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model-incorporation-request

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UpdatedJuly 1, 2026 at 09:08

Open a model request issue on ersilia-os/ersilia for a new model to be incorporated into the Ersilia Model Hub. Use this skill whenever a user wants to request a new model, open a model request, or start the model incorporation pipeline. The skill reads the publication PDF and source code repository to propose all required fields, asks the user to confirm, then opens the GitHub issue mimicking the official ersilia-os/ersilia model request form. Trigger on phrases like "request a model", "open a model request", "add a new model to the hub", "start model incorporation", or "open an issue for a new model".

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SKILL.md

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name	model-incorporation-request
description	Open a model request issue on ersilia-os/ersilia for a new model to be incorporated into the Ersilia Model Hub. Use this skill whenever a user wants to request a new model, open a model request, or start the model incorporation pipeline. The skill reads the publication PDF and source code repository to propose all required fields, asks the user to confirm, then opens the GitHub issue mimicking the official ersilia-os/ersilia model request form. Trigger on phrases like "request a model", "open a model request", "add a new model to the hub", "start model incorporation", or "open an issue for a new model".
allowed-tools	["Bash","Read","WebFetch","WebSearch","AskUserQuestion"]

Model Incorporation Request

Your job is to open a model request issue on ersilia-os/ersilia that exactly mirrors the official model request form, using information extracted from the publication and source code repository.

Parse Arguments

--pdf <pdf-path> (required): local path to the publication PDF
--publication <url> (required): URL to the publication (DOI, arXiv, journal)
--source <url> (required): URL to the source code repository (GitHub, GitLab, Zenodo, etc.)

If any argument is missing, ask the user before proceeding.

Phase 1 – Extract Information

1a. Read the PDF

Extract:

Model name / what it does (for Title and Name)
What the model predicts or computes — in plain language (for Description)
Application areas and relevant keywords (for Tags)

1b. Fetch the source code repository

Use WebFetch on the repository URL (README and root files) to extract:

License — look for a LICENSE file or license field in pyproject.toml / setup.py / package.json
Any additional context for the description or tags

1c. Fetch the valid tag and license lists

Fetch both files at runtime:

https://raw.githubusercontent.com/ersilia-os/ersilia/master/ersilia/hub/content/metadata/tag.txt
https://raw.githubusercontent.com/ersilia-os/ersilia/master/ersilia/hub/content/metadata/license.txt

Both are newline-separated. Keep both lists in memory — you will validate tags and the license against them.

Phase 2 – Propose All Fields and Confirm

Present all proposed values in a single table and wait for the user's feedback before proceeding. Do not open the issue until the user explicitly confirms.

Field	Proposed value
Title	`🦠 Model Request: <Name>`
Name	...
Slug	...
Description	...
Tags	...
Publication	(from --publication argument)
Source Code	(from --source argument)
License	...

Field rules:

Title / Name <Name> should be concise (2–5 words), title-case, describing what the model does. The Name field is the same <Name> without the emoji prefix.

Slug Lowercase, hyphens only, 2–4 words maximum. Keep it short and memorable — it becomes part of the model's permanent identifier. Propose a single best option (e.g. mt-gnn-adme, morgan-fingerprints). If you find yourself using more than 4 words, trim ruthlessly.

Description 200–600 characters (hard limits from the GitHub form). Plain English, focused on what a user gets from running this model on a molecule. Do not start with "This model...". Do not include a character count in the table — just show the description text.

Tags Pick only from the tag list fetched in Phase 1c. Choose 2–4 tags maximum — only the most directly relevant ones. Do not tag everything that loosely applies; prefer precision over coverage. At least one is required.

License Use only values from the license.txt list fetched in Phase 1c. Use None if no LICENSE file is found.

After presenting the table, ask: "Does this look correct? Let me know any changes and I'll open the issue."

