Added CLI for CombineH5 along with a test

Made required modifications, added check_src flag

Made newer changes

Made newer changes

Removed unnecessary includes

Changes

src/IO/H5/CombineH5.cpp

@@ -1,6 +1,8 @@
 // Distributed under the MIT License.
 // See LICENSE.txt for details.
 
+#include "IO/H5/CombineH5.hpp"
+
 #include <boost/program_options.hpp>
 #include <cstddef>
 #include <cstdlib>
@@ -46,23 +48,25 @@ size_t get_number_of_elements(const std::vector<std::string>& input_filenames,
   }
   return total_elements;
 }
-}
+} //namespace
 namespace h5 {
 
 void combine_h5(const std::string& file_prefix, const std::string& subfile_name,
-                const std::string& output) {
+                const std::string& output, const bool check_src) {
   // Parses for and stores all input files to be looped over
   const std::vector<std::string>& file_names =
       file_system::glob(file_prefix + "[0-9]*.h5");
   Parallel::printf("Processing files:\n%s\n",
                    std::string{MakeString{} << file_names}.c_str());
 
   // Checks that volume data was generated with identical versions of SpECTRE
-  if (!h5::check_src_files_match(file_names)) {
+  if (check_src){
+    if (!h5::check_src_files_match(file_names)) {
     ERROR(
         "One or more of your files were found to have differing src.tar.gz "
         "files, meaning that they may be from differing versions of SpECTRE.");
   }
+  }
 
   // Checks that volume data files contain the same observation ids
   if (!h5::check_observation_ids_match(file_names, subfile_name)) {

src/IO/H5/CombineH5.hpp

@@ -1,28 +1,13 @@
 // Distributed under the MIT License.
 // See LICENSE.txt for details.
+
 #pragma once
 
-#include <boost/program_options.hpp>
-#include <cstddef>
-#include <cstdlib>
-#include <iterator>
 #include <string>
-#include <vector>
-
-#include "DataStructures/DataVector.hpp"
-#include "IO/H5/AccessType.hpp"
-#include "IO/H5/CheckH5PropertiesMatch.hpp"
-#include "IO/H5/File.hpp"
-#include "IO/H5/SourceArchive.hpp"
-#include "IO/H5/VolumeData.hpp"
-#include "Parallel/Printf.hpp"
-#include "Utilities/FileSystem.hpp"
-#include "Utilities/MakeString.hpp"
-#include "Utilities/StdHelpers.hpp"
 
 namespace h5 {
 
 void combine_h5(const std::string& file_prefix, const std::string& subfile_name,
-                const std::string& output);
+                const std::string& output, const bool check_src = true);
 
 }  // namespace h5

src/IO/H5/Python/CombineH5.cpp

@@ -15,6 +15,6 @@ namespace py_bindings {
 void bind_h5combine(py::module& m) {
   // Wrapper for combining h5 files
   m.def("combine_h5", &h5::combine_h5, py::arg("file_prefix"),
-        py::arg("subfile_name"), py::arg("output"));
+        py::arg("subfile_name"), py::arg("output"), py::arg("check_src"));
 }
 }  // namespace py_bindings

src/IO/H5/Python/CombineH5.py

@@ -0,0 +1,71 @@
+# Distributed under the MIT License.
+# See LICENSE.txt for details.
+
+import logging
+import os
+
+import click
+import rich
+
+import spectre.IO.H5 as spectre_h5
+
+
+@click.command(name="combine-h5")
+@click.option(
+    "--file-prefix",
+    required=True,
+    type=str,
+    help="prefix of the files to be combined (omit number and file extension)",
+)
+@click.option(
+    "--subfile-name",
+    "-d",
+    type=str,
+    help="subfile name of the volume file in the H5 file (omit file extension)",
+)
+@click.option(
+    "--output",
+    "-o",
+    required=True,
+    type=click.Path(
+        exists=False,
+        file_okay=True,
+        dir_okay=False,
+        writable=True,
+        readable=True,
+    ),
+    help="combined output filename (omit file extension)",
+)
+@click.option(
+    "--check-src/--no-check-src",
+    default=True,
+    show_default=True,
+    help=(
+        "flag to check src files, True implies src files exist and can be"
+        " checked, False implies no src files to check."
+    ),
+)
+def combine_h5_command(file_prefix, subfile_name, output, check_src):
+    """Combines multiple HDF5 volume files
+
+    This executable is used for combining a series of HDF5 volume files into one
+    continuous dataset to be stored in a single HDF5 volume file."""
+
+    # Print available subfile names and exit
+    filename = file_prefix + "0.h5"
+    if not subfile_name:
+        if os.path.exists(filename):
+            spectre_file = spectre_h5.H5File(filename, "r")
+            import rich.columns
+
+            rich.print(rich.columns.Columns(spectre_file.all_vol_files()))
+            return
+
+    if subfile_name[0] == "/":
+        subfile_name = subfile_name[1:]
+
+    spectre_h5.combine_h5(file_prefix, subfile_name, output, check_src)
+
+
+if __name__ == "__main__":
+    combine_h5_command(help_option_names=["-h", "--help"])

