Merge pull request #706 from dimitri-yatsenko/master

Fix #698 and #699

Author: guzman-raphael

CHANGELOG.md

@@ -1,5 +1,10 @@
 ## Release notes
 
+## 0.12.3 -- Nov 22, 2019
+* Bugfix #675 (PR #705) networkx 2.4+ is now supported
+* Bugfix #698 and #699 (PR #706) display table definition in doc string and help
+* Bugfix #701 (PR #702) job reservation works with native python datatype support disabled
+
 ### 0.12.2 -- Nov 11, 2019
 * Bugfix - Convoluted error thrown if there is a reference to a non-existent table attribute (#691)
 * Bugfix - Insert into external does not trim leading slash if defined in `dj.config['stores']['<store>']['location']` (#692)

datajoint/blob.py

@@ -152,10 +152,8 @@ def pack_blob(self, obj):
             return self.pack_array(np.array(obj))
         if isinstance(obj, (bool, np.bool, np.bool_)):
             return self.pack_array(np.array(obj))
-        if isinstance(obj, float):
-            return self.pack_array(np.array(obj, dtype=np.float64))
-        if isinstance(obj, int):
-            return self.pack_array(np.array(obj, dtype=np.int64))
+        if isinstance(obj, (float, int, complex)):
+            return self.pack_array(np.array(obj))
         if isinstance(obj, (datetime.datetime, datetime.date, datetime.time)):
             return self.pack_datetime(obj)
         if isinstance(obj, Decimal):

datajoint/heading.py

@@ -247,7 +247,10 @@ def init_from_database(self, conn, database, table_name, context):
                     category = next(c for c in SPECIAL_TYPES if TYPE_PATTERN[c].match(attr['type']))
                 except StopIteration:
                     if attr['type'].startswith('external'):
-                        raise DataJointError('Legacy datatype `{type}`.'.format(**attr)) from None
+                        url = "https://docs.datajoint.io/python/admin/5-blob-config.html" \
+                              "#migration-between-datajoint-v0-11-and-v0-12"
+                        raise DataJointError('Legacy datatype `{type}`. Migrate your external stores to '
+                                             'datajoint 0.12: {url}'.format(url=url, **attr)) from None
                     raise DataJointError('Unknown attribute type `{type}`'.format(**attr)) from None
                 if category == 'FILEPATH' and not _support_filepath_types():
                     raise DataJointError("""

datajoint/schema.py

@@ -191,6 +191,10 @@ def process_table_class(self, table_class, context, assert_declared=False):
                 instance.declare(context)
         is_declared = is_declared or instance.is_declared
 
+        # add table definition to the doc string
+        if isinstance(table_class.definition, str):
+            table_class.__doc__ = (table_class.__doc__ or "") + "\nTable definition:\n\n" + table_class.definition
+
         # fill values in Lookup tables from their contents property
         if isinstance(instance, Lookup) and hasattr(instance, 'contents') and is_declared:
             contents = list(instance.contents)

datajoint/table.py

@@ -45,14 +45,9 @@ def heading(self):
         """
         if self._heading is None:
             self._heading = Heading()  # instance-level heading
-        if not self._heading:  # lazy loading of heading
-            if self.connection is None:
-                raise DataJointError(
-                    'DataJoint class is missing a database connection. '
-                    'Missing schema decorator on the class? (e.g. @schema)')
-            else:
-                self._heading.init_from_database(
-                    self.connection, self.database, self.table_name, self.declaration_context)
+        if not self._heading and self.connection is not None:  # lazy loading of heading
+            self._heading.init_from_database(
+                self.connection, self.database, self.table_name, self.declaration_context)
         return self._heading
 
     def declare(self, context=None):
@@ -411,7 +406,7 @@ def delete(self, verbose=True):
             print('About to delete:')
 
