datajoint · guzman-raphael · Mar 25, 2022 · Feb 15, 2022 · Feb 15, 2022 · Feb 15, 2022
diff --git a/.github/workflows/development.yaml b/.github/workflows/development.yaml
@@ -30,7 +30,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install flake8
+          pip install flake8 black
       - name: Run syntax tests
         run: flake8 datajoint --count --select=E9,F63,F7,F82 --show-source --statistics
       - name: Run primary tests
@@ -47,5 +47,7 @@ jobs:
         run: docker-compose -f LNX-docker-compose.yml up --build --exit-code-from app
       - name: Run style tests
         run: |
-          flake8 --ignore=E121,E123,E126,E226,E24,E704,W503,W504,E722,F401,W605 datajoint \
+          flake8 --ignore=E203,E722,F401,W503 datajoint \
                  --count --max-complexity=62 --max-line-length=127 --statistics
+          black datajoint --check -v
+          black tests --check -v
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,10 +1,11 @@
 ## Release notes
 
-### 0.13.4 -- March, 25 2022
+### 0.13.4 -- March, 28 2022
 * Add - Allow reading blobs produced by legacy 32-bit compiled mYm library for matlab. PR #995
 * Bugfix - Add missing `jobs` argument for multiprocessing PR #997
 * Add - Test for multiprocessing PR #1008
 * Bugfix - Fix external store key name doesn't allow '-' (#1005) PR #1006
+* Add - Adopted black formatting into code base PR #998
 
 ### 0.13.3 -- Feb 9, 2022
 * Bugfix - Fix error in listing ancestors, descendants with part tables.

diff --git a/datajoint/__init__.py b/datajoint/__init__.py
@@ -16,15 +16,40 @@
 
 __author__ = "DataJoint Contributors"
 __date__ = "November 7, 2020"
-__all__ = ['__author__', '__version__',
-           'config', 'conn', 'Connection',
-           'Schema', 'schema', 'VirtualModule', 'create_virtual_module',
-           'list_schemas', 'Table', 'FreeTable',
-           'Manual', 'Lookup', 'Imported', 'Computed', 'Part',
-           'Not', 'AndList', 'U', 'Diagram', 'Di', 'ERD',
-           'set_password', 'kill',
-           'MatCell', 'MatStruct', 'AttributeAdapter',
-           'errors', 'DataJointError', 'key', 'key_hash']
+__all__ = [
+    "__author__",
+    "__version__",
+    "config",
+    "conn",
+    "Connection",
+    "Schema",
+    "schema",
+    "VirtualModule",
+    "create_virtual_module",
+    "list_schemas",
+    "Table",
+    "FreeTable",
+    "Manual",
+    "Lookup",
+    "Imported",
+    "Computed",
+    "Part",
+    "Not",
+    "AndList",
+    "U",
+    "Diagram",
+    "Di",
+    "ERD",
+    "set_password",
+    "kill",
+    "MatCell",
+    "MatStruct",
+    "AttributeAdapter",
+    "errors",
+    "DataJointError",
+    "key",
+    "key_hash",
+]
 
 from .version import __version__
 from .settings import config
@@ -44,6 +69,6 @@
 from .errors import DataJointError
 from .migrate import migrate_dj011_external_blob_storage_to_dj012
 
-ERD = Di = Diagram   # Aliases for Diagram
-schema = Schema   # Aliases for Schema
-create_virtual_module = VirtualModule   # Aliases for VirtualModule
+ERD = Di = Diagram  # Aliases for Diagram
+schema = Schema  # Aliases for Schema
+create_virtual_module = VirtualModule  # Aliases for VirtualModule
diff --git a/datajoint/admin.py b/datajoint/admin.py
@@ -5,19 +5,23 @@
 from .utils import user_choice
 
 
-def set_password(new_password=None, connection=None, update_config=None):   # pragma: no cover
+def set_password(
+    new_password=None, connection=None, update_config=None
+):  # pragma: no cover
     connection = conn() if connection is None else connection
     if new_password is None:
-        new_password = getpass('New password: ')
-        confirm_password = getpass('Confirm password: ')
+        new_password = getpass("New password: ")
+        confirm_password = getpass("Confirm password: ")
         if new_password != confirm_password:
-            print('Failed to confirm the password! Aborting password change.')
+            print("Failed to confirm the password! Aborting password change.")
             return
     connection.query("SET PASSWORD = PASSWORD('%s')" % new_password)
-    print('Password updated.')
+    print("Password updated.")
 
-    if update_config or (update_config is None and user_choice('Update local setting?') == 'yes'):
-        config['database.password'] = new_password
+    if update_config or (
+        update_config is None and user_choice("Update local setting?") == "yes"
+    ):
+        config["database.password"] = new_password
         config.save_local(verbose=True)
 
 
@@ -40,24 +44,32 @@ def kill(restriction=None, connection=None, order_by=None):  # pragma: no cover
         connection = conn()
 
     if order_by is not None and not isinstance(order_by, str):
-        order_by = ','.join(order_by)
+        order_by = ",".join(order_by)
 
