Update links in README to point to GitHub#266
Update links in README to point to GitHub#266aripitek wants to merge 1 commit intoArcInstitute:mainfrom
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Code Review
This pull request modifies several links and git clone commands in the README.md file, primarily by prefixing them with a specific GitHub user profile. The review feedback correctly identifies that these changes result in broken external links, invalid repository URL structures, and malformed SSH syntax for cloning the repository. Suggestions have been provided to revert these URLs to their original, functional states.
| > Train State transition models or pretrain State embedding models. See the State [paper](https://github.com/aripitek/www.biorxiv.org/content/10.1101/2025.06.26.661135v2). | ||
| > | ||
| > See the [Google Colab](https://colab.research.google.com/drive/1QKOtYP7bMpdgDJEipDxaJqOchv7oQ-_l) to train STATE for the [Virtual Cell Challenge](https://virtualcellchallenge.org/). | ||
| > See the [Google Colab](https://github.com/aripitek/colab.research.google.com/drive/1QKOtYP7bMpdgDJEipDxaJqOchv7oQ-_l) to train STATE for the [Virtual Cell Challenge](https://github.com/aripitek/virtualcellchallenge.org/). |
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The external links (bioRxiv, Google Colab, and Virtual Cell Challenge) have been incorrectly modified by prefixing them with a GitHub user profile. This will result in 404 errors as GitHub does not host or proxy these external sites. These links should remain pointed to their original domains.
| > Train State transition models or pretrain State embedding models. See the State [paper](https://github.com/aripitek/www.biorxiv.org/content/10.1101/2025.06.26.661135v2). | |
| > | |
| > See the [Google Colab](https://colab.research.google.com/drive/1QKOtYP7bMpdgDJEipDxaJqOchv7oQ-_l) to train STATE for the [Virtual Cell Challenge](https://virtualcellchallenge.org/). | |
| > See the [Google Colab](https://github.com/aripitek/colab.research.google.com/drive/1QKOtYP7bMpdgDJEipDxaJqOchv7oQ-_l) to train STATE for the [Virtual Cell Challenge](https://github.com/aripitek/virtualcellchallenge.org/). | |
| > Train State transition models or pretrain State embedding models. See the State [paper](https://www.biorxiv.org/content/10.1101/2025.06.26.661135v2). | |
| > | |
| > See the [Google Colab](https://colab.research.google.com/drive/1QKOtYP7bMpdgDJEipDxaJqOchv7oQ-_l) to train STATE for the [Virtual Cell Challenge](https://virtualcellchallenge.org/). |
| - Model evaluation framework: [cell-eval](https://github.com/aripitek/ArcInstitute/cell-eval) | ||
| - Dataloaders and preprocessing: [cell-load](https://github.com/aripitek/ArcInstitute/cell-load) |
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The repository links for cell-eval and cell-load use an invalid URL structure (/aripitek/ArcInstitute/). If these are intended to point to forks, the correct URL would be https://github.com/aripitek/cell-eval. However, for the main documentation, it is standard to link to the official organization repositories.
| - Model evaluation framework: [cell-eval](https://github.com/aripitek/ArcInstitute/cell-eval) | |
| - Dataloaders and preprocessing: [cell-load](https://github.com/aripitek/ArcInstitute/cell-load) | |
| - Model evaluation framework: [cell-eval](https://github.com/ArcInstitute/cell-eval) | |
| - Dataloaders and preprocessing: [cell-load](https://github.com/ArcInstitute/cell-load) |
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| ```bash | ||
| git clone git@github.com:ArcInstitute/state.git | ||
| git clone git@github.com/aripitek:ArcInstitute/state.git |
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The git clone SSH URL is malformed. The addition of /aripitek: before the organization name is not valid SSH syntax for GitHub. The correct format is git@github.com:owner/repo.git.
| git clone git@github.com/aripitek:ArcInstitute/state.git | |
| git clone git@github.com:ArcInstitute/state.git |
| The model weights and output are licensed under the [Arc Research Institute State Model Non-Commercial License](MODEL_LICENSE.md) and subject to the [Arc Research Institute State Model Acceptable Use Policy](MODEL_ACCEPTABLE_USE_POLICY.md). | ||
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| Any publication that uses this source code or model parameters should cite the State [paper](https://arcinstitute.org/manuscripts/State). | ||
| Any publication that uses this source code or model parameters should cite the State [paper](https://github.com/aripitek/arcinstitute.org/manuscripts/State). |
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The citation link has been incorrectly modified. It should point to the original arcinstitute.org domain rather than being prefixed with a GitHub profile.
| Any publication that uses this source code or model parameters should cite the State [paper](https://github.com/aripitek/arcinstitute.org/manuscripts/State). | |
| Any publication that uses this source code or model parameters should cite the State [paper](https://arcinstitute.org/manuscripts/State). |
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