@@ -282,65 +282,6 @@ CATPRED_MODAL_TOKEN=<your-token>
282282CATPRED_MODAL_FALLBACK_TO_LOCAL=0
283283```
284284
285- #### CI/CD (GitHub Actions + Vercel + Modal)
286-
287- This repo includes two GitHub Actions workflows:
288-
289- - ` .github/workflows/ci.yml `
290- - Runs on every PR and push to ` main ` .
291- - Installs minimal API dependencies, compiles all Python files, and smoke-tests API entrypoints.
292- - ` .github/workflows/deploy-modal.yml `
293- - Runs on push to ` main ` when backend files change (and manually via ` workflow_dispatch ` ).
294- - Deploys ` modal_app.py ` automatically.
295-
296- To enable automatic Modal deploys from GitHub Actions, add repository secrets:
297-
298- - ` MODAL_TOKEN_ID `
299- - ` MODAL_TOKEN_SECRET `
300-
301- Create these from Modal:
302-
303- 1 . Go to [ https://modal.com/settings/tokens ] ( https://modal.com/settings/tokens ) .
304- 2 . Create a token with deploy permissions for your workspace.
305- 3 . Copy token ID and secret into GitHub repo settings:
306- ` Settings -> Secrets and variables -> Actions -> New repository secret ` .
307-
308- Vercel deployment remains automatic from the connected GitHub branch (` main ` ).
309-
310- ### 🧪 Fine-Tuning On Custom Data
311-
312- You can fine-tune CatPred on your own regression targets using ` train.py ` .
313-
314- 1 . Prepare train/val/test CSVs with at least:
315- - ` SMILES `
316- - ` sequence `
317- - ` pdbpath ` (unique per unique sequence)
318- - one numeric target column (for example: ` log10kcat_max ` )
319-
320- 2 . Build a protein-records file that covers all ` pdbpath ` values in your splits:
321-
322- ``` bash
323- python ./scripts/create_pdbrecords.py --data_file < combined_or_train_csv> --out_file < protein_records.json.gz>
324- ```
325-
326- 3 . Train:
327-
328- ``` bash
329- python train.py \
330- --protein_records_path < protein_records.json.gz> \
331- --data_path < train.csv> \
332- --separate_val_path < val.csv> \
333- --separate_test_path < test.csv> \
334- --dataset_type regression \
335- --smiles_columns SMILES \
336- --target_columns < target_column_name> \
337- --add_esm_feats \
338- --loss_function mve \
339- --save_dir < output_checkpoint_dir>
340- ```
341-
342- For working end-to-end examples, see the training commands in scripts such as ` scripts/reproduce_figS10_catpred.sh ` .
343-
344285### 🔄 Reproducing Publication Results <a name =" reproduce " ></a >
345286
346287We provide three separate ways for reproducing the results of the publication.
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