fix(server): apply default_instruction in the remaining flash embedders

[svonava]

Problem

This is a follow-up to #621, which fixed Qwen2FlashAdapter. The other flash embedding adapters that format texts with the shared extract_texts helper also never read the default_instruction runtime option. A query with no explicit instruction is formatted with an empty instruction slot.

User impact

NovaSearch/stella_en_400M_v5 is served by RoPEFlashAdapter and configures both a query template and a default instruction. On CUDA, its queries were embedded as:

Instruct: 
Query: what is sie?

instead of

Instruct: Given a web search query, retrieve relevant passages that answer the query.
Query: what is sie?

The CPU fallback (SentenceTransformerDenseAdapter) already applied the default, so the same model embedded queries differently on CPU and on CUDA.

BertFlashAdapter, ModernBERTFlashAdapter, NomicFlashAdapter, GTESparseFlashAdapter and SPLADEFlashAdapter have the same gap. No shipped model config sets default_instruction for them today, but a custom config that sets one would be silently ignored.

Fix

• Add _utils.resolve_query_instruction(instruction, options, *, is_query). It returns the request instruction when one is given; an explicit "" counts as given. When the request gives none, queries get the default_instruction runtime option and documents get nothing. The rule matches XLMRobertaFlashAdapter, SentenceTransformerDenseAdapter and fix(server): apply default_instruction to qwen2_flash queries #621.
• Pass the resolved instruction to extract_texts in RoPEFlashAdapter, BertFlashAdapter, ModernBERTFlashAdapter, NomicFlashAdapter, GTESparseFlashAdapter and SPLADEFlashAdapter.
• Switch Qwen2FlashAdapter from its inline check (fix(server): apply default_instruction to qwen2_flash queries #621) to the same helper. Its behaviour does not change, and it joins the parametrized tests.

For every shipped model config, only stella_en_400M_v5 changes behaviour, because none of the other configs on these adapters sets default_instruction. Documents are unchanged everywhere.

Adapters reviewed and left unchanged

These adapters do not format query text with an {instruction} template, so a default instruction has nothing to fill. No shipped config sets default_instruction for any of them:

• ColBERTAdapter, ColBERTModernBERTFlashAdapter and ColBERTRotaryFlashAdapter use fixed query and document prefixes in their own _extract_texts, and prepend only an explicit instruction.
• The BGE-M3 adapters (bge_m3, bge_m3_flash, bge_m3_flag) prepend only an explicit instruction.
• TopkEmbedAdapter rejects instructions; it applies its own fixed templates.
• The vision and multimodal embedders (CLIP, SigLIP, ColPali, ColQwen, ColSmol, NeMo ColEmbed, st_sparse_vision) take no query template.
• The remote SIE adapter forwards the request; the remote server applies its own defaults.
• XLMRobertaFlashAdapter, SentenceTransformerDenseAdapter, PyTorchEmbeddingAdapter, SGLangEmbeddingAdapter, Qwen3VLEmbeddingAdapter and the Candle worker already apply default_instruction.

Tests

The new file packages/sie_server/tests/adapters/test_flash_default_instruction.py runs on CPU and loads no models. Each adapter is stopped right after it formats its texts, and the test checks the exact strings it would tokenize. The cases are parametrized over the six adapters above and Qwen2FlashAdapter:

• A query uses the default instruction.
• An explicit instruction wins.
• An explicit "" is kept.
• A document gets no default, even with an {instruction} doc template.
• A query with a template but no default keeps the previous empty slot.

Two more tests cover the shipped config and the helper:

• A stella_en_400M_v5 query, with options built from the shipped YAML through merge_runtime_options, gets the profile instruction.
• Unit cases for resolve_query_instruction.

Before the adapter changes, the default-instruction cases fail for every adapter. All pass with the fix.

Validation

• mise run lint: passed
• mise run typecheck: passed
• mise run test: 12654 passed, 564 skipped, 5 failed. The 5 failures are the same macOS-local PermissionErrors in config/test_serving_artifacts.py and core/test_model_loader_cache.py noted in fix(server): apply default_instruction to qwen2_flash queries #621, and they are unrelated. After rebasing on fix(server): apply default_instruction to qwen2_flash queries #621 and switching qwen2_flash to the helper, mise run test -- packages/sie_server/tests/adapters/ gives 4585 passed, 57 skipped.

Compatibility

No public API, wire or config changes. Query embeddings change only where a profile or request sets default_instruction; for shipped models that is stella_en_400M_v5 on CUDA. Document embeddings and indexes are unaffected.

Summary by CodeRabbit

• New Features
  • Queries can use a configured default instruction when no instruction is provided. Explicit instructions, including an empty instruction, are preserved.
• Bug Fixes
  • Document encoding remains separate from query defaults, so configured query instructions aren’t applied to documents.
• Tests
  • Added coverage for default and explicit instructions across supported adapters, including model-profile behavior.

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📝 Walkthrough

Walkthrough

A shared helper resolves query instructions for seven flash adapters. Explicit instructions take precedence, including empty strings. When no instruction is supplied, queries use the configured default; documents do not.

Changes

Query instruction defaults

Layer / File(s)	Summary
Instruction resolution packages/sie_server/src/sie_server/adapters/_utils.py, packages/sie_server/tests/adapters/test_flash_default_instruction.py	Added resolve_query_instruction to select an explicit instruction, a query’s default_instruction, or no instruction. Tests cover explicit values, empty strings, document inputs, and missing defaults.
Flash adapter integration packages/sie_server/src/sie_server/adapters/{bert_flash,gte_sparse_flash,modernbert_flash,nomic_flash,qwen2_flash,rope_flash,splade_flash}/..., packages/sie_server/tests/adapters/test_flash_default_instruction.py	Seven adapters use the resolver before extracting text. Tests check query and document formatting, explicit instructions, missing defaults, and the Stella 400M profile.

Suggested reviewers: dragosboca

Priority: ➖ Normal

Merge Risk: 🔵 Low · up to 16347

The change fixes query formatting for the Stella profile and looks safe to merge. The remaining note about keeping package initializers empty is a maintainability follow-up, not a behavior risk.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 42.11% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 19 functions across 9 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly identifies the main change: applying default_instruction to the remaining flash embedders. It is concise and specific.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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Inline comments:
Review comments at
@packages/sie_server/src/sie_server/adapters/rope_flash/__init__.py:
- Line 17: Move the adapter implementations out of the six non-empty package
initializers and leave each initializer empty. For rope_flash (lines 17–17),
move the RoPE implementation and update the Stella adapter path; for bert_flash
(lines 33–33), gte_sparse_flash (lines 16–16), modernbert_flash (lines 28–28),
nomic_flash (lines 18–18), and qwen2_flash (lines 18–18), move each
implementation to a regular module and update its entrypoints to import from
that module.

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📥 Commits

Reviewing files that changed from the base of the PR and between db4c0a8 and 1634727.

📒 Files selected for processing (9)

• packages/sie_server/src/sie_server/adapters/_utils.py
• packages/sie_server/src/sie_server/adapters/bert_flash/__init__.py
• packages/sie_server/src/sie_server/adapters/gte_sparse_flash/__init__.py
• packages/sie_server/src/sie_server/adapters/modernbert_flash/__init__.py
• packages/sie_server/src/sie_server/adapters/nomic_flash/__init__.py
• packages/sie_server/src/sie_server/adapters/qwen2_flash/__init__.py
• packages/sie_server/src/sie_server/adapters/rope_flash/__init__.py
• packages/sie_server/src/sie_server/adapters/splade_flash/adapter.py
• packages/sie_server/tests/adapters/test_flash_default_instruction.py

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