         if not already_in_transaction:
-            self.connection.start_transaction()
+            conn.start_transaction()
         total = 0
         try:
             for name, table in reversed(list(delete_list.items())):
@@ -423,25 +418,25 @@ def delete(self, verbose=True):
         except:
             # Delete failed, perhaps due to insufficient privileges. Cancel transaction.
             if not already_in_transaction:
-                self.connection.cancel_transaction()
+                conn.cancel_transaction()
             raise
         else:
             assert not (already_in_transaction and safe)
             if not total:
                 print('Nothing to delete')
                 if not already_in_transaction:
-                    self.connection.cancel_transaction()
+                    conn.cancel_transaction()
             else:
                 if already_in_transaction:
                     if verbose:
                         print('The delete is pending within the ongoing transaction.')
                 else:
                     if not safe or user_choice("Proceed?", default='no') == 'yes':
-                        self.connection.commit_transaction()
+                        conn.commit_transaction()
                         if verbose or safe:
                             print('Committed.')
                     else:
-                        self.connection.cancel_transaction()
+                        conn.cancel_transaction()
                         if verbose or safe:
                             print('Cancelled deletes.')
 

datajoint/user_tables.py

@@ -13,7 +13,7 @@
 # attributes that trigger instantiation of user classes
 supported_class_attrs = {
     'key_source', 'describe', 'alter', 'heading', 'populate', 'progress', 'primary_key', 'proj', 'aggr',
-    'fetch', 'fetch1','head', 'tail',
+    'fetch', 'fetch1', 'head', 'tail',
     'insert', 'insert1', 'drop', 'drop_quick', 'delete', 'delete_quick'}
 
 
@@ -92,7 +92,7 @@ def table_name(cls):
 
     @ClassProperty
     def full_table_name(cls):
-        if cls not in {Manual, Imported, Lookup, Computed, Part}:
+        if cls not in {Manual, Imported, Lookup, Computed, Part, UserTable}:
             if cls.database is None:
                 raise DataJointError('Class %s is not properly declared (schema decorator not applied?)' % cls.__name__)
             return r"`{0:s}`.`{1:s}`".format(cls.database, cls.table_name)

datajoint/version.py

@@ -1,3 +1,3 @@
-__version__ = "0.12.2"
+__version__ = "0.12.3"
 
 assert len(__version__) <= 10  # The log table limits version to the 10 characters

docs-parts/intro/Releases_lang1.rst

@@ -1,4 +1,11 @@
-0.12.1 -- Nov 11, 2019
+0.12.3 -- Nov 22, 2019
+----------------------
+* Bugfix - networkx 2.4 causes error in diagrams (#675) PR #705
+* Bugfix - include definition in doc string and help (#698, #699) PR #706
+* Bugfix - job reservation fails when native python datatype support is disabled (#701) PR #702 
+
+
+0.12.2 -- Nov 11, 2019
 -------------------------
 * Bugfix - Convoluted error thrown if there is a reference to a non-existent table attribute (#691)
 * Bugfix - Insert into external does not trim leading slash if defined in `dj.config['stores']['<store>']['location']` (#692)

tests/schema.py

@@ -13,6 +13,9 @@
 
 @schema
 class TTest(dj.Lookup):
+    """
+    doc string
+    """
     definition = """
     key   :   int     # key
     ---

tests/test_blob.py

@@ -23,6 +23,9 @@ def test_pack():
     x = np.random.randn(10)
     assert_array_equal(x, unpack(pack(x)), "Arrays do not match!")
 
+    x = 7j
+    assert_equal(x, unpack(pack(x)), "Complex scalar does not match")
+
     x = np.float32(np.random.randn(3, 4, 5))
     assert_array_equal(x, unpack(pack(x)), "Arrays do not match!")
 

tests/test_declare.py

@@ -22,6 +22,20 @@ def test_schema_decorator():
         assert_true(issubclass(Subject, dj.Lookup))
         assert_true(not issubclass(Subject, dj.Part))
 
+    @staticmethod
+    def test_class_help():
+        help(TTest)
+        help(TTest2)
+        assert_true(TTest.definition in TTest.__doc__)
+        assert_true(TTest.definition in TTest2.__doc__)
+
+    @staticmethod
+    def test_instance_help():
+        help(TTest())
+        help(TTest2())
+        assert_true(TTest().definition in TTest().__doc__)
+        assert_true(TTest2().definition in TTest2().__doc__)
+
     @staticmethod
     def test_describe():
         """real_definition should match original definition"""