biomero-dev

name	biomero-dev
description	BIOMERO core library (pylib) development runbook for the surf branch. Use when changing biomero/slurm_client.py or related modules, adding or migrating a config option, writing or running pytest tests, following TDD, or building the Sphinx docs. Covers the config precedence pattern (code default -> ini -> env), the existing pytest fixture style, the venvTest test runner, and the docs build.

BIOMERO Core Development

Use this skill for development work on the BIOMERO Python library in this repo (biomero/), especially biomero/slurm_client.py. Favor matching existing conventions over inventing new ones: read the surrounding code, mirror the nearest existing example, then make the smallest change that is correct and backward compatible.

Backward compatibility is a hard requirement. Every new option must default to the current behavior so existing deployments are byte-for-byte unaffected unless they opt in.

Environment

Tests and docs run from the repo-local venvTest. Run everything from this repository's root (the folder containing this .agents directory). The terminal cwd can reset between calls, so re-set it to the repo root first if needed (PowerShell):

# from the repo root
.\venvTest\Scripts\python.exe -m pytest tests/unit/test_slurm_client.py -q

Reference Routing

Read only the relevant reference before acting:

• references/testing.md: pytest fixture style, the factory fixtures, TDD red/green discipline, the exact-kwargs test_from_config guard, and how to run a narrow vs full slice.
• references/config-pattern.md: the _get_config_value() precedence helper and the full checklist of touch points for adding or migrating a config option.
• references/docs.md: every place a setting must be documented (sample ini, both Sphinx rst files, deployment inis, and the OMERO.biomero admin UI), the cross-surface consistency checklist, and how to build the Sphinx site.

Core Rules

• New config follows the precedence pattern: code default -> slurm-config.ini -> environment variable, resolved by _get_config_value(). Never hand-roll os.getenv precedence in from_config().
• A new constructor parameter on SlurmClient requires updating the exact-kwargs assertion in test_from_config (it asserts the full call to the constructor).
• TDD means writing tests that FAIL first, then implementing until they pass. If you batch the implementation with the tests, prove the tests are meaningful by temporarily disabling the new code and observing the red, then restore.
• Keep pep8/line-length style consistent with the file you edit; the module already carries many pre-existing long-line lints, so do not reflow unrelated code.
• Any change to an ini setting (new option, migration, or a change to its scope/precedence/meaning) is not done until every documentation and config surface is updated to match: the sample resources/slurm-config.ini, both Sphinx docs (slurm-configuration.rst, configuration-reference.rst), the deployment inis (e.g. NL-BIOMERO/web/slurm-config.ini), and the OMERO.biomero admin UI (SettingsForm.js) when the setting is editable there. See references/docs.md for the full cross-surface checklist.