Deprecate plink functions (#1324)

* Deprecate plink functions

* Update changlog

Author: tomwhite

docs/api.rst

@@ -23,6 +23,10 @@ BGEN
 PLINK
 -----
 
+.. deprecated:: 0.11.0
+   Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+   and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
+
 .. currentmodule:: sgkit.io.plink
 .. autosummary::
    :toctree: generated/

docs/changelog.rst

@@ -14,8 +14,12 @@ Changelog
 .. Breaking changes
 .. ~~~~~~~~~~~~~~~~
 
-.. Deprecations
-.. ~~~~~~~~~~~~
+Deprecations
+~~~~~~~~~~~~
+
+- Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+  and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
+  (:user:`tomwhite`, :pr:`1324`, :issue:`1318`)
 
 .. Improvements
 .. ~~~~~~~~~~~~

sgkit/io/plink/__init__.py

@@ -1,3 +1,11 @@
+import warnings
+
+warnings.warn(
+    "Functions for reading and writing plink are deprecated, please use the bio2zarr and vcztools packages.",
+    DeprecationWarning,
+    stacklevel=2,
+)
+
 try:
     from .plink_reader import plink_to_zarr, read_plink
     from .plink_writer import write_plink, zarr_to_plink

sgkit/io/plink/plink_reader.py

@@ -147,6 +147,10 @@ def read_plink(
     Loads a single PLINK dataset as dask arrays within a Dataset
     from bed, bim, and fam files.
 
+    .. deprecated:: 0.11.0
+        Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+        and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
+
     Parameters
     ----------
     path
@@ -328,6 +332,10 @@ def plink_to_zarr(
 
     Refer to :func:`read_plink` for details and limitations.
 
+    .. deprecated:: 0.11.0
+        Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+        and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
+
     Parameters
     ----------
     path

sgkit/io/plink/plink_writer.py

@@ -49,6 +49,10 @@ def write_plink(
     - ``sample_phenotype``: Phenotype code equal to 1 for control, 2 for case,
         and -1 for missing
 
+    .. deprecated:: 0.11.0
+        Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+        and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
+
     Parameters
     ----------
     ds
@@ -146,6 +150,10 @@ def zarr_to_plink(
 
     Refer to :func:`write_plink` for details and limitations.
 
+    .. deprecated:: 0.11.0
+        Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+        and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
+
     Parameters
     ----------
     input