From 55317355e91d8d6130636c849b4b6d46bd9d8cd5 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Sat, 1 Aug 2020 01:41:24 +0530
Subject: [PATCH 01/40] Added redis, zarr, mongodb backeneds

---
 signac/core/mongodbcollection.py | 149 +++++++++++++++++++++++++++++++
 signac/core/rediscollection.py   | 142 +++++++++++++++++++++++++++++
 signac/core/zarrcollection.py    | 135 ++++++++++++++++++++++++++++
 tests/test_synced_collection.py  |  43 +++++++++
 4 files changed, 469 insertions(+)
 create mode 100644 signac/core/mongodbcollection.py
 create mode 100644 signac/core/rediscollection.py
 create mode 100644 signac/core/zarrcollection.py

diff --git a/signac/core/mongodbcollection.py b/signac/core/mongodbcollection.py
new file mode 100644
index 000000000..3bac399c3
--- /dev/null
+++ b/signac/core/mongodbcollection.py
@@ -0,0 +1,149 @@
+# Copyright (c) 2020 The Regents of the University of Michigan
+# All rights reserved.
+# This software is licensed under the BSD 3-Clause License.
+"""Implements Mongo-backend.
+
+This implements the Mongo-backend for SyncedCollection API by
+implementing sync and load methods.
+"""
+import json
+import pymongo
+
+from .synced_collection import SyncedCollection
+from .syncedattrdict import SyncedAttrDict
+from .synced_list import SyncedList
+
+
+class MongoCollection(SyncedCollection):
+    """Implement sync and load using a Mongo backend."""
+
+    backend = __name__  # type: ignore
+
+    def __init__(self, name=None, client=None, database='signac_db', collection='collection'
+                 mongo_kwargs=None, **kwargs):
+        if client is None:
+            mongo_kwargs = mongo_kwargs if mongo_kwargs is not None else {}
+            self._client = pymongo.MongoClient(**mongo_kwargs)
+        else:
+            self._client = client
+        self._db = self._client.get_database(database)
+        self._collection = self._db.get_collection(collection)
+        self._name = name
+        self._key = 'name'
+        if (name is None) == (self._parent is None):
+            raise ValueError(
+                "Illegal argument combination, one of the two arguments, "
+                "parent or name must be None, but not both.")
+        super().__init__(**kwargs)
+
+
+    def _load(self):
+        """Load the data from a Mongo-database."""
+        blob = self._collection.find_one({self._key: self._name})
+        return blob['data'] if blob is not None else None
+
+    def _sync(self):
+        """Write the data from Mongo-database."""
+        data = self.to_base()
+        data_to_insert = {self._key: self._name, 'data': data}
+        self._collection.replace_one({self._key: self._name}, data_to_insert, True)
+
+
+class MongoDict(MongoCollection, SyncedAttrDict):
+    """A dict-like mapping interface to a persistent Mongo-database.
+
+    The MongoDict inherits from :class:`~core.collection_api.MongoCollection`
+    and :class:`~core.syncedattrdict.SyncedAttrDict`.
+
+    .. code-block:: python
+
+        doc = MongoDict('data')
+        doc['foo'] = "bar"
+        assert doc.foo == doc['foo'] == "bar"
+        assert 'foo' in doc
+        del doc['foo']
+
+    .. code-block:: python
+
+        >>> doc['foo'] = dict(bar=True)
+        >>> doc
+        {'foo': {'bar': True}}
+        >>> doc.foo.bar = False
+        {'foo': {'bar': False}}
+
+    .. warning::
+
+        While the MongoDict object behaves like a dictionary, there are
+        important distinctions to remember. In particular, because operations
+        are reflected as changes to an underlying database, copying (even deep
+        copying) a MongoDict instance may exhibit unexpected behavior. If a
+        true copy is required, you should use the `to_base()` method to get a
+        dictionary representation, and if necessary construct a new MongoDict
+        instance: `new_dict = MongoDict(old_dict.to_base())`.
+
+    Parameters
+    ----------
+    name: str
+        The name of the  collection (Default value = None).
+    client:
+        A Mongo client.
+    mongo_kwargs: dict
+        kwargs arguments passed through to the `pymongo.MongoClient` function.
+    database : string
+        Name of database (Default value = 'signac_db').
+    collection : string 
+        Name of collection (Default value = 'collection')
+    data: mapping, optional
+        The intial data pass to MOngoDict. Defaults to `dict()`
+    parent: object, optional
+        A parent instance of MongoDict or None (Default value = None).
+    """
+    pass
+
+
+class MongoList(MongoCollection, SyncedList):
+    """A non-string sequence interface to a persistent Mongo file.
+
+    The MongoDict inherits from :class:`~core.synced_collection.SyncedCollection`
+    and :class:`~core.syncedlist.SyncedList`.
+
+    .. code-block:: python
+
+        synced_list = RedisList('data')
+        synced_list.append("bar")
+        assert synced_list[0] == "bar"
+        assert len(synced_list) == 1
+        del synced_list[0]
+
+    .. warning::
+
+        While the MongoList object behaves like a list, there are
+        important distinctions to remember. In particular, because operations
+        are reflected as changes to an underlying database, copying (even deep
+        copying) a MongoList instance may exhibit unexpected behavior. If a
+        true copy is required, you should use the `to_base()` method to get a
+        dictionary representation, and if necessary construct a new MongoList
+        instance: `new_list = MongoList(old_list.to_base())`.
+
+    Parameters
+    ----------
+    name: str
+        The name of the  collection (Default value = None).
+    client:
+        A Mongo client.
+    Mongo_kwargs: dict
+        kwargs arguments passed through to the `Mongo.Mongo` function.
+    database : string
+        Name of database (Default value = 'signac_db').
+    collection : string 
+        Name of collection (Default value = 'collection')
+    data: mapping, optional
+        The intial data pass to MongoDict. Defaults to `list()`
+    parent: object, optional
+        A parent instance of MongoDict or None (Default value = None).
+    """
+
+    pass
+
+
+SyncedCollection.register(MongoDict, MongoList)
diff --git a/signac/core/rediscollection.py b/signac/core/rediscollection.py
new file mode 100644
index 000000000..e2a6d3281
--- /dev/null
+++ b/signac/core/rediscollection.py
@@ -0,0 +1,142 @@
+# Copyright (c) 2020 The Regents of the University of Michigan
+# All rights reserved.
+# This software is licensed under the BSD 3-Clause License.
+"""Implements Redis-backend.
+
+This implements the Redis-backend for SyncedCollection API by
+implementing sync and load methods.
+"""
+import json
+import redis
+
+from .synced_collection import SyncedCollection
+from .syncedattrdict import SyncedAttrDict
+from .synced_list import SyncedList
+
+
+class RedisCollection(SyncedCollection):
+    """Implement sync and load using a Redis backend."""
+
+    backend = __name__  # type: ignore
+
+    def __init__(self, name=None, client=None, redis_kwargs=None, **kwargs):
+        if client is None:
+            redis_kwargs = redis_kwargs if redis_kwargs is not None else {}
+            self._client = redis.Redis(**redis_kwargs)
+        else:
+            self._client = client
+        self._name = name
+        super().__init__(**kwargs)
+        if (name is None) == (self._parent is None):
+            raise ValueError(
+                "Illegal argument combination, one of the two arguments, "
+                "parent or name must be None, but not both.")
+
+    def _load(self):
+        """Load the data from a Redis-database."""
+        blob = self._client.get(self._name)
+        return json.loads(blob) if blob is not None else blob
+
+    def _sync(self):
+        """Write the data from Redis-database."""
+        data = self.to_base()
+        # Serialize data:
+        blob = json.dumps(data).encode()
+
+        self._client.set(self._name, blob)
+
+
+class RedisDict(RedisCollection, SyncedAttrDict):
+    """A dict-like mapping interface to a persistent Redis-database.
+
+    The RedisDict inherits from :class:`~core.rediscollection.RedisCollection`
+    and :class:`~core.syncedattrdict.SyncedAttrDict`.
+
+    .. code-block:: python
+
+        doc = RedisDict('data')
+        doc['foo'] = "bar"
+        assert doc.foo == doc['foo'] == "bar"
+        assert 'foo' in doc
+        del doc['foo']
+
+    .. code-block:: python
+
+        >>> doc['foo'] = dict(bar=True)
+        >>> doc
+        {'foo': {'bar': True}}
+        >>> doc.foo.bar = False
+        {'foo': {'bar': False}}
+
+    .. warning::
+
+        While the RedisDict object behaves like a dictionary, there are
+        important distinctions to remember. In particular, because operations
+        are reflected as changes to an underlying database, copying (even deep
+        copying) a RedisDict instance may exhibit unexpected behavior. If a
+        true copy is required, you should use the `to_base()` method to get a
+        dictionary representation, and if necessary construct a new RedisDict
+        instance: `new_dict = RedisDict(old_dict.to_base())`.
+
+    Parameters
+    ----------
+    name: str
+        The name of the  collection (Default value = None).
+    client:
+        A redis client.
+    redis_kwargs: dict
+        kwargs arguments passed through to the `redis.Redis` function.
+    data: mapping, optional
+        The intial data pass to RedisDict. Defaults to `dict()`
+    parent: object, optional
+        A parent instance of RedisDict or None (Default value = None).
+
+
+    """
+
+    pass
+
+
+class RedisList(RedisCollection, SyncedList):
+    """A non-string sequence interface to a persistent Redis file.
+
+    The RedisDict inherits from :class:`~core.collection_api.SyncedCollection`
+    and :class:`~core.syncedlist.SyncedList`.
+
+    .. code-block:: python
+
+        synced_list = RedisList('data')
+        synced_list.append("bar")
+        assert synced_list[0] == "bar"
+        assert len(synced_list) == 1
+        del synced_list[0]
+
+    .. warning::
+
+        While the RedisList object behaves like a list, there are
+        important distinctions to remember. In particular, because operations
+        are reflected as changes to an underlying database, copying (even deep
+        copying) a RedisList instance may exhibit unexpected behavior. If a
+        true copy is required, you should use the `to_base()` method to get a
+        dictionary representation, and if necessary construct a new RedisList
+        instance: `new_list = RedisList(old_list.to_base())`.
+
+    Parameters
+    ----------
+    name: str
+        The name of the  collection (Default value = None).
+    client:
+        A redis client.
+    redis_kwargs: dict
+        kwargs arguments passed through to the `redis.Redis` function.
+    data: mapping, optional
+        The intial data pass to RedisDict. Defaults to `list()`
+    parent: object, optional
+        A parent instance of RedisDict or None (Default value = None).
+
+    """
+
+    pass
+
+
+SyncedCollection.register(RedisDict, RedisList)
diff --git a/signac/core/zarrcollection.py b/signac/core/zarrcollection.py
new file mode 100644
index 000000000..3902fd81b
--- /dev/null
+++ b/signac/core/zarrcollection.py
@@ -0,0 +1,135 @@
+# Copyright (c) 2020 The Regents of the University of Michigan
+# All rights reserved.
+# This software is licensed under the BSD 3-Clause License.
+"""Implements Zarr-backend.
+
+This implements the Zarr-backend for SyncedCollection API by
+implementing sync and load methods.
+"""
+import zarr
+import numcodecs
+
+from .synced_collection import SyncedCollection
+from .syncedattrdict import SyncedAttrDict
+from .synced_list import SyncedList
+
+
+class ZarrCollection(SyncedCollection):
+    """Implement sync and load using a Zarr backend."""
+
+    backend = __name__  # type: ignore
+
+    def __init__(self, name=None, store=None, **kwargs):
+        self._root = zarr.group(store=store)
+        self._name = name
+        super().__init__(**kwargs)
+        if (name is None) == (self._parent is None):
+            raise ValueError(
+                "Illegal argument combination, one of the two arguments, "
+                "parent or name must be None, but not both.")
+
+    def _load(self):
+        """Load the data from a Radis-database."""
+        try:
+            dataset = self._root[self._name]
+            data = dataset[0]
+        except KeyError:
+            data = None
+        return data
+
+    def _sync(self):
+        """Write the data from Radis-database."""
+        data = self.to_base()
+        # Serialize data:
+        dataset = self._root.require_dataset(
+            self._name, overwrite=True, shape=1, dtype='object', object_codec=numcodecs.JSON())
+        dataset[0] = data
+
+
+class ZarrDict(ZarrCollection, SyncedAttrDict):
+    """A dict-like mapping interface to a persistent Zarr-database.
+
+    The ZarrDict inherits from :class:`~core.collection_api.ZarrCollection`
+    and :class:`~core.syncedattrdict.SyncedAttrDict`.
+
+    .. code-block:: python
+
+        doc = ZarrDict('data')
+        doc['foo'] = "bar"
+        assert doc.foo == doc['foo'] == "bar"
+        assert 'foo' in doc
+        del doc['foo']
+
+    .. code-block:: python
+
+        >>> doc['foo'] = dict(bar=True)
+        >>> doc
+        {'foo': {'bar': True}}
+        >>> doc.foo.bar = False
+        {'foo': {'bar': False}}
+
+    .. warning::
+
+        While the ZarrDict object behaves like a dictionary, there are
+        important distinctions to remember. In particular, because operations
+        are reflected as changes to an underlying database, copying (even deep
+        copying) a ZarrDict instance may exhibit unexpected behavior. If a
+        true copy is required, you should use the `to_base()` method to get a
+        dictionary representation, and if necessary construct a new ZarrDict
+        instance: `new_dict = ZarrDict(old_dict.to_base())`.
+
+    Parameters
+    ----------
+    name: str, optional
+        The name of the  collection (Default value = None).
+    data: mapping, optional
+        The intial data pass to ZarrDict. Defaults to `dict()`.
+    store: mapping
+        A zarr store to synchronise the data
+    parent: object, optional
+        A parent instance of ZarrDict or None (Default value = None).
+    """
+
+    pass
+
+
+class ZarrList(ZarrCollection, SyncedList):
+    """A non-string sequence interface to a persistent Zarr file.
+
+    The ZarrDict inherits from :class:`~core.collection_api.ZarrCollection`
+    and :class:`~core.syncedlist.SyncedList`.
+
+    .. code-block:: python
+
+        synced_list = ZarrList('data')
+        synced_list.append("bar")
+        assert synced_list[0] == "bar"
+        assert len(synced_list) == 1
+        del synced_list[0]
+
+    .. warning::
+
+        While the ZarrList object behaves like a list, there are
+        important distinctions to remember. In particular, because operations
+        are reflected as changes to an underlying database, copying (even deep
+        copying) a ZarrList instance may exhibit unexpected behavior. If a
+        true copy is required, you should use the `to_base()` method to get a
+        dictionary representation, and if necessary construct a new ZarrList
+        instance: `new_list = ZarrList(old_list.to_base())`.
+
+    Parameters
+    ----------
+    name: str
+        The name of the  collection.
+    data: mapping, optional
+        The intial data pass to ZarrDict. Defaults to `list()`.
+    store: mapping
+        A zarr store to synchronise the data
+    parent: object, optional
+        A parent instance of ZarrDict or None (Default value = None).
+    """
+
+    pass
+
+
+SyncedCollection.register(ZarrDict, ZarrList)
diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index 0792be926..65dda35cd 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -5,6 +5,7 @@
 import uuid
 import os
 import json
+import numcodecs
 from tempfile import TemporaryDirectory
 from collections.abc import MutableMapping
 from collections.abc import MutableSequence
@@ -13,6 +14,8 @@
 from signac.core.synced_list import SyncedCollection
 from signac.core.jsoncollection import JSONDict
 from signac.core.jsoncollection import JSONList
+from signac.core.zarrcollection import ZarrDict
+from signac.core.zarrcollection import ZarrList
 from signac.errors import InvalidKeyError
 from signac.errors import KeyTypeError
 
