Normalize subfile path in H5 lib

This has bothered me for a long time. A leading slash and
_no_ extension for subfile names was required before,
and failing to do this lead to rather useless error messages.
Now, the leading slash and the extension are handled
within the H5 lib, so it should be much easier to use.

src/IO/Exporter/Exporter.cpp

@@ -151,7 +151,7 @@ template <size_t Dim>
 std::vector<std::vector<double>> interpolate_to_points(
     const std::variant<std::vector<std::string>, std::string>&
         volume_files_or_glob,
-    std::string subfile_name,
+    const std::string& subfile_name,
     const std::variant<ObservationId, ObservationStep>& observation,
     const std::vector<std::string>& tensor_components,
     const std::array<std::vector<double>, Dim>& target_points,
@@ -173,15 +173,6 @@ std::vector<std::vector<double>> interpolate_to_points(
     ERROR_NO_TRACE("No volume files found. Specify at least one volume file.");
   }
 
-  // Normalize subfile name
-  if (subfile_name.size() > 4 &&
-      subfile_name.substr(subfile_name.size() - 4) == ".vol") {
-    subfile_name = subfile_name.substr(0, subfile_name.size() - 4);
-  }
-  if (subfile_name.front() != '/') {
-    subfile_name = '/' + subfile_name;
-  }
-
   // Retrieve info from the first volume file
   const h5::H5File<h5::AccessType::ReadOnly> first_h5file(filenames.front());
   const auto& first_volfile = first_h5file.get<h5::VolumeData>(subfile_name);
@@ -278,7 +269,7 @@ std::vector<std::vector<double>> interpolate_to_points(
   template std::vector<std::vector<double>> interpolate_to_points<DIM(data)>( \
       const std::variant<std::vector<std::string>, std::string>&              \
           volume_files_or_glob,                                               \
-      std::string subfile_name,                                               \
+      const std::string& subfile_name,                                        \
       const std::variant<ObservationId, ObservationStep>& observation,        \
       const std::vector<std::string>& tensor_components,                      \
       const std::array<std::vector<double>, DIM(data)>& target_points,        \

src/IO/Exporter/Exporter.hpp

@@ -58,7 +58,7 @@ template <size_t Dim>
 std::vector<std::vector<double>> interpolate_to_points(
     const std::variant<std::vector<std::string>, std::string>&
         volume_files_or_glob,
-    std::string subfile_name,
+    const std::string& subfile_name,
     const std::variant<ObservationId, ObservationStep>& observation,
     const std::vector<std::string>& tensor_components,
     const std::array<std::vector<double>, Dim>& target_points,

src/IO/H5/File.hpp

@@ -209,7 +209,7 @@ class H5File {
 
   template <typename ObjectType>
   std::tuple<bool, detail::OpenGroup, std::string> check_if_object_exists(
-      const std::string& path) const;
+      std::string path) const;
 
   std::string file_name_;
   // NOLINTNEXTLINE(spectre-mutable)
@@ -392,7 +392,16 @@ const ObjectType& H5File<Access_t>::convert_to_derived(
 template <AccessType Access_t>
 template <typename ObjectType>
 std::tuple<bool, detail::OpenGroup, std::string>
-H5File<Access_t>::check_if_object_exists(const std::string& path) const {
+H5File<Access_t>::check_if_object_exists(std::string path) const {
+  // Normalize path to have a leading slash and the correct extension
+  if (path.front() != '/') {
+    path = '/' + path;
+  }
+  const size_t extension_length = ObjectType::extension().size();
+  if (path.size() > extension_length and
+      path.substr(path.size() - extension_length) == ObjectType::extension()) {
+    path = path.substr(0, path.size() - extension_length);
+  }
   std::string name_only = "/";
   if (path != "/") {
     name_only = file_system::get_file_name(path);

src/IO/H5/Python/CombineH5.py

@@ -78,11 +78,6 @@ def combine_h5_vol_command(h5files, subfile_name, output, check_src):
         rich.print(rich.columns.Columns(spectre_file.all_vol_files()))
         return
 