Phase 3 – Open the GitHub Issue

Use gh issue create to open the issue on ersilia-os/ersilia. Format the body to match exactly what the GitHub form produces when submitted — each field as a level-3 heading followed by its value:

### Model Name

<name>

### Model Description

<description>

### Slug

<slug>

### Tag

<tag1>, <tag2>

### Publication

<publication-url>

### Source Code

<source-url>

### License

<license>

Use a HEREDOC to pass the body:

gh issue create \
  --repo ersilia-os/ersilia \
  --title "<title>" \
  --label "new-model" \
  --body "$(cat <<'EOF'
<body>
EOF
)"

Phase 4 – Tell the User What Happens Next

After the issue is opened, print the issue URL and explain the next steps:

An Ersilia admin will review and approve the request
Once approved, a new model repository (eosXXXX) is created under ersilia-os
Fork that repository and clone it locally
Run /model-incorporation-metadata to fill in the metadata
Run /model-incorporation-code to wire up the model code
Run /ersilia-model-test to validate the model runs correctly before submitting a PR
Run /model-incorporation-reproduce to verify the model performs as reported in the paper

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name	model-incorporation-request
description	Open a model request issue on ersilia-os/ersilia for a new model to be incorporated into the Ersilia Model Hub. Use this skill whenever a user wants to request a new model, open a model request, or start the model incorporation pipeline. The skill reads the publication PDF and source code repository to propose all required fields, asks the user to confirm, then opens the GitHub issue mimicking the official ersilia-os/ersilia model request form. Trigger on phrases like "request a model", "open a model request", "add a new model to the hub", "start model incorporation", or "open an issue for a new model".
allowed-tools	["Bash","Read","WebFetch","WebSearch","AskUserQuestion"]

Model Incorporation Request

Your job is to open a model request issue on ersilia-os/ersilia that exactly mirrors the official model request form, using information extracted from the publication and source code repository.

Parse Arguments

--pdf <pdf-path> (required): local path to the publication PDF
--publication <url> (required): URL to the publication (DOI, arXiv, journal)
--source <url> (required): URL to the source code repository (GitHub, GitLab, Zenodo, etc.)

If any argument is missing, ask the user before proceeding.

Phase 1 – Extract Information

1a. Read the PDF

Extract:

Model name / what it does (for Title and Name)
What the model predicts or computes — in plain language (for Description)
Application areas and relevant keywords (for Tags)

1b. Fetch the source code repository

Use WebFetch on the repository URL (README and root files) to extract:

License — look for a LICENSE file or license field in pyproject.toml / setup.py / package.json
Any additional context for the description or tags

1c. Fetch the valid tag and license lists

Fetch both files at runtime:

https://raw.githubusercontent.com/ersilia-os/ersilia/master/ersilia/hub/content/metadata/tag.txt
https://raw.githubusercontent.com/ersilia-os/ersilia/master/ersilia/hub/content/metadata/license.txt

Both are newline-separated. Keep both lists in memory — you will validate tags and the license against them.

Phase 2 – Propose All Fields and Confirm

Present all proposed values in a single table and wait for the user's feedback before proceeding. Do not open the issue until the user explicitly confirms.

Field	Proposed value
Title	`🦠 Model Request: <Name>`
Name	...
Slug	...
Description	...
Tags	...
Publication	(from --publication argument)
Source Code	(from --source argument)
License	...

Field rules:

Title / Name <Name> should be concise (2–5 words), title-case, describing what the model does. The Name field is the same <Name> without the emoji prefix.

License Use only values from the license.txt list fetched in Phase 1c. Use None if no LICENSE file is found.

After presenting the table, ask: "Does this look correct? Let me know any changes and I'll open the issue."

Phase 3 – Open the GitHub Issue

### Model Name

<name>

### Model Description

<description>

### Slug

<slug>

### Tag

<tag1>, <tag2>

### Publication

<publication-url>

### Source Code

<source-url>

### License

<license>

Use a HEREDOC to pass the body:

gh issue create \
  --repo ersilia-os/ersilia \
  --title "<title>" \
  --label "new-model" \
  --body "$(cat <<'EOF'
<body>
EOF
)"

Phase 4 – Tell the User What Happens Next

After the issue is opened, print the issue URL and explain the next steps:

An Ersilia admin will review and approve the request
Once approved, a new model repository (eosXXXX) is created under ersilia-os
Fork that repository and clone it locally
Run /model-incorporation-metadata to fill in the metadata
Run /model-incorporation-code to wire up the model code
Run /ersilia-model-test to validate the model runs correctly before submitting a PR
Run /model-incorporation-reproduce to verify the model performs as reported in the paper