@@ -22,6 +25,12 @@
 except ImportError:
     NUMPY = False
 
+try:
+    import zarr
+    Zarr = True
+except ImportError:
+    Zarr = False
+
 FN_JSON = 'test.json'
 
 
@@ -602,3 +611,37 @@ def synced_list(self):
         self._backend_kwargs = {'filename': self._fn_, 'write_concern': True}
         yield JSONList(**self._backend_kwargs)
         self._tmp_dir.cleanup()
+
+
+@pytest.mark.skipif(not Zarr, reason='test requires the zarr package')
+class TestZarrDict(TestJSONDict):
+
+    @pytest.fixture(autouse=True)
+    def synced_dict(self):
+        self._tmp_dir = TemporaryDirectory(prefix='jsondict_')
+        self._store = zarr.DirectoryStore(self._tmp_dir.name)
+        self._backend_kwargs = {'name': 'test', 'store': self._store}
+        yield ZarrDict(**self._backend_kwargs)
+        self._tmp_dir.cleanup()
+
+    def store(self, data):
+        dataset = zarr.group(self._store).require_dataset(
+            'test', overwrite=True, shape=1, dtype='object', object_codec=numcodecs.JSON())
+        dataset[0] = data
+
+
+@pytest.mark.skipif(not Zarr, reason='test requires the zarr package')
+class TestZarrList(TestJSONList):
+
+    @pytest.fixture(autouse=True)
+    def synced_list(self):
+        self._tmp_dir = TemporaryDirectory(prefix='jsondict_')
+        self._store = zarr.DirectoryStore(self._tmp_dir.name)
+        self._backend_kwargs = {'name': 'test', 'store': self._store}
+        yield ZarrList(**self._backend_kwargs)
+        self._tmp_dir.cleanup()
+
+    def store(self, data):
+        dataset = zarr.group(self._store).require_dataset(
+            'test', overwrite=True, shape=1, dtype='object', object_codec=numcodecs.JSON())
+        dataset[0] = data

From 22c4235e040c56055500bba0077c1a1cd45f48ad Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Sat, 1 Aug 2020 01:43:23 +0530
Subject: [PATCH 02/40] Added redis, zarr, mongodb backeneds

---
 signac/core/mongodbcollection.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/signac/core/mongodbcollection.py b/signac/core/mongodbcollection.py
index 3bac399c3..f2c797f68 100644
--- a/signac/core/mongodbcollection.py
+++ b/signac/core/mongodbcollection.py
@@ -19,7 +19,7 @@ class MongoCollection(SyncedCollection):
 
     backend = __name__  # type: ignore
 
-    def __init__(self, name=None, client=None, database='signac_db', collection='collection'
+    def __init__(self, name=None, client=None, database='signac_db', collection='collection',
                  mongo_kwargs=None, **kwargs):
         if client is None:
             mongo_kwargs = mongo_kwargs if mongo_kwargs is not None else {}
@@ -36,7 +36,6 @@ def __init__(self, name=None, client=None, database='signac_db', collection='col
                 "parent or name must be None, but not both.")
         super().__init__(**kwargs)
 
-
     def _load(self):
         """Load the data from a Mongo-database."""
         blob = self._collection.find_one({self._key: self._name})
@@ -91,7 +90,7 @@ class MongoDict(MongoCollection, SyncedAttrDict):
         kwargs arguments passed through to the `pymongo.MongoClient` function.
     database : string
         Name of database (Default value = 'signac_db').
-    collection : string 
+    collection : string
         Name of collection (Default value = 'collection')
     data: mapping, optional
         The intial data pass to MOngoDict. Defaults to `dict()`
@@ -135,7 +134,7 @@ class MongoList(MongoCollection, SyncedList):
         kwargs arguments passed through to the `Mongo.Mongo` function.
     database : string
         Name of database (Default value = 'signac_db').
-    collection : string 
+    collection : string
         Name of collection (Default value = 'collection')
     data: mapping, optional
         The intial data pass to MongoDict. Defaults to `list()`

From 80ef22dda559daf83d09ad8cc0d6b20d8be16d7c Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Sat, 1 Aug 2020 01:44:35 +0530
Subject: [PATCH 03/40] Removed extra import

---
 signac/core/mongodbcollection.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/signac/core/mongodbcollection.py b/signac/core/mongodbcollection.py
index f2c797f68..f72b3da96 100644
--- a/signac/core/mongodbcollection.py
+++ b/signac/core/mongodbcollection.py
@@ -6,7 +6,6 @@
 This implements the Mongo-backend for SyncedCollection API by
 implementing sync and load methods.
 """
-import json
 import pymongo
 
 from .synced_collection import SyncedCollection

From 0203f28fd680c31b8e173e9f4c20ad918e3096e7 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Sat, 1 Aug 2020 01:56:24 +0530
Subject: [PATCH 04/40] Added zarr, redis to requirement-dev.txt

---
 requirements-dev.txt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/requirements-dev.txt b/requirements-dev.txt
index 1a3af8ef1..b506f78f1 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -11,3 +11,5 @@ pytest-subtests==0.3.1
 pydocstyle==5.0.2
 pytest-cov==2.10.0
 pymongo==3.10.1
+zarr==2.4.0
+redis 3.5.3

From 113b27401fb4dc884a92b7255464ced2b930a001 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Sat, 1 Aug 2020 01:57:34 +0530
Subject: [PATCH 05/40] Correction requirement-dev.txt

---
 requirements-dev.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements-dev.txt b/requirements-dev.txt
index b506f78f1..affb371f9 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -12,4 +12,4 @@ pydocstyle==5.0.2
 pytest-cov==2.10.0
 pymongo==3.10.1
 zarr==2.4.0
-redis 3.5.3
+redis==3.5.3

From b1795f6bfdf86095d74fef8d7a90890eb3d04196 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Sat, 1 Aug 2020 02:06:06 +0530
Subject: [PATCH 06/40]  moved numcodecs import in tests

---
 signac/core/mongodbcollection.py | 1 -
 tests/test_synced_collection.py  | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/signac/core/mongodbcollection.py b/signac/core/mongodbcollection.py
index f72b3da96..1f5ce8f54 100644
--- a/signac/core/mongodbcollection.py
+++ b/signac/core/mongodbcollection.py
@@ -6,7 +6,6 @@
 This implements the Mongo-backend for SyncedCollection API by
 implementing sync and load methods.
 """
-import pymongo
 
 from .synced_collection import SyncedCollection
 from .syncedattrdict import SyncedAttrDict
diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index 65dda35cd..dfccc238e 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -5,7 +5,6 @@
 import uuid
 import os
 import json
-import numcodecs
 from tempfile import TemporaryDirectory
 from collections.abc import MutableMapping
 from collections.abc import MutableSequence
@@ -27,6 +26,7 @@
 
 try:
     import zarr
+    import numcodecs # zarr depends on numcodecs 
     Zarr = True
 except ImportError:
     Zarr = False

From 84ec0b51381c87684f4501a4173af038339560e2 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Sat, 1 Aug 2020 02:07:33 +0530
Subject: [PATCH 07/40] Linting error

---
 signac/core/mongodbcollection.py | 1 +
 tests/test_synced_collection.py  | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/signac/core/mongodbcollection.py b/signac/core/mongodbcollection.py
index 1f5ce8f54..f72b3da96 100644
--- a/signac/core/mongodbcollection.py
+++ b/signac/core/mongodbcollection.py
@@ -6,6 +6,7 @@
 This implements the Mongo-backend for SyncedCollection API by
 implementing sync and load methods.
 """
+import pymongo
 
 from .synced_collection import SyncedCollection
 from .syncedattrdict import SyncedAttrDict
diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index dfccc238e..bde125884 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -26,7 +26,7 @@
 
 try:
     import zarr
-    import numcodecs # zarr depends on numcodecs 
+    import numcodecs  # zarr depends on numcodecs
     Zarr = True
 except ImportError:
     Zarr = False

From 8c0d31ba33fd7a3628ec12693385fc88a6747479 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Mon, 3 Aug 2020 02:32:04 +0530
Subject: [PATCH 08/40] Renamed zarr temp dir

---
 tests/test_synced_collection.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index bde125884..97354a6b1 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -635,7 +635,7 @@ class TestZarrList(TestJSONList):
 
     @pytest.fixture(autouse=True)
     def synced_list(self):
-        self._tmp_dir = TemporaryDirectory(prefix='jsondict_')
+        self._tmp_dir = TemporaryDirectory(prefix='zarrdict_')
         self._store = zarr.DirectoryStore(self._tmp_dir.name)
         self._backend_kwargs = {'name': 'test', 'store': self._store}
         yield ZarrList(**self._backend_kwargs)

From 83492a4b84a27f543395af1b30f9695babbb7067 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Wed, 5 Aug 2020 01:37:41 +0530
Subject: [PATCH 09/40] Added test for redis

---
 tests/test_synced_collection.py | 56 +++++++++++++++++++++++++++++----
 1 file changed, 50 insertions(+), 6 deletions(-)

diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index 97354a6b1..6882b975b 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -15,6 +15,8 @@
 from signac.core.jsoncollection import JSONList
 from signac.core.zarrcollection import ZarrDict
 from signac.core.zarrcollection import ZarrList
+from signac.core.rediscollection import RedisDict
+from signac.core.rediscollection import RedisList
 from signac.errors import InvalidKeyError
 from signac.errors import KeyTypeError
 
@@ -27,9 +29,23 @@
 try:
     import zarr
     import numcodecs  # zarr depends on numcodecs
-    Zarr = True
+    ZARR = True
 except ImportError:
-    Zarr = False
+    ZARR = False
+
+try:
+    import redis
+    try:
+        RedisClient = redis.Redis()
+        test_key = str(uuid.uuid4())
+        RedisClient.set(test_key, 0)
+        assert json.loads(RedisClient.get(test_key)) == 0
+        RedisClient.flushall()
+        REDIS = True
+    except (redis.exceptions.ConnectionError, AssertionError) :
+        REDIS = False
+except ImportError:
+    REDIS = False
 
 FN_JSON = 'test.json'
 
@@ -630,18 +646,46 @@ def store(self, data):
         dataset[0] = data
 
 
-@pytest.mark.skipif(not Zarr, reason='test requires the zarr package')
+@pytest.mark.skipif(not ZARR, reason='test requires the zarr package')
 class TestZarrList(TestJSONList):
 
     @pytest.fixture(autouse=True)
     def synced_list(self):
-        self._tmp_dir = TemporaryDirectory(prefix='zarrdict_')
+        self._tmp_dir = TemporaryDirectory(prefix='zarrlist_')
         self._store = zarr.DirectoryStore(self._tmp_dir.name)
-        self._backend_kwargs = {'name': 'test', 'store': self._store}
-        yield ZarrList(**self._backend_kwargs)
+        self._name = 'test'
+        yield ZarrList(name=self._name, store=self._store)
         self._tmp_dir.cleanup()
 
     def store(self, data):
         dataset = zarr.group(self._store).require_dataset(
             'test', overwrite=True, shape=1, dtype='object', object_codec=numcodecs.JSON())
         dataset[0] = data
+
+
+@pytest.mark.skipif(not REDIS, reason='test requires the redis package and running redis-server')
+class TestRedisDict(TestJSONDict):
+    
+    @pytest.fixture
+    def synced_dict(self, request):
+        self._client = RedisClient
+        request.addfinalizer(self._client.flushall)
+        self._name ='test'
+        yield RedisDict(name=self._name, client=self._client)
+
+    def store(self, data):
+        self._client.set(self._name, json.dumps(data).encode())
+
+
+@pytest.mark.skipif(not REDIS, reason='test requires the redis package and running redis-server')
+class TestRedisList(TestJSONList):
+
+    @pytest.fixture
+    def synced_list(self, request):
+        self._client = RedisClient
+        request.addfinalizer(self._client.flushall)
+        self._name ='test'
+        yield RedisList(name=self._name, client=self._client)
+
+    def store(self, data):
+        self._client.set(self._name, json.dumps(data).encode())

From 456878f93af1a366b15d2de87833baef5fe9552e Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Wed, 5 Aug 2020 01:41:15 +0530
Subject: [PATCH 10/40] Added test for redis

---
 tests/test_synced_collection.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index 6882b975b..2414aff68 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -29,9 +29,9 @@
 try:
     import zarr
     import numcodecs  # zarr depends on numcodecs
-    ZARR = True
+    Zarr = True
 except ImportError:
-    ZARR = False
+    Zarr = False
 
 try:
     import redis
@@ -42,7 +42,7 @@
         assert json.loads(RedisClient.get(test_key)) == 0
         RedisClient.flushall()
         REDIS = True
-    except (redis.exceptions.ConnectionError, AssertionError) :
+    except (redis.exceptions.ConnectionError, AssertionError):
         REDIS = False
 except ImportError:
     REDIS = False
@@ -670,7 +670,7 @@ class TestRedisDict(TestJSONDict):
     def synced_dict(self, request):
         self._client = RedisClient
         request.addfinalizer(self._client.flushall)
-        self._name ='test'
+        self._name = 'test'
         yield RedisDict(name=self._name, client=self._client)
 
     def store(self, data):
@@ -684,7 +684,7 @@ class TestRedisList(TestJSONList):
     def synced_list(self, request):
         self._client = RedisClient
         request.addfinalizer(self._client.flushall)
-        self._name ='test'
+        self._name = 'test'
         yield RedisList(name=self._name, client=self._client)
 
     def store(self, data):

From 5275f3acfcbccf7bf5090cab8fbca10106291efa Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Wed, 5 Aug 2020 01:42:47 +0530
Subject: [PATCH 11/40] Added test for redis-backend

---
 tests/test_synced_collection.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index 2414aff68..14d372188 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -646,7 +646,7 @@ def store(self, data):
         dataset[0] = data
 
 
-@pytest.mark.skipif(not ZARR, reason='test requires the zarr package')
+@pytest.mark.skipif(not Zarr, reason='test requires the zarr package')
 class TestZarrList(TestJSONList):
 
     @pytest.fixture(autouse=True)

From 0c8cc25239f6d7dc0edfe01d7efb9ace50d3526e Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Wed, 5 Aug 2020 01:46:52 +0530
Subject: [PATCH 12/40] Added test for redis backend and changed Zarr to ZARR

---
 tests/test_synced_collection.py | 35 ++++++++++++++++++++-------------
 1 file changed, 21 insertions(+), 14 deletions(-)

diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index 14d372188..cb22b5cea 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -8,7 +8,7 @@
 from tempfile import TemporaryDirectory
 from collections.abc import MutableMapping
 from collections.abc import MutableSequence
-from copy import deepcopy
+from copy import copy
 
 from signac.core.synced_list import SyncedCollection
 from signac.core.jsoncollection import JSONDict
@@ -60,22 +60,29 @@ class TestSyncedCollectionBase:
     # this fixture sets temprary directory for tests
     @pytest.fixture(autouse=True)
     def synced_collection(self):
-        self._tmp_dir = TemporaryDirectory(prefix='jsondict_')
+        self._tmp_dir = TemporaryDirectory(prefix='synced_collection_')
         self._fn_ = os.path.join(self._tmp_dir.name, FN_JSON)
         yield
         self._tmp_dir.cleanup()
 
