🚧 Deprecate augur filter --metadata-chunk-size

DEPRECATED.md

@@ -4,6 +4,12 @@ These features are deprecated, which means they are no longer maintained and
 will go away in a future major version of Augur. They are currently still
 available for backwards compatibility, but should not be used in new code.
 
+## `augur filter --metadata-chunk-size`
+
+*Deprecated in version X.X.X. Planned for removal in September 2024 or after.*
+
+FIXME: add description here
+
 ## `augur parse` preference of `name` over `strain` as the sequence ID field
 
 *Deprecated in February 2024. Planned to be reordered June 2024 or after.*

augur/filter/__init__.py

@@ -18,7 +18,7 @@ def register_arguments(parser):
     input_group.add_argument('--metadata', required=True, metavar="FILE", help="sequence metadata")
     input_group.add_argument('--sequences', '-s', help="sequences in FASTA or VCF format")
     input_group.add_argument('--sequence-index', help="sequence composition report generated by augur index. If not provided, an index will be created on the fly.")
-    input_group.add_argument('--metadata-chunk-size', type=int, default=100000, help="maximum number of metadata records to read into memory at a time. Increasing this number can speed up filtering at the cost of more memory used.")
+    input_group.add_argument('--metadata-chunk-size', help="[DEPRECATED] Previously used to specify maximum number of metadata records to read into memory at a time. This no longer has an effect.")
     input_group.add_argument('--metadata-id-columns', default=DEFAULT_ID_COLUMNS, nargs="+", help="names of possible metadata columns containing identifier information, ordered by priority. Only one ID column will be inferred.")
     input_group.add_argument('--metadata-delimiters', default=DEFAULT_DELIMITERS, nargs="+", help="delimiters to accept when reading a metadata file. Only one delimiter will be inferred.")
 

augur/filter/validate_arguments.py

@@ -1,4 +1,5 @@
 from augur.errors import AugurError
+from augur.io.print import print_err
 from augur.io.vcf import is_vcf as filename_is_vcf
 
 
@@ -16,6 +17,9 @@ def validate_arguments(args):
     args : argparse.Namespace
         Parsed arguments from argparse
     """
+    if args.metadata_chunk_size:
+        print_err("WARNING: --metadata-chunk-size is no longer necessary and will be removed in a future version.")
+
     # Don't allow sequence output when no sequence input is provided.
     if args.output and not args.sequences:
         raise AugurError("You need to provide sequences to output sequences.")