proteins readme

Author: aditya0by0

README.md

@@ -1,2 +1,146 @@
-# python-chebai-proteins
-Protein-related extension of the chebai framework
+
+# 🧪 ChEB-AI Proteins
+
+`python-chebai-proteins` repository for protein prediction and classification, built on top of the [`python-chebai`](https://github.com/ChEB-AI/python-chebai) codebase.
+
+
+## 🔧 Installation
+
+
+To install, follow these steps:
+
+1. Clone the repository:
+```
+git clone https://github.com/ChEB-AI/python-chebai-proteins.git
+```
+
+2. Install the package:
+
+```
+cd python-chebai
+pip install .
+```
+
+## 🗂 Recommended Folder Structure
+
+To combine configuration files from both `python-chebai` and `python-chebai-proteins`, structure your project like this:
+
+```
+my_projects/
+├── python-chebai/
+│   ├── chebai/
+│   ├── configs/
+│   └── ...
+└── python-chebai-proteins/
+    ├── chebai_proteins/
+    ├── configs/
+    └── ...
+```
+
+This setup enables shared access to data and model configurations.
+
+
+
+## 🚀 Training & Pretraining Guide
+
+### ⚠️ Important Setup Instructions
+
+Before running any training scripts, ensure the environment is correctly configured:
+
+* Either:
+
+  * Install the `python-chebai` repository as a package using:
+
+    ```bash
+    pip install .
+    ```
+* **OR**
+
+  * Manually set the `PYTHONPATH` environment variable if working across multiple directories (`python-chebai` and `python-chebai-proteins`):
+
+    * If your current working directory is `python-chebai-proteins`, set:
+
+      ```bash
+      export PYTHONPATH=path/to/python-chebai
+      ```
+      or vice versa.
+      
+    * If you're working within both repositories simultaneously or facing module not found errors,  we **recommend configuring both directories**:
+
+      ```bash
+      # Linux/macOS
+      export PYTHONPATH=path/to/python-chebai:path/to/python-chebai-proteins
+
+      # Windows (use semicolon instead of colon)
+      set PYTHONPATH=path\to\python-chebai;path\to\python-chebai-proteins
+      ```
+
+> 🔎 See the [PYTHONPATH Explained](#-pythonpath-explained) section below for more details.
+
+
+### 📊 SCOPE hierarchy prediction
+
+Assuming your current working directory is `python-chebai-proteins`, run the following command to start training:
+```bash
+python -m chebai fit --trainer=../configs/training/default_trainer.yml --trainer.callbacks=../configs/training/default_callbacks.yml --trainer.logger.init_args.name=scope50  --trainer.accumulate_grad_batches=4 --trainer.logger=../configs/training/wandb_logger.yml --trainer.min_epochs=100 --trainer.max_epochs=100 --data=configs/data/scope/scope50.yml --data.init_args.batch_size=32  --data.init_args.num_workers=10 --model=../configs/model/electra.yml --model.train_metrics=../configs/metrics/micro-macro-f1.yml --model.test_metrics=../configs/metrics/micro-macro-f1.yml --model.val_metrics=../configs/metrics/micro-macro-f1.yml  --model.pass_loss_kwargs=false --model.criterion=../configs/loss/bce.yml --model.criterion.init_args.beta=0.99
+```
+
+Same command can be used for **DeepGO** just by changing the config path for data.
+
+
+
+
+
+
+
+## 🧭 PYTHONPATH Explained
+
+### What is `PYTHONPATH`?
+
+`PYTHONPATH` is an environment variable that tells Python where to search for modules that aren't installed via `pip` or not in your current working directory.
+
+### Why You Need It
+
+If your config refers to a custom module like:
+
+```yaml
+class_path: chebai_proteins.preprocessing.datasets.scope.scope.SCOPe50
+```
+
+...and you're running the code from `python-chebai`, Python won't know where to find