support/Python/__main__.py

@@ -21,6 +21,7 @@ class Cli(click.MultiCommand):
     def list_commands(self, ctx):
         return [
             "clean-output",
+            "combine-h5",
             "delete-subfiles",
             "extend-connectivity",
             "extract-dat",
@@ -44,6 +45,10 @@ def get_command(self, ctx, name):
             from spectre.tools.CleanOutput import clean_output_command
 
             return clean_output_command
+        elif name == "combine-h5":
+            from spectre.IO.H5.CombineH5 import combine_h5_command
+
+            return combine_h5_command
         elif name == "delete-subfiles":
             from spectre.IO.H5.DeleteSubfiles import delete_subfiles_command
 

tests/Unit/IO/H5/CMakeLists.txt

@@ -42,12 +42,10 @@ spectre_add_python_bindings_test(
   )
 
 if(${BUILD_PYTHON_BINDINGS})
-  # Test is a bit slow because it writes a bunch of plot files to verify
-  # the argument handling works.
   set_tests_properties(
     "Unit.IO.H5.CombineH5.Python"
     PROPERTIES
-    TIMEOUT 80
+    TIMEOUT 10
     )
 endif()
 

tests/Unit/IO/H5/Test_CombineH5.py

@@ -5,11 +5,13 @@
 import unittest
 
 import numpy as np
+from click.testing import CliRunner
 
 import spectre.IO.H5 as spectre_h5
 from spectre import Informer
 from spectre.DataStructures import DataVector
 from spectre.IO.H5 import ElementVolumeData, TensorComponent, combine_h5
+from spectre.IO.H5.CombineH5 import combine_h5_command
 from spectre.Spectral import Basis, Quadrature
 
 
@@ -38,15 +40,20 @@ def setUp(self):
 
         # Initializing attributes
         grid_names1 = ["[B0(L0I0,L0I0,L1I0)]"]
-        grid_names2 = ["[B0(L1I0,L0I0,L0I0)]"]
+        grid_names2 = ["[B1(L1I0,L0I0,L0I0)]"]
         observation_values = {0: 7.0, 1: 1.3}
         basis = Basis.Legendre
         quad = Quadrature.Gauss
         self.observation_ids = [0, 1]
 
         # Writing ElementVolume data and TensorComponent Data to first file
         self.h5_file1 = spectre_h5.H5File(file_name=self.file_name1, mode="a")
-        self.tensor_component_data1 = np.array([[0.0], [0.3], [0.6]])
+        self.tensor_component_data1 = np.array(
+            [
+                [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7],
+                [0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08],
+            ]
+        )
         self.h5_file1.insert_vol("/element_data", version=0)
         self.h5_file1.close_current_object()
         self.vol_file1 = self.h5_file1.get_vol(path="/element_data")
@@ -60,7 +67,7 @@ def setUp(self):
                     ),
                     TensorComponent(
                         "field_2",
-                        DataVector(self.tensor_component_data1[i + 1]),
+                        DataVector(self.tensor_component_data1[i]),
                     ),
                 ],
                 extents=3 * [2],
@@ -89,7 +96,12 @@ def setUp(self):
 
