Pathlib support (#768)

* Tests for pathlib use

* Allow pathlib use in convenience and filesystem stores

* Rename Path newtype to PathType

With the use of pathlib.Path in the library, this could get confusing.

* Use os.PathLike instead of Path for type checks

* Document PathLike usage in convenience

* Revert "Document PathLike usage in convenience"

This reverts commit 7292604.

* Revert "Rename Path newtype to PathType"

This reverts commit 515951c.

* Use pathlib.Path explicitly

This makes a more obvious contrast opposed to zarr's built-in `Path`
type annotation (for internal keys).

Author: clbarnes

zarr/convenience.py

@@ -1,6 +1,7 @@
 """Convenience functions for storing and loading data."""
 import io
 import itertools
+import os
 import re
 from collections.abc import Mapping
 
@@ -100,6 +101,10 @@ def open(store=None, mode='a', **kwargs):
             raise PathNotFoundError(path)
 
 
+def _might_close(path):
+    return isinstance(path, (str, os.PathLike))
+
+
 def save_array(store, arr, **kwargs):
     """Convenience function to save a NumPy array to the local file system, following a
     similar API to the NumPy save() function.
@@ -131,7 +136,7 @@ def save_array(store, arr, **kwargs):
         array([   0,    1,    2, ..., 9997, 9998, 9999])
 
     """
-    may_need_closing = isinstance(store, str)
+    may_need_closing = _might_close(store)
     store = normalize_store_arg(store, clobber=True)
     try:
         _create_array(arr, store=store, overwrite=True, **kwargs)
@@ -202,7 +207,7 @@ def save_group(store, *args, **kwargs):
     if len(args) == 0 and len(kwargs) == 0:
         raise ValueError('at least one array must be provided')
     # handle polymorphic store arg
-    may_need_closing = isinstance(store, str)
+    may_need_closing = _might_close(store)
     store = normalize_store_arg(store, clobber=True)
     try:
         grp = _create_group(store, overwrite=True)

zarr/creation.py

@@ -1,3 +1,4 @@
+import os
 from warnings import warn
 
 import numpy as np
@@ -148,7 +149,9 @@ def create(shape, chunks=True, dtype=None, compressor='default',
 def normalize_store_arg(store, clobber=False, storage_options=None, mode='w'):
     if store is None:
         return dict()
-    elif isinstance(store, str):
+    if isinstance(store, os.PathLike):
+        store = os.fspath(store)
+    if isinstance(store, str):
         mode = mode if clobber else "r"
         if "://" in store or "::" in store:
             return FSStore(store, mode=mode, **(storage_options or {}))

zarr/tests/conftest.py

@@ -0,0 +1,8 @@
+import pathlib
+
+import pytest
+
+
+@pytest.fixture(params=[str, pathlib.Path])
+def path_type(request):
+    return request.param

zarr/tests/test_convenience.py

@@ -27,10 +27,11 @@
                           atexit_rmtree, getsize)
 
 
-def test_open_array():
+def test_open_array(path_type):
 
     store = tempfile.mkdtemp()
     atexit.register(atexit_rmtree, store)
+    store = path_type(store)
 
     # open array, create if doesn't exist
     z = open(store, mode='a', shape=100)
@@ -53,10 +54,11 @@ def test_open_array():
         open('doesnotexist', mode='r')
 
 
-def test_open_group():
+def test_open_group(path_type):
 
     store = tempfile.mkdtemp()
     atexit.register(atexit_rmtree, store)
+    store = path_type(store)
 
     # open group, create if doesn't exist
     g = open(store, mode='a')

zarr/tests/test_storage.py

@@ -2,6 +2,7 @@
 import atexit
 import json
 import os
+import pathlib
 import sys
 import pickle
 import shutil
@@ -836,6 +837,11 @@ def test_filesystem_path(self):
             with pytest.raises(ValueError):
                 DirectoryStore(f.name)
 
+    def test_init_pathlib(self):
+        path = tempfile.mkdtemp()
+        atexit.register(atexit_rmtree, path)
+        DirectoryStore(pathlib.Path(path))
+
     def test_pickle_ext(self):
         store = self.create_store()
         store2 = pickle.loads(pickle.dumps(store))