datajoint 0.14.3__py3-none-any.whl → 0.14.5__py3-none-any.whl

datajoint/__init__.py

@@ -55,24 +55,23 @@ __all__ = [
     "cli",
 ]
 
-from .logging import logger
-from .version import __version__
-from .settings import config
-from .connection import conn, Connection
-from .schemas import Schema
-from .schemas import VirtualModule, list_schemas
-from .table import Table, FreeTable
-from .user_tables import Manual, Lookup, Imported, Computed, Part
-from .expression import Not, AndList, U, Top
-from .diagram import Diagram
-from .admin import set_password, kill
+from . import errors
+from .admin import kill, set_password
+from .attribute_adapter import AttributeAdapter
 from .blob import MatCell, MatStruct
+from .cli import cli
+from .connection import Connection, conn
+from .diagram import Diagram
+from .errors import DataJointError
+from .expression import AndList, Not, Top, U
 from .fetch import key
 from .hash import key_hash
-from .attribute_adapter import AttributeAdapter
-from . import errors
-from .errors import DataJointError
-from .cli import cli
+from .logging import logger
+from .schemas import Schema, VirtualModule, list_schemas
+from .settings import config
+from .table import FreeTable, Table
+from .user_tables import Computed, Imported, Lookup, Manual, Part
+from .version import __version__
 
 ERD = Di = Diagram  # Aliases for Diagram
 schema = Schema  # Aliases for Schema

datajoint/admin.py

@@ -1,10 +1,12 @@
-import pymysql
+import logging
 from getpass import getpass
+
+import pymysql
 from packaging import version
+
 from .connection import conn
 from .settings import config
 from .utils import user_choice
-import logging
 
 logger = logging.getLogger(__name__.split(".")[0])
 

datajoint/attribute_adapter.py

@@ -1,4 +1,5 @@
 import re
+
 from .errors import DataJointError, _support_adapted_types
 from .plugin import type_plugins
 

datajoint/autopopulate.py

@@ -1,17 +1,20 @@
 """This module defines class dj.AutoPopulate"""
 
-import logging
+import contextlib
 import datetime
-import traceback
-import random
 import inspect
+import logging
+import multiprocessing as mp
+import random
+import signal
+import traceback
+
+import deepdiff
 from tqdm import tqdm
-from .hash import key_hash
-from .expression import QueryExpression, AndList
+
 from .errors import DataJointError, LostConnectionError
-import signal
-import multiprocessing as mp
-import contextlib
+from .expression import AndList, QueryExpression
+from .hash import key_hash
 
 # noinspection PyExceptionInherit,PyCallingNonCallable
 
@@ -92,13 +95,76 @@ class AutoPopulate:
 
     def make(self, key):
         """
-        Derived classes must implement method `make` that fetches data from tables
-        above them in the dependency hierarchy, restricting by the given key,
-        computes secondary attributes, and inserts the new tuples into self.
+        This method must be implemented by derived classes to perform automated computation.
+        The method must implement the following three steps:
+
+        1. Fetch data from tables above in the dependency hierarchy, restricted by the given key.
+        2. Compute secondary attributes based on the fetched data.
+        3. Insert the new tuple(s) into the current table.
+
+        The method can be implemented either as:
+        (a) Regular method: All three steps are performed in a single database transaction.
+            The method must return None.
+        (b) Generator method:
+            The make method is split into three functions:
+            - `make_fetch`: Fetches data from the parent tables.
+            - `make_compute`: Computes secondary attributes based on the fetched data.
+            - `make_insert`: Inserts the computed data into the current table.
+
+            Then populate logic is executes as follows:
+
+            <pseudocode>
+            fetched_data1 = self.make_fetch(key)
+            computed_result = self.make_compute(key, *fetched_data1)
+            begin transaction:
+                fetched_data2 = self.make_fetch(key)
+                if fetched_data1 != fetched_data2:
+                    cancel transaction
+                else:
+                    self.make_insert(key, *computed_result)
+                    commit_transaction
+            <pseudocode>
+
+        Importantly, the output of make_fetch is a tuple that serves as the input into `make_compute`.
+        The output of `make_compute` is a tuple that serves as the input into `make_insert`.
+
+        The functionality must be strictly divided between these three methods:
+        - All database queries must be completed in `make_fetch`.
+        - All computation must be completed in `make_compute`.
+        - All database inserts must be completed in `make_insert`.
+
+        DataJoint may programmatically enforce this separation in the future.
+
+        :param key: The primary key value used to restrict the data fetching.
+        :raises NotImplementedError: If the derived class does not implement the required methods.
         """
-        raise NotImplementedError(
-            "Subclasses of AutoPopulate must implement the method `make`"
-        )
+
+        if not (
+            hasattr(self, "make_fetch")
+            and hasattr(self, "make_insert")
+            and hasattr(self, "make_compute")
+        ):
+            # user must implement `make`
+            raise NotImplementedError(
+                "Subclasses of AutoPopulate must implement the method `make` "
+                "or (`make_fetch` + `make_compute` + `make_insert`)"
+            )
+
+        # User has implemented `_fetch`, `_compute`, and `_insert` methods instead
+
+        # Step 1: Fetch data from parent tables
+        fetched_data = self.make_fetch(key)  # fetched_data is a tuple
+        computed_result = yield fetched_data  # passed as input into make_compute
+
+        # Step 2: If computed result is not passed in, compute the result
+        if computed_result is None:
+            # this is only executed in the first invocation
+            computed_result = self.make_compute(key, *fetched_data)
+            yield computed_result  # this is passed to the second invocation of make
+
+        # Step 3: Insert the computed result into the current table.
+        self.make_insert(key, *computed_result)
+        yield
 
     @property
     def target(self):
@@ -200,9 +266,8 @@ class AutoPopulate:
             self.connection.schemas[self.target.database].jobs if reserve_jobs else None
         )
 
-        # define and set up signal handler for SIGTERM:
         if reserve_jobs:
-
+            # Define a signal handler for SIGTERM
             def handler(signum, frame):
                 logger.info("Populate terminated by SIGTERM")
                 raise SystemExit("SIGTERM received")
@@ -262,13 +327,16 @@ class AutoPopulate:
                 # spawn multiple processes
                 self.connection.close()  # disconnect parent process from MySQL server
                 del self.connection._conn.ctx  # SSLContext is not pickleable
-                with mp.Pool(
-                    processes, _initialize_populate, (self, jobs, populate_kwargs)
-                ) as pool, (
-                    tqdm(desc="Processes: ", total=nkeys)
-                    if display_progress
-                    else contextlib.nullcontext()
-                ) as progress_bar:
+                with (
+                    mp.Pool(
+                        processes, _initialize_populate, (self, jobs, populate_kwargs)
+                    ) as pool,
+                    (
+                        tqdm(desc="Processes: ", total=nkeys)
+                        if display_progress
+                        else contextlib.nullcontext()
+                    ) as progress_bar,
+                ):
                     for status in pool.imap(_call_populate1, keys, chunksize=1):
                         if status is True:
                             success_list.append(1)
@@ -309,17 +377,47 @@ class AutoPopulate:
         ):
             return False
 
-        self.connection.start_transaction()
+        # if make is a generator, it transaction can be delayed until the final stage
+        is_generator = inspect.isgeneratorfunction(make)
+        if not is_generator:
+            self.connection.start_transaction()
+
         if key in self.target:  # already populated
-            self.connection.cancel_transaction()
+            if not is_generator:
+                self.connection.cancel_transaction()
             if jobs is not None:
                 jobs.complete(self.target.table_name, self._job_key(key))
             return False
 
         logger.debug(f"Making {key} -> {self.target.full_table_name}")
         self.__class__._allow_insert = True
+
         try:
-            make(dict(key), **(make_kwargs or {}))
+            if not is_generator:
+                make(dict(key), **(make_kwargs or {}))
+            else:
+                # tripartite make - transaction is delayed until the final stage
+                gen = make(dict(key), **(make_kwargs or {}))
+                fetched_data = next(gen)
+                fetch_hash = deepdiff.DeepHash(
+                    fetched_data, ignore_iterable_order=False
+                )[fetched_data]
+                computed_result = next(gen)  # perform the computation
+                # fetch and insert inside a transaction
+                self.connection.start_transaction()
+                gen = make(dict(key), **(make_kwargs or {}))  # restart make
+                fetched_data = next(gen)
+                if (
+                    fetch_hash
+                    != deepdiff.DeepHash(fetched_data, ignore_iterable_order=False)[
+                        fetched_data
+                    ]
+                ):  # raise error if fetched data has changed
+                    raise DataJointError(
+                        "Referential integrity failed! The `make_fetch` data has changed"
+                    )
+                gen.send(computed_result)  # insert
+
         except (KeyboardInterrupt, SystemExit, Exception) as error:
             try:
                 self.connection.cancel_transaction()

datajoint/blob.py

@@ -3,17 +3,18 @@
 compatibility with Matlab-based serialization implemented by mYm.
 """
 
-import zlib
-from itertools import repeat
 import collections
-from decimal import Decimal
 import datetime
 import uuid
+import zlib
+from decimal import Decimal
+from itertools import repeat
+
 import numpy as np
+
 from .errors import DataJointError
 from .settings import config
 
-
 deserialize_lookup = {
     0: {"dtype": None, "scalar_type": "UNKNOWN"},
     1: {"dtype": None, "scalar_type": "CELL"},
@@ -139,7 +140,7 @@ class Blob:
                 "S": self.read_struct,  # matlab struct array
                 "C": self.read_cell_array,  # matlab cell array
                 # basic data types
-                "\xFF": self.read_none,  # None
+                "\xff": self.read_none,  # None
                 "\x01": self.read_tuple,  # a Sequence (e.g. tuple)
                 "\x02": self.read_list,  # a MutableSequence (e.g. list)
                 "\x03": self.read_set,  # a Set
@@ -204,7 +205,7 @@ class Blob:
             return self.pack_dict(obj)
         if isinstance(obj, str):
             return self.pack_string(obj)
-        if isinstance(obj, collections.abc.ByteString):
+        if isinstance(obj, (bytes, bytearray)):
             return self.pack_bytes(obj)
         if isinstance(obj, collections.abc.MutableSequence):
             return self.pack_list(obj)
@@ -400,7 +401,7 @@ class Blob:
 
     @staticmethod
     def pack_none():
-        return b"\xFF"
+        return b"\xff"
 
     def read_tuple(self):
         return tuple(

datajoint/cli.py

@@ -1,6 +1,7 @@
 import argparse
 from code import interact
 from collections import ChainMap
+
 import datajoint as dj
 
 

datajoint/condition.py

@@ -1,17 +1,19 @@
-""" methods for generating SQL WHERE clauses from datajoint restriction conditions """
+"""methods for generating SQL WHERE clauses from datajoint restriction conditions"""
 
-import inspect
 import collections
-import re
-import uuid
 import datetime
 import decimal
+import inspect
+import json
+import re
+import uuid
+from dataclasses import dataclass
+from typing import List, Union
+
 import numpy
 import pandas
-import json
+
 from .errors import DataJointError
-from typing import Union, List
-from dataclasses import dataclass
 
 JSON_PATTERN = re.compile(
     r"^(?P<attr>\w+)(\.(?P<path>[\w.*\[\]]+))?(:(?P<type>[\w(,\s)]+))?$"
@@ -143,7 +145,7 @@ def make_condition(query_expression, condition, columns):
         condition.
     :return: an SQL condition string or a boolean value.
     """
-    from .expression import QueryExpression, Aggregation, U
+    from .expression import Aggregation, QueryExpression, U
 
     def prep_value(k, v):
         """prepare SQL condition"""

datajoint/connection.py

@@ -3,20 +3,22 @@ This module contains the Connection class that manages the connection to the dat
 the ``conn`` function that provides access to a persistent connection in datajoint.
 """
 
+import logging
+import pathlib
+import re
 import warnings
 from contextlib import contextmanager
-import pymysql as client
-import logging
 from getpass import getpass
-import re
-import pathlib
 
-from .settings import config
+import pymysql as client
+
 from . import errors
-from .dependencies import Dependencies
 from .blob import pack, unpack
+from .dependencies import Dependencies
 from .hash import uuid_from_buffer
 from .plugin import connection_plugins
+from .settings import config
+from .version import __version__
 
 logger = logging.getLogger(__name__.split(".")[0])
 query_log_max_length = 300
@@ -190,15 +192,20 @@ class Connection:
         self.conn_info["ssl_input"] = use_tls
         self.conn_info["host_input"] = host_input
         self.init_fun = init_fun
-        logger.info("Connecting {user}@{host}:{port}".format(**self.conn_info))
         self._conn = None
         self._query_cache = None
         connect_host_hook(self)
         if self.is_connected:
-            logger.info("Connected {user}@{host}:{port}".format(**self.conn_info))
+            logger.info(
+                "DataJoint {version} connected to {user}@{host}:{port}".format(
+                    version=__version__, **self.conn_info
+                )
+            )
             self.connection_id = self.query("SELECT connection_id()").fetchone()[0]
         else:
-            raise errors.LostConnectionError("Connection failed.")
+            raise errors.LostConnectionError(
+                "Connection failed {user}@{host}:{port}".format(**self.conn_info)
+            )
         self._in_transaction = False
         self.schemas = dict()
         self.dependencies = Dependencies(self)
@@ -344,7 +351,7 @@ class Connection:
         except errors.LostConnectionError:
             if not reconnect:
                 raise
-            logger.warning("MySQL server has gone away. Reconnecting to the server.")
+            logger.warning("Reconnecting to MySQL server.")
             connect_host_hook(self)
             if self._in_transaction:
                 self.cancel_transaction()

datajoint/declare.py

@@ -3,13 +3,15 @@ This module hosts functions to convert DataJoint table definitions into mysql ta
 declare the corresponding mysql tables.
 """
 
-import re
-import pyparsing as pp
 import logging
+import re
 from hashlib import sha1
-from .errors import DataJointError, _support_filepath_types, FILEPATH_FEATURE_SWITCH
+
+import pyparsing as pp
+
 from .attribute_adapter import get_adapter
 from .condition import translate_attribute
+from .errors import FILEPATH_FEATURE_SWITCH, DataJointError, _support_filepath_types
 from .settings import config
 
 UUID_DATA_TYPE = "binary(16)"
@@ -163,8 +165,8 @@ def compile_foreign_key(
     :param index_sql: list of INDEX declaration statements, duplicate or redundant indexes are ok.
     """
     # Parse and validate
-    from .table import Table
     from .expression import QueryExpression
+    from .table import Table
 
     try:
         result = foreign_key_parser.parseString(line)

datajoint/dependencies.py

@@ -1,7 +1,9 @@
-import networkx as nx
 import itertools
 import re
 from collections import defaultdict
+
+import networkx as nx
+
 from .errors import DataJointError
 
 

datajoint/diagram.py

@@ -1,14 +1,14 @@
-import networkx as nx
 import functools
+import inspect
 import io
 import logging
-import inspect
-from .table import Table
+
+import networkx as nx
+
 from .dependencies import topo_sort
-from .user_tables import Manual, Imported, Computed, Lookup, Part, _get_tier, _AliasNode
 from .errors import DataJointError
-from .table import lookup_class_name
-
+from .table import Table, lookup_class_name
+from .user_tables import Computed, Imported, Lookup, Manual, Part, _AliasNode, _get_tier
 
 try:
     from matplotlib import pyplot as plt
@@ -35,7 +35,7 @@ if not diagram_active:
         Entity relationship diagram, currently disabled due to the lack of required packages: matplotlib and pygraphviz.
 
         To enable Diagram feature, please install both matplotlib and pygraphviz. For instructions on how to install
-        these two packages, refer to https://datajoint.com/docs/core/datajoint-python/0.14/client/install/
+        these two packages, refer to https://docs.datajoint.com/core/datajoint-python/0.14/client/install/
         """
 
         def __init__(self, *args, **kwargs):

datajoint/expression.py

@@ -1,23 +1,24 @@
-from itertools import count
-import logging
-import inspect
 import copy
+import inspect
+import logging
 import re
-from .settings import config
-from .errors import DataJointError
-from .fetch import Fetch, Fetch1
-from .preview import preview, repr_html
+from itertools import count
+
 from .condition import (
     AndList,
-    Top,
     Not,
-    make_condition,
+    PromiscuousOperand,
+    Top,
     assert_join_compatibility,
     extract_column_names,
-    PromiscuousOperand,
+    make_condition,
     translate_attribute,
 )
 from .declare import CONSTANT_LITERALS
+from .errors import DataJointError
+from .fetch import Fetch, Fetch1
+from .preview import preview, repr_html
+from .settings import config
 
 logger = logging.getLogger(__name__.split(".")[0])
 

datajoint/external.py

@@ -1,15 +1,17 @@
-from pathlib import Path, PurePosixPath, PureWindowsPath
+import logging
 from collections.abc import Mapping
+from pathlib import Path, PurePosixPath, PureWindowsPath
+
 from tqdm import tqdm
-import logging
-from .settings import config
+
+from . import errors, s3
+from .declare import EXTERNAL_TABLE_ROOT
 from .errors import DataJointError, MissingExternalFile
 from .hash import uuid_from_buffer, uuid_from_file
-from .table import Table, FreeTable
 from .heading import Heading
-from .declare import EXTERNAL_TABLE_ROOT
-from . import s3, errors
-from .utils import safe_write, safe_copy
+from .settings import config
+from .table import FreeTable, Table
+from .utils import safe_copy, safe_write
 
 logger = logging.getLogger(__name__.split(".")[0])
 
@@ -22,7 +24,7 @@ SUPPORT_MIGRATED_BLOBS = True  # support blobs migrated from datajoint 0.11.*
 
 def subfold(name, folds):
     """
-    subfolding for external storage:   e.g.  subfold('aBCdefg', (2, 3))  -->  ['ab','cde']
+    subfolding for external storage: e.g.  subfold('aBCdefg', (2, 3))  -->  ['ab','cde']
     """
     return (
         (name[: folds[0]].lower(),) + subfold(name[folds[0] :], folds[1:])
@@ -278,7 +280,7 @@ class ExternalTable(Table):
 
         # check if the remote file already exists and verify that it matches
         check_hash = (self & {"hash": uuid}).fetch("contents_hash")
-        if check_hash:
+        if check_hash.size:
             # the tracking entry exists, check that it's the same file as before
             if contents_hash != check_hash[0]:
                 raise DataJointError(

datajoint/fetch.py

@@ -1,13 +1,15 @@
-from functools import partial
-from pathlib import Path
-import pandas
 import itertools
 import json
-import numpy as np
-import uuid
 import numbers
+import uuid
+from functools import partial
+from pathlib import Path
+
+import numpy as np
+import pandas
 
 from datajoint.condition import Top
+
 from . import blob, hash
 from .errors import DataJointError
 from .settings import config

datajoint/hash.py

@@ -1,6 +1,6 @@
 import hashlib
-import uuid
 import io
+import uuid
 from pathlib import Path
 
 

datajoint/heading.py

@@ -1,18 +1,19 @@
-import numpy as np
-from collections import namedtuple, defaultdict
-from itertools import chain
-import re
 import logging
-from .errors import DataJointError, _support_filepath_types, FILEPATH_FEATURE_SWITCH
+import re
+from collections import defaultdict, namedtuple
+from itertools import chain
+
+import numpy as np
+
+from .attribute_adapter import AttributeAdapter, get_adapter
 from .declare import (
-    UUID_DATA_TYPE,
-    SPECIAL_TYPES,
-    TYPE_PATTERN,
     EXTERNAL_TYPES,
     NATIVE_TYPES,
+    SPECIAL_TYPES,
+    TYPE_PATTERN,
+    UUID_DATA_TYPE,
 )
-from .attribute_adapter import get_adapter, AttributeAdapter
-
+from .errors import FILEPATH_FEATURE_SWITCH, DataJointError, _support_filepath_types
 
 logger = logging.getLogger(__name__.split(".")[0])
 

datajoint/jobs.py

@@ -1,10 +1,11 @@
 import os
-from .hash import key_hash
 import platform
-from .table import Table
-from .settings import config
+
 from .errors import DuplicateError
+from .hash import key_hash
 from .heading import Heading
+from .settings import config
+from .table import Table
 
 ERROR_MESSAGE_LENGTH = 2047
 TRUNCATION_APPENDIX = "...truncated"

datajoint/plugin.py

@@ -1,9 +1,11 @@
-from .settings import config
-import pkg_resources
+import logging
 from pathlib import Path
+
+import pkg_resources
 from cryptography.exceptions import InvalidSignature
 from otumat import hash_pkg, verify
-import logging
+
+from .settings import config
 
 logger = logging.getLogger(__name__.split(".")[0])
 

datajoint/preview.py

@@ -1,4 +1,4 @@
-""" methods for generating previews of query expression results in python command line and Jupyter """
+"""methods for generating previews of query expression results in python command line and Jupyter"""
 
 from .settings import config
 

datajoint/s3.py

@@ -2,12 +2,14 @@
 AWS S3 operations
 """
 
+import logging
+import uuid
 from io import BytesIO
+from pathlib import Path
+
 import minio  # https://docs.minio.io/docs/python-client-api-reference
 import urllib3
-import uuid
-import logging
-from pathlib import Path
+
 from . import errors
 
 logger = logging.getLogger(__name__.split(".")[0])

datajoint/schemas.py

@@ -1,19 +1,20 @@
-import warnings
-import logging
-import inspect
-import re
 import collections
+import inspect
 import itertools
+import logging
+import re
+import types
+import warnings
+
 from .connection import conn
-from .settings import config
-from .errors import DataJointError, AccessError
-from .jobs import JobTable
+from .errors import AccessError, DataJointError
 from .external import ExternalMapping
 from .heading import Heading
-from .utils import user_choice, to_camel_case
-from .user_tables import Part, Computed, Imported, Manual, Lookup, _get_tier
-from .table import lookup_class_name, Log, FreeTable
-import types
+from .jobs import JobTable
+from .settings import config
+from .table import FreeTable, Log, lookup_class_name
+from .user_tables import Computed, Imported, Lookup, Manual, Part, _get_tier
+from .utils import to_camel_case, user_choice
 
 logger = logging.getLogger(__name__.split(".")[0])
 
@@ -482,8 +483,8 @@ class Schema:
         return [
             t
             for d, t in (
-                full_t.replace("`", "").split(".")
-                for full_t in self.connection.dependencies.topo_sort()
+                table_name.replace("`", "").split(".")
+                for table_name in self.connection.dependencies.topo_sort()
             )
             if d == self.database
         ]

datajoint/settings.py

@@ -1,14 +1,15 @@
 """
-Settings for DataJoint.
+Settings for DataJoint
 """
 
-from contextlib import contextmanager
+import collections
 import json
+import logging
 import os
 import pprint
-import logging
-import collections
+from contextlib import contextmanager
 from enum import Enum
+
 from .errors import DataJointError
 
 LOCALCONFIG = "dj_local_conf.json"
@@ -48,7 +49,8 @@ default = dict(
         "database.use_tls": None,
         "enable_python_native_blobs": True,  # python-native/dj0 encoding support
         "add_hidden_timestamp": False,
-        "filepath_checksum_size_limit": None,  # file size limit for when to disable checksums
+        # file size limit for when to disable checksums
+        "filepath_checksum_size_limit": None,
     }
 )
 
@@ -117,6 +119,7 @@ class Config(collections.abc.MutableMapping):
         if filename is None:
             filename = LOCALCONFIG
         with open(filename, "r") as fid:
+            logger.info(f"DataJoint is configured from {os.path.abspath(filename)}")
             self._conf.update(json.load(fid))
 
     def save_local(self, verbose=False):
@@ -236,7 +239,8 @@ class Config(collections.abc.MutableMapping):
 
         def __init__(self, *args, **kwargs):
             self._conf = dict(default)
-            self._conf.update(dict(*args, **kwargs))  # use the free update to set keys
+            # use the free update to set keys
+            self._conf.update(dict(*args, **kwargs))
 
         def __getitem__(self, key):
             return self._conf[key]
@@ -250,7 +254,9 @@ class Config(collections.abc.MutableMapping):
             valid_logging_levels = {"DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"}
             if key == "loglevel":
                 if value not in valid_logging_levels:
-                    raise ValueError(f"{'value'} is not a valid logging value")
+                    raise ValueError(
+                        f"'{value}' is not a valid logging value {tuple(valid_logging_levels)}"
+                    )
                 logger.setLevel(value)
 
 
@@ -260,11 +266,9 @@ config_files = (
     os.path.expanduser(n) for n in (LOCALCONFIG, os.path.join("~", GLOBALCONFIG))
 )
 try:
-    config_file = next(n for n in config_files if os.path.exists(n))
+    config.load(next(n for n in config_files if os.path.exists(n)))
 except StopIteration:
-    pass
-else:
-    config.load(config_file)
+    logger.info("No config file was found.")
 
 # override login credentials with environment variables
 mapping = {
@@ -292,6 +296,8 @@ mapping = {
     )
     if v is not None
 }
-config.update(mapping)
+if mapping:
+    logger.info(f"Overloaded settings {tuple(mapping)} from environment variables.")
+    config.update(mapping)
 
 logger.setLevel(log_levels[config["loglevel"]])

datajoint/table.py

@@ -1,30 +1,32 @@
 import collections
-import itertools
+import csv
 import inspect
-import platform
-import numpy as np
-import pandas
+import itertools
+import json
 import logging
-import uuid
-import csv
+import platform
 import re
-import json
+import uuid
 from pathlib import Path
-from .settings import config
-from .declare import declare, alter
-from .condition import make_condition
-from .expression import QueryExpression
+from typing import Union
+
+import numpy as np
+import pandas
+
 from . import blob
-from .utils import user_choice, get_master, is_camel_case
-from .heading import Heading
+from .condition import make_condition
+from .declare import alter, declare
 from .errors import (
-    DuplicateError,
     AccessError,
     DataJointError,
-    UnknownAttributeError,
+    DuplicateError,
     IntegrityError,
+    UnknownAttributeError,
 )
-from typing import Union
+from .expression import QueryExpression
+from .heading import Heading
+from .settings import config
+from .utils import get_master, is_camel_case, user_choice
 from .version import __version__ as version
 
 logger = logging.getLogger(__name__.split(".")[0])
@@ -135,7 +137,7 @@ class Table(QueryExpression):
         sql, external_stores = alter(self.definition, old_definition, context)
         if not sql:
             if prompt:
-                logger.warn("Nothing to alter.")
+                logger.warning("Nothing to alter.")
         else:
             sql = "ALTER TABLE {tab}\n\t".format(
                 tab=self.full_table_name
@@ -518,7 +520,13 @@ class Table(QueryExpression):
                 try:
                     delete_count = table.delete_quick(get_count=True)
                 except IntegrityError as error:
-                    match = foreign_key_error_regexp.match(error.args[0]).groupdict()
+                    match = foreign_key_error_regexp.match(error.args[0])
+                    if match is None:
+                        raise DataJointError(
+                            "Cascading deletes failed because the error message is missing foreign key information."
+                            "Make sure you have REFERENCES privilege to all dependent tables."
+                        ) from None
+                    match = match.groupdict()
                     # if schema name missing, use table
                     if "`.`" not in match["child"]:
                         match["child"] = "{}.{}".format(
@@ -641,7 +649,7 @@ class Table(QueryExpression):
         # Confirm and commit
         if delete_count == 0:
             if safemode:
-                logger.warn("Nothing to delete.")
+                logger.warning("Nothing to delete.")
             if transaction:
                 self.connection.cancel_transaction()
         elif not transaction:
@@ -651,12 +659,12 @@ class Table(QueryExpression):
                 if transaction:
                     self.connection.commit_transaction()
                 if safemode:
-                    logger.info("Deletes committed.")
+                    logger.info("Delete committed.")
             else:
                 if transaction:
                     self.connection.cancel_transaction()
                 if safemode:
-                    logger.warn("Deletes cancelled")
+                    logger.warning("Delete cancelled")
         return delete_count
 
     def drop_quick(self):
@@ -724,11 +732,6 @@ class Table(QueryExpression):
         ).fetchone()
         return ret["Data_length"] + ret["Index_length"]
 
-    def show_definition(self):
-        raise AttributeError(
-            "show_definition is deprecated. Use the describe method instead."
-        )
-
     def describe(self, context=None, printout=False):
         """
         :return:  the definition string for the query using DataJoint DDL.

datajoint/user_tables.py

@@ -3,10 +3,11 @@ Hosts the table tiers, user tables should be derived from.
 """
 
 import re
-from .table import Table
+
 from .autopopulate import AutoPopulate
-from .utils import from_camel_case, ClassProperty
 from .errors import DataJointError
+from .table import Table
+from .utils import ClassProperty, from_camel_case
 
 _base_regexp = r"[a-z][a-z0-9]*(_[a-z][a-z0-9]*)*"
 

datajoint/utils.py

@@ -1,8 +1,9 @@
 """General-purpose utilities"""
 
 import re
-from pathlib import Path
 import shutil
+from pathlib import Path
+
 from .errors import DataJointError
 
 
@@ -146,3 +147,5 @@ def parse_sql(filepath):
                     if line.endswith(delimiter):
                         yield " ".join(statement)
                         statement = []
+        if statement:
+            yield " ".join(statement)

datajoint/version.py

@@ -1,3 +1,6 @@
-__version__ = "0.14.3"
+# version bump auto managed by Github Actions:
+# label_prs.yaml(prep), release.yaml(bump), post_release.yaml(edit)
+# manually set this version will be eventually overwritten by the above actions
+__version__ = "0.14.5"
 
 assert len(__version__) <= 10  # The log table limits version to the 10 characters

{datajoint-0.14.3.dist-info → datajoint-0.14.5.dist-info}/METADATA

@@ -1,11 +1,11 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: datajoint
-Version: 0.14.3
-Summary: A relational data pipeline framework.
+Version: 0.14.5
+Summary: DataJoint for Python is a framework for scientific workflow management based on relational principles. DataJoint is built on the foundation of the relational data model and prescribes a consistent method for organizing, populating, computing, and querying data.
 Author: Raphael Guzman, Edgar Walker
 Author-email: Dimitri Yatsenko <dimitri@datajoint.com>, DataJoint Contributors <support@datajoint.com>
 Maintainer-email: Dimitri Yatsenko <dimitri@datajoint.com>, DataJoint Contributors <support@datajoint.com>
-License: GNU LESSER GENERAL PUBLIC LICENSE
+License:  GNU LESSER GENERAL PUBLIC LICENSE
                                Version 2.1, February 1999
         
          Copyright (C) 1991, 1999 Free Software Foundation, Inc.
@@ -510,55 +510,165 @@ License: GNU LESSER GENERAL PUBLIC LICENSE
         
         That's all there is to it!
         
-Project-URL: Homepage, https://datajoint.com/docs
-Project-URL: Documentation, https://datajoint.com/docs
+Project-URL: Homepage, https://docs.datajoint.com/
+Project-URL: Documentation, https://docs.datajoint.com/
 Project-URL: Repository, https://github.com/datajoint/datajoint-python
 Project-URL: Bug Tracker, https://github.com/datajoint/datajoint-python/issues
-Project-URL: Changelog, https://github.com/datajoint/datajoint-python/blob/master/CHANGELOG.md
-Keywords: database,data pipelines,scientific computing,automated research workflows
+Project-URL: Release Notes, https://github.com/datajoint/datajoint-python/releases
+Keywords: database,automated,automation,compute,data,pipeline,workflow,scientific,science,research,neuroscience,bioinformatics,bio-informatics,datajoint
 Classifier: Programming Language :: Python
-Requires-Python: <4.0,>=3.8
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: <4.0,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: numpy
-Requires-Dist: pymysql >=0.7.2
+Requires-Dist: pymysql>=0.7.2
+Requires-Dist: deepdiff
 Requires-Dist: pyparsing
 Requires-Dist: ipython
 Requires-Dist: pandas
 Requires-Dist: tqdm
 Requires-Dist: networkx
 Requires-Dist: pydot
-Requires-Dist: minio >=7.0.0
+Requires-Dist: minio>=7.0.0
 Requires-Dist: matplotlib
 Requires-Dist: otumat
 Requires-Dist: faker
 Requires-Dist: cryptography
 Requires-Dist: urllib3
+Requires-Dist: setuptools
 Provides-Extra: test
-Requires-Dist: pytest ; extra == 'test'
-Requires-Dist: pytest-cov ; extra == 'test'
-Requires-Dist: black ==24.2.0 ; extra == 'test'
-Requires-Dist: flake8 ; extra == 'test'
-
-[![DOI](https://zenodo.org/badge/16774/datajoint/datajoint-python.svg)](https://zenodo.org/badge/latestdoi/16774/datajoint/datajoint-python)
-[![Coverage Status](https://coveralls.io/repos/datajoint/datajoint-python/badge.svg?branch=master&service=github)](https://coveralls.io/github/datajoint/datajoint-python?branch=master)
-[![PyPI version](https://badge.fury.io/py/datajoint.svg)](http://badge.fury.io/py/datajoint)
-[![Slack](https://img.shields.io/badge/slack-chat-green.svg)](https://datajoint.slack.com/)
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: black==24.2.0; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: codespell; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Dynamic: license-file
 
 # Welcome to DataJoint for Python!
 
-DataJoint for Python is a framework for scientific workflow management based on 
-relational principles. DataJoint is built on the foundation of the relational data 
-model and prescribes a consistent method for organizing, populating, computing, and 
+<table>
+<!-- Thank Zarr for providing badge insights! -->
+<!-- https://github.com/zarr-developers/zarr-python/blob/main/README.md -->
+<tr>
+  <td>PyPI</td>
+  <td>
+    <a href="https://pypi.org/project/datajoint/">
+      <img src="https://img.shields.io/pypi/v/datajoint?color=blue" alt="pypi release" />
+    </a>
+    <br>
+    <a href="https://pypi.org/project/datajoint/">
+      <img src="https://img.shields.io/pypi/dm/datajoint?color=yellow" alt="pypi downloads" />
+    </a>
+  </td>
+</tr>
+<tr>
+  <td>Conda Forge</td>
+  <td>
+    <a href="https://anaconda.org/conda-forge/datajoint">
+      <img src="https://img.shields.io/conda/vn/conda-forge/datajoint?color=brightgreen" alt="conda-forge release" />
+    </a>
+    <br>
+    <a href="https://anaconda.org/conda-forge/datajoint">
+      <img src="https://img.shields.io/conda/dn/conda-forge/datajoint?color=brightgreen" alt="conda-forge downloads" />
+    </a>
+  </td>
+</tr>
+<tr>
+  <td>Since Release</td>
+  <td>
+    <a id="commit-since-release-link" href="https://github.com/datajoint/datajoint-python/compare/v0.14.5...master">
+      <img id="commit-since-release-img" src="https://img.shields.io/github/commits-since/datajoint/datajoint-python/v0.14.5?color=red" alt="commit since last release" />
+    </a>
+  </td>
+</tr>
+<tr>
+  <td>Test Status</td>
+  <td>
+    <a href="https://github.com/datajoint/datajoint-python/actions/workflows/test.yaml">
+      <img src="https://github.com/datajoint/datajoint-python/actions/workflows/test.yaml/badge.svg" alt="test status" />
+    </a>
+  </td>
+</tr>
+<tr>
+  <td>Release Status</td>
+  <td>
+    <a href="https://github.com/datajoint/datajoint-python/actions/workflows/post_draft_release_published.yaml">
+      <img src="https://github.com/datajoint/datajoint-python/actions/workflows/post_draft_release_published.yaml/badge.svg" alt="release status" />
+    </a>
+  </td>
+</tr>
+<tr>
+  <td>Doc Status</td>
+  <td>
+    <a href="https://docs.datajoint.com">
+      <img src="https://github.com/datajoint/datajoint-python/actions/workflows/pages/pages-build-deployment/badge.svg" alt="doc status" />
+    </a>
+  </td>
+</tr>
+<tr>
+  <td>Coverage</td>
+  <td>
+    <a href="https://coveralls.io/github/datajoint/datajoint-python?branch=master">
+      <img src="https://coveralls.io/repos/datajoint/datajoint-python/badge.svg?branch=master&service=github"/ alt="coverage">
+    </a>
+  </td>
+</tr>
+<tr>
+ <td>Developer Chat</td>
+ <td>
+  <a href="https://datajoint.slack.com/">
+      <img src="https://img.shields.io/badge/slack-datajoint-purple.svg" alt="datajoint slack"/>
+  </a>
+ </td>
+</tr>
+<tr>
+  <td>License</td>
+  <td>
+    <a href="https://github.com/datajoint/datajoint-python/blob/master/LICENSE.txt">
+      <img src="https://img.shields.io/github/license/datajoint/datajoint-python" alt="LGPL-2.1" />
+    </a>
+  </td>
+</tr>
+<tr>
+ <td>Citation</td>
+ <td>
+  <a href="https://doi.org/10.1101/031658">
+   <img src="https://img.shields.io/badge/DOI-10.1101/bioRxiv.031658-B31B1B.svg" alt="bioRxiv">
+  </a>
+    <br>
+    <a href="https://doi.org/10.5281/zenodo.6829062">
+      <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.6829062.svg" alt="zenodo">
+  </a>
+ </td>
+</tr>
+
+</table>
+
+DataJoint for Python is a framework for scientific workflow management based on
+relational principles. DataJoint is built on the foundation of the relational data
+model and prescribes a consistent method for organizing, populating, computing, and
 querying data.
 
-DataJoint was initially developed in 2009 by Dimitri Yatsenko in Andreas Tolias' Lab at 
-Baylor College of Medicine for the distributed processing and management of large 
-volumes of data streaming from regular experiments. Starting in 2011, DataJoint has 
-been available as an open-source project adopted by other labs and improved through 
+DataJoint was initially developed in 2009 by Dimitri Yatsenko in Andreas Tolias' Lab at
+Baylor College of Medicine for the distributed processing and management of large
+volumes of data streaming from regular experiments. Starting in 2011, DataJoint has
+been available as an open-source project adopted by other labs and improved through
 contributions from several developers.
-Presently, the primary developer of DataJoint open-source software is the company 
-DataJoint (https://datajoint.com).
+Presently, the primary developer of DataJoint open-source software is the company
+DataJoint (<https://datajoint.com>).
 
 ## Data Pipeline Example
 
@@ -580,13 +690,13 @@ DataJoint (https://datajoint.com).
      pip install datajoint
      ```
 
-- [Documentation & Tutorials](https://datajoint.com/docs/core/datajoint-python/)
+- [Documentation & Tutorials](https://docs.datajoint.com/core/datajoint-python/)
 
 - [Interactive Tutorials](https://github.com/datajoint/datajoint-tutorials) on GitHub Codespaces
 
-- [DataJoint Elements](https://datajoint.com/docs/elements/) - Catalog of example pipelines for neuroscience experiments
+- [DataJoint Elements](https://docs.datajoint.com/elements/) - Catalog of example pipelines for neuroscience experiments
 
 - Contribute
-  - [Development Environment](https://datajoint.com/docs/core/datajoint-python/latest/develop/)
+  - [Contribution Guidelines](https://docs.datajoint.com/about/contribute/)
 
-  - [Guidelines](https://datajoint.com/docs/about/contribute/)
+  - [Developer Guide](https://docs.datajoint.com/core/datajoint-python/latest/develop/)

datajoint-0.14.5.dist-info/RECORD

@@ -0,0 +1,34 @@
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+datajoint/utils.py,sha256=m-tnRa65dkwdCV6qqUG7kYHsIaFJGPSVr22QpHzeCZc,4576
+datajoint/version.py,sha256=0J3S_RIdt9bVt0MteMQlEy0auezr5cWmUqFiP90qpzw,302
+datajoint-0.14.5.dist-info/licenses/LICENSE.txt,sha256=7VXUyqv9idbgJNkr3OFy0vfuSqZa3JHmC2TpSavBpss,26444
+datajoint-0.14.5.dist-info/METADATA,sha256=vnpbGSX4jahjFspaxbLoq972sKd5qKxi4hl_r_iU5UA,37822
+datajoint-0.14.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+datajoint-0.14.5.dist-info/entry_points.txt,sha256=RLoyQD_Hz9HdlKG-ei0SlHDxuaTpasDJ6gZcvj9iZG0,71
+datajoint-0.14.5.dist-info/top_level.txt,sha256=GLPeIbF_-lu3lpcSazCl0KUco1v2rr5uyUvieYAniLU,10
+datajoint-0.14.5.dist-info/RECORD,,

{datajoint-0.14.3.dist-info → datajoint-0.14.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

datajoint-0.14.3.dist-info/RECORD

@@ -1,34 +0,0 @@
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-datajoint/condition.py,sha256=KzeVfbCSfb0FUL04-pdbdsIvP_tt1R85W-wb8MmJzgs,11848
-datajoint/connection.py,sha256=CXQeGob99CI92ZSkhmu29-eGBTGxtNDD8Y-ZH6HOYJk,15869
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