Bug: conda-forge Python 3.13 | ModuleNotFoundError: No module named 'pkg_resources'

[drewyangdev]

Bug Report

Description

While working with conda-forge release, I found the datajoint-feedtest test would fail for me on python 3.13

python -c 'import datajoint as dj; assert dj.diagram.diagram_active'
# ModuleNotFoundError: No module named 'pkg_resources'

Reproducibility

Include:

• OS (Linux)
• Python Version 3.13
• DataJoint Version Unreleased 3e39771
• Minimum number of steps to reliably reproduce the issue

which conda
# /home/drewyang/miniconda3/condabin/conda
conda --version
# conda 25.1.1
conda create -n dj313 -c conda-forge python=3.13 # installed from conda-forge instead of the defaults channel 'conda-forge/linux-64::python-3.13.2-hf636f53_101_cp313'
conda activate dj313
# cd <datajoint-python repo>
git checkout 3e3977147aedcef735561427664a4c7a81d3862f # latest master as of 20250320
pip install -e .
python -c 'import datajoint as dj; assert dj.diagram.diagram_active'

• Complete error stack as a result of evaluating the above steps

Traceback (most recent call last):
  File "<string>", line 1, in <module>
    import datajoint as dj; assert dj.diagram.diagram_active
    ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/drewyang/Documents/DataJoint/datajoint-python/datajoint/__init__.py", line 59, in <module>
    from .admin import kill, set_password
  File "/home/drewyang/Documents/DataJoint/datajoint-python/datajoint/admin.py", line 7, in <module>
    from .connection import conn
  File "/home/drewyang/Documents/DataJoint/datajoint-python/datajoint/connection.py", line 19, in <module>
    from .plugin import connection_plugins
  File "/home/drewyang/Documents/DataJoint/datajoint-python/datajoint/plugin.py", line 4, in <module>
    import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'

Expected Behavior

which conda
# /home/drewyang/miniconda3/condabin/conda
conda --version
# conda 25.1.1
conda create -n dj312 -c conda-forge python=3.12 # installed from conda-forge instead of the defaults channel 'conda-forge/linux-64::python-3.13.2-hf636f53_101_cp313'
conda activate dj312
# cd <datajoint-python repo>
git checkout 3e3977147aedcef735561427664a4c7a81d3862f # latest main as of 20250320
pip install -e .
python -c 'import datajoint as dj; assert dj.diagram.diagram_active'

# No output or error

Additional Research and Context

setuptools isn't a default dependency of Python 3.13 anymore, suggest to add to the pyproject.toml.
However, I also tried the same on Mac, which installed the conda default channel's python 3.13 for osx-64, it does include setuptools, which didn't cause the same issue.

I suggest we explicitly include setuptools in pyproject.yaml as a dependency(not a build dependency, but a package dependency)

Also setuptools.pkg_resources will be deprecated.

Use of pkg_resources is deprecated in favor of importlib.resources, importlib.metadata and their backports (importlib_resources, importlib_metadata). Some useful APIs are also provided by packaging (e.g. requirements and version parsing). Users should refrain from new usage of pkg_resources and should work to port to importlib-based solutions.

[timonmerk]

I still get the issue installing the package using pip:

In [2]: import datajoint

ModuleNotFoundError Traceback (most recent call last)
Cell In[2], line 1
----> 1 import datajoint

File ~/Documents/datajoint_playground/.venv/lib/python3.12/site-packages/datajoint/init.py:61
59 from .version import version
60 from .settings import config
---> 61 from .connection import conn, Connection
62 from .schemas import Schema
63 from .schemas import VirtualModule, list_schemas

File ~/Documents/datajoint_playground/.venv/lib/python3.12/site-packages/datajoint/connection.py:19
17 from .blob import pack, unpack
18 from .hash import uuid_from_buffer
---> 19 from .plugin import connection_plugins
21 logger = logging.getLogger(name.split(".")[0])
22 query_log_max_length = 300

File ~/Documents/datajoint_playground/.venv/lib/python3.12/site-packages/datajoint/plugin.py:2
1 from .settings import config
----> 2 import pkg_resources
3 from pathlib import Path
4 from cryptography.exceptions import InvalidSignature

ModuleNotFoundError: No module named 'pkg_resources'