Merge branch 'main' into ipython-docs

Author: GbotemiB

.gitignore

@@ -35,7 +35,6 @@ pip-delete-this-directory.txt
 
 # Unit test / coverage reports
 htmlcov/
-.tox/
 .coverage
 .coverage.*
 .cache

docs/contributing.rst

@@ -212,9 +212,12 @@ Test coverage
 
 Zarr maintains 100% test coverage under the latest Python stable release (currently
 Python 3.8). Both unit tests and docstring doctests are included when computing
-coverage. Running ``tox -e py38`` will automatically run the test suite with coverage
-and produce a coverage report. This should be 100% before code can be accepted into the
-main code base.
+coverage. Running::
+    
+    $ python -m pytest -v --cov=zarr --cov-config=.coveragerc zarr
+    
+will automatically run the test suite with coverage and produce a coverage report.
+This should be 100% before code can be accepted into the main code base.
 
 When submitting a pull request, coverage will also be collected across all supported
 Python versions via the Codecov service, and will be reported back within the pull
@@ -243,9 +246,10 @@ notes (``docs/release.rst``).
 
 The documentation can be built locally by running::
 
-    $ tox -e docs
+    $ cd docs
+    $ make clean; make html
 
-The resulting built documentation will be available in the ``.tox/docs/tmp/html`` folder.
+The resulting built documentation will be available in the ``docs/_build/html`` folder.
 
 Development best practices, policies and procedures
 ---------------------------------------------------

docs/index.rst

@@ -130,6 +130,7 @@ Contents
     contributing
     release
     license
+    View homepage <https://zarr.dev/>
 
