Dev

[madina1203]

PR Type

configuration changes

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Description

• Add new configuration section for llm_gpt_5

• Update configuration parameters in params.ini

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Diagram Walkthrough

flowchart LR
  A["Existing Configuration"] -- "Add new section" --> B["Configuration for llm_gpt_5"]

Loading

File Walkthrough

	Relevant files
Configuration changes	params.ini Add configuration for `llm_gpt_5` model                                    app/config/params.ini Added new section [llm_gpt_5] Set id, temperature, and max_retries for gpt-5 +5/-0

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[qodo-code-review]

PR Reviewer Guide 🔍

(Review updated until commit daef213)

Here are some key observations to aid the review process:

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

🔒 No security concerns identified

⚡ Recommended focus areas for review Config Consistency Please verify that the new configuration section for llm_gpt_5 adheres to the existing parameter conventions and that the provided values are consistent with system expectations. [llm_gpt_5] id = gpt-5 temperature = 1 max_retries = 3

[github-actions]

Persistent review updated to latest commit daef213

[github-actions]

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

docs/index.md (1)

21-21: Nit: standardize trailing slash with Quickstart

Quickstart uses a trailing slash; this one doesn’t. If the site canonicalizes to one form, mirror it here for consistency and cleaner link checking.

Apply if you choose trailing slashes:

-👉 **Try the MetaboT Web App**: [https://metabot.holobiomicslab.eu](https://metabot.holobiomicslab.eu)
+👉 **Try the MetaboT Web App**: [https://metabot.holobiomicslab.eu/](https://metabot.holobiomicslab.eu/)

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between c2e0761 and daef213.

⛔ Files ignored due to path filters (1)

• app/config/params.ini is excluded by !**/*.ini

📒 Files selected for processing (2)

• docs/getting-started/quickstart.md (1 hunks)
• docs/index.md (1 hunks)

🔇 Additional comments (2)

docs/getting-started/quickstart.md (1)

5-5: URL update LGTM

Switch to holobiomicslab.eu looks correct.

docs/index.md (1)

21-21: URL update LGTM

Good swap to holobiomicslab.eu.

[coderabbitai]

💡 Verification agent

🧩 Analysis chain

Consistency: align trailing slash across docs

This link includes a trailing slash, while docs/index.md (Line 21) does not. Pick one style to avoid mixed canonicals.

Run to confirm all old domains are gone and the new URL resolves:

---

🏁 Script executed:

#!/bin/bash
set -euo pipefail

echo "Searching for any lingering cnrs.fr references..."
rg -nI --hidden --glob '!.git' 'holobiomicslab\.cnrs\.fr' || echo "No cnrs.fr references found."

echo "Checking new endpoint reachability and canonicalization..."
for url in "https://metabot.holobiomicslab.eu" "https://metabot.holobiomicslab.eu/"; do
  echo -e "\nHEAD $url"
  curl -sI "$url" | sed -n '1p;/^location:/Ip'
done

Length of output: 392

---

🏁 Script executed:

#!/bin/bash
set -euo pipefail

echo "Searching for lingering cnrs.fr references..."
rg -n 'holobiomicslab\.cnrs\.fr' || echo "No cnrs.fr references found."

echo "Checking all occurrences of metabot.holobiomicslab.eu in docs/index.md"
rg -n -C1 'metabot\.holobiomicslab\.eu' docs/index.md

Length of output: 997

---

Fix legacy domain in README and standardize trailing slash in Quickstart

• In docs/getting-started/quickstart.md (Line 5), remove the trailing slash so the link matches docs/index.md:
  change
  [https://metabot.holobiomicslab.eu/](https://metabot.holobiomicslab.eu/)
  to
  [https://metabot.holobiomicslab.eu](https://metabot.holobiomicslab.eu)
• In README.md (Line 16), replace the old “holobiomicslab.cnrs.fr” URL with “metabot.holobiomicslab.eu” to remove the legacy domain reference.

🤖 Prompt for AI Agents

In docs/getting-started/quickstart.md around line 5 and README.md around line
16, update the demo links to the canonical metabot domain: in quickstart.md
remove the trailing slash so the link becomes
[https://metabot.holobiomicslab.eu](https://metabot.holobiomicslab.eu) (no
trailing slash) to match docs/index.md, and in README.md replace any occurrence
of the legacy holobiomicslab.cnrs.fr URL with https://metabot.holobiomicslab.eu
to remove the legacy domain reference.