector<hsize_t>& chunkLayout, uint64 i = 0)
+inline Result<> RecursivelyWriteChunks(nx::core::HDF5::DatasetWriter& datasetWriter, const AbstractDataStore<T>& store, const nx::core::HDF5::DatasetWriter::DimsType& h5dims,
+                                       const nx::core::HDF5::DatasetWriter::DimsType& chunkDims, IDataStore::ShapeType index, const nx::core::HDF5::DatasetWriter::DimsType& chunkLayout, uint64 i = 0)
 {
   // uint64 rank = chunkLayout.size();
   const uint64 rank = chunkDims.size();
@@ -117,7 +117,7 @@ inline Result<> RecursivelyWriteChunks(nx::core::HDF5::DatasetWriter& datasetWri
 }
 
 template <typename T>
-inline Result<> WriteDataStoreChunks(nx::core::HDF5::DatasetWriter& datasetWriter, const AbstractDataStore<T>& store, const std::vector<hsize_t>& h5dims)
+inline Result<> WriteDataStoreChunks(nx::core::HDF5::DatasetWriter& datasetWriter, const AbstractDataStore<T>& store, const nx::core::HDF5::DatasetWriter::DimsType& h5dims)
 {
   auto shapeDims = store.getTupleShape();
   const auto componentDims = store.getComponentShape();
@@ -128,7 +128,7 @@ inline Result<> WriteDataStoreChunks(nx::core::HDF5::DatasetWriter& datasetWrite
 
   usize rank = shapeDims.size();
 
-  std::vector<hsize_t> chunkLayout(rank);
+  nx::core::HDF5::DatasetWriter::DimsType chunkLayout(rank);
   for(usize i = 0; i < rank; i++)
   {
     const bool hasRemainder = (shapeDims[i] % chunkDims[i] != 0);
@@ -163,7 +163,7 @@ inline Result<> WriteDataStore(nx::core::HDF5::DatasetWriter& datasetWriter, con
 
   // Consolidate the Tuple and Component Dims into a single array which is used
   // to write the entire data array to HDF5
-  std::vector<hsize_t> h5dims;
+  nx::core::HDF5::DatasetWriter::DimsType h5dims;
   for(const auto& value : dataStore.getTupleShape())
   {
     h5dims.push_back(static_cast<hsize_t>(value));

src/simplnx/Utilities/FileUtilities.cpp

@@ -25,7 +25,7 @@ int64 LinesInFile(const std::string& filepath)
   // Check if the very last character is NOT a newline character
   fseek(fd, -1, SEEK_END);
   char last[1];
-  fread(last, 1, 1, fd);
+  auto bytsRead = fread(last, 1, 1, fd);
   if(last[0] != '\n')
   {
     lines++;

src/simplnx/Utilities/Parsing/HDF5/IO/AttributeIO.cpp

@@ -6,6 +6,7 @@
 
 #include <H5Apublic.h>
 
+#include <algorithm>
 #include <iostream>
 #include <numeric>
 #include <vector>
@@ -414,7 +415,10 @@ Result<> AttributeIO::writeVector(const DimsVector& dims, const std::vector<T>&
     return MakeErrorResult(-102, "DataType was unkown");
   }
 
-  hid_t dataspaceId = H5Screate_simple(rank, dims.data(), nullptr);
+  std::vector<hsize_t> hDims(dims.size());
+  std::transform(dims.begin(), dims.end(), hDims.begin(), [](DimsVector::value_type x) { return static_cast<hsize_t>(x); });
+  hid_t dataspaceId = H5Screate_simple(rank, hDims.data(), nullptr);
+
   if(dataspaceId >= 0)
   {
     // Delete any existing attribute

src/simplnx/Utilities/Parsing/HDF5/IO/DatasetIO.cpp

@@ -465,10 +465,12 @@ std::vector<hsize_t> DatasetIO::getDimensions() const
   return dims;
 }
 