 Indices and tables
 ------------------

docs/release.rst

@@ -17,6 +17,9 @@ Unreleased
 Maintenance
 ~~~~~~~~~~~
 
+* Simplify if/else statement.
+  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1227`.
+
 * Migrate to ``pyproject.toml`` and remove redundant infrastructure.
   By :user:`Saransh Chopra <Saransh-cpp>` :issue:`1158`.
 

release.txt

@@ -1,4 +1,3 @@
-tox
 # version=x.x.x
 echo $version
 git tag -a v$version -m v$version

requirements_dev_minimal.txt

@@ -5,4 +5,4 @@ numcodecs==0.10.2
 msgpack-python==0.5.6
 setuptools-scm==7.0.5
 # test requirements
-pytest==7.1.3
+pytest==7.2.0

requirements_dev_optional.txt

@@ -13,7 +13,6 @@ types-redis
 types-setuptools
 pymongo==4.3.2
 # optional test requirements
-tox==3.26.0
 coverage
 flake8==5.0.4
 pytest-cov==4.0.0

tox.ini

@@ -487,12 +487,11 @@ def __init__(self, log):
         elif isinstance(log, str):
             self.log_file = io.open(log, mode='w')
             self.needs_closing = True
-        else:
-            if not hasattr(log, 'write'):
-                raise TypeError('log must be a callable function, file path or '
-                                'file-like object, found %r' % log)
+        elif hasattr(log, 'write'):
             self.log_file = log
-            self.needs_closing = False
+        else:
+            raise TypeError('log must be a callable function, file path or '
+                            'file-like object, found %r' % log)
 
     def __enter__(self):
         return self

zarr/convenience.py

@@ -1,3 +1,4 @@
+from typing import Optional
 from warnings import warn
 
 import numpy as np
@@ -17,7 +18,7 @@
 
 
 def create(shape, chunks=True, dtype=None, compressor='default',
-           fill_value=0, order='C', store=None, synchronizer=None,
+           fill_value: Optional[int] = 0, order='C', store=None, synchronizer=None,
            overwrite=False, path=None, chunk_store=None, filters=None,
            cache_metadata=True, cache_attrs=True, read_only=False,
            object_codec=None, dimension_separator=None, write_empty_chunks=True,

zarr/creation.py

@@ -1,5 +1,3 @@
-
-
 class MetadataError(Exception):
     pass
 

zarr/errors.py

@@ -157,6 +157,7 @@ def __init__(self, store, path=None, read_only=False, chunk_store=None,
             raise ContainsArrayError(path)
 
         # initialize metadata
+        mkey = None
         try:
             mkey = _prefix_to_group_key(self._store, self._key_prefix)
             assert not mkey.endswith("root/.group")
@@ -633,26 +634,26 @@ def _array_iter(self, keys_only, method, recurse):
                     yield _key if keys_only else (_key, self[key])
                 elif recurse and contains_group(self._store, path):
                     group = self[key]
-                    for i in getattr(group, method)(recurse=recurse):
-                        yield i
+                    yield from getattr(group, method)(recurse=recurse)
         else:
             dir_name = meta_root + self._path
             array_sfx = '.array' + self._metadata_key_suffix
+            group_sfx = '.group' + self._metadata_key_suffix
+
             for key in sorted(listdir(self._store, dir_name)):
                 if key.endswith(array_sfx):
                     key = key[:-len(array_sfx)]
+                    _key = key.rstrip("/")
+                    yield _key if keys_only else (_key, self[key])
+
                 path = self._key_prefix + key
                 assert not path.startswith("meta/")
-                if key.endswith('.group' + self._metadata_key_suffix):
+                if key.endswith(group_sfx):
                     # skip group metadata keys
                     continue
-                if contains_array(self._store, path):
-                    _key = key.rstrip("/")
-                    yield _key if keys_only else (_key, self[key])
                 elif recurse and contains_group(self._store, path):
                     group = self[key]
-                    for i in getattr(group, method)(recurse=recurse):
-                        yield i
+                    yield from getattr(group, method)(recurse=recurse)
 
     def visitvalues(self, func):
         """Run ``func`` on each object.
@@ -686,8 +687,7 @@ def _visit(obj):
             yield obj
             keys = sorted(getattr(obj, "keys", lambda: [])())
             for k in keys:
-                for v in _visit(obj[k]):
-                    yield v
+                yield from _visit(obj[k])
 
         for each_obj in islice(_visit(self), 1, None):
             value = func(each_obj)
@@ -1277,6 +1277,7 @@ def group(store=None, overwrite=False, chunk_store=None,
 
     path = normalize_storage_path(path)
 
+    requires_init = None
     if zarr_version == 2:
         requires_init = overwrite or not contains_group(store)
     elif zarr_version == 3:

zarr/hierarchy.py

@@ -161,13 +161,13 @@ def normalize_store_arg(store: Any, storage_options=None, mode="r", *,
     if zarr_version is None:
         # default to v2 store for backward compatibility
         zarr_version = getattr(store, "_store_version", DEFAULT_ZARR_VERSION)
-    elif zarr_version not in [2, 3]:
-        raise ValueError("zarr_version must be either 2 or 3")
     if zarr_version == 2:
         normalize_store = _normalize_store_arg_v2
     elif zarr_version == 3:
         from zarr._storage.v3 import _normalize_store_arg_v3
         normalize_store = _normalize_store_arg_v3
+    else:
+        raise ValueError("zarr_version must be either 2 or 3")
     return normalize_store(store, storage_options, mode)
 
 
@@ -597,7 +597,7 @@ def init_group(
     store: StoreLike,
     overwrite: bool = False,
     path: Path = None,
-    chunk_store: StoreLike = None,
+    chunk_store: Optional[StoreLike] = None,
 ):
     """Initialize a group store. Note that this is a low-level function and there should be no
     need to call this directly from user code.
@@ -644,7 +644,7 @@ def _init_group_metadata(
     store: StoreLike,
     overwrite: Optional[bool] = False,
     path: Optional[str] = None,
-    chunk_store: StoreLike = None,
+    chunk_store: Optional[StoreLike] = None,
 ):
 
     store_version = getattr(store, '_store_version', 2)
@@ -702,8 +702,7 @@ def _dict_store_keys(d: Dict, prefix="", cls=dict):
     for k in d.keys():
         v = d[k]
         if isinstance(v, cls):
-            for sk in _dict_store_keys(v, prefix + k + '/', cls):
-                yield sk
+            yield from _dict_store_keys(v, prefix + k + '/', cls)
         else:
             yield prefix + k
 
@@ -863,8 +862,7 @@ def __eq__(self, other):
         )
 
     def keys(self):
-        for k in _dict_store_keys(self.root, cls=self.cls):
-            yield k
+        yield from _dict_store_keys(self.root, cls=self.cls)
 
     def __iter__(self):
         return self.keys()
@@ -1462,7 +1460,7 @@ def listdir(self, path=None):
                     return sorted(new_children)
                 else:
                     return children
-        except IOError:
+        except OSError:
             return []
 
     def rmdir(self, path=None):
@@ -1794,8 +1792,7 @@ def keylist(self):
             return sorted(self.zf.namelist())
 
     def keys(self):
-        for key in self.keylist():
-            yield key
+        yield from self.keylist()
 
     def __iter__(self):
         return self.keys()
@@ -2270,8 +2267,7 @@ def keys(self):
     def values(self):
         with self.db.begin(buffers=self.buffers) as txn:
             with txn.cursor() as cursor:
-                for v in cursor.iternext(keys=False, values=True):
-                    yield v
+                yield from cursor.iternext(keys=False, values=True)
 
     def __iter__(self):
         return self.keys()
@@ -2581,8 +2577,7 @@ def __contains__(self, key):
 
     def items(self):
         kvs = self.cursor.execute('SELECT k, v FROM zarr')
-        for k, v in kvs:
-            yield k, v
+        yield from kvs
 
     def keys(self):
         ks = self.cursor.execute('SELECT k FROM zarr')
@@ -2796,12 +2791,10 @@ def keylist(self):
                 for key in self.client.keys(self._key('*'))]
 
     def keys(self):
-        for key in self.keylist():
-            yield key
+        yield from self.keylist()
 
     def __iter__(self):
-        for key in self.keys():
-            yield key
+        yield from self.keys()
 
     def __len__(self):
         return len(self.keylist())