-    def test_from_base(self):
+    def test_from_base_json(self):
         sd = SyncedCollection.from_base(filename=self._fn_,
                                         data={'a': 0}, backend='signac.core.jsoncollection')
         assert isinstance(sd, JSONDict)
         assert 'a' in sd
         assert sd['a'] == 0
 
-        # invalid input
-        with pytest.raises(ValueError):
-            SyncedCollection.from_base(data={'a': 0}, filename=self._fn_)
+    @pytest.mark.skipif(not ZARR, reason='test requires the zarr package')
+    def test_from_base_zarr(self):
+        sd = SyncedCollection.from_base(name='test',
+                                        data={'a': 0}, backend='signac.core.zarrcollection')
+        assert isinstance(sd, ZarrDict)
+        assert 'a' in sd
+        assert sd['a'] == 0
 
+    def test_from_base_no_backend(self):
+        with pytest.raises(ValueError):
+            SyncedCollection.from_base(data={'a': 0})
 
 class TestJSONDict:
 
@@ -304,7 +311,7 @@ def test_call(self, synced_dict, testdata):
     def test_reopen(self, synced_dict, testdata):
         key = 'reopen'
         synced_dict[key] = testdata
-        synced_dict2 = deepcopy(synced_dict)
+        synced_dict2 = copy(synced_dict)
         synced_dict.sync()
         del synced_dict  # possibly unsafe
         synced_dict2.load()
@@ -399,7 +406,7 @@ class TestJSONList:
 
     @pytest.fixture
     def synced_list(self):
-        self._tmp_dir = TemporaryDirectory(prefix='jsondict_')
+        self._tmp_dir = TemporaryDirectory(prefix='jsonlist_')
         self._fn_ = os.path.join(self._tmp_dir.name, FN_JSON)
         self._backend_kwargs = {'filename': self._fn_, 'write_concern': self._write_concern}
         yield JSONList(**self._backend_kwargs)
@@ -545,14 +552,14 @@ def test_update_recursive(self, synced_list):
         self.store(data1)
         assert synced_list == data1
 
-        # inavlid data in file
+        # invalid data in file
         data2 = {'a': 1}
         self.store(data2)
         with pytest.raises(ValueError):
             synced_list.load()
 
     def test_reopen(self, synced_list, testdata):
-        synced_list2 = deepcopy(synced_list)
+        synced_list2 = copy(synced_list)
         synced_list.append(testdata)
         synced_list.sync()
         del synced_list  # possibly unsafe
@@ -629,15 +636,15 @@ def synced_list(self):
         self._tmp_dir.cleanup()
 
 
-@pytest.mark.skipif(not Zarr, reason='test requires the zarr package')
+@pytest.mark.skipif(not ZARR, reason='test requires the zarr package')
 class TestZarrDict(TestJSONDict):
 
     @pytest.fixture(autouse=True)
     def synced_dict(self):
-        self._tmp_dir = TemporaryDirectory(prefix='jsondict_')
+        self._tmp_dir = TemporaryDirectory(prefix='zarrdict_')
         self._store = zarr.DirectoryStore(self._tmp_dir.name)
-        self._backend_kwargs = {'name': 'test', 'store': self._store}
-        yield ZarrDict(**self._backend_kwargs)
+        self._name = 'test'
+        yield ZarrDict(name=self._name, store=self._store)
         self._tmp_dir.cleanup()
 
     def store(self, data):

From dc7f8aedc8be8cd04e3ff207cd20f6ba5483471d Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Wed, 5 Aug 2020 01:48:08 +0530
Subject: [PATCH 13/40] Linting changes

---
 tests/test_synced_collection.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index cb22b5cea..d9a80aae1 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -29,9 +29,9 @@
 try:
     import zarr
     import numcodecs  # zarr depends on numcodecs
-    Zarr = True
+    ZARR = True
 except ImportError:
-    Zarr = False
+    ZARR = False
 
 try:
     import redis
@@ -653,7 +653,7 @@ def store(self, data):
         dataset[0] = data
 
 
-@pytest.mark.skipif(not Zarr, reason='test requires the zarr package')
+@pytest.mark.skipif(not ZARR, reason='test requires the zarr package')
 class TestZarrList(TestJSONList):
 
     @pytest.fixture(autouse=True)
@@ -672,7 +672,7 @@ def store(self, data):
 
 @pytest.mark.skipif(not REDIS, reason='test requires the redis package and running redis-server')
 class TestRedisDict(TestJSONDict):
-    
+
     @pytest.fixture
     def synced_dict(self, request):
         self._client = RedisClient

From dd2e4fa5ef4d4884921d9291b317e1107f7ad5d1 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Wed, 5 Aug 2020 01:48:58 +0530
Subject: [PATCH 14/40] Linting changes

---
 tests/test_synced_collection.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index d9a80aae1..5fcb33746 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -84,6 +84,7 @@ def test_from_base_no_backend(self):
         with pytest.raises(ValueError):
             SyncedCollection.from_base(data={'a': 0})
 
+
 class TestJSONDict:
 
     @pytest.fixture

From 5d765b4eed0909559cb403ff59608ad3c2c827f1 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 6 Aug 2020 23:25:42 +0530
Subject: [PATCH 15/40] Added test for mongocollection

---
 signac/core/mongodbcollection.py |  5 ++-
 tests/test_synced_collection.py  | 76 ++++++++++++++++++++++++++++++++
 2 files changed, 79 insertions(+), 2 deletions(-)

diff --git a/signac/core/mongodbcollection.py b/signac/core/mongodbcollection.py
index f72b3da96..6a4cc8f28 100644
--- a/signac/core/mongodbcollection.py
+++ b/signac/core/mongodbcollection.py
@@ -28,12 +28,13 @@ def __init__(self, name=None, client=None, database='signac_db', collection='col
         self._db = self._client.get_database(database)
         self._collection = self._db.get_collection(collection)
         self._name = name
-        self._key = 'name'
+        self._key = type(self).__name__ + '::name'
+        super().__init__(**kwargs)
         if (name is None) == (self._parent is None):
             raise ValueError(
                 "Illegal argument combination, one of the two arguments, "
                 "parent or name must be None, but not both.")
-        super().__init__(**kwargs)
+
 
     def _load(self):
         """Load the data from a Mongo-database."""
diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index 5fcb33746..9145be9c8 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -17,6 +17,8 @@
 from signac.core.zarrcollection import ZarrList
 from signac.core.rediscollection import RedisDict
 from signac.core.rediscollection import RedisList
+from signac.core.mongodbcollection import MongoDict
+from signac.core.mongodbcollection import MongoList
 from signac.errors import InvalidKeyError
 from signac.errors import KeyTypeError
 
@@ -47,6 +49,14 @@
 except ImportError:
     REDIS = False
 
+try:
+    import pymongo
+    import bson  # required for invalid data error
+    MongoClient = pymongo.MongoClient()
+    PYMONGO = True
+except ImportError:
+    PYMONGO = False
+
 FN_JSON = 'test.json'
 
 
@@ -80,6 +90,23 @@ def test_from_base_zarr(self):
         assert 'a' in sd
         assert sd['a'] == 0
 
+    @pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package.')
+    def test_from_base_mongo(self):
+        sd = SyncedCollection.from_base(name='test', data={'a': 0}, client=MongoClient,
+                                        backend='signac.core.mongodbcollection')
+        assert isinstance(sd, MongoDict)
+        assert 'a' in sd
+        assert sd['a'] == 0
+
+    @pytest.mark.skipif(not REDIS, reason='test requires the redis package '
+                                          'and running redis-server')
+    def test_from_base_redis(self):
+        sd = SyncedCollection.from_base(name='test', data={'a': 0}, client=RedisClient,
+                                        backend='signac.core.rediscollection')
+        assert isinstance(sd, ResisDict)
+        assert 'a' in sd
+        assert sd['a'] == 0
+
     def test_from_base_no_backend(self):
         with pytest.raises(ValueError):
             SyncedCollection.from_base(data={'a': 0})
@@ -697,3 +724,52 @@ def synced_list(self, request):
 
     def store(self, data):
         self._client.set(self._name, json.dumps(data).encode())
+
+
+@pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package')
+class TestMongoDict(TestJSONDict):
+
+    @pytest.fixture
+    def synced_dict(self, request):
+        self._client = MongoClient
+        self._name = 'test'
+        yield MongoDict(name=self._name, client=self._client,
+                        database='test_db', collection='test_dict')
+        self._client.test_db.test_dict.drop()
+
+    def store(self, data):
+        data_to_insert = {'MongoDict::name': self._name, 'data': data}
+        self._client.test_db.test_dict.replace_one({'MongoDict::name': self._name}, data_to_insert)
+
+
+    def test_write_invalid_type(self, synced_dict, testdata):
+        # mongodict return InvalidDocument error for objects
+        class Foo(object):
+            pass
+
+        key = 'write_invalid_type'
+        synced_dict[key] = testdata
+        assert len(synced_dict) == 1
+        assert synced_dict[key] == testdata
+        d2 = Foo()
+        with pytest.raises(bson.errors.InvalidDocument):
+            synced_dict[key + '2'] = d2
+        assert len(synced_dict) == 1
+        assert synced_dict[key] == testdata
+
+
+
+@pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package')
+class TestMongoList(TestJSONList):
+
+    @pytest.fixture
+    def synced_list(self, request):
+        self._client = MongoClient
+        self._name = 'test'
+        yield MongoList(name=self._name, client=self._client,
+                        database='test_db', collection='test_list')
+        self._client.test_db.test_list.drop()
+
+    def store(self, data):
+        data_to_insert = {'MongoList::name': self._name, 'data': data}
+        self._client.test_db.test_list.replace_one({'MongoList::name': self._name}, data_to_insert)
\ No newline at end of file

From 5dd9e154d4a5fe65fdb6feb2a6fc910f98f08465 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 6 Aug 2020 23:28:25 +0530
Subject: [PATCH 16/40] Linting Changes

---
 signac/core/mongodbcollection.py | 1 -
 tests/test_synced_collection.py  | 4 +---
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/signac/core/mongodbcollection.py b/signac/core/mongodbcollection.py
index 6a4cc8f28..041440c90 100644
--- a/signac/core/mongodbcollection.py
+++ b/signac/core/mongodbcollection.py
@@ -35,7 +35,6 @@ def __init__(self, name=None, client=None, database='signac_db', collection='col
                 "Illegal argument combination, one of the two arguments, "
                 "parent or name must be None, but not both.")
 
-
     def _load(self):
         """Load the data from a Mongo-database."""
         blob = self._collection.find_one({self._key: self._name})
diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index 9145be9c8..cc37c3abb 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -103,7 +103,7 @@ def test_from_base_mongo(self):
     def test_from_base_redis(self):
         sd = SyncedCollection.from_base(name='test', data={'a': 0}, client=RedisClient,
                                         backend='signac.core.rediscollection')
-        assert isinstance(sd, ResisDict)
+        assert isinstance(sd, RedisDict)
         assert 'a' in sd
         assert sd['a'] == 0
 
@@ -741,7 +741,6 @@ def store(self, data):
         data_to_insert = {'MongoDict::name': self._name, 'data': data}
         self._client.test_db.test_dict.replace_one({'MongoDict::name': self._name}, data_to_insert)
 
-
     def test_write_invalid_type(self, synced_dict, testdata):
         # mongodict return InvalidDocument error for objects
         class Foo(object):
@@ -758,7 +757,6 @@ class Foo(object):
         assert synced_dict[key] == testdata
 
 
-
 @pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package')
 class TestMongoList(TestJSONList):
 

From c1ded73d027b845524fba12baffece4435f18619 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 6 Aug 2020 23:29:41 +0530
Subject: [PATCH 17/40] Added comments

---
 tests/test_synced_collection.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index cc37c3abb..a075d566e 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -38,11 +38,12 @@
 try:
     import redis
     try:
+        # try to connect to server
         RedisClient = redis.Redis()
         test_key = str(uuid.uuid4())
         RedisClient.set(test_key, 0)
-        assert json.loads(RedisClient.get(test_key)) == 0
-        RedisClient.flushall()
+        assert RedisClient.get(test_key) == b'0'  # redis store data as bytes
+        RedisClient.delete(test_key)
         REDIS = True
     except (redis.exceptions.ConnectionError, AssertionError):
         REDIS = False
@@ -770,4 +771,4 @@ def synced_list(self, request):
 
     def store(self, data):
         data_to_insert = {'MongoList::name': self._name, 'data': data}
-        self._client.test_db.test_list.replace_one({'MongoList::name': self._name}, data_to_insert)
\ No newline at end of file
+        self._client.test_db.test_list.replace_one({'MongoList::name': self._name}, data_to_insert)

From 1a1b0751e6880aa9fe03cf7255097cfdaae0c33b Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Fri, 7 Aug 2020 01:01:42 +0530
Subject: [PATCH 18/40] Added test for mongodb server

---
 tests/test_synced_collection.py | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index a075d566e..f6a71b72f 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -53,8 +53,17 @@
 try:
     import pymongo
     import bson  # required for invalid data error
-    MongoClient = pymongo.MongoClient()
-    PYMONGO = True
+    try:
+        # test the mongodb server
+        MongoClient = pymongo.MongoClient()
+        tmp_collection = MongoClient['test_db']['test']
+        tmp_collection.insert_one({'test': '0'})
+        ret = tmp_collection.find_one({'test': '0'})
+        assert ret['test'] == '0'
+        tmp_collection.drop()
+        PYMONGO = True
+    except (pymongo.errors.ServerSelectionTimeoutError, AssertionError):
+        PYMONGO = False
 except ImportError:
     PYMONGO = False
 
@@ -727,7 +736,7 @@ def store(self, data):
         self._client.set(self._name, json.dumps(data).encode())
 
 
-@pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package')
+@pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package and mongodb server')
 class TestMongoDict(TestJSONDict):
 
     @pytest.fixture
@@ -758,7 +767,7 @@ class Foo(object):
         assert synced_dict[key] == testdata
 
 
-@pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package')
+@pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package and mongodb server')
 class TestMongoList(TestJSONList):
 
     @pytest.fixture

From c17abb8bcd31ca16bf963884132daec7c12769a3 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Fri, 7 Aug 2020 01:04:17 +0530
Subject: [PATCH 19/40] Moved import to class __init__

