TYP: add string annotations in io.pytables (pandas-dev#29682)

Author: jbrockmendel

pandas/io/pytables.py

@@ -9,7 +9,7 @@
 import os
 import re
 import time
-from typing import List, Optional, Type, Union
+from typing import TYPE_CHECKING, Any, Dict, List, Optional, Type, Union
 import warnings
 
 import numpy as np
@@ -55,6 +55,10 @@
 from pandas.io.common import _stringify_path
 from pandas.io.formats.printing import adjoin, pprint_thing
 
+if TYPE_CHECKING:
+    from tables import File  # noqa:F401
+
+
 # versioning attribute
 _version = "0.15.2"
 
@@ -465,6 +469,8 @@ class HDFStore:
     >>> store.close()
     """
 
+    _handle: Optional["File"]
+
     def __init__(
         self,
         path,
@@ -535,7 +541,7 @@ def __getattr__(self, name):
             )
         )
 
-    def __contains__(self, key):
+    def __contains__(self, key: str):
         """ check for existence of this key
               can match the exact pathname or the pathnm w/o the leading '/'
               """
@@ -560,7 +566,7 @@ def __enter__(self):
     def __exit__(self, exc_type, exc_value, traceback):
         self.close()
 
-    def keys(self):
+    def keys(self) -> List[str]:
         """
         Return a list of keys corresponding to objects stored in HDFStore.
 
@@ -698,13 +704,13 @@ def flush(self, fsync: bool = False):
                 except OSError:
                     pass
 
-    def get(self, key):
+    def get(self, key: str):
         """
         Retrieve pandas object stored in file.
 
         Parameters
         ----------
-        key : object
+        key : str
 
         Returns
         -------
@@ -718,7 +724,7 @@ def get(self, key):
 
     def select(
         self,
-        key,
+        key: str,
         where=None,
         start=None,
         stop=None,
@@ -733,7 +739,7 @@ def select(
 
         Parameters
         ----------
-        key : object
+        key : str
                 Object being retrieved from file.
         where : list, default None
                 List of Term (or convertible) objects, optional.
@@ -784,13 +790,15 @@ def func(_start, _stop, _where):
 
         return it.get_result()
 
-    def select_as_coordinates(self, key, where=None, start=None, stop=None, **kwargs):
+    def select_as_coordinates(
+        self, key: str, where=None, start=None, stop=None, **kwargs
+    ):
         """
         return the selection as an Index
 
         Parameters
         ----------
-        key : object
+        key : str
         where : list of Term (or convertible) objects, optional
         start : integer (defaults to None), row number to start selection
         stop  : integer (defaults to None), row number to stop selection
@@ -800,15 +808,16 @@ def select_as_coordinates(self, key, where=None, start=None, stop=None, **kwargs
             where=where, start=start, stop=stop, **kwargs
         )
 
-    def select_column(self, key, column, **kwargs):
+    def select_column(self, key: str, column: str, **kwargs):
         """
         return a single column from the table. This is generally only useful to
         select an indexable
 
         Parameters
         ----------
-        key : object
-        column: the column of interest
+        key : str
+        column: str
+            The column of interest.
 
         Raises
         ------
@@ -966,7 +975,7 @@ def put(self, key, value, format=None, append=False, **kwargs):
         kwargs = self._validate_format(format, kwargs)
         self._write_to_group(key, value, append=append, **kwargs)
 
-    def remove(self, key, where=None, start=None, stop=None):
+    def remove(self, key: str, where=None, start=None, stop=None):
         """
         Remove pandas object partially by specifying the where condition
 
@@ -1152,16 +1161,17 @@ def append_to_multiple(
 
             self.append(k, val, data_columns=dc, **kwargs)
 
-    def create_table_index(self, key, **kwargs):
-        """ Create a pytables index on the table
+    def create_table_index(self, key: str, **kwargs):
+        """
+        Create a pytables index on the table.
+
         Parameters
         ----------
-        key : object (the node to index)
+        key : str
 
         Raises
         ------
-        raises if the node is not a table
-
+        TypeError: raises if the node is not a table
         """
 
         # version requirements
@@ -1247,17 +1257,19 @@ def walk(self, where="/"):
 
             yield (g._v_pathname.rstrip("/"), groups, leaves)
 
-    def get_node(self, key):
+    def get_node(self, key: str):
         """ return the node with the key or None if it does not exist """
         self._check_if_open()
+        if not key.startswith("/"):
+            key = "/" + key
+
+        assert self._handle is not None
         try:
-            if not key.startswith("/"):
-                key = "/" + key
             return self._handle.get_node(self.root, key)
-        except _table_mod.exceptions.NoSuchNodeError:
+        except _table_mod.exceptions.NoSuchNodeError:  # type: ignore
             return None
 
-    def get_storer(self, key):
+    def get_storer(self, key: str):
         """ return the storer object for a key, raise if not in the file """
         group = self.get_node(key)
         if group is None:
@@ -1481,7 +1493,7 @@ def error(t):
 
     def _write_to_group(
         self,
-        key,
+        key: str,
         value,
         format,
         index=True,
@@ -1492,6 +1504,10 @@ def _write_to_group(
     ):
         group = self.get_node(key)
 
+        # we make this assertion for mypy; the get_node call will already
+        #  have raised if this is incorrect
+        assert self._handle is not None
+
         # remove the node if we are not appending
         if group is not None and not append:
             self._handle.remove_node(group, recursive=True)
@@ -2691,7 +2707,7 @@ def f(values, freq=None, tz=None):
 
         return klass
 
-    def validate_read(self, kwargs):
+    def validate_read(self, kwargs: Dict[str, Any]) -> Dict[str, Any]:
         """
         remove table keywords from kwargs and return
         raise if any keywords are passed which are not-None
@@ -2733,7 +2749,7 @@ def get_attrs(self):
     def write(self, obj, **kwargs):
         self.set_attrs()
 
-    def read_array(self, key, start=None, stop=None):
+    def read_array(self, key: str, start=None, stop=None):
         """ read an array for the specified node (off of group """
         import tables
 
@@ -4008,7 +4024,7 @@ def read_coordinates(self, where=None, start=None, stop=None, **kwargs):
 
         return Index(coords)
 
-    def read_column(self, column, where=None, start=None, stop=None):
+    def read_column(self, column: str, where=None, start=None, stop=None):
         """return a single column from the table, generally only indexables
         are interesting
         """
@@ -4642,8 +4658,8 @@ def _convert_index(index, encoding=None, errors="strict", format_type=None):
             converted,
             "datetime64",
             _tables().Int64Col(),
-            freq=getattr(index, "freq", None),
-            tz=getattr(index, "tz", None),
+            freq=index.freq,
+            tz=index.tz,
             index_name=index_name,
         )
     elif isinstance(index, TimedeltaIndex):
@@ -4652,7 +4668,7 @@ def _convert_index(index, encoding=None, errors="strict", format_type=None):
             converted,
             "timedelta64",
             _tables().Int64Col(),
-            freq=getattr(index, "freq", None),
+            freq=index.freq,
             index_name=index_name,
         )
     elif isinstance(index, (Int64Index, PeriodIndex)):