Undocument a few methods in the dataset

Author: jeromekelleher

sc2ts/dataset.py

@@ -233,6 +233,7 @@ class Variant:
 
 
 class Dataset(collections.abc.Mapping):
+
     def __init__(self, path, chunk_cache_size=1, date_field=None):
         """
         Open a sc2ts VCF Zarr dataset for convenient access to alignments and metadata.
@@ -385,11 +386,6 @@ def copy(
         sample_id=None,
         show_progress=False,
     ):
-        """
-        Copy this dataset to the specified path.
-
-        If sample_id is specified, only include these samples in the specified order.
-        """
         if samples_chunk_size is None:
             samples_chunk_size = self.samples_chunk_size
         if variants_chunk_size is None:
@@ -414,20 +410,6 @@ def copy(
         Dataset.add_metadata(path, df)
 
     def reorder(self, path, additional_fields=list(), show_progress=False):
-        """
-        Write a copy of this dataset reordered by date and optional metadata fields.
-
-        Samples are sorted primarily by the dataset's ``date_field`` and then
-        by any ``additional_fields`` provided, and written to a new dataset at
-        ``path``.
-
-        :param str path: Output path for the reordered dataset.
-        :param list additional_fields: Metadata field names to use as
-            secondary sort keys after ``date_field``. Defaults to an
-            empty list.
-        :param bool show_progress: If True, show a progress bar while
-            copying samples. Defaults to False.
-        """
         sample_id = self.metadata.sample_id_array[:]
         sort_key = [self.date_field] + list(additional_fields)
         logger.info(f"Reorder sort key = {sort_key})")
@@ -436,19 +418,6 @@ def reorder(self, path, additional_fields=list(), show_progress=False):
 
     @staticmethod
     def new(path, samples_chunk_size=None, variants_chunk_size=None):
-        """
-        Create an empty sc2ts dataset at the specified path.
-
-        The resulting Zarr store is initialised with variant coordinates and
-        empty sample/genotype arrays, ready for use with
-        :meth:`Dataset.append_alignments` and :meth:`Dataset.add_metadata`.
-
-        :param str path: Path at which to create the new dataset.
-        :param int samples_chunk_size: Chunk size for the samples dimension;
-            if ``None``, a reasonable default is used.
-        :param int variants_chunk_size: Chunk size for the variants
-            dimension; if ``None``, a reasonable default is used.
-        """
         if samples_chunk_size is None:
             samples_chunk_size = 10_000
         if variants_chunk_size is None:
@@ -535,10 +504,6 @@ def new(path, samples_chunk_size=None, variants_chunk_size=None):
 
     @staticmethod
     def append_alignments(path, alignments):
-        """
-        Append alignments to the store. If this method fails then the store
-        should be considered corrupt.
-        """
         if len(alignments) == 0:
             return
         store = zarr.DirectoryStore(path)
@@ -565,10 +530,6 @@ def append_alignments(path, alignments):
 
     @staticmethod
     def add_metadata(path, df, field_descriptions=dict()):
-        """
-        Add metadata from the specified dataframe, indexed by sample ID.
-        Each column will be added as a new array with prefix ``sample_``.
-        """
         store = zarr.DirectoryStore(path)
         root = zarr.open(store, mode="a")
 
@@ -608,15 +569,6 @@ def add_metadata(path, df, field_descriptions=dict()):
 
     @staticmethod
     def create_zip(in_path, out_path):
-        """
-        Create a zipped version of a directory-backed dataset.
-
-        The contents of ``in_path`` are written into a ZIP file at
-        ``out_path`` in a form suitable for use with :class:`Dataset`.
-
-        :param str in_path: Path to an existing directory-backed dataset.
-        :param str out_path: Path to the output ``.zip`` file.
-        """
         # Based on https://github.com/python/cpython/blob/3.13/Lib/zipfile/__init__.py
         def add_to_zip(zf, path, zippath):
             if os.path.isfile(path):