---
 signac/core/mongodbcollection.py | 4 ++--
 signac/core/rediscollection.py   | 3 ++-
 signac/core/zarrcollection.py    | 6 +++---
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/signac/core/mongodbcollection.py b/signac/core/mongodbcollection.py
index 041440c90..62315a438 100644
--- a/signac/core/mongodbcollection.py
+++ b/signac/core/mongodbcollection.py
@@ -6,8 +6,6 @@
 This implements the Mongo-backend for SyncedCollection API by
 implementing sync and load methods.
 """
-import pymongo
-
 from .synced_collection import SyncedCollection
 from .syncedattrdict import SyncedAttrDict
 from .synced_list import SyncedList
@@ -20,6 +18,8 @@ class MongoCollection(SyncedCollection):
 
     def __init__(self, name=None, client=None, database='signac_db', collection='collection',
                  mongo_kwargs=None, **kwargs):
+        import pymongo
+
         if client is None:
             mongo_kwargs = mongo_kwargs if mongo_kwargs is not None else {}
             self._client = pymongo.MongoClient(**mongo_kwargs)
diff --git a/signac/core/rediscollection.py b/signac/core/rediscollection.py
index e2a6d3281..647822d88 100644
--- a/signac/core/rediscollection.py
+++ b/signac/core/rediscollection.py
@@ -7,7 +7,6 @@
 implementing sync and load methods.
 """
 import json
-import redis
 
 from .synced_collection import SyncedCollection
 from .syncedattrdict import SyncedAttrDict
@@ -20,6 +19,8 @@ class RedisCollection(SyncedCollection):
     backend = __name__  # type: ignore
 
     def __init__(self, name=None, client=None, redis_kwargs=None, **kwargs):
+        import redis
+
         if client is None:
             redis_kwargs = redis_kwargs if redis_kwargs is not None else {}
             self._client = redis.Redis(**redis_kwargs)
diff --git a/signac/core/zarrcollection.py b/signac/core/zarrcollection.py
index 3902fd81b..ad74c40ea 100644
--- a/signac/core/zarrcollection.py
+++ b/signac/core/zarrcollection.py
@@ -6,9 +6,6 @@
 This implements the Zarr-backend for SyncedCollection API by
 implementing sync and load methods.
 """
-import zarr
-import numcodecs
-
 from .synced_collection import SyncedCollection
 from .syncedattrdict import SyncedAttrDict
 from .synced_list import SyncedList
@@ -20,6 +17,9 @@ class ZarrCollection(SyncedCollection):
     backend = __name__  # type: ignore
 
     def __init__(self, name=None, store=None, **kwargs):
+        import zarr
+        import numcodecs
+
         self._root = zarr.group(store=store)
         self._name = name
         super().__init__(**kwargs)

From 8632cdbc3c614d3fe9b04ff3a734ebbf6f6c846d Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Fri, 7 Aug 2020 01:10:34 +0530
Subject: [PATCH 20/40]  removed numcodec import error

---
 signac/core/zarrcollection.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/signac/core/zarrcollection.py b/signac/core/zarrcollection.py
index ad74c40ea..15af4c937 100644
--- a/signac/core/zarrcollection.py
+++ b/signac/core/zarrcollection.py
@@ -18,10 +18,11 @@ class ZarrCollection(SyncedCollection):
 
     def __init__(self, name=None, store=None, **kwargs):
         import zarr
-        import numcodecs
+        import numcodecs  # zarr depends on numcodecs
 
         self._root = zarr.group(store=store)
         self._name = name
+        self._object_codec = numcodecs.JSON()
         super().__init__(**kwargs)
         if (name is None) == (self._parent is None):
             raise ValueError(
@@ -42,7 +43,7 @@ def _sync(self):
         data = self.to_base()
         # Serialize data:
         dataset = self._root.require_dataset(
-            self._name, overwrite=True, shape=1, dtype='object', object_codec=numcodecs.JSON())
+            self._name, overwrite=True, shape=1, dtype='object', object_codec=self._object_codec)
         dataset[0] = data
 
 

From 6cdb6f4b5e39df35c6e788a622e4244991e02b6f Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Fri, 7 Aug 2020 01:30:21 +0530
Subject: [PATCH 21/40] Updated documentation

---
 signac/core/mongodbcollection.py | 12 ++++++------
 signac/core/rediscollection.py   | 10 ++++------
 signac/core/zarrcollection.py    |  4 ++--
 tests/test_synced_collection.py  |  2 +-
 4 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/signac/core/mongodbcollection.py b/signac/core/mongodbcollection.py
index 62315a438..3c0a926da 100644
--- a/signac/core/mongodbcollection.py
+++ b/signac/core/mongodbcollection.py
@@ -83,7 +83,7 @@ class MongoDict(MongoCollection, SyncedAttrDict):
     ----------
     name: str
         The name of the  collection (Default value = None).
-    client:
+    client: object
         A Mongo client.
     mongo_kwargs: dict
         kwargs arguments passed through to the `pymongo.MongoClient` function.
@@ -92,7 +92,7 @@ class MongoDict(MongoCollection, SyncedAttrDict):
     collection : string
         Name of collection (Default value = 'collection')
     data: mapping, optional
-        The intial data pass to MOngoDict. Defaults to `dict()`
+        The intial data pass to MongoDict. Defaults to `dict()`
     parent: object, optional
         A parent instance of MongoDict or None (Default value = None).
     """
@@ -107,7 +107,7 @@ class MongoList(MongoCollection, SyncedList):
 
     .. code-block:: python
 
-        synced_list = RedisList('data')
+        synced_list = MongoList('data')
         synced_list.append("bar")
         assert synced_list[0] == "bar"
         assert len(synced_list) == 1
@@ -130,15 +130,15 @@ class MongoList(MongoCollection, SyncedList):
     client:
         A Mongo client.
     Mongo_kwargs: dict
-        kwargs arguments passed through to the `Mongo.Mongo` function.
+        kwargs arguments passed through to the `pymongo.MongoClient` function.
     database : string
         Name of database (Default value = 'signac_db').
     collection : string
         Name of collection (Default value = 'collection')
     data: mapping, optional
-        The intial data pass to MongoDict. Defaults to `list()`
+        The intial data pass to MongoList. Defaults to `list()`
     parent: object, optional
-        A parent instance of MongoDict or None (Default value = None).
+        A parent instance of MongoList or None (Default value = None).
     """
 
     pass
diff --git a/signac/core/rediscollection.py b/signac/core/rediscollection.py
index 647822d88..7cc387382 100644
--- a/signac/core/rediscollection.py
+++ b/signac/core/rediscollection.py
@@ -83,7 +83,7 @@ class RedisDict(RedisCollection, SyncedAttrDict):
     ----------
     name: str
         The name of the  collection (Default value = None).
-    client:
+    client: object
         A redis client.
     redis_kwargs: dict
         kwargs arguments passed through to the `redis.Redis` function.
@@ -91,8 +91,6 @@ class RedisDict(RedisCollection, SyncedAttrDict):
         The intial data pass to RedisDict. Defaults to `dict()`
     parent: object, optional
         A parent instance of RedisDict or None (Default value = None).
-
-
     """
 
     pass
@@ -126,14 +124,14 @@ class RedisList(RedisCollection, SyncedList):
     ----------
     name: str
         The name of the  collection (Default value = None).
-    client:
+    client: object
         A redis client.
     redis_kwargs: dict
         kwargs arguments passed through to the `redis.Redis` function.
     data: mapping, optional
-        The intial data pass to RedisDict. Defaults to `list()`
+        The intial data pass to RedisList. Defaults to `list()`
     parent: object, optional
-        A parent instance of RedisDict or None (Default value = None).
+        A parent instance of RedisList or None (Default value = None).
 
     """
 
diff --git a/signac/core/zarrcollection.py b/signac/core/zarrcollection.py
index 15af4c937..f835a45c2 100644
--- a/signac/core/zarrcollection.py
+++ b/signac/core/zarrcollection.py
@@ -123,11 +123,11 @@ class ZarrList(ZarrCollection, SyncedList):
     name: str
         The name of the  collection.
     data: mapping, optional
-        The intial data pass to ZarrDict. Defaults to `list()`.
+        The intial data pass to ZarrList. Defaults to `list()`.
     store: mapping
         A zarr store to synchronise the data
     parent: object, optional
-        A parent instance of ZarrDict or None (Default value = None).
+        A parent instance of ZarrList or None (Default value = None).
     """
 
     pass
diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index f6a71b72f..8ae494b77 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -52,7 +52,7 @@
 
 try:
     import pymongo
-    import bson  # required for invalid data error
+    import bson  # required for invalid data error in test_write_invalid_type
     try:
         # test the mongodb server
         MongoClient = pymongo.MongoClient()

From f1134523fb587a1aafc259d5405fe37b9fb06410 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Wed, 12 Aug 2020 01:59:07 +0530
Subject: [PATCH 22/40] Changed API as suggested

---
 .../{jsoncollection.py => collection_json.py} |  0
 ...odbcollection.py => collection_mongodb.py} | 42 +++++--------------
 ...rediscollection.py => collection_redis.py} | 22 ++--------
 .../{zarrcollection.py => collection_zarr.py} | 20 ++++-----
 4 files changed, 23 insertions(+), 61 deletions(-)
 rename signac/core/{jsoncollection.py => collection_json.py} (100%)
 rename signac/core/{mongodbcollection.py => collection_mongodb.py} (75%)
 rename signac/core/{rediscollection.py => collection_redis.py} (84%)
 rename signac/core/{zarrcollection.py => collection_zarr.py} (91%)

diff --git a/signac/core/jsoncollection.py b/signac/core/collection_json.py
similarity index 100%
rename from signac/core/jsoncollection.py
rename to signac/core/collection_json.py
diff --git a/signac/core/mongodbcollection.py b/signac/core/collection_mongodb.py
similarity index 75%
rename from signac/core/mongodbcollection.py
rename to signac/core/collection_mongodb.py
index 3c0a926da..26ae88b3a 100644
--- a/signac/core/mongodbcollection.py
+++ b/signac/core/collection_mongodb.py
@@ -1,9 +1,9 @@
 # Copyright (c) 2020 The Regents of the University of Michigan
 # All rights reserved.
 # This software is licensed under the BSD 3-Clause License.
-"""Implements Mongo-backend.
+"""Implements MongoDB-backend.
 
-This implements the Mongo-backend for SyncedCollection API by
+This implements the MongoDB-backend for SyncedCollection API by
 implementing sync and load methods.
 """
 from .synced_collection import SyncedCollection
@@ -11,22 +11,13 @@
 from .synced_list import SyncedList
 
 
-class MongoCollection(SyncedCollection):
-    """Implement sync and load using a Mongo backend."""
+class MongoDBCollection(SyncedCollection):
+    """Implement sync and load using a MongoDB backend."""
 
     backend = __name__  # type: ignore
 
-    def __init__(self, name=None, client=None, database='signac_db', collection='collection',
-                 mongo_kwargs=None, **kwargs):
-        import pymongo
-
-        if client is None:
-            mongo_kwargs = mongo_kwargs if mongo_kwargs is not None else {}
-            self._client = pymongo.MongoClient(**mongo_kwargs)
-        else:
-            self._client = client
-        self._db = self._client.get_database(database)
-        self._collection = self._db.get_collection(collection)
+    def __init__(self, name=None, collection, **kwargs):
+        self._collection = collection
         self._name = name
         self._key = type(self).__name__ + '::name'
         super().__init__(**kwargs)
@@ -83,19 +74,14 @@ class MongoDict(MongoCollection, SyncedAttrDict):
     ----------
     name: str
         The name of the  collection (Default value = None).
-    client: object
-        A Mongo client.
-    mongo_kwargs: dict
-        kwargs arguments passed through to the `pymongo.MongoClient` function.
-    database : string
-        Name of database (Default value = 'signac_db').
-    collection : string
-        Name of collection (Default value = 'collection')
+    collection : object
+        A pymongo.Collection instance
     data: mapping, optional
         The intial data pass to MongoDict. Defaults to `dict()`
     parent: object, optional
         A parent instance of MongoDict or None (Default value = None).
     """
+
     pass
 
 
@@ -127,14 +113,8 @@ class MongoList(MongoCollection, SyncedList):
     ----------
     name: str
         The name of the  collection (Default value = None).
-    client:
-        A Mongo client.
-    Mongo_kwargs: dict
-        kwargs arguments passed through to the `pymongo.MongoClient` function.
-    database : string
-        Name of database (Default value = 'signac_db').
-    collection : string
-        Name of collection (Default value = 'collection')
+    collection : object
+        A pymongo.Collection instance
     data: mapping, optional
         The intial data pass to MongoList. Defaults to `list()`
     parent: object, optional
diff --git a/signac/core/rediscollection.py b/signac/core/collection_redis.py
similarity index 84%
rename from signac/core/rediscollection.py
rename to signac/core/collection_redis.py
index 7cc387382..d9c161b49 100644
--- a/signac/core/rediscollection.py
+++ b/signac/core/collection_redis.py
@@ -18,14 +18,8 @@ class RedisCollection(SyncedCollection):
 
     backend = __name__  # type: ignore
 
-    def __init__(self, name=None, client=None, redis_kwargs=None, **kwargs):
-        import redis
-
-        if client is None:
-            redis_kwargs = redis_kwargs if redis_kwargs is not None else {}
-            self._client = redis.Redis(**redis_kwargs)
-        else:
-            self._client = client
+    def __init__(self, name=None, client=None **kwargs):
+        self._client = client
         self._name = name
         super().__init__(**kwargs)
         if (name is None) == (self._parent is None):
@@ -36,15 +30,11 @@ def __init__(self, name=None, client=None, redis_kwargs=None, **kwargs):
     def _load(self):
         """Load the data from a Redis-database."""
         blob = self._client.get(self._name)
-        return json.loads(blob) if blob is not None else blob
+        return None if blob is None else json.loads(blob)
 
     def _sync(self):
         """Write the data from Redis-database."""
-        data = self.to_base()
-        # Serialize data:
-        blob = json.dumps(data).encode()
-
-        self._client.set(self._name, blob)
+        self._client.set(self._name, json.dumps(self.to_base()).encode())
 
 
 class RedisDict(RedisCollection, SyncedAttrDict):
@@ -85,8 +75,6 @@ class RedisDict(RedisCollection, SyncedAttrDict):
         The name of the  collection (Default value = None).
     client: object
         A redis client.
-    redis_kwargs: dict
-        kwargs arguments passed through to the `redis.Redis` function.
     data: mapping, optional
         The intial data pass to RedisDict. Defaults to `dict()`
     parent: object, optional
@@ -126,8 +114,6 @@ class RedisList(RedisCollection, SyncedList):
         The name of the  collection (Default value = None).
     client: object
         A redis client.
-    redis_kwargs: dict
-        kwargs arguments passed through to the `redis.Redis` function.
     data: mapping, optional
         The intial data pass to RedisList. Defaults to `list()`
     parent: object, optional
diff --git a/signac/core/zarrcollection.py b/signac/core/collection_zarr.py
similarity index 91%
rename from signac/core/zarrcollection.py
rename to signac/core/collection_zarr.py
index f835a45c2..ea712b22c 100644
--- a/signac/core/zarrcollection.py
+++ b/signac/core/collection_zarr.py
@@ -16,11 +16,10 @@ class ZarrCollection(SyncedCollection):
 
     backend = __name__  # type: ignore
 
-    def __init__(self, name=None, store=None, **kwargs):
-        import zarr
+    def __init__(self, name=None, group=None, **kwargs):
         import numcodecs  # zarr depends on numcodecs
 
