utility code in its own module

utils/encoder.py

@@ -0,0 +1,16 @@
+import numpy as np
+
+
+# Convert non-json-encodable types to built-in types
+
+
+def json_encode(val):
+
+    if isinstance(val, np.integer):
+        return int(val)
+    elif isinstance(val, np.floating):
+        return float(val)
+    elif isinstance(val, np.ndarray):
+        return val.tolist()
+    else:
+        return val

utils/parser.py

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+# parser for netcdf_to_zarr
+
+import argparse
+
+
+def configure(args):
+
+    class toList(argparse.Action):
+        def __init__(self, option_strings, dest, nargs=None, **kwargs):
+            if nargs is not None:
+                raise ValueError("nargs not allowed")
+            super(toList, self).__init__(option_strings, dest, **kwargs)
+
+        def __call__(self, parser, namespace, values, option_string=None):
+            setattr(namespace, self.dest, values.split(' '))
+
+    desc = ('This script converts netCDF4 into zarr files\n'
+            'It is possible to specify a list of netCDF4 files\n'
+            'to merge them into a single zarr file.\n'
+            'to do so, the variables in the netCD4 file\n'
+            'must have a common shape and run along the same dimension.\n'
+            '\nExamples:\n'
+            '  -convert.py src.nc dst.nc [-options]\n'
+            '  -convert.py "src1.nc src2.nc src3.nc" dst.zarr [-options]\n')
+
+    parser = argparse.ArgumentParser(description=desc,
+                                     formatter_class=argparse.RawTextHelpFormatter)
+
+    parser.add_argument('src',
+                        help='source netCDF4 file/files',
+                        action=toList,
+                        default=[])
+
+    parser.add_argument('dst',
+                        help='target zarr file',
+                        default='')
+
+    parser.add_argument('-a',
+                        '--axis',
+                        metavar='axis',
+                        help='axis name to append along',
+                        default=None)
+
+    parser.add_argument('-n',
+                        '--nested',
+                        help='chunks are located into a nested path',
+                        action='store_true',
+                        default=False)
+
+    parser.add_argument('-m',
+                        '--mode',
+                        metavar='mode',
+                        help='use processes or threads',
+                        choices=('threads', 'processes'),
+                        default='serial')
+
+    return parser.parse_args(args)