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1a17418 c3b49d6 1a17418 7177af3 49f5c84 7177af3 49f5c84 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 | """
Constants for CodeAct agent.
"""
import os
# Available packages with descriptions
LIBRARY_CONTENT_DICT = {
"numpy": "[Python Package] The fundamental package for scientific computing with Python, providing support for arrays, matrices, and mathematical functions.",
"scipy": "[Python Package] A Python library for scientific and technical computing, including modules for optimization, linear algebra, integration, and statistics.",
}
def _load_system_prompt() -> str:
"""Load the system prompt template from prompts.yaml at the project root."""
import yaml
# core/constants.py lives at <root>/core/ (before move) or <root>/src/core/ (after move).
# Two or three levels up is the project root in both cases.
here = os.path.dirname(os.path.abspath(__file__))
for levels in (1, 2):
candidate = os.path.normpath(os.path.join(here, *[".."] * levels, "prompts.yaml"))
if os.path.exists(candidate):
with open(candidate, encoding="utf-8") as f:
data = yaml.safe_load(f)
return data["system_prompt"]
raise FileNotFoundError("prompts.yaml not found relative to core/constants.py")
SYSTEM_PROMPT_TEMPLATE = _load_system_prompt()
# Standing decoupleR method limitations.
#
# This block is true of EVERY decoupleR run, so it is appended deterministically
# in code to the final solution — it is NOT generated by the model. The model is
# instructed (see prompts.yaml, Example 6 / Reporting Results) to write only
# run-specific caveats (sample sizes, contrast, exclusions). Keeping the standing
# text here guarantees it is byte-for-byte identical on every run and can never be
# softened or dropped.
#
# If the computation changes (PROGENy pathway count, default scoring model, or
# regulon source), update this text to match — it must describe what the pipeline
# actually does.
# The trailing half is identical on every path; only the sentence describing
# *what was scored* differs (see below).
_DISCLAIMER_TAIL = (
"ULM p-values are liberal and scale "
"with regulon size, so rank results by effect size rather than by how small "
"padj is. PROGENy: 14-pathway model. Regulons: CollecTRI. These outputs "
"require independent validation before any biological or clinical conclusion."
)
_DISCLAIMER_HEAD = "**Method limitations (decoupleR).** All TF and pathway values are *inferred* "
# Path-neutral wording. This is the block the workflow engine appends to every
# <solution>, where the scoring path taken during the run is not known — so it
# must be true of BOTH paths. Do not re-add the "derived from
# differential-expression statistics" clause here: that is false for the
# per-sample path (dataset_score_bulk_samples scores the expression matrix
# directly, without computing DE statistics first).
DECOUPLER_DISCLAIMER = (
_DISCLAIMER_HEAD + "regulon/gene-set activities — not direct measurements of "
"protein activity, nuclear localization, or pathway flux. " + _DISCLAIMER_TAIL
)
# DE-based enrichment tools (decoupler_tf_enrichment_collectri,
# decoupler_pathway_enrichment_progeny, decoupler_hallmark_enrichment): the ULM
# fit is over per-contrast DE statistics, so scores are contrast-level.
DECOUPLER_DISCLAIMER_DE = (
_DISCLAIMER_HEAD + "regulon/gene-set activities derived from "
"differential-expression statistics via the ULM model — not direct measurements "
"of protein activity, nuclear localization, or pathway flux. " + _DISCLAIMER_TAIL
)
# Per-sample scoring path (dataset_score_bulk_samples / dataset_score_signature):
# the ULM fit is over the normalised expression matrix itself, so scores are
# per-sample and relative to the rest of the cohort — there is no contrast.
DECOUPLER_DISCLAIMER_PER_SAMPLE = (
_DISCLAIMER_HEAD + "regulon/gene-set activities scored directly from the "
"normalised expression matrix (no differential-expression step) — not direct "
"measurements of protein activity, nuclear localization, or pathway flux. "
"Per-sample scores are relative to the rest of the scored cohort, so they are "
"comparable across samples within this run but not across runs or datasets. " + _DISCLAIMER_TAIL
)
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