-        self._root = zarr.group(store=store)
+        self._root = group
         self._name = name
         self._object_codec = numcodecs.JSON()
         super().__init__(**kwargs)
@@ -32,16 +31,13 @@ def __init__(self, name=None, store=None, **kwargs):
     def _load(self):
         """Load the data from a Radis-database."""
         try:
-            dataset = self._root[self._name]
-            data = dataset[0]
+            return self._root[self._name][0]
         except KeyError:
-            data = None
-        return data
+            return None
 
     def _sync(self):
         """Write the data from Radis-database."""
         data = self.to_base()
-        # Serialize data:
         dataset = self._root.require_dataset(
             self._name, overwrite=True, shape=1, dtype='object', object_codec=self._object_codec)
         dataset[0] = data
@@ -85,8 +81,8 @@ class ZarrDict(ZarrCollection, SyncedAttrDict):
         The name of the  collection (Default value = None).
     data: mapping, optional
         The intial data pass to ZarrDict. Defaults to `dict()`.
-    store: mapping
-        A zarr store to synchronise the data
+    group: object
+        A zarr.hierarchy.Group instance
     parent: object, optional
         A parent instance of ZarrDict or None (Default value = None).
     """
@@ -124,8 +120,8 @@ class ZarrList(ZarrCollection, SyncedList):
         The name of the  collection.
     data: mapping, optional
         The intial data pass to ZarrList. Defaults to `list()`.
-    store: mapping
-        A zarr store to synchronise the data
+    group: object
+        A zarr.hierarchy.Group instance
     parent: object, optional
         A parent instance of ZarrList or None (Default value = None).
     """

From 3dc74131fa3a9b663abb0c3cbd68971d9641ebd4 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Wed, 12 Aug 2020 02:01:57 +0530
Subject: [PATCH 23/40] Documentation changes

---
 signac/core/collection_mongodb.py | 2 +-
 signac/core/collection_redis.py   | 2 +-
 signac/core/collection_zarr.py    | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index 26ae88b3a..96c3fde5f 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -16,7 +16,7 @@ class MongoDBCollection(SyncedCollection):
 
     backend = __name__  # type: ignore
 
-    def __init__(self, name=None, collection, **kwargs):
+    def __init__(self, collection, name=None, **kwargs):
         self._collection = collection
         self._name = name
         self._key = type(self).__name__ + '::name'
diff --git a/signac/core/collection_redis.py b/signac/core/collection_redis.py
index d9c161b49..262496a50 100644
--- a/signac/core/collection_redis.py
+++ b/signac/core/collection_redis.py
@@ -18,7 +18,7 @@ class RedisCollection(SyncedCollection):
 
     backend = __name__  # type: ignore
 
-    def __init__(self, name=None, client=None **kwargs):
+    def __init__(self, name=None, client=None, **kwargs):
         self._client = client
         self._name = name
         super().__init__(**kwargs)
diff --git a/signac/core/collection_zarr.py b/signac/core/collection_zarr.py
index ea712b22c..9482d3f23 100644
--- a/signac/core/collection_zarr.py
+++ b/signac/core/collection_zarr.py
@@ -29,14 +29,14 @@ def __init__(self, name=None, group=None, **kwargs):
                 "parent or name must be None, but not both.")
 
     def _load(self):
-        """Load the data from a Radis-database."""
+        """Load the data."""
         try:
             return self._root[self._name][0]
         except KeyError:
             return None
 
     def _sync(self):
-        """Write the data from Radis-database."""
+        """Write the data."""
         data = self.to_base()
         dataset = self._root.require_dataset(
             self._name, overwrite=True, shape=1, dtype='object', object_codec=self._object_codec)

From 6ff7ecb664e9d9afca290193fdfacc6946c92494 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Wed, 12 Aug 2020 02:03:40 +0530
Subject: [PATCH 24/40] Change name MongoCollection to MongoDBCollection

---
 signac/core/collection_mongodb.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index 96c3fde5f..756eaa512 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -38,7 +38,7 @@ def _sync(self):
         self._collection.replace_one({self._key: self._name}, data_to_insert, True)
 
 
-class MongoDict(MongoCollection, SyncedAttrDict):
+class MongoDict(MongoDBCollection, SyncedAttrDict):
     """A dict-like mapping interface to a persistent Mongo-database.
 
     The MongoDict inherits from :class:`~core.collection_api.MongoCollection`
@@ -85,7 +85,7 @@ class MongoDict(MongoCollection, SyncedAttrDict):
     pass
 
 
-class MongoList(MongoCollection, SyncedList):
+class MongoList(MongoDBCollection, SyncedList):
     """A non-string sequence interface to a persistent Mongo file.
 
     The MongoDict inherits from :class:`~core.synced_collection.SyncedCollection`

From db8a96e2fe0e0b71c73e640b5c4d61da8c5c6dc6 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 13 Aug 2020 00:46:05 +0530
Subject: [PATCH 25/40] Moved error for name and parent to synced_collection

---
 signac/core/collection_json.py    | 7 ++-----
 signac/core/collection_mongodb.py | 8 +++-----
 signac/core/collection_redis.py   | 7 +------
 signac/core/collection_zarr.py    | 7 +------
 signac/core/synced_collection.py  | 7 ++++++-
 signac/core/syncedattrdict.py     | 2 +-
 6 files changed, 14 insertions(+), 24 deletions(-)

diff --git a/signac/core/collection_json.py b/signac/core/collection_json.py
index 0a7e02121..d51ff970d 100644
--- a/signac/core/collection_json.py
+++ b/signac/core/collection_json.py
@@ -23,13 +23,10 @@ class JSONCollection(SyncedCollection):
     backend = __name__  # type: ignore
 
     def __init__(self, filename=None, write_concern=False, **kwargs):
-        self._filename = os.path.realpath(filename) if filename is not None else None
+        self._filename = None if filename is None else os.path.realpath(filename)
         self._write_concern = write_concern
+        kwargs['name'] = filename
         super().__init__(**kwargs)
-        if (filename is None) == (self._parent is None):
-            raise ValueError(
-                "Illegal argument combination, one of the two arguments, "
-                "parent or filename must be None, but not both.")
 
     def _load(self):
         """Load the data from a JSON-file."""
diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index 756eaa512..51c67ea5d 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -17,14 +17,12 @@ class MongoDBCollection(SyncedCollection):
     backend = __name__  # type: ignore
 
     def __init__(self, collection, name=None, **kwargs):
+        import bson # for InvalidDocument
+
         self._collection = collection
-        self._name = name
+        self._errors = bson.errors
         self._key = type(self).__name__ + '::name'
         super().__init__(**kwargs)
-        if (name is None) == (self._parent is None):
-            raise ValueError(
-                "Illegal argument combination, one of the two arguments, "
-                "parent or name must be None, but not both.")
 
     def _load(self):
         """Load the data from a Mongo-database."""
diff --git a/signac/core/collection_redis.py b/signac/core/collection_redis.py
index 262496a50..c0327dd45 100644
--- a/signac/core/collection_redis.py
+++ b/signac/core/collection_redis.py
@@ -18,14 +18,9 @@ class RedisCollection(SyncedCollection):
 
     backend = __name__  # type: ignore
 
-    def __init__(self, name=None, client=None, **kwargs):
+    def __init__(self, client=None, **kwargs):
         self._client = client
-        self._name = name
         super().__init__(**kwargs)
-        if (name is None) == (self._parent is None):
-            raise ValueError(
-                "Illegal argument combination, one of the two arguments, "
-                "parent or name must be None, but not both.")
 
     def _load(self):
         """Load the data from a Redis-database."""
diff --git a/signac/core/collection_zarr.py b/signac/core/collection_zarr.py
index 9482d3f23..5b14932e6 100644
--- a/signac/core/collection_zarr.py
+++ b/signac/core/collection_zarr.py
@@ -16,17 +16,12 @@ class ZarrCollection(SyncedCollection):
 
     backend = __name__  # type: ignore
 
-    def __init__(self, name=None, group=None, **kwargs):
+    def __init__(self, group=None, **kwargs):
         import numcodecs  # zarr depends on numcodecs
 
         self._root = group
-        self._name = name
         self._object_codec = numcodecs.JSON()
         super().__init__(**kwargs)
-        if (name is None) == (self._parent is None):
-            raise ValueError(
-                "Illegal argument combination, one of the two arguments, "
-                "parent or name must be None, but not both.")
 
     def _load(self):
         """Load the data."""
diff --git a/signac/core/synced_collection.py b/signac/core/synced_collection.py
index f275238a7..52eb7c81a 100644
--- a/signac/core/synced_collection.py
+++ b/signac/core/synced_collection.py
@@ -31,10 +31,15 @@ class SyncedCollection(Collection):
 
     backend = None
 
-    def __init__(self, parent=None):
+    def __init__(self, name=None, parent=None):
         self._data = None
         self._parent = parent
+        self._name = name
         self._suspend_sync_ = 0
+        if (name is None) == (parent is None):
+            raise ValueError(
+                "Illegal argument combination, one of the two arguments, "
+                "parent or name must be None, but not both.")
 
     @classmethod
     def register(cls, *args):
diff --git a/signac/core/syncedattrdict.py b/signac/core/syncedattrdict.py
index ffc592eb6..206650450 100644
--- a/signac/core/syncedattrdict.py
+++ b/signac/core/syncedattrdict.py
@@ -35,7 +35,7 @@ class SyncedAttrDict(SyncedCollection, MutableMapping):
         dictionary representation, and if necessary construct a new SyncedAttrDict.
     """
 
-    _PROTECTED_KEYS = ('_data', '_suspend_sync_', '_load', '_sync', '_parent')
+    _PROTECTED_KEYS = ('_data', '_name', '_suspend_sync_', '_load', '_sync', '_parent')
 
     VALID_KEY_TYPES = (str, int, bool, type(None))
 

From 064eafc2f2732347e4a4d430a637765c449cb8db Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 13 Aug 2020 00:47:29 +0530
Subject: [PATCH 26/40] Removed pass

---
 signac/core/collection_json.py    | 4 ----
 signac/core/collection_mongodb.py | 6 +-----
 signac/core/collection_redis.py   | 5 -----
 signac/core/collection_zarr.py    | 4 ----
 4 files changed, 1 insertion(+), 18 deletions(-)

diff --git a/signac/core/collection_json.py b/signac/core/collection_json.py
index d51ff970d..8fd70bacd 100644
--- a/signac/core/collection_json.py
+++ b/signac/core/collection_json.py
@@ -102,8 +102,6 @@ class JSONDict(JSONCollection, SyncedAttrDict):
         first, before replacing the original file (Default value = None).
     """
 
-    pass
-
 
 class JSONList(JSONCollection, SyncedList):
     """A non-string sequence interface to a persistent JSON file.
@@ -142,7 +140,5 @@ class JSONList(JSONCollection, SyncedList):
         first, before replacing the original file (Default value = None).
     """
 
-    pass
-
 
 SyncedCollection.register(JSONDict, JSONList)
diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index 51c67ea5d..ea8754ab7 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -17,7 +17,7 @@ class MongoDBCollection(SyncedCollection):
     backend = __name__  # type: ignore
 
     def __init__(self, collection, name=None, **kwargs):
-        import bson # for InvalidDocument
+        import bson  # for InvalidDocument
 
         self._collection = collection
         self._errors = bson.errors
@@ -80,8 +80,6 @@ class MongoDict(MongoDBCollection, SyncedAttrDict):
         A parent instance of MongoDict or None (Default value = None).
     """
 
-    pass
-
 
 class MongoList(MongoDBCollection, SyncedList):
     """A non-string sequence interface to a persistent Mongo file.
@@ -119,7 +117,5 @@ class MongoList(MongoDBCollection, SyncedList):
         A parent instance of MongoList or None (Default value = None).
     """
 
-    pass
-
 
 SyncedCollection.register(MongoDict, MongoList)
diff --git a/signac/core/collection_redis.py b/signac/core/collection_redis.py
index c0327dd45..8aec36f36 100644
--- a/signac/core/collection_redis.py
+++ b/signac/core/collection_redis.py
@@ -76,8 +76,6 @@ class RedisDict(RedisCollection, SyncedAttrDict):
         A parent instance of RedisDict or None (Default value = None).
     """
 
-    pass
-
 
 class RedisList(RedisCollection, SyncedList):
     """A non-string sequence interface to a persistent Redis file.
@@ -113,10 +111,7 @@ class RedisList(RedisCollection, SyncedList):
         The intial data pass to RedisList. Defaults to `list()`
     parent: object, optional
         A parent instance of RedisList or None (Default value = None).
-
     """
 
-    pass
-
 
 SyncedCollection.register(RedisDict, RedisList)
diff --git a/signac/core/collection_zarr.py b/signac/core/collection_zarr.py
index 5b14932e6..69baf1884 100644
--- a/signac/core/collection_zarr.py
+++ b/signac/core/collection_zarr.py
@@ -82,8 +82,6 @@ class ZarrDict(ZarrCollection, SyncedAttrDict):
         A parent instance of ZarrDict or None (Default value = None).
     """
 
-    pass
-
 
 class ZarrList(ZarrCollection, SyncedList):
     """A non-string sequence interface to a persistent Zarr file.
@@ -121,7 +119,5 @@ class ZarrList(ZarrCollection, SyncedList):
         A parent instance of ZarrList or None (Default value = None).
     """
 
-    pass
-
 
 SyncedCollection.register(ZarrDict, ZarrList)

From a61a5ebb2e330ed1a9edf531b6ac3c03340767c6 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 13 Aug 2020 00:49:09 +0530
Subject: [PATCH 27/40] Implemented deepcopy for MongodbCollection and
 RedisCollection

---
 signac/core/collection_mongodb.py | 9 ++++++++-
 signac/core/collection_redis.py   | 3 +++
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index ea8754ab7..5fdf7841a 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -33,7 +33,14 @@ def _sync(self):
         """Write the data from Mongo-database."""
         data = self.to_base()
         data_to_insert = {self._key: self._name, 'data': data}
-        self._collection.replace_one({self._key: self._name}, data_to_insert, True)
+        try:
+            self._collection.replace_one({self._key: self._name}, data_to_insert, True)
+        except self._errors.InvalidDocument as err:
+            raise TypeError(str(err))
+
+    def __deepcopy__(self, memo):
+        return type(self)(client=self._collection, name=self._name, data=self.to_base()
+                          parent=deepcopy(self._parent, memo))
 
 
 class MongoDict(MongoDBCollection, SyncedAttrDict):
diff --git a/signac/core/collection_redis.py b/signac/core/collection_redis.py
index 8aec36f36..2c442da7e 100644
--- a/signac/core/collection_redis.py
+++ b/signac/core/collection_redis.py
@@ -31,6 +31,9 @@ def _sync(self):
         """Write the data from Redis-database."""
         self._client.set(self._name, json.dumps(self.to_base()).encode())
 
+    def __deepcopy__(self, memo):
+        return type(self)(client=self._client, name=self._name, data=self.to_base()
+                          parent=deepcopy(self._parent, memo))
 
 class RedisDict(RedisCollection, SyncedAttrDict):
     """A dict-like mapping interface to a persistent Redis-database.