-IdType DatasetIO::CreateDatasetChunkProperties(nonstd::span<const hsize_t> dims)
+IdType DatasetIO::CreateDatasetChunkProperties(const DimsType& dims)
 {
+  std::vector<hsize_t> hDims(dims.size());
+  std::transform(dims.begin(), dims.end(), hDims.begin(), [](DimsType::value_type x) { return static_cast<hsize_t>(x); });
   auto cparms = H5Pcreate(H5P_DATASET_CREATE);
-  auto status = H5Pset_chunk(cparms, dims.size(), dims.data());
+  auto status = H5Pset_chunk(cparms, hDims.size(), hDims.data());
   if(status < 0)
   {
     return H5P_DEFAULT;
@@ -505,7 +507,9 @@ Result<> DatasetIO::writeSpan(const DimsType& dims, nonstd::span<const T> values
     return MakeErrorResult(-105, "DataType was unknown");
   }
 
-  hid_t dataspaceId = H5Screate_simple(rank, dims.data(), nullptr);
+  std::vector<hsize_t> hDims(dims.size());
+  std::transform(dims.begin(), dims.end(), hDims.begin(), [](DimsType::value_type x) { return static_cast<hsize_t>(x); });
+  hid_t dataspaceId = H5Screate_simple(rank, hDims.data(), nullptr);
   if(dataspaceId >= 0)
   {
     Result<> result = findAndDeleteAttribute();
@@ -558,7 +562,9 @@ Result<> DatasetIO::writeChunk(const DimsType& dims, nonstd::span<const T> value
     return MakeErrorResult(-100, "DataType was unknown");
   }
 
-  hid_t dataspaceId = H5Screate_simple(rank, dims.data(), nullptr);
+  std::vector<hsize_t> hDims(dims.size());
+  std::transform(dims.begin(), dims.end(), hDims.begin(), [](DimsType::value_type x) { return static_cast<hsize_t>(x); });
+  hid_t dataspaceId = H5Screate_simple(rank, hDims.data(), nullptr);
   if(dataspaceId >= 0)
   {
     Result<> result = findAndDeleteAttribute();

src/simplnx/Utilities/Parsing/HDF5/IO/DatasetIO.hpp

@@ -291,7 +291,7 @@ class SIMPLNX_EXPORT DatasetIO : public ObjectIO
    * @param dims
    * @return Returns the property ID if successful. Returns H5P_DEFAULT otherwise.
    */
-  static IdType CreateDatasetChunkProperties(nonstd::span<const hsize_t> dims);
+  static IdType CreateDatasetChunkProperties(const DimsType& dims);
 
   static IdType CreateTransferChunkProperties(const DimsType& chunkDims);
 

src/simplnx/Utilities/Parsing/HDF5/IO/GroupIO.cpp

@@ -111,13 +111,13 @@ size_t GroupIO::getNumChildren() const
     return 0;
   }
 
-  SizeType numChildren;
+  hsize_t numChildren;
   auto err = H5Gget_num_objs(getId(), &numChildren);
   if(err < 0)
   {
     return 0;
   }
-  return numChildren;
+  return static_cast<size_t>(numChildren);
 }
 
 std::vector<std::string> GroupIO::getChildNames() const

src/simplnx/Utilities/Parsing/HDF5/Readers/GroupReader.cpp

@@ -72,13 +72,13 @@ size_t GroupReader::getNumChildren() const
     return 0;
   }
 