-    query = 'SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()' + (
-        "" if restriction is None else ' AND (%s)' % restriction) + (
-            ' ORDER BY %s' % (order_by or 'id'))
+    query = (
+        "SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()"
+        + ("" if restriction is None else " AND (%s)" % restriction)
+        + (" ORDER BY %s" % (order_by or "id"))
+    )
 
     while True:
-        print('  ID USER         HOST          STATE         TIME    INFO')
-        print('+--+ +----------+ +-----------+ +-----------+ +-----+')
-        cur = ({k.lower(): v for k, v in elem.items()}
-               for elem in connection.query(query, as_dict=True))
+        print("  ID USER         HOST          STATE         TIME    INFO")
+        print("+--+ +----------+ +-----------+ +-----------+ +-----+")
+        cur = (
+            {k.lower(): v for k, v in elem.items()}
+            for elem in connection.query(query, as_dict=True)
+        )
         for process in cur:
             try:
-                print('{id:>4d} {user:<12s} {host:<12s} {state:<12s} {time:>7d}  {info}'.format(**process))
+                print(
+                    "{id:>4d} {user:<12s} {host:<12s} {state:<12s} {time:>7d}  {info}".format(
+                        **process
+                    )
+                )
             except TypeError:
                 print(process)
         response = input('process to kill or "q" to quit > ')
-        if response == 'q':
+        if response == "q":
             break
         if response:
             try:
@@ -66,9 +78,9 @@ def kill(restriction=None, connection=None, order_by=None):  # pragma: no cover
                 pass  # ignore non-numeric input
             else:
                 try:
-                    connection.query('kill %d' % pid)
+                    connection.query("kill %d" % pid)
                 except pymysql.err.InternalError:
-                    print('Process not found')
+                    print("Process not found")
 
 
 def kill_quick(restriction=None, connection=None):
@@ -86,13 +98,17 @@ def kill_quick(restriction=None, connection=None):
     if connection is None:
         connection = conn()
 
-    query = 'SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()' + (
-        "" if restriction is None else ' AND (%s)' % restriction)
+    query = (
+        "SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()"
+        + ("" if restriction is None else " AND (%s)" % restriction)
+    )
 
-    cur = ({k.lower(): v for k, v in elem.items()}
-           for elem in connection.query(query, as_dict=True))
+    cur = (
+        {k.lower(): v for k, v in elem.items()}
+        for elem in connection.query(query, as_dict=True)
+    )
     nkill = 0
     for process in cur:
-        connection.query('kill %d' % process['id'])
+        connection.query("kill %d" % process["id"])
         nkill += 1
     return nkill
diff --git a/datajoint/attribute_adapter.py b/datajoint/attribute_adapter.py
@@ -7,48 +7,62 @@ class AttributeAdapter:
     """
     Base class for adapter objects for user-defined attribute types.
     """
+
     @property
     def attribute_type(self):
         """
         :return: a supported DataJoint attribute type to use; e.g. "longblob", "blob@store"
         """
-        raise NotImplementedError('Undefined attribute adapter')
+        raise NotImplementedError("Undefined attribute adapter")
 
     def get(self, value):
         """
         convert value retrieved from the the attribute in a table into the adapted type
         :param value: value from the database
         :return: object of the adapted type
         """
-        raise NotImplementedError('Undefined attribute adapter')
+        raise NotImplementedError("Undefined attribute adapter")
 
     def put(self, obj):
         """
         convert an object of the adapted type into a value that DataJoint can store in a table attribute
         :param obj: an object of the adapted type
         :return: value to store in the database
         """
-        raise NotImplementedError('Undefined attribute adapter')
+        raise NotImplementedError("Undefined attribute adapter")
 
 
 def get_adapter(context, adapter_name):
     """
     Extract the AttributeAdapter object by its name from the context and validate.
     """
     if not _support_adapted_types():
-        raise DataJointError('Support for Adapted Attribute types is disabled.')
-    adapter_name = adapter_name.lstrip('<').rstrip('>')
+        raise DataJointError("Support for Adapted Attribute types is disabled.")
+    adapter_name = adapter_name.lstrip("<").rstrip(">")
     try:
-        adapter = (context[adapter_name] if adapter_name in context
-                   else type_plugins[adapter_name]['object'].load())
+        adapter = (
+            context[adapter_name]
+            if adapter_name in context
+            else type_plugins[adapter_name]["object"].load()
+        )
     except KeyError:
         raise DataJointError(
-            "Attribute adapter '{adapter_name}' is not defined.".format(adapter_name=adapter_name))
+            "Attribute adapter '{adapter_name}' is not defined.".format(
+                adapter_name=adapter_name
+            )
+        )
     if not isinstance(adapter, AttributeAdapter):
         raise DataJointError(
             "Attribute adapter '{adapter_name}' must be an instance of datajoint.AttributeAdapter".format(
-                adapter_name=adapter_name))
-    if not isinstance(adapter.attribute_type, str) or not re.match(r'^\w', adapter.attribute_type):
-        raise DataJointError("Invalid attribute type {type} in attribute adapter '{adapter_name}'".format(
-            type=adapter.attribute_type, adapter_name=adapter_name))
+                adapter_name=adapter_name
+            )
+        )
+    if not isinstance(adapter.attribute_type, str) or not re.match(
+        r"^\w", adapter.attribute_type
+    ):
+        raise DataJointError(
+            "Invalid attribute type {type} in attribute adapter '{adapter_name}'".format(
+                type=adapter.attribute_type, adapter_name=adapter_name
+            )
+        )
     return adapter