From 25b1139bdcd9c7d18cfdebb021f20b48d372ef2b Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 13 Aug 2020 00:50:55 +0530
Subject: [PATCH 28/40] Moved testdata to confest.py

---
 signac/core/collection_mongodb.py | 2 +-
 signac/core/collection_redis.py   | 3 ++-
 tests/conftest.py                 | 6 ++++++
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index 5fdf7841a..5f22f4ea4 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -39,7 +39,7 @@ def _sync(self):
             raise TypeError(str(err))
 
     def __deepcopy__(self, memo):
-        return type(self)(client=self._collection, name=self._name, data=self.to_base()
+        return type(self)(client=self._collection, name=self._name, data=self.to_base(),
                           parent=deepcopy(self._parent, memo))
 
 
diff --git a/signac/core/collection_redis.py b/signac/core/collection_redis.py
index 2c442da7e..ccecfde81 100644
--- a/signac/core/collection_redis.py
+++ b/signac/core/collection_redis.py
@@ -32,9 +32,10 @@ def _sync(self):
         self._client.set(self._name, json.dumps(self.to_base()).encode())
 
     def __deepcopy__(self, memo):
-        return type(self)(client=self._client, name=self._name, data=self.to_base()
+        return type(self)(client=self._client, name=self._name, data=self.to_base(),
                           parent=deepcopy(self._parent, memo))
 
+
 class RedisDict(RedisCollection, SyncedAttrDict):
     """A dict-like mapping interface to a persistent Redis-database.
 
diff --git a/tests/conftest.py b/tests/conftest.py
index e94b7439f..b6a9210a4 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -2,6 +2,7 @@
 from packaging import version
 import signac
 import pytest
+import uuid
 
 
 @contextmanager
@@ -11,3 +12,8 @@ def deprecated_in_version(version_string):
             yield
     else:
         yield
+
+
+@pytest.fixture
+def testdata():
+    return str(uuid.uuid4())
\ No newline at end of file

From 3bea2601d3f9e3761583dc0085641605950922b0 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 13 Aug 2020 00:54:01 +0530
Subject: [PATCH 29/40] Moved backend test to specific file

---
 signac/core/collection_mongodb.py |   2 +
 signac/core/collection_redis.py   |   1 +
 tests/conftest.py                 |   2 +-
 tests/test_mongo_collection.py    |  57 +++++++++
 tests/test_redis_collection.py    |  52 ++++++++
 tests/test_synced_collection.py   | 201 ++----------------------------
 tests/test_zarr_collection.py     |  51 ++++++++
 7 files changed, 172 insertions(+), 194 deletions(-)
 create mode 100644 tests/test_mongo_collection.py
 create mode 100644 tests/test_redis_collection.py
 create mode 100644 tests/test_zarr_collection.py

diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index 5f22f4ea4..77962a064 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -6,6 +6,8 @@
 This implements the MongoDB-backend for SyncedCollection API by
 implementing sync and load methods.
 """
+from copy impport deepcopy
+
 from .synced_collection import SyncedCollection
 from .syncedattrdict import SyncedAttrDict
 from .synced_list import SyncedList
diff --git a/signac/core/collection_redis.py b/signac/core/collection_redis.py
index ccecfde81..6f87e7ba8 100644
--- a/signac/core/collection_redis.py
+++ b/signac/core/collection_redis.py
@@ -7,6 +7,7 @@
 implementing sync and load methods.
 """
 import json
+from copy import deepcopy
 
 from .synced_collection import SyncedCollection
 from .syncedattrdict import SyncedAttrDict
diff --git a/tests/conftest.py b/tests/conftest.py
index b6a9210a4..fe2f608e8 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -16,4 +16,4 @@ def deprecated_in_version(version_string):
 
 @pytest.fixture
 def testdata():
-    return str(uuid.uuid4())
\ No newline at end of file
+    return str(uuid.uuid4())
diff --git a/tests/test_mongo_collection.py b/tests/test_mongo_collection.py
new file mode 100644
index 000000000..b4c093840
--- /dev/null
+++ b/tests/test_mongo_collection.py
@@ -0,0 +1,57 @@
+# Copyright (c) 2020 The Regents of the University of Michigan
+# All rights reserved.
+# This software is licensed under the BSD 3-Clause License.
+import pytest
+
+from signac.core.collection_mongodb import MongoDict
+from signac.core.collection_mongodb import MongoList
+from test_synced_collection import TestJSONDict
+from test_synced_collection import TestJSONList
+
+try:
+    import pymongo
+    try:
+        # test the mongodb server
+        MongoClient = pymongo.MongoClient()
+        tmp_collection = MongoClient['test_db']['test']
+        tmp_collection.insert_one({'test': '0'})
+        ret = tmp_collection.find_one({'test': '0'})
+        assert ret['test'] == '0'
+        tmp_collection.drop()
+        PYMONGO = True
+    except (pymongo.errors.ServerSelectionTimeoutError, AssertionError):
+        PYMONGO = False
+except ImportError:
+    PYMONGO = False
+
+
+@pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package and mongodb server')
+class TestMongoDict(TestJSONDict):
+
+    @pytest.fixture
+    def synced_dict(self, request):
+        self._client = MongoClient
+        self._name = 'test'
+        self._collection = self._client.test_db.test_dict
+        yield MongoDict(name=self._name, collection= self._collection)
+        self._collection.drop()
+
+    def store(self, data):
+        data_to_insert = {'MongoDict::name': self._name, 'data': data}
+        self._collection.replace_one({'MongoDict::name': self._name}, data_to_insert)
+
+
+@pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package and mongodb server')
+class TestMongoList(TestJSONList):
+
+    @pytest.fixture
+    def synced_list(self, request):
+        self._client = MongoClient
+        self._name = 'test'
+        self._collection = self._client.test_db.test_list
+        yield MongoList(name=self._name, collection=self._collection)
+        self._collection.drop()
+
+    def store(self, data):
+        data_to_insert = {'MongoList::name': self._name, 'data': data}
+        self._collection.replace_one({'MongoList::name': self._name}, data_to_insert)
diff --git a/tests/test_redis_collection.py b/tests/test_redis_collection.py
new file mode 100644
index 000000000..4c70cb140
--- /dev/null
+++ b/tests/test_redis_collection.py
@@ -0,0 +1,52 @@
+# Copyright (c) 2020 The Regents of the University of Michigan
+# All rights reserved.
+# This software is licensed under the BSD 3-Clause License.
+import pytest
+
+from signac.core.collection_redis import RedisDict
+from signac.core.collection_redis import RedisList
+from test_synced_collection import TestJSONDict
+from test_synced_collection import TestJSONList
+
+try:
+    import redis
+    try:
+        # try to connect to server
+        RedisClient = redis.Redis()
+        test_key = str(uuid.uuid4())
+        RedisClient.set(test_key, 0)
+        assert RedisClient.get(test_key) == b'0'  # redis store data as bytes
+        RedisClient.delete(test_key)
+        REDIS = True
+    except (redis.exceptions.ConnectionError, AssertionError):
+        REDIS = False
+except ImportError:
+    REDIS = False
+
+
+@pytest.mark.skipif(not REDIS, reason='test requires the redis package and running redis-server')
+class TestRedisDict(TestJSONDict):
+
+    @pytest.fixture
+    def synced_dict(self, request):
+        self._client = RedisClient
+        request.addfinalizer(self._client.flushall)
+        self._name = 'test'
+        yield RedisDict(name=self._name, client=self._client)
+
+    def store(self, data):
+        self._client.set(self._name, json.dumps(data).encode())
+
+
+@pytest.mark.skipif(not REDIS, reason='test requires the redis package and running redis-server')
+class TestRedisList(TestJSONList):
+
+    @pytest.fixture
+    def synced_list(self, request):
+        self._client = RedisClient
+        request.addfinalizer(self._client.flushall)
+        self._name = 'test'
+        yield RedisList(name=self._name, client=self._client)
+
+    def store(self, data):
+        self._client.set(self._name, json.dumps(data).encode())
diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index 8ae494b77..5cace5d55 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -2,23 +2,16 @@
 # All rights reserved.
 # This software is licensed under the BSD 3-Clause License.
 import pytest
-import uuid
 import os
 import json
 from tempfile import TemporaryDirectory
 from collections.abc import MutableMapping
 from collections.abc import MutableSequence
-from copy import copy
+from copy import deepcopy
 
 from signac.core.synced_list import SyncedCollection
-from signac.core.jsoncollection import JSONDict
-from signac.core.jsoncollection import JSONList
-from signac.core.zarrcollection import ZarrDict
-from signac.core.zarrcollection import ZarrList
-from signac.core.rediscollection import RedisDict
-from signac.core.rediscollection import RedisList
-from signac.core.mongodbcollection import MongoDict
-from signac.core.mongodbcollection import MongoList
+from signac.core.collection_json import JSONDict
+from signac.core.collection_json import JSONList
 from signac.errors import InvalidKeyError
 from signac.errors import KeyTypeError
 
@@ -28,56 +21,12 @@
 except ImportError:
     NUMPY = False
 
-try:
-    import zarr
-    import numcodecs  # zarr depends on numcodecs
-    ZARR = True
-except ImportError:
-    ZARR = False
-
-try:
-    import redis
-    try:
-        # try to connect to server
-        RedisClient = redis.Redis()
-        test_key = str(uuid.uuid4())
-        RedisClient.set(test_key, 0)
-        assert RedisClient.get(test_key) == b'0'  # redis store data as bytes
-        RedisClient.delete(test_key)
-        REDIS = True
-    except (redis.exceptions.ConnectionError, AssertionError):
-        REDIS = False
-except ImportError:
-    REDIS = False
-
-try:
-    import pymongo
-    import bson  # required for invalid data error in test_write_invalid_type
-    try:
-        # test the mongodb server
-        MongoClient = pymongo.MongoClient()
-        tmp_collection = MongoClient['test_db']['test']
-        tmp_collection.insert_one({'test': '0'})
-        ret = tmp_collection.find_one({'test': '0'})
-        assert ret['test'] == '0'
-        tmp_collection.drop()
-        PYMONGO = True
-    except (pymongo.errors.ServerSelectionTimeoutError, AssertionError):
-        PYMONGO = False
-except ImportError:
-    PYMONGO = False
-
 FN_JSON = 'test.json'
 
 
-@pytest.fixture
-def testdata():
-    return str(uuid.uuid4())
-
+class TestJSONCollectionBase:
 
-class TestSyncedCollectionBase:
-
-    # this fixture sets temprary directory for tests
+    # this fixture sets temporary directory for tests
     @pytest.fixture(autouse=True)
     def synced_collection(self):
         self._tmp_dir = TemporaryDirectory(prefix='synced_collection_')
@@ -87,36 +36,11 @@ def synced_collection(self):
 
     def test_from_base_json(self):
         sd = SyncedCollection.from_base(filename=self._fn_,
-                                        data={'a': 0}, backend='signac.core.jsoncollection')
+                                        data={'a': 0}, backend='signac.core.collection_json')
         assert isinstance(sd, JSONDict)
         assert 'a' in sd
         assert sd['a'] == 0
 
-    @pytest.mark.skipif(not ZARR, reason='test requires the zarr package')
-    def test_from_base_zarr(self):
-        sd = SyncedCollection.from_base(name='test',
-                                        data={'a': 0}, backend='signac.core.zarrcollection')
-        assert isinstance(sd, ZarrDict)
-        assert 'a' in sd
-        assert sd['a'] == 0
-
-    @pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package.')
-    def test_from_base_mongo(self):
-        sd = SyncedCollection.from_base(name='test', data={'a': 0}, client=MongoClient,
-                                        backend='signac.core.mongodbcollection')
-        assert isinstance(sd, MongoDict)
-        assert 'a' in sd
-        assert sd['a'] == 0
-
-    @pytest.mark.skipif(not REDIS, reason='test requires the redis package '
-                                          'and running redis-server')
-    def test_from_base_redis(self):
-        sd = SyncedCollection.from_base(name='test', data={'a': 0}, client=RedisClient,
-                                        backend='signac.core.rediscollection')
-        assert isinstance(sd, RedisDict)
-        assert 'a' in sd
-        assert sd['a'] == 0
-
     def test_from_base_no_backend(self):
         with pytest.raises(ValueError):
             SyncedCollection.from_base(data={'a': 0})
@@ -349,7 +273,7 @@ def test_call(self, synced_dict, testdata):
     def test_reopen(self, synced_dict, testdata):
         key = 'reopen'
         synced_dict[key] = testdata
-        synced_dict2 = copy(synced_dict)
+        synced_dict2 = deepcopy(synced_dict)
         synced_dict.sync()
         del synced_dict  # possibly unsafe
         synced_dict2.load()
@@ -597,7 +521,7 @@ def test_update_recursive(self, synced_list):
             synced_list.load()
 
     def test_reopen(self, synced_list, testdata):
-        synced_list2 = copy(synced_list)
+        synced_list2 = deepcopy(synced_list)
         synced_list.append(testdata)
         synced_list.sync()
         del synced_list  # possibly unsafe
@@ -672,112 +596,3 @@ def synced_list(self):
         self._backend_kwargs = {'filename': self._fn_, 'write_concern': True}
         yield JSONList(**self._backend_kwargs)
         self._tmp_dir.cleanup()
-
-
-@pytest.mark.skipif(not ZARR, reason='test requires the zarr package')
-class TestZarrDict(TestJSONDict):
-
-    @pytest.fixture(autouse=True)
-    def synced_dict(self):
-        self._tmp_dir = TemporaryDirectory(prefix='zarrdict_')
-        self._store = zarr.DirectoryStore(self._tmp_dir.name)
-        self._name = 'test'
-        yield ZarrDict(name=self._name, store=self._store)
-        self._tmp_dir.cleanup()
-
-    def store(self, data):
-        dataset = zarr.group(self._store).require_dataset(
-            'test', overwrite=True, shape=1, dtype='object', object_codec=numcodecs.JSON())
-        dataset[0] = data
-
-
-@pytest.mark.skipif(not ZARR, reason='test requires the zarr package')
-class TestZarrList(TestJSONList):
-
-    @pytest.fixture(autouse=True)
-    def synced_list(self):
-        self._tmp_dir = TemporaryDirectory(prefix='zarrlist_')
-        self._store = zarr.DirectoryStore(self._tmp_dir.name)
-        self._name = 'test'
-        yield ZarrList(name=self._name, store=self._store)
-        self._tmp_dir.cleanup()
-
-    def store(self, data):
-        dataset = zarr.group(self._store).require_dataset(
-            'test', overwrite=True, shape=1, dtype='object', object_codec=numcodecs.JSON())
-        dataset[0] = data
-
-
-@pytest.mark.skipif(not REDIS, reason='test requires the redis package and running redis-server')
-class TestRedisDict(TestJSONDict):
-
-    @pytest.fixture
-    def synced_dict(self, request):
-        self._client = RedisClient
-        request.addfinalizer(self._client.flushall)
-        self._name = 'test'
-        yield RedisDict(name=self._name, client=self._client)
-
-    def store(self, data):
-        self._client.set(self._name, json.dumps(data).encode())
-
-
-@pytest.mark.skipif(not REDIS, reason='test requires the redis package and running redis-server')
-class TestRedisList(TestJSONList):
-
-    @pytest.fixture
-    def synced_list(self, request):
-        self._client = RedisClient
-        request.addfinalizer(self._client.flushall)
-        self._name = 'test'
-        yield RedisList(name=self._name, client=self._client)
-
-    def store(self, data):
-        self._client.set(self._name, json.dumps(data).encode())
-
-
-@pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package and mongodb server')
-class TestMongoDict(TestJSONDict):
-
-    @pytest.fixture
-    def synced_dict(self, request):
-        self._client = MongoClient
-        self._name = 'test'
-        yield MongoDict(name=self._name, client=self._client,
-                        database='test_db', collection='test_dict')
-        self._client.test_db.test_dict.drop()
-
-    def store(self, data):
-        data_to_insert = {'MongoDict::name': self._name, 'data': data}
-        self._client.test_db.test_dict.replace_one({'MongoDict::name': self._name}, data_to_insert)
-
-    def test_write_invalid_type(self, synced_dict, testdata):
-        # mongodict return InvalidDocument error for objects
-        class Foo(object):
-            pass
-
-        key = 'write_invalid_type'
-        synced_dict[key] = testdata
-        assert len(synced_dict) == 1
-        assert synced_dict[key] == testdata
-        d2 = Foo()
-        with pytest.raises(bson.errors.InvalidDocument):
-            synced_dict[key + '2'] = d2
-        assert len(synced_dict) == 1
-        assert synced_dict[key] == testdata
-
-
-@pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package and mongodb server')
-class TestMongoList(TestJSONList):
-
-    @pytest.fixture
-    def synced_list(self, request):
-        self._client = MongoClient
-        self._name = 'test'
-        yield MongoList(name=self._name, client=self._client,
-                        database='test_db', collection='test_list')
-        self._client.test_db.test_list.drop()
-
-    def store(self, data):
-        data_to_insert = {'MongoList::name': self._name, 'data': data}
-        self._client.test_db.test_list.replace_one({'MongoList::name': self._name}, data_to_insert)
diff --git a/tests/test_zarr_collection.py b/tests/test_zarr_collection.py
new file mode 100644
index 000000000..db109b03a
--- /dev/null
+++ b/tests/test_zarr_collection.py
@@ -0,0 +1,51 @@
+# Copyright (c) 2020 The Regents of the University of Michigan
+# All rights reserved.
+# This software is licensed under the BSD 3-Clause License.
+import pytest
+from tempfile import TemporaryDirectory
+
+from signac.core.collection_zarr import ZarrDict
+from signac.core.collection_zarr import ZarrList
+from test_synced_collection import TestJSONDict
+from test_synced_collection import TestJSONList
+
+try:
+    import zarr
+    import numcodecs  # zarr depends on numcodecs
+    ZARR = True
+except ImportError:
+    ZARR = False
+
+
+@pytest.mark.skipif(not ZARR, reason='test requires the zarr package')
+class TestZarrDict(TestJSONDict):
+
+    @pytest.fixture(autouse=True)
+    def synced_dict(self):
+        self._tmp_dir = TemporaryDirectory(prefix='zarrdict_')
+        self._group = zarr.group(zarr.DirectoryStore(self._tmp_dir.name))
+        self._name = 'test'
+        yield ZarrDict(name=self._name, group=self._group)
+        self._tmp_dir.cleanup()
+
+    def store(self, data):
+        dataset = self._group.require_dataset(
+            'test', overwrite=True, shape=1, dtype='object', object_codec=numcodecs.JSON())
+        dataset[0] = data
+
+
+@pytest.mark.skipif(not ZARR, reason='test requires the zarr package')
+class TestZarrList(TestJSONList):
+
+    @pytest.fixture(autouse=True)
+    def synced_list(self):
+        self._tmp_dir = TemporaryDirectory(prefix='zarrlist_')
+        self._group = zarr.group(zarr.DirectoryStore(self._tmp_dir.name))
+        self._name = 'test'
+        yield ZarrList(name=self._name, group=self._group)
+        self._tmp_dir.cleanup()
+
+    def store(self, data):
+        dataset = self._group.require_dataset(
+            'test', overwrite=True, shape=1, dtype='object', object_codec=numcodecs.JSON())
+        dataset[0] = data