-    if not subfile_name.startswith("/"):
-        subfile_name = "/" + subfile_name
-    if subfile_name.endswith(".vol"):
-        subfile_name = subfile_name[:-4]
-
     if not output.endswith(".h5"):
         output += ".h5"
 

src/IO/H5/Python/ExtendConnectivityData.py

@@ -40,11 +40,6 @@ def extend_connectivity_data_command(filename, subfile_name):
     files, the combine-h5 executable must be run first. The extend-connectivity
     command can then be run on the newly generated HDF5 file.
     """
-    # Ensure that the format of the subfile is correct
-    if subfile_name.endswith(".vol"):
-        subfile_name = subfile_name[:-4]
-    if subfile_name[0] != "/":
-        subfile_name = "/" + subfile_name
     # Read the h5 file and extract the volume file from it
     h5_file = spectre_h5.H5File(filename, "r+")
     vol_file = h5_file.get_vol(subfile_name)

src/Visualization/Python/OpenVolfiles.py

@@ -168,12 +168,6 @@ def command(
                     rich.print(rich.columns.Columns(available_subfiles))
                     return
 
-            # Normalize subfile name
-            if subfile_name.endswith(".vol"):
-                subfile_name = subfile_name[:-4]
-            if not subfile_name.startswith("/"):
-                subfile_name = "/" + subfile_name
-
             # Print available observations/times and exit
             if list_times:
                 import rich.columns

src/Visualization/Python/Render1D.py

@@ -310,11 +310,6 @@ def render_1d_command(
         rich.print(rich.columns.Columns(open_h5_files[0].all_vol_files()))
         return
 
-    if subfile_name.endswith(".vol"):
-        subfile_name = subfile_name[:-4]
-    if not subfile_name.startswith("/"):
-        subfile_name = "/" + subfile_name
-
     volfiles = [h5file.get_vol(subfile_name) for h5file in open_h5_files]
     dim = volfiles[0].get_dimension()
     assert (

src/Visualization/Python/TransformVolumeData.py

@@ -800,11 +800,6 @@ def shift_magnitude(
             rich.print(rich.columns.Columns())
             return
 
-    if subfile_name.endswith(".vol"):
-        subfile_name = subfile_name[:-4]
-    if not subfile_name.startswith("/"):
-        subfile_name = "/" + subfile_name
-
     volfiles = [h5file.get_vol(subfile_name) for h5file in open_h5_files]
 
     # Load kernels

tests/Unit/IO/H5/Test_Dat.cpp

@@ -321,7 +321,9 @@ void test_dat_read() {
     error_file.append(std::vector<double>{0.33, 0.66, 0.77, 0.90});
   }
   h5::H5File<h5::AccessType::ReadOnly> my_file(h5_file_name);
-  const auto& error_file = my_file.get<h5::Dat>("/L2_errors");
+  // No leading slash should also find the subfile, and a ".dat" extension as
+  // well
+  const auto& error_file = my_file.get<h5::Dat>("L2_errors.dat");
   CHECK(error_file.subfile_path() == "/L2_errors");
 
   // Check version info is correctly retrieved from Dat file

tests/Unit/IO/H5/Test_VolumeData.cpp

@@ -264,9 +264,10 @@ void test() {
     my_file.close_current_object();
   }
   // Open the read volume file and check that the observation id and values are
-  // correct.
+  // correct. No leading slash should also find the subfile, and a ".vol"
+  // extension as well.
   const auto& volume_file =
-      my_file.get<h5::VolumeData>("/element_data", version_number);
+      my_file.get<h5::VolumeData>("element_data.vol", version_number);
   CHECK(volume_file.subfile_path() == "/element_data");
   const auto read_observation_ids = volume_file.list_observation_ids();
   // The observation IDs should be sorted by their observation value