feat: utils to repack and replace .h5 and .hdf5 files

pyproject.toml

@@ -88,6 +88,7 @@ gwk_ess_evolution_plot = "gwkokab_scripts.ess_evolution_plot:main"
 gwk_ess_plot = "gwkokab_scripts.ess_plot:main"
 gwk_flowMC_cfg_template = "gwkokab.analysis.core.inference_io._sampler:_dump_flowMC_cfg"
 gwk_flowMC_info = "gwkokab_scripts.flowMC_info:main"
+gwk_h5repack = "gwkokab_scripts.h5repack:main"
 gwk_hist_overplot = "gwkokab_scripts.hist_overplot:main"
 gwk_joint_plot = "gwkokab_scripts.joint_plot:main"
 gwk_numpyro_cfg_template = "gwkokab.analysis.core.inference_io._sampler:_dump_numpyro_cfg"

src/gwkokab_scripts/h5repack.py

@@ -0,0 +1,62 @@
+# Copyright 2023 The GWKokab Authors
+# SPDX-License-Identifier: Apache-2.0
+
+
+import argparse
+import os
+import shutil
+import subprocess
+
+
+def main():
+    description = r"""Repack an HDF5 file using `h5repack` if available.
+
+It is equivalent to the following shell script:
+
+```sh
+#!/bin/bash
+
+file=$1
+temp_file="${file}.tmp"
+
+h5repack [options] "$file" "$temp_file"
+
+if [ $? -eq 0 ]; then
+    mv "$temp_file" "$file"
+else
+    rm -f "$temp_file"
+fi
+```
+"""
+    parser = argparse.ArgumentParser(
+        description=description,
+        epilog="Example usage: gwk_h5repack -- -f GZIP=9 -f SHUF data.h5",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+    parser.add_argument(
+        "options",
+        nargs=argparse.REMAINDER,
+        help="Additional options to pass to h5repack (e.g., '-f GZIP=9 -f SHUF')",
+    )
+    parser.add_argument("file", help="Path to the HDF5 file to repack")
+    args, options = parser.parse_known_args()
+
+    filename = args.file
+
+    if not shutil.which("h5repack"):
+        raise OSError("'h5repack' command not found in PATH.")
+
+    if not os.path.exists(filename):
+        raise FileNotFoundError(f"File '{filename}' does not exist.")
+
+    temp_file = f"{filename}.tmp"
+
+    cmd = ["h5repack"] + options + [filename, temp_file]
+
+    try:
+        subprocess.run(cmd, check=True)
+        shutil.move(temp_file, filename)
+    except (subprocess.CalledProcessError, OSError) as e:
+        if os.path.exists(temp_file):
+            os.remove(temp_file)
+        raise e