docs: add config file for PR agent

[BioGeek]

PR Type

Enhancement

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Description

• Add .pr_agent.toml config file

• Configure GitHub App PR triggers

• Define default PR agent commands

• Enable original user description

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Changes walkthrough 📝

	Relevant files
Configuration changes	.pr_agent.toml Add PR agent configuration                                                              .pr_agent.toml Created new config file for PR agent Set handle_pr_actions for PR events Specified default pr_commands Enabled add_original_user_description +10/-0

---

Need help?

Type /help how to ... in the comments thread for any questions about PR-Agent usage.

Check out the documentation for more information.

[BioGeek]

/describe

[instadeep-pr-agent]

PR Description updated to latest commit (b33bc31)

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
__init__.py	0	0	100%
constants.py	8	0	100%
data_types.py	4	0	100%
calibration
__init__.py	0	0	100%
calibration_features.py	263	11	95%	163–164, 317–319, 546–548, 997–999
calibrator.py	84	10	88%	69–70, 95–96, 98, 123–124, 128, 155–156
datasets
__init__.py	0	0	100%
calibration_dataset.py	80	11	86%	184, 186–187, 193–196, 198–201
data_loaders.py	190	190	0%	7–11, 13–17, 19–20, 24, 27, 30–31, 42, 44, 49, 54, 56–57, 67, 70–71, 73–74, 79, 85–86, 95, 98, 108, 113–114, 124, 129–131, 133, 137–138, 140–141, 146, 149, 156, 162, 164–165, 174, 176–179, 181, 185–186, 188, 190, 192–193, 204–206, 215, 217–218, 230, 236, 245–246, 250, 252–253, 263–264, 267, 270–271, 278, 287, 289, 305–306, 308–310, 312–314, 316–317, 319, 322, 346, 357–358, 364–365, 374–375, 377–378, 387–388, 390–393, 395, 399–400, 402, 404, 420–421, 423–424, 427–429, 434, 437–438, 441–442, 448–449, 451, 453, 463, 466, 478–479, 486, 492, 496, 498, 501, 505, 507, 523, 535, 548–549, 551–552, 555–557, 567–568, 570, 572–574, 576, 587, 589, 600–601, 605, 609, 611, 623, 630, 643, 653–654, 665, 698, 704, 724, 727, 740–741, 743–746, 749, 752, 759, 767–770, 772–773
interfaces.py	3	3	0%	6–8
psm_dataset.py	25	0	100%
fdr
__init__.py	0	0	100%
base.py	58	15	74%	81, 85–86, 91, 98–99, 105, 126, 129–130, 135, 137–138, 144, 186
database_grounded.py	22	0	100%
nonparametric.py	25	4	84%	62, 68–69, 72
scripts
__init__.py	0	0	100%
main.py	137	137	0%	2, 9–11, 17–19, 21–30, 34–37, 40, 43–46, 49–50, 53, 56–57, 60–61, 64–65, 68–69, 72–73, 76–77, 80, 83–84, 88–89, 91–93, 95, 103, 119–122, 125, 128–129, 132, 136–137, 140, 144–145, 148, 153, 156, 159, 168–169, 177, 180, 198–200, 205, 212, 217–218, 221, 228–230, 232, 236–241, 244, 246–247, 252–253, 300–301, 306, 309–310, 315, 318–319, 322–324, 327, 331, 385–386, 391, 395–397, 400–401, 403–404, 406–408, 411–414, 422, 424, 430–434, 437, 439–442
TOTAL	899	381	57%

Tests	Skipped	Failures	Errors	Time
126	0 💤	0 ❌	0 🔥	36.397s ⏱️

[JemmaLDaniel]

/review

[instadeep-pr-agent]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 1 🔵⚪⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Schema Validation Ensure that the new .pr_agent.toml file is validated against the expected configuration schema to prevent misconfiguration and runtime errors. [github_app] handle_pr_actions = ["opened", "reopened", "ready_for_review"] pr_commands = [ "/describe --pr_description.final_update_message=false", "/review", "/improve", ] Documentation Consider adding comments or explanations for each configuration option to guide users on valid values and expected behavior. [github_app] handle_pr_actions = ["opened", "reopened", "ready_for_review"] pr_commands = [ "/describe --pr_description.final_update_message=false", "/review", "/improve", ] [pr_description] add_original_user_description=true