-  SizeType numChildren;
+  hsize_t numChildren;
   auto err = H5Gget_num_objs(getId(), &numChildren);
   if(err < 0)
   {
     return 0;
   }
-  return numChildren;
+  return static_cast<size_t>(numChildren);
 }
 
 std::vector<std::string> GroupReader::getChildNames() const

src/simplnx/Utilities/Parsing/HDF5/Writers/AttributeWriter.hpp

@@ -1,5 +1,6 @@
 #pragma once
 
+#include <algorithm>
 #include <any>
 #include <string>
 #include <vector>
@@ -161,8 +162,9 @@ class SIMPLNX_EXPORT AttributeWriter
     {
       return MakeErrorResult(-101, "Unknown data type");
     }
-
-    hid_t dataspaceId = H5Screate_simple(rank, dims.data(), nullptr);
+    std::vector<hsize_t> hDims(dims.size());
+    std::transform(dims.begin(), dims.end(), hDims.begin(), [](DimsVector::value_type x) { return static_cast<hsize_t>(x); });
+    hid_t dataspaceId = H5Screate_simple(rank, hDims.data(), nullptr);
     if(dataspaceId >= 0)
     {
       // Delete any existing attribute

src/simplnx/Utilities/Parsing/HDF5/Writers/DatasetWriter.cpp

@@ -127,10 +127,12 @@ void DatasetWriter::createOrOpenDataset(IdType typeId, IdType dataspaceId, IdTyp
   }
 }
 
-IdType DatasetWriter::CreateDatasetChunkProperties(nonstd::span<const hsize_t> dims)
+IdType DatasetWriter::CreateDatasetChunkProperties(const DimsType& chunkDims)
 {
+  std::vector<hsize_t> hDims(chunkDims.size());
+  std::transform(chunkDims.begin(), chunkDims.end(), hDims.begin(), [](DimsType::value_type x) { return static_cast<hsize_t>(x); });
   auto cparms = H5Pcreate(H5P_DATASET_CREATE);
-  auto status = H5Pset_chunk(cparms, dims.size(), dims.data());
+  auto status = H5Pset_chunk(cparms, hDims.size(), hDims.data());
   if(status < 0)
   {
     return H5P_DEFAULT;

src/simplnx/Utilities/Parsing/HDF5/Writers/DatasetWriter.hpp

@@ -91,8 +91,10 @@ class SIMPLNX_EXPORT DatasetWriter : public ObjectWriter
     {
       return MakeErrorResult(-1, "DataType was unknown");
     }
+    std::vector<hsize_t> hDims(dims.size());
+    std::transform(dims.begin(), dims.end(), hDims.begin(), [](DimsType::value_type x) { return static_cast<hsize_t>(x); });
+    hid_t dataspaceId = H5Screate_simple(rank, hDims.data(), nullptr);
 
-    hid_t dataspaceId = H5Screate_simple(rank, dims.data(), nullptr);
     if(dataspaceId >= 0)
     {
       auto result = findAndDeleteAttribute();
@@ -144,8 +146,9 @@ class SIMPLNX_EXPORT DatasetWriter : public ObjectWriter
     {
       return MakeErrorResult(-100, "DataType was unkown");
     }
-
-    hid_t dataspaceId = H5Screate_simple(rank, dims.data(), nullptr);
+    std::vector<hsize_t> hDims(dims.size());
+    std::transform(dims.begin(), dims.end(), hDims.begin(), [](DimsType::value_type x) { return static_cast<hsize_t>(x); });
+    hid_t dataspaceId = H5Screate_simple(rank, hDims.data(), nullptr);
     if(dataspaceId >= 0)
     {
       auto result = findAndDeleteAttribute();
@@ -221,11 +224,16 @@ class SIMPLNX_EXPORT DatasetWriter : public ObjectWriter
 
   /**
    * @brief Applies chunking to the dataset and sets the chunk dimensions.
-   * @param dims
+   * @param chunkDims
    * @return Returns the property ID if successful. Returns H5P_DEFAULT otherwise.
    */
-  static IdType CreateDatasetChunkProperties(nonstd::span<const hsize_t> dims);
+  static IdType CreateDatasetChunkProperties(const DimsType& chunkDims);
 
+  /**
+   * @brief
+   * @param chunkDims
+   * @return Returns the property ID if successful. Returns H5P_DEFAULT otherwise.
+   */
   static IdType CreateTransferChunkProperties(const DimsType& chunkDims);
 
   /**