[arthurmccray]

Move to electronmicroscopy: rename, config, stores, weights, contribution tooling

Branch rename -> main. Version 0.5.0.dev0. Breaking, pre-1.0.

Rename

• Package, distribution and repo are all emdatabase. import em_database no longer works.
• datasets/ (the YAML index) is index/ and is not an importable package.
• _build_docs.py moved out of the package into docs/source/; doc/ is docs/.
• Links point at electronmicroscopy/emdatabase.

Config

• Dask-style config replaces Settings: emdatabase.config.get/set/write, ~/.config/emdatabase/*.yaml (or $EMDATABASE_CONFIG), EMDATABASE_* env vars with __ nesting. Precedence: shipped defaults < files < env < set.
• Removed: settings, save(), reset(), get_setting/set_setting, EM_DATABASE_* env vars, the /etc system file, the settings widget. set_data_dir(path) no longer takes persist=; use config.write().
• Default data directory is pooch.os_cache("emdatabase"), with a one-time notice on first run.
• Named stores: stores: {group: /path} are searched before data_dir; a copy found in a store reports the store name as its location.

Model weights

• Entries carry kind (dataset or weights, always written), version, and for weights a model block (class, framework, quantem). Schema enforces model on weights only.
• list_weights(), filter(kind=...), a Model Weights docs page, widget badge.
• First entry: TutorialUNet_v1 (the U-Net from neural_networks_02_unet.ipynb).
• Optional url field for download links that are not source/file (Google Drive).

Contributing

• One validator (metadata.validate_document) used by the tests, the issue action, the CLI and (via node) the web form.
• index/TEMPLATE.yaml; python -m emdatabase.new_dataset URL fetches size and checksum, prompts for metadata, validates and writes the file; --validate PATH.
• Web form and issue form cover every schema field including weights and url. Issue workflow: trigger checked the body for the label name and never fired; body is now passed through an env var rather than shell interpolation.
• docs/contributing.rst, root CONTRIBUTING.md.

Tests

239 passed, 25 deselected (20 network, 5 slow). Sphinx build clean with -W.

Not in this PR

• Release: tag 0.5.0, PyPI, Pages source switched to gh-pages.
• Polymer peak-detection weights entry (waiting on the Zenodo version with a separate .pt).
• Other tutorials pulling example data from emdatabase.

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