intermine314 0.1.1

Modernized InterMine WebService client (Python 3.14+)

intermine314

Python 3.14+ client for InterMine web services.

This package modernizes the historical InterMine Python client for current Python runtimes, with a focus on practical reliability for research use.

Ownership and Credit

Copyright (c) 2026 Monash University, Plant Energy and Biotechnology Lab.

Project ownership and stewardship:

• Kris Kari
• Dr. Maria Ermakova
• Plant Energy and Biotechnology Lab, Monash University
• Contact: [e-mail]

Original credit:

• The original InterMine team and community contributors are credited for foundational work that this package builds upon.

License

Licensed under the MIT License (see LICENSE-LGPL, which now contains the active MIT license text and notice).

Requirements

• Python 3.14+

Supported Mines

Priority support is focused on:

• MaizeMine
• ThaleMine
• LegumeMine
• OakMine
• WheatMine

Installation

pip install intermine314

Repository: https://github.com/kriskari/intermine314

Quick Example

from intermine314.webservice import Service

service = Service("https://www.flymine.org/query/service")
query = service.new_query("Gene")
query.add_view("Gene.symbol", "Gene.length")

for row in query.run_parallel(page_size=2000, max_workers=16, prefetch=16):
    print(row)

Parallel Worker Defaults

intermine314 defaults parallel query workflows to 16 workers.

You can tune this per query based on your hardware and network:

• Smaller machines or constrained environments: use 4 to 8.
• High-core desktops/workstations with stable network: use 16 to 32.
• If remote endpoints rate-limit aggressively, lower workers to reduce retries/timeouts.

rows = query.run_parallel(
    row="dict",
    page_size=2000,
    max_workers=16,  # override per machine/workload
    prefetch=16,     # typically match max_workers
)

Testing

Run unit tests against the local mock service:

python setup.py test

Run live tests:

python setup.py livetest

Upgrades for Python 3.14

The following package upgrades were applied in this modernization cycle:

• Raised runtime baseline to Python 3.14 (pyproject.toml, README.md, CI, tox).
• Updated packaging metadata toward modern PEP 621 layout.
• Simplified dependency management (requirements.txt, optional extras in pyproject.toml).
• Removed Python 2 compatibility remnants from runtime modules.
• Removed Python 2 compatibility remnants from tests.
• Modernized query parallel execution behavior in intermine314/query.py:
  • bounded in-flight work
  • configurable prefetch
  • fixed edge handling for start and size=None
  • used executor.map(..., buffersize=...) for ordered mode
• Updated CI configuration for Python 3.14.
• Verified local unit test suite and live mine connectivity checks.

Notes

Documentation/tutorial links from legacy upstream sources are intentionally omitted for now while docs are being updated for the Python 3.14 package line.