<commit_before>from Database import Database
from pymongo import MongoClient
from pymongo import ASCENDING
from pymongo import GEO2D
import numpy as np
import rtree
import time
import os

class Mongodb(Database):
    """ Provides a :class:`Database` interface to ``pymongo``

    Arguments
    ----------
    path: str
        The file path to store and access the database
    RUNTIME: :class:`RUNTIME`
        Gets stored as :data:`RUNTIME`

    Attributes
    -----------
    RUNTIME: :class:`RUNTIME`
        With keywords needed to load files and use tables
    synapse_rtree: rtree.index.Index
        Keeps all synapse positions for spatial indexing
    mongo_db: pymongo.database
        Keeps all full collections of neurons and synapses
    log: :class:`MakeLog`.``logging``
        All formats for log messages
    """<commit_msg>do not include rtree in Mongodb<commit_after>from Database import Database
from pymongo import MongoClient
from pymongo import ASCENDING
from pymongo import GEO2D
import numpy as np
import time
import os

class Mongodb(Database):
    """ Provides a :class:`Database` interface to ``pymongo``

    Arguments
    ----------
    path: str
        The file path to store and access the database
    RUNTIME: :class:`RUNTIME`
        Gets stored as :data:`RUNTIME`

    Attributes
    -----------
    RUNTIME: :class:`RUNTIME`
        With keywords needed to load files and use tables
    synapse_rtree: rtree.index.Index
        Keeps all synapse positions for spatial indexing
    mongo_db: pymongo.database
        Keeps all full collections of neurons and synapses
    log: :class:`MakeLog`.``logging``
        All formats for log messages
    """
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