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Remove CI/CD section and incorrect fine-tuning section from README
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README.md

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@@ -282,65 +282,6 @@ CATPRED_MODAL_TOKEN=<your-token>
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CATPRED_MODAL_FALLBACK_TO_LOCAL=0
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```
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#### CI/CD (GitHub Actions + Vercel + Modal)
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This repo includes two GitHub Actions workflows:
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- `.github/workflows/ci.yml`
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- Runs on every PR and push to `main`.
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- Installs minimal API dependencies, compiles all Python files, and smoke-tests API entrypoints.
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- `.github/workflows/deploy-modal.yml`
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- Runs on push to `main` when backend files change (and manually via `workflow_dispatch`).
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- Deploys `modal_app.py` automatically.
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To enable automatic Modal deploys from GitHub Actions, add repository secrets:
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- `MODAL_TOKEN_ID`
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- `MODAL_TOKEN_SECRET`
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Create these from Modal:
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1. Go to [https://modal.com/settings/tokens](https://modal.com/settings/tokens).
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2. Create a token with deploy permissions for your workspace.
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3. Copy token ID and secret into GitHub repo settings:
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`Settings -> Secrets and variables -> Actions -> New repository secret`.
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Vercel deployment remains automatic from the connected GitHub branch (`main`).
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### 🧪 Fine-Tuning On Custom Data
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You can fine-tune CatPred on your own regression targets using `train.py`.
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1. Prepare train/val/test CSVs with at least:
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- `SMILES`
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- `sequence`
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- `pdbpath` (unique per unique sequence)
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- one numeric target column (for example: `log10kcat_max`)
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2. Build a protein-records file that covers all `pdbpath` values in your splits:
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```bash
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python ./scripts/create_pdbrecords.py --data_file <combined_or_train_csv> --out_file <protein_records.json.gz>
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```
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3. Train:
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```bash
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python train.py \
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--protein_records_path <protein_records.json.gz> \
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--data_path <train.csv> \
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--separate_val_path <val.csv> \
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--separate_test_path <test.csv> \
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--dataset_type regression \
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--smiles_columns SMILES \
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--target_columns <target_column_name> \
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--add_esm_feats \
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--loss_function mve \
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--save_dir <output_checkpoint_dir>
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```
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For working end-to-end examples, see the training commands in scripts such as `scripts/reproduce_figS10_catpred.sh`.
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### 🔄 Reproducing Publication Results <a name="reproduce"></a>
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We provide three separate ways for reproducing the results of the publication.

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