OpenVariant | New feature Multiple fields for a single plugin

[dmartmillan]

Be able to create plugins that modify multiple fields, added along with a small example and documentation explaining the use case.

The main change is how Annotation (annotation._annotation) is stored:

Previous version (each plugin has its individual field):

{
'TYPE': ('PLUGIN', ....), 
'POSITION': ('PLUGIN', ....), 
'VARIANT': ('PLUGIN', ....), 
'HGVS': ('INTERNAL',, ....)
}

Now (a tuple is created as a key, it encompass multiple fields to a unique plugin function):

{
('TYPE', 'POSITION', 'VARIANT'): ('PLUGIN', ....), 
'HGVS': ('INTERNAL', ....)
}

With this simple change, we can distinguish which fields are grouped under each plugin. This makes parsing straightforward, as we know which plugin function to execute and which fields it should apply to.
In the first example, the plugin is executed three times in separate processes; now, it runs just once for multiple fields.

The filedSource was discarted because the field from inputs can be used as follow (and being access by the plugin):

annotation:
- type: plugin
  plugin: HGVS_decoder
  field: 
  - TYPE
  - POSITION
  - VARIANT
- type: internal
  field: HGVS
  fieldSource:
  - 'HGVS Consequence'
  - HGVSp

[dmartmillan]

Not merge yet!
Need to add more docs info and fix a bug on the plugin example.

[dmartmillan]

Ready!

[Copilot]

Pull Request Overview

This PR introduces support for plugins that target multiple output fields in a single invocation by keying plugins on tuples of field names and updating parsing, annotation loading, and documentation accordingly.

• Key changes:
  • Annotation storage now uses tuple keys for multi‐field plugins and updates header extraction and parsing in variant.py.
  • Annotation loader in annotation.py now accepts list‐style field declarations and normalizes into tuple keys.
  • Examples and documentation expanded to show multi‐field plugin usage and fixed sample notebooks/READMEs.

Reviewed Changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
openvariant/variant/variant.py	Updated header and parser logic to unpack tuple‐keyed plugins.
openvariant/annotation/annotation.py	Accept list fields, normalize keys, and verify columns.
examples/plugin_system/HGVS_decoder/init.py	Added example init for multi‐field plugin (syntax needs fix).
examples/plugin_system/README.md	Updated README with new plugins section (spelling error).
docs/user_guide/annotation_structure.rst	Expanded docs for multi‐field plugin (duplicate word issue).

Comments suppressed due to low confidence (2)

examples/plugin_system/HGVS_decoder/init.py:1

• This import syntax is invalid; change to from .multi_test import Multi_testPlugin to correctly import the plugin class.

import .multi_test from Multi_testPlugin

docs/examples/plugin_system/HGVS_decoder/init.py:1

• Invalid import syntax in docs example; update to from .multi_test import Multi_testPlugin to match real code.

import .multi_test from Multi_testPlugin

[dmartmillan]

Can we merge it? or it needs revision?

[FedericaBrando]

Hi David, it still needs revision and testing. We've been quite busy lately.