From 4789b37f92c58f1f1e03407b017b5389c2fa3916 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 13 Aug 2020 00:56:28 +0530
Subject: [PATCH 30/40] Linting errors

---
 signac/core/collection_mongodb.py | 2 +-
 tests/test_mongo_collection.py    | 2 +-
 tests/test_redis_collection.py    | 2 ++
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index 77962a064..9d35d81bf 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -6,7 +6,7 @@
 This implements the MongoDB-backend for SyncedCollection API by
 implementing sync and load methods.
 """
-from copy impport deepcopy
+from copy import deepcopy
 
 from .synced_collection import SyncedCollection
 from .syncedattrdict import SyncedAttrDict
diff --git a/tests/test_mongo_collection.py b/tests/test_mongo_collection.py
index b4c093840..5767230a2 100644
--- a/tests/test_mongo_collection.py
+++ b/tests/test_mongo_collection.py
@@ -33,7 +33,7 @@ def synced_dict(self, request):
         self._client = MongoClient
         self._name = 'test'
         self._collection = self._client.test_db.test_dict
-        yield MongoDict(name=self._name, collection= self._collection)
+        yield MongoDict(name=self._name, collection=self._collection)
         self._collection.drop()
 
     def store(self, data):
diff --git a/tests/test_redis_collection.py b/tests/test_redis_collection.py
index 4c70cb140..cc1cca1d4 100644
--- a/tests/test_redis_collection.py
+++ b/tests/test_redis_collection.py
@@ -2,6 +2,8 @@
 # All rights reserved.
 # This software is licensed under the BSD 3-Clause License.
 import pytest
+import json
+import uuid
 
 from signac.core.collection_redis import RedisDict
 from signac.core.collection_redis import RedisList

From 813fe90d38ea370c2741e841c4e41a51ef09e60b Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 13 Aug 2020 01:02:36 +0530
Subject: [PATCH 31/40] Error correction

---
 signac/core/collection_mongodb.py                             | 4 ++--
 .../{test_mongo_collection.py => test_mongodb_collection.py}  | 0
 2 files changed, 2 insertions(+), 2 deletions(-)
 rename tests/{test_mongo_collection.py => test_mongodb_collection.py} (100%)

diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index 9d35d81bf..796a63e59 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -18,7 +18,7 @@ class MongoDBCollection(SyncedCollection):
 
     backend = __name__  # type: ignore
 
-    def __init__(self, collection, name=None, **kwargs):
+    def __init__(self, collection=None, **kwargs):
         import bson  # for InvalidDocument
 
         self._collection = collection
@@ -41,7 +41,7 @@ def _sync(self):
             raise TypeError(str(err))
 
     def __deepcopy__(self, memo):
-        return type(self)(client=self._collection, name=self._name, data=self.to_base(),
+        return type(self)(collection=self._collection, name=self._name, data=self.to_base(),
                           parent=deepcopy(self._parent, memo))
 
 
diff --git a/tests/test_mongo_collection.py b/tests/test_mongodb_collection.py
similarity index 100%
rename from tests/test_mongo_collection.py
rename to tests/test_mongodb_collection.py

From c9b659a16f22eaca36e24910cdbf6e82ac5790b2 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 13 Aug 2020 01:25:30 +0530
Subject: [PATCH 32/40] Added __deepcopy__ for zarr

---
 signac/core/collection_zarr.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/signac/core/collection_zarr.py b/signac/core/collection_zarr.py
index 69baf1884..8fc911704 100644
--- a/signac/core/collection_zarr.py
+++ b/signac/core/collection_zarr.py
@@ -6,6 +6,8 @@
 This implements the Zarr-backend for SyncedCollection API by
 implementing sync and load methods.
 """
+from copy import deepcopy
+
 from .synced_collection import SyncedCollection
 from .syncedattrdict import SyncedAttrDict
 from .synced_list import SyncedList
@@ -37,6 +39,10 @@ def _sync(self):
             self._name, overwrite=True, shape=1, dtype='object', object_codec=self._object_codec)
         dataset[0] = data
 
+    def __deepcopy__(self, memo):
+        return type(self)(group=self._root, name=self._name, data=self.to_base(),
+                          parent=deepcopy(self._parent, memo))
+
 
 class ZarrDict(ZarrCollection, SyncedAttrDict):
     """A dict-like mapping interface to a persistent Zarr-database.

From a0f28aa2034736fc4a4ecef6555de3a4c4eccf6f Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 13 Aug 2020 23:31:55 +0530
Subject: [PATCH 33/40] Changed name of MongoDict and MongoList to MongoDBDict
 and MongoDBList

---
 signac/core/collection_mongodb.py | 10 +++++-----
 tests/test_mongodb_collection.py  | 12 ++++++------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index 796a63e59..c7df89dcc 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -27,12 +27,12 @@ def __init__(self, collection=None, **kwargs):
         super().__init__(**kwargs)
 
     def _load(self):
-        """Load the data from a Mongo-database."""
+        """Load the data from a MongoDB."""
         blob = self._collection.find_one({self._key: self._name})
         return blob['data'] if blob is not None else None
 
     def _sync(self):
-        """Write the data from Mongo-database."""
+        """Write the data from MongoDB."""
         data = self.to_base()
         data_to_insert = {self._key: self._name, 'data': data}
         try:
@@ -45,7 +45,7 @@ def __deepcopy__(self, memo):
                           parent=deepcopy(self._parent, memo))
 
 
-class MongoDict(MongoDBCollection, SyncedAttrDict):
+class MongoDBDict(MongoDBCollection, SyncedAttrDict):
     """A dict-like mapping interface to a persistent Mongo-database.
 
     The MongoDict inherits from :class:`~core.collection_api.MongoCollection`
@@ -90,7 +90,7 @@ class MongoDict(MongoDBCollection, SyncedAttrDict):
     """
 
 
-class MongoList(MongoDBCollection, SyncedList):
+class MongoDBList(MongoDBCollection, SyncedList):
     """A non-string sequence interface to a persistent Mongo file.
 
     The MongoDict inherits from :class:`~core.synced_collection.SyncedCollection`
@@ -127,4 +127,4 @@ class MongoList(MongoDBCollection, SyncedList):
     """
 
 
-SyncedCollection.register(MongoDict, MongoList)
+SyncedCollection.register(MongoDBDict, MongoDBList)
diff --git a/tests/test_mongodb_collection.py b/tests/test_mongodb_collection.py
index 5767230a2..5511baab6 100644
--- a/tests/test_mongodb_collection.py
+++ b/tests/test_mongodb_collection.py
@@ -3,8 +3,8 @@
 # This software is licensed under the BSD 3-Clause License.
 import pytest
 
-from signac.core.collection_mongodb import MongoDict
-from signac.core.collection_mongodb import MongoList
+from signac.core.collection_mongodb import MongoDBDict
+from signac.core.collection_mongodb import MongoDBList
 from test_synced_collection import TestJSONDict
 from test_synced_collection import TestJSONList
 
@@ -26,14 +26,14 @@
 
 
 @pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package and mongodb server')
-class TestMongoDict(TestJSONDict):
+class TestMongoDBDict(TestJSONDict):
 
     @pytest.fixture
     def synced_dict(self, request):
         self._client = MongoClient
         self._name = 'test'
         self._collection = self._client.test_db.test_dict
-        yield MongoDict(name=self._name, collection=self._collection)
+        yield MongoDBDict(name=self._name, collection=self._collection)
         self._collection.drop()
 
     def store(self, data):
@@ -42,14 +42,14 @@ def store(self, data):
 
 
 @pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package and mongodb server')
-class TestMongoList(TestJSONList):
+class TestMongoDBList(TestJSONList):
 
     @pytest.fixture
     def synced_list(self, request):
         self._client = MongoClient
         self._name = 'test'
         self._collection = self._client.test_db.test_list
-        yield MongoList(name=self._name, collection=self._collection)
+        yield MongoDBList(name=self._name, collection=self._collection)
         self._collection.drop()
 
     def store(self, data):

From c2e402e9510d573739f75c97e5598867986d59f1 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Thu, 13 Aug 2020 23:33:32 +0530
Subject: [PATCH 34/40] Changed documentation and __deepcopy__ in zarr
 collection

---
 signac/core/collection_zarr.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/signac/core/collection_zarr.py b/signac/core/collection_zarr.py
index 8fc911704..7250192e3 100644
--- a/signac/core/collection_zarr.py
+++ b/signac/core/collection_zarr.py
@@ -26,21 +26,21 @@ def __init__(self, group=None, **kwargs):
         super().__init__(**kwargs)
 
     def _load(self):
-        """Load the data."""
+        """Load the data from zarr-store."""
         try:
             return self._root[self._name][0]
         except KeyError:
             return None
 
     def _sync(self):
-        """Write the data."""
+        """Write the data to zarr-store."""
         data = self.to_base()
         dataset = self._root.require_dataset(
             self._name, overwrite=True, shape=1, dtype='object', object_codec=self._object_codec)
         dataset[0] = data
 
     def __deepcopy__(self, memo):
-        return type(self)(group=self._root, name=self._name, data=self.to_base(),
+        return type(self)(group=deepcopy(self._root, memo), name=self._name, data=self.to_base(),
                           parent=deepcopy(self._parent, memo))
 
 

From d9b3304a80e727ee7b8ad4db20249efd8d677624 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Sat, 15 Aug 2020 03:26:28 +0530
Subject: [PATCH 35/40] Added _psuedo_deepcopy for redis and mongodb

---
 signac/core/collection_mongodb.py |  2 +-
 signac/core/collection_redis.py   |  2 +-
 tests/test_synced_collection.py   | 12 ++++++++++--
 3 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index c7df89dcc..e71318aff 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -40,7 +40,7 @@ def _sync(self):
         except self._errors.InvalidDocument as err:
             raise TypeError(str(err))
 
-    def __deepcopy__(self, memo):
+    def _pseudo_deepcopy(self, memo=None):
         return type(self)(collection=self._collection, name=self._name, data=self.to_base(),
                           parent=deepcopy(self._parent, memo))
 
diff --git a/signac/core/collection_redis.py b/signac/core/collection_redis.py
index 6f87e7ba8..bd130b94a 100644
--- a/signac/core/collection_redis.py
+++ b/signac/core/collection_redis.py
@@ -32,7 +32,7 @@ def _sync(self):
         """Write the data from Redis-database."""
         self._client.set(self._name, json.dumps(self.to_base()).encode())
 
-    def __deepcopy__(self, memo):
+    def _pseudo_deepcopy(self, memo=None):
         return type(self)(client=self._client, name=self._name, data=self.to_base(),
                           parent=deepcopy(self._parent, memo))
 
diff --git a/tests/test_synced_collection.py b/tests/test_synced_collection.py
index 5cace5d55..0ba22c431 100644
--- a/tests/test_synced_collection.py
+++ b/tests/test_synced_collection.py
@@ -273,7 +273,11 @@ def test_call(self, synced_dict, testdata):
     def test_reopen(self, synced_dict, testdata):
         key = 'reopen'
         synced_dict[key] = testdata
-        synced_dict2 = deepcopy(synced_dict)
+        try:
+            synced_dict2 = deepcopy(synced_dict)
+        except TypeError:
+            # Use fallback implementation, deepcopy not supported by backend.
+            synced_dict2 = synced_dict._pseudo_deepcopy()
         synced_dict.sync()
         del synced_dict  # possibly unsafe
         synced_dict2.load()
@@ -521,7 +525,11 @@ def test_update_recursive(self, synced_list):
             synced_list.load()
 
     def test_reopen(self, synced_list, testdata):
-        synced_list2 = deepcopy(synced_list)
+        try:
+            synced_list2 = deepcopy(synced_list)
+        except TypeError:
+            # Use fallback implementation, deepcopy not supported by backend.
+            synced_list2 = synced_list._pseudo_deepcopy()
         synced_list.append(testdata)
         synced_list.sync()
         del synced_list  # possibly unsafe

From c8b82cf499f442af63867cfd92ac428f548cfd4a Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Sat, 15 Aug 2020 03:37:22 +0530
Subject: [PATCH 36/40] Changed name MongoX to MongoDBX in
 test_mongodb_collection

