Check make cf conventions configurable

README.md

@@ -29,20 +29,22 @@ new_data = rechunk_dataset(dset)
 
 ```bash
 rechunk-data --help
-usage: rechunk-data [-h] [--output OUTPUT] [--netcdf-engine {h5netcdf,netcdf4}] [-v] [-V] input
+usage: rechunk-data [-h] [--output OUTPUT] [--netcdf-engine {h5netcdf,netcdf4}] [--skip-cf-convention] [-v] [-V] input
 
 Rechunk input netcdf data to optimal chunk-size. approx. 126 MB per chunk
 
 positional arguments:
   input                 Input file/directory. If a directory is given all ``.nc`` files in all sub directories will be processed
 
-optional arguments:
+options:
   -h, --help            show this help message and exit
-  --output OUTPUT       Output file/directory of the chunked netcdf file(s). Note: If ``input`` is a directory output should be a
-                        directory. If None given (default) the ``input`` is overidden. (default: None)
+  --output OUTPUT       Output file/directory of the chunked netcdf file(s).
+                        Note: If ``input`` is a directory output should be a directory.
+                        If None given (default) the ``input`` is overidden. (default: None)
   --netcdf-engine {h5netcdf,netcdf4}
-                        The netcdf engine used to create the new netcdf file. (default: h5netcdf)
-  -v
+                        The netcdf engine used to create the new netcdf file. (default: netcdf4)
+  --skip-cf-convention  Do not assume assume data variables follow CF conventions. (default: False)
+  -v                    Increase verbosity (default: 0)
   -V, --version         show program's version number and exit
 ```
 

src/rechunk_data/__init__.py

@@ -51,10 +51,17 @@ def parse_args(argv: Optional[List[str]]) -> argparse.Namespace:
         default="netcdf4",
         type=str,
     )
+    parser.add_argument(
+        "--skip-cf-convention",
+        help="Do not assume assume data variables follow CF conventions.",
+        action="store_true",
+        default=False,
+    )
     parser.add_argument(
         "-v",
         action="count",
         default=0,
+        help="Increase verbosity",
     )
     parser.add_argument(
         "-V",
@@ -63,11 +70,16 @@ def parse_args(argv: Optional[List[str]]) -> argparse.Namespace:
         version=f"%(prog)s {__version__}",
     )
     args = parser.parse_args(argv)
-    logger.setLevel(max(logging.ERROR - (10 + args.v * 10), 0))
+    logger.setLevel(max(logging.ERROR - (10 + args.v * 10), 10))
     return args
 
 
 def cli(argv: Optional[List[str]] = None) -> None:
     """Command line interface calling the rechunking method."""
     args = parse_args(argv)
-    rechunk_netcdf_file(args.input, args.output, engine=args.netcdf_engine)
+    rechunk_netcdf_file(
+        args.input,
+        args.output,
+        engine=args.netcdf_engine,
+        decode_cf=args.skip_cf_convention is False,
+    )

src/rechunk_data/_rechunk.py

@@ -92,13 +92,21 @@ def _rechunk_dataset(
         ) from error
     for data_var in dset.data_vars:
         var = str(data_var)
-        if not isinstance(dset[var].data, Array):
+        if (
+            not isinstance(dset[var].data, Array)
+            or "bnds" in var
+            or "rotated_pole" in var
+        ):
             logger.debug("Skipping rechunking variable %s", var)
             continue
         logger.debug("Rechunking variable %s", var)
         chunks: Dict[int, Optional[str]] = {}
         for i, dim in enumerate(map(str, dset[var].dims)):
-            if "lon" in dim.lower() or "lat" in dim.lower() or "bnds" in dim.lower():
+            if (
+                "lon" in dim.lower()
+                or "lat" in dim.lower()
+                or "bnds" in dim.lower()
+            ):
                 chunks[i] = None
             else:
                 chunks[i] = "auto"
@@ -116,9 +124,14 @@ def _rechunk_dataset(
         )
         logger.debug("Settings encoding of variable %s", var)
         encoding[data_var] = {
-            str(k): v for k, v in dset[var].encoding.items() if str(k) in _keywords
+            str(k): v
+            for k, v in dset[var].encoding.items()
+            if str(k) in _keywords
         }
-        if engine != "netcdf4" or encoding[data_var].get("contiguous", False) is False:
+        if (
+            engine != "netcdf4"
+            or encoding[data_var].get("contiguous", False) is False
+        ):
             encoding[data_var]["chunksizes"] = new_chunks
     return dset, encoding
 
@@ -146,6 +159,7 @@ def rechunk_dataset(
 def rechunk_netcdf_file(
     input_path: os.PathLike,
     output_path: Optional[os.PathLike] = None,
+    decode_cf: bool = True,
     engine: Literal["h5netcdf", "netcdf4"] = "netcdf4",
 ) -> None:
     """Rechunk netcdf files.
@@ -159,6 +173,9 @@ def rechunk_netcdf_file(
         Output file/directory of the chunked netcdf file(s). Note: If ``input``
         is a directory output should be a directory. If None given (default)
         the ``input`` is overidden.
+    decode_cf: bool, default: True
+        Whether to decode these variables, assuming they were saved according
+        to CF conventions.
     engine: str, default: netcdf4
         The netcdf engine used to create the new netcdf file.
     """
@@ -175,7 +192,10 @@ def rechunk_netcdf_file(
         output_file.parent.mkdir(exist_ok=True, parents=True)
         try:
             with xr.open_mfdataset(
-                str(input_file), decode_cf=True, parallel=True
+                str(input_file),
+                parallel=True,
+                decode_cf=decode_cf,
+                inline_array=True,
             ) as nc_data:
                 new_data, encoding = _rechunk_dataset(nc_data, engine)
                 if encoding: