datajoint 0.14.3__tar.gz → 0.14.5__tar.gz

{datajoint-0.14.3 → datajoint-0.14.5}/PKG-INFO

@@ -1,7 +1,7 @@
-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>
@@ -510,18 +510,27 @@ 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: deepdiff
 Requires-Dist: pyparsing
 Requires-Dist: ipython
 Requires-Dist: pandas
@@ -534,31 +543,132 @@ 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/)
+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/README.md

@@ -0,0 +1,143 @@
+# Welcome to DataJoint for Python!
+
+<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
+contributions from several developers.
+Presently, the primary developer of DataJoint open-source software is the company
+DataJoint (<https://datajoint.com>).
+
+## Data Pipeline Example
+
+![pipeline](https://raw.githubusercontent.com/datajoint/datajoint-python/master/images/pipeline.png)
+
+[Yatsenko et al., bioRxiv 2021](https://doi.org/10.1101/2021.03.30.437358)
+
+## Getting Started
+
+- Install with Conda
+
+     ```bash
+     conda install -c conda-forge datajoint
+     ```
+
+- Install with pip
+
+     ```bash
+     pip install datajoint
+     ```
+
+- [Documentation & Tutorials](https://docs.datajoint.com/core/datajoint-python/)
+
+- [Interactive Tutorials](https://github.com/datajoint/datajoint-tutorials) on GitHub Codespaces
+
+- [DataJoint Elements](https://docs.datajoint.com/elements/) - Catalog of example pipelines for neuroscience experiments
+
+- Contribute
+  - [Contribution Guidelines](https://docs.datajoint.com/about/contribute/)
+
+  - [Developer Guide](https://docs.datajoint.com/core/datajoint-python/latest/develop/)

{datajoint-0.14.3 → datajoint-0.14.5}/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-0.14.3 → datajoint-0.14.5}/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-0.14.3 → datajoint-0.14.5}/datajoint/attribute_adapter.py

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

{datajoint-0.14.3 → datajoint-0.14.5}/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-0.14.3 → datajoint-0.14.5}/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-0.14.3 → datajoint-0.14.5}/datajoint/cli.py

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