         # Writing ElementVolume data and TensorComponent Data to second file
         self.h5_file2 = spectre_h5.H5File(file_name=self.file_name2, mode="a")
-        self.tensor_component_data2 = np.array([[1.0], [0.13], [0.16]])
+        self.tensor_component_data2 = np.array(
+            [
+                [0.1, 0.12, 0.22, 0.32, 0.42, 0.52, 0.62, 0.72],
+                [0.011, 0.021, 0.031, 0.041, 0.051, 0.061, 0.079, 0.089],
+            ]
+        )
         self.h5_file2.insert_vol("/element_data", version=0)
         self.h5_file2.close_current_object()
         self.vol_file2 = self.h5_file2.get_vol(path="/element_data")
@@ -103,7 +115,7 @@ def setUp(self):
                     ),
                     TensorComponent(
                         "field_2",
-                        DataVector(self.tensor_component_data2[i + 1]),
+                        DataVector(self.tensor_component_data2[i]),
                     ),
                 ],
                 extents=3 * [2],
@@ -138,9 +150,112 @@ def test_combine_h5(self):
         # Run the combine_h5 command and check if any feature (for eg.
         # connectivity length has increased due to combining two files)
 
-        combine_h5(self.file_name1[:-4], "element_data", self.output_file)
+        combine_h5(
+            self.file_name1[:-4], "element_data", self.output_file, False
+        )
+        h5_output = spectre_h5.H5File(
+            file_name=self.output_file + "0.h5", mode="r"
+        )
+        output_vol = h5_output.get_vol(path="/element_data")
+
+        # Test observation ids
+
+        actual_obs_ids = output_vol.list_observation_ids()
+        actual_obs_ids.sort()
+
+        expected_obs_ids = [0, 1]
+
+        self.assertEqual(actual_obs_ids, expected_obs_ids)
+
+        # Test observation values
+
+        obs_id = actual_obs_ids[0]
+
+        actual_obs_value = output_vol.get_observation_value(obs_id)
+        expected_obs_value = 7.0
+
+        self.assertEqual(actual_obs_value, expected_obs_value)
+
+        # Test tensor components
+
+        actual_tensor_component_names = output_vol.list_tensor_components(
+            obs_id
+        )
+
+        expected_tensor_component_names = ["field_1", "field_2"]
+
+        self.assertEqual(
+            actual_tensor_component_names, expected_tensor_component_names
+        )
+
+        expected_tensor_components = np.array(
+            [
+                (
+                    0,
+                    0.1,
+                    0.2,
+                    0.3,
+                    0.4,
+                    0.5,
+                    0.6,
+                    0.7,
+                    0.1,
+                    0.12,
+                    0.22,
+                    0.32,
+                    0.42,
+                    0.52,
+                    0.62,
+                    0.72,
+                ),
+                (
+                    0.01,
+                    0.02,
+                    0.03,
+                    0.04,
+                    0.05,
+                    0.06,
+                    0.07,
+                    0.08,
+                    0.011,
+                    0.021,
+                    0.031,
+                    0.041,
+                    0.051,
+                    0.061,
+                    0.079,
+                    0.089,
+                ),
+            ]
+        )
+        for i in range(len(expected_tensor_components)):
+            value = (
+                output_vol.get_tensor_component(
+                    i, actual_tensor_component_names[i]
+                ).data
+                == expected_tensor_components[i]
+            )
+            self.assertEqual(value, True)
+
+    def test_cli(self):
+        # Checks if the CLI for CombineH5 runs properly
+        runner = CliRunner()
+        result = runner.invoke(
+            combine_h5_command,
+            [
+                "--file-prefix",
+                self.file_name1[:-4],
+                "-d",
+                "element_data",
+                "-o",
+                self.output_file,
+                "--check-src",
+            ],
+            catch_exceptions=False,
+        )
+
         h5_output = spectre_h5.H5File(
-            file_name=self.output_file + "0.h5", mode="a"
+            file_name=self.output_file + "0.h5", mode="r"
         )
         output_vol = h5_output.get_vol(path="/element_data")
 
@@ -153,6 +268,24 @@ def test_combine_h5(self):
         ).data
 
         assert len(self.initial_h5_connectivity) < len(final_h5_connectivity)
+        self.assertEqual(result.exit_code, 0, result.output)
+
+    def test_cli2(self):
+        # Checks that if no subfile name is given, the CLI prints
+        # available subfiles correctly
+        runner = CliRunner()
+        result = runner.invoke(
+            combine_h5_command,
+            [
+                "--file-prefix",
+                self.file_name1[:-4],
+                "-o",
+                self.output_file,
+                "--check-src",
+            ],
+            catch_exceptions=False,
+        )
+        assert result.output is not None
 
 
 if __name__ == "__main__":