Merge pull request #811 from dimitri-yatsenko/master

make dtype=object for adapted attributes.

Author: guzman-raphael

README.md

@@ -114,6 +114,7 @@ GID=1000
 * `cp local-docker-compose.yml docker-compose.yml`
 * `docker-compose up -d` (Note configured `JUPYTER_PASSWORD`)
 * Select a means of running Tests e.g. Docker Terminal, or Local Terminal (see bottom)
+* Add entry in `/etc/hosts` for `127.0.0.1 fakeservices.datajoint.io`
 * Run desired tests. Some examples are as follows:
 
 | Use Case                     | Shell Code                                                                    |
@@ -137,4 +138,4 @@ GID=1000
 ### Launch Jupyter Notebook for Interactive Use
 * Navigate to `localhost:8888`
 * Input Jupyter password
-* Launch a notebook i.e. `New > Python 3`
+* Launch a notebook i.e. `New > Python 3`

datajoint/attribute_adapter.py

@@ -24,7 +24,7 @@ def get(self, value):
     def put(self, obj):
         """
         convert an object of the adapted type into a value that DataJoint can store in a table attribute
-        :param object: an object of the adapted type
+        :param obj: an object of the adapted type
         :return: value to store in the database
         """
         raise NotImplementedError('Undefined attribute adapter')

datajoint/dependencies.py

@@ -8,8 +8,8 @@ class Dependencies(nx.DiGraph):
     """
     The graph of dependencies (foreign keys) between loaded tables.
 
-    Note: the 'connnection' argument should normally be supplied;
-    Empty use is permitted to facilliate use of networkx algorithms which
+    Note: the 'connection' argument should normally be supplied;
+    Empty use is permitted to facilitate use of networkx algorithms which
     internally create objects with the expectation of empty constructors.
     See also: https://github.com/datajoint/datajoint-python/pull/443
     """
@@ -107,7 +107,6 @@ def descendants(self, full_table_name):
         """
         nodes = self.subgraph(
             nx.algorithms.dag.descendants(self, full_table_name))
-
         return [full_table_name] + list(
             nx.algorithms.dag.topological_sort(nodes))
 

datajoint/heading.py

@@ -279,7 +279,7 @@ def init_from_database(self, conn, database, table_name, context):
 
             # fill out dtype. All floats and non-nullable integers are turned into specific dtypes
             attr['dtype'] = object
-            if attr['numeric']:
+            if attr['numeric'] and not attr['adapter']:
                 is_integer = TYPE_PATTERN['INTEGER'].match(attr['type'])
                 is_float = TYPE_PATTERN['FLOAT'].match(attr['type'])
                 if is_integer and not attr['nullable'] or is_float:

datajoint/version.py

@@ -1,3 +1,3 @@
-__version__ = "0.12.6"
+__version__ = "0.12.7"
 
 assert len(__version__) <= 10  # The log table limits version to the 10 characters

setup.py

@@ -6,13 +6,13 @@
 min_py_version = (3, 5)
 
 if sys.version_info <  min_py_version:
-    sys.exit('DataJoint is only supported on Python {}.{} or higher'.format(*min_py_version))
+    sys.exit('DataJoint is only supported for Python {}.{} or higher'.format(*min_py_version))
 
 here = path.abspath(path.dirname(__file__))
 
 long_description = "A relational data framework for scientific data pipelines with MySQL backend."
 
-# read in version number
+# read in version number into __version__
 with open(path.join(here, 'datajoint', 'version.py')) as f:
     exec(f.read())
 

tests/__init__.py

@@ -26,17 +26,17 @@
 
 # Connection for testing
 CONN_INFO = dict(
-    host=environ.get('DJ_TEST_HOST', 'localhost'),
+    host=environ.get('DJ_TEST_HOST', 'fakeservices.datajoint.io'),
     user=environ.get('DJ_TEST_USER', 'datajoint'),
     password=environ.get('DJ_TEST_PASSWORD', 'datajoint'))
 
 CONN_INFO_ROOT = dict(
-    host=environ.get('DJ_HOST', 'localhost'),
+    host=environ.get('DJ_HOST', 'fakeservices.datajoint.io'),
     user=environ.get('DJ_USER', 'root'),
     password=environ.get('DJ_PASS', 'simple'))
 
 S3_CONN_INFO = dict(
-    endpoint=environ.get('S3_ENDPOINT', 'localhost:9000'),
+    endpoint=environ.get('S3_ENDPOINT', 'fakeservices.datajoint.io'),
     access_key=environ.get('S3_ACCESS_KEY', 'datajoint'),
     secret_key=environ.get('S3_SECRET_KEY', 'datajoint'),
     bucket=environ.get('S3_BUCKET', 'datajoint.test'))
@@ -132,7 +132,7 @@ def setup_package():
     # Add old S3
     source = Path(
         Path(__file__).resolve().parent,
-        'external-legacy-data','s3')
+        'external-legacy-data', 's3')
     region = "us-east-1"
     try:
         minioClient.make_bucket(S3_MIGRATE_BUCKET, location=region)
@@ -144,7 +144,7 @@ def setup_package():
         if os.path.isfile(str(path)) and ".sql" not in str(path):
             minioClient.fput_object(
                     S3_MIGRATE_BUCKET, str(Path(
-                        os.path.relpath(str(path),str(Path(source,S3_MIGRATE_BUCKET))))
+                        os.path.relpath(str(path), str(Path(source, S3_MIGRATE_BUCKET))))
                                 .as_posix()), str(path))
     # Add S3
     try:

tests/test_reconnection.py

@@ -4,10 +4,8 @@
 
 from nose.tools import assert_true, assert_false, assert_equal, raises
 import datajoint as dj
-import numpy as np
 from datajoint import DataJointError
-from . import CONN_INFO, PREFIX
-
+from . import CONN_INFO
 
 
 class TestReconnect:
@@ -18,20 +16,17 @@ class TestReconnect:
     def setup(self):
         self.conn = dj.conn(reset=True, **CONN_INFO)
 
-
     def test_close(self):
         assert_true(self.conn.is_connected, "Connection should be alive")
         self.conn.close()
         assert_false(self.conn.is_connected, "Connection should now be closed")
 
-
     def test_reconnect(self):
         assert_true(self.conn.is_connected, "Connection should be alive")
         self.conn.close()
         self.conn.query('SHOW DATABASES;', reconnect=True).fetchall()
         assert_true(self.conn.is_connected, "Connection should be alive")
 
-
     @raises(DataJointError)
     def test_reconnect_throws_error_in_transaction(self):
         assert_true(self.conn.is_connected, "Connection should be alive")