---
 tests/test_mongodb_collection.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_mongodb_collection.py b/tests/test_mongodb_collection.py
index 5511baab6..328ebc06f 100644
--- a/tests/test_mongodb_collection.py
+++ b/tests/test_mongodb_collection.py
@@ -37,8 +37,8 @@ def synced_dict(self, request):
         self._collection.drop()
 
     def store(self, data):
-        data_to_insert = {'MongoDict::name': self._name, 'data': data}
-        self._collection.replace_one({'MongoDict::name': self._name}, data_to_insert)
+        data_to_insert = {'MongoDBDict::name': self._name, 'data': data}
+        self._collection.replace_one({'MongoDBDict::name': self._name}, data_to_insert)
 
 
 @pytest.mark.skipif(not PYMONGO, reason='test requires the pymongo package and mongodb server')
@@ -53,5 +53,5 @@ def synced_list(self, request):
         self._collection.drop()
 
     def store(self, data):
-        data_to_insert = {'MongoList::name': self._name, 'data': data}
-        self._collection.replace_one({'MongoList::name': self._name}, data_to_insert)
+        data_to_insert = {'MongoDBList::name': self._name, 'data': data}
+        self._collection.replace_one({'MongoDBList::name': self._name}, data_to_insert)

From 62c346a0d32c1d5cf0938e38fd0427f3d1f2c64d Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Mon, 17 Aug 2020 03:08:40 +0530
Subject: [PATCH 37/40] Added docstring for _pseudo_deepcopy

---
 signac/core/collection_mongodb.py | 9 +++++++--
 signac/core/collection_redis.py   | 9 +++++++--
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index e71318aff..d8a7a06ca 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -40,9 +40,14 @@ def _sync(self):
         except self._errors.InvalidDocument as err:
             raise TypeError(str(err))
 
-    def _pseudo_deepcopy(self, memo=None):
+    def _pseudo_deepcopy(self):
+        """Return a copy of instance.
+
+        It is a psuedo implementation for `deepcopy` because 
+        `pymongo.Collection` do not support `deepcopy`. 
+        """
         return type(self)(collection=self._collection, name=self._name, data=self.to_base(),
-                          parent=deepcopy(self._parent, memo))
+                          parent=deepcopy(self._parent))
 
 
 class MongoDBDict(MongoDBCollection, SyncedAttrDict):
diff --git a/signac/core/collection_redis.py b/signac/core/collection_redis.py
index bd130b94a..26835235c 100644
--- a/signac/core/collection_redis.py
+++ b/signac/core/collection_redis.py
@@ -32,9 +32,14 @@ def _sync(self):
         """Write the data from Redis-database."""
         self._client.set(self._name, json.dumps(self.to_base()).encode())
 
-    def _pseudo_deepcopy(self, memo=None):
+    def _pseudo_deepcopy(self):
+        """Return a copy of instance.
+
+        It is a psuedo implementation for `deepcopy` because
+        `redis.Redis` do not support `deepcopy`.
+        """
         return type(self)(client=self._client, name=self._name, data=self.to_base(),
-                          parent=deepcopy(self._parent, memo))
+                          parent=deepcopy(self._parent))
 
 
 class RedisDict(RedisCollection, SyncedAttrDict):

From 49f2dffa752c9dd7065bff617e2f71abfda46b65 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Mon, 17 Aug 2020 03:09:41 +0530
Subject: [PATCH 38/40] Removed trailing space

---
 signac/core/collection_mongodb.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index d8a7a06ca..7dd2f5d71 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -43,8 +43,8 @@ def _sync(self):
     def _pseudo_deepcopy(self):
         """Return a copy of instance.
 
-        It is a psuedo implementation for `deepcopy` because 
-        `pymongo.Collection` do not support `deepcopy`. 
+        It is a psuedo implementation for `deepcopy` because
+        `pymongo.Collection` do not support `deepcopy`.
         """
         return type(self)(collection=self._collection, name=self._name, data=self.to_base(),
                           parent=deepcopy(self._parent))

From 663781ca03d8b475ed9a1a02f4252870c1d3a49d Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Mon, 17 Aug 2020 23:47:32 +0530
Subject: [PATCH 39/40] Changes the docstring of _pseudo_deepcopy

---
 signac/core/collection_mongodb.py | 2 +-
 signac/core/collection_redis.py   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index 7dd2f5d71..a2b855d52 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -44,7 +44,7 @@ def _pseudo_deepcopy(self):
         """Return a copy of instance.
 
         It is a psuedo implementation for `deepcopy` because
-        `pymongo.Collection` do not support `deepcopy`.
+        `pymongo.Collection` does not support `deepcopy` method.
         """
         return type(self)(collection=self._collection, name=self._name, data=self.to_base(),
                           parent=deepcopy(self._parent))
diff --git a/signac/core/collection_redis.py b/signac/core/collection_redis.py
index 26835235c..b340c1d5a 100644
--- a/signac/core/collection_redis.py
+++ b/signac/core/collection_redis.py
@@ -36,7 +36,7 @@ def _pseudo_deepcopy(self):
         """Return a copy of instance.
 
         It is a psuedo implementation for `deepcopy` because
-        `redis.Redis` do not support `deepcopy`.
+        `redis.Redis` does not support `deepcopy` method.
         """
         return type(self)(client=self._client, name=self._name, data=self.to_base(),
                           parent=deepcopy(self._parent))

From 36787edf64b8f486be460eaf131617e49e75d009 Mon Sep 17 00:00:00 2001
From: unknown <vishavsharma1771@gmail.com>
Date: Wed, 19 Aug 2020 01:56:32 +0530
Subject: [PATCH 40/40] Changes the order of Parameters in documentation and
 minor corrections

---
 signac/core/collection_json.py    | 20 ++++++-------
 signac/core/collection_mongodb.py | 48 +++++++++++++++----------------
 signac/core/collection_redis.py   | 24 ++++++++--------
 signac/core/collection_zarr.py    | 21 +++++++-------
 4 files changed, 57 insertions(+), 56 deletions(-)

diff --git a/signac/core/collection_json.py b/signac/core/collection_json.py
index 8fd70bacd..18bcd7de2 100644
--- a/signac/core/collection_json.py
+++ b/signac/core/collection_json.py
@@ -93,20 +93,20 @@ class JSONDict(JSONCollection, SyncedAttrDict):
     ----------
     filename: str, optional
         The filename of the associated JSON file on disk (Default value = None).
+    write_concern: bool, optional
+        Ensure file consistency by writing changes back to a temporary file
+        first, before replacing the original file (Default value = None).
     data: mapping, optional
         The intial data pass to JSONDict. Defaults to `list()`
     parent: object, optional
         A parent instance of JSONDict or None (Default value = None).
-    write_concern: bool, optional
-        Ensure file consistency by writing changes back to a temporary file
-        first, before replacing the original file (Default value = None).
     """
 
 
 class JSONList(JSONCollection, SyncedList):
     """A non-string sequence interface to a persistent JSON file.
 
-    The JSONDict inherits from :class:`~core.collection_api.SyncedCollection`
+    The JSONList inherits from :class:`~core.collection_api.SyncedCollection`
     and :class:`~core.syncedlist.SyncedList`.
 
     .. code-block:: python
@@ -129,15 +129,15 @@ class JSONList(JSONCollection, SyncedList):
 
     Parameters
     ----------
-    filename: str
+    filename: str, optional
         The filename of the associated JSON file on disk (Default value = None).
-    data: non-str Sequence
-        The intial data pass to JSONDict
-    parent: object
-        A parent instance of JSONDict or None (Default value = None).
-    write_concern: bool
+    write_concern: bool, optional
         Ensure file consistency by writing changes back to a temporary file
         first, before replacing the original file (Default value = None).
+    data: non-str Sequence, optional
+        The intial data pass to JSONList
+    parent: object, optional
+        A parent instance of JSONList or None (Default value = None).
     """
 
 
diff --git a/signac/core/collection_mongodb.py b/signac/core/collection_mongodb.py
index a2b855d52..83897e71c 100644
--- a/signac/core/collection_mongodb.py
+++ b/signac/core/collection_mongodb.py
@@ -53,12 +53,12 @@ def _pseudo_deepcopy(self):
 class MongoDBDict(MongoDBCollection, SyncedAttrDict):
     """A dict-like mapping interface to a persistent Mongo-database.
 
-    The MongoDict inherits from :class:`~core.collection_api.MongoCollection`
+    The MongoDBDict inherits from :class:`~core.collection_api.MongoCollection`
     and :class:`~core.syncedattrdict.SyncedAttrDict`.
 
     .. code-block:: python
 
-        doc = MongoDict('data')
+        doc = MongoDBDict('data')
         doc['foo'] = "bar"
         assert doc.foo == doc['foo'] == "bar"
         assert 'foo' in doc
@@ -74,36 +74,36 @@ class MongoDBDict(MongoDBCollection, SyncedAttrDict):
 
     .. warning::
 
-        While the MongoDict object behaves like a dictionary, there are
+        While the MongoDBDict object behaves like a dictionary, there are
         important distinctions to remember. In particular, because operations
         are reflected as changes to an underlying database, copying (even deep
-        copying) a MongoDict instance may exhibit unexpected behavior. If a
+        copying) a MongoDBDict instance may exhibit unexpected behavior. If a
         true copy is required, you should use the `to_base()` method to get a
-        dictionary representation, and if necessary construct a new MongoDict
-        instance: `new_dict = MongoDict(old_dict.to_base())`.
+        dictionary representation, and if necessary construct a new MongoDBDict
+        instance: `new_dict = MongoDBDict(old_dict.to_base())`.
 
     Parameters
     ----------
-    name: str
-        The name of the  collection (Default value = None).
-    collection : object
-        A pymongo.Collection instance
+    collection : object, optional
+        A pymongo.Collection instance.
     data: mapping, optional
-        The intial data pass to MongoDict. Defaults to `dict()`
+        The intial data pass to MongoDBDict. Defaults to `dict()`.
+    name: str, optional
+        The name of the  collection (Default value = None).
     parent: object, optional
-        A parent instance of MongoDict or None (Default value = None).
+        A parent instance of MongoDBDict (Default value = None).
     """
 
 
 class MongoDBList(MongoDBCollection, SyncedList):
     """A non-string sequence interface to a persistent Mongo file.
 
-    The MongoDict inherits from :class:`~core.synced_collection.SyncedCollection`
+    The MongoDBList inherits from :class:`~core.synced_collection.SyncedCollection`
     and :class:`~core.syncedlist.SyncedList`.
 
     .. code-block:: python
 
-        synced_list = MongoList('data')
+        synced_list = MongoDBList('data')
         synced_list.append("bar")
         assert synced_list[0] == "bar"
         assert len(synced_list) == 1
@@ -111,24 +111,24 @@ class MongoDBList(MongoDBCollection, SyncedList):
 
     .. warning::
 
-        While the MongoList object behaves like a list, there are
+        While the MongoDBList object behaves like a list, there are
         important distinctions to remember. In particular, because operations
         are reflected as changes to an underlying database, copying (even deep
-        copying) a MongoList instance may exhibit unexpected behavior. If a
+        copying) a MongoDBList instance may exhibit unexpected behavior. If a
         true copy is required, you should use the `to_base()` method to get a
-        dictionary representation, and if necessary construct a new MongoList
-        instance: `new_list = MongoList(old_list.to_base())`.
+        dictionary representation, and if necessary construct a new MongoDBList
+        instance: `new_list = MongoDBList(old_list.to_base())`.
 
     Parameters
     ----------
-    name: str
+    collection : object, optional
+        A pymongo.Collection instance (Default value = None).
+    data: non-str Sequence, optional
+        The intial data pass to MongoDBList. Defaults to `list()`.
+    name: str, optional
         The name of the  collection (Default value = None).
-    collection : object
-        A pymongo.Collection instance
-    data: mapping, optional
-        The intial data pass to MongoList. Defaults to `list()`
     parent: object, optional
-        A parent instance of MongoList or None (Default value = None).
+        A parent instance of MongoDBList (Default value = None).
     """
 
 
diff --git a/signac/core/collection_redis.py b/signac/core/collection_redis.py
index b340c1d5a..1dc9e504d 100644
--- a/signac/core/collection_redis.py
+++ b/signac/core/collection_redis.py
@@ -76,21 +76,21 @@ class RedisDict(RedisCollection, SyncedAttrDict):
 
     Parameters
     ----------
-    name: str
-        The name of the  collection (Default value = None).
-    client: object
-        A redis client.
+    client: object, optional
+        A redis client (Default value = None).
     data: mapping, optional
         The intial data pass to RedisDict. Defaults to `dict()`
+    name: str, optional
+        The name of the  collection (Default value = None).
     parent: object, optional
-        A parent instance of RedisDict or None (Default value = None).
+        A parent instance of RedisDict (Default value = None).
     """
 
 
 class RedisList(RedisCollection, SyncedList):
     """A non-string sequence interface to a persistent Redis file.
 
-    The RedisDict inherits from :class:`~core.collection_api.SyncedCollection`
+    The RedisList inherits from :class:`~core.collection_api.SyncedCollection`
     and :class:`~core.syncedlist.SyncedList`.
 
     .. code-block:: python
@@ -113,14 +113,14 @@ class RedisList(RedisCollection, SyncedList):
 
     Parameters
     ----------
-    name: str
-        The name of the  collection (Default value = None).
-    client: object
-        A redis client.
-    data: mapping, optional
+    client: object, optional
+        A redis client (Default value = None).
+    data: non-str Sequence, optional
         The intial data pass to RedisList. Defaults to `list()`
+    name: str, optional
+        The name of the  collection (Default value = None).
     parent: object, optional
-        A parent instance of RedisList or None (Default value = None).
+        A parent instance of RedisList (Default value = None).
     """
 
 
diff --git a/signac/core/collection_zarr.py b/signac/core/collection_zarr.py
index 7250192e3..3cfef408d 100644
--- a/signac/core/collection_zarr.py
+++ b/signac/core/collection_zarr.py
@@ -78,12 +78,12 @@ class ZarrDict(ZarrCollection, SyncedAttrDict):
 
     Parameters
     ----------
-    name: str, optional
-        The name of the  collection (Default value = None).
+    group: object, optional
+        A zarr.hierarchy.Group instance (Default value = None).
     data: mapping, optional
         The intial data pass to ZarrDict. Defaults to `dict()`.
-    group: object
-        A zarr.hierarchy.Group instance
+    name: str, optional
+        The name of the  collection (Default value = None).
     parent: object, optional
         A parent instance of ZarrDict or None (Default value = None).
     """
@@ -92,7 +92,7 @@ class ZarrDict(ZarrCollection, SyncedAttrDict):
 class ZarrList(ZarrCollection, SyncedList):
     """A non-string sequence interface to a persistent Zarr file.
 
-    The ZarrDict inherits from :class:`~core.collection_api.ZarrCollection`
+    The ZarrList inherits from :class:`~core.collection_api.ZarrCollection`
     and :class:`~core.syncedlist.SyncedList`.
 
     .. code-block:: python
@@ -115,12 +115,13 @@ class ZarrList(ZarrCollection, SyncedList):
 
     Parameters
     ----------
-    name: str
-        The name of the  collection.
-    data: mapping, optional
+
+    group: object, optional
+        A zarr.hierarchy.Group instance (Default value = None).
+    data: non-str Sequence, optional
         The intial data pass to ZarrList. Defaults to `list()`.
-    group: object
-        A zarr.hierarchy.Group instance
+    name: str, optional
+        The name of the  collection (Default value = None).
     parent: object, optional
         A parent instance of ZarrList or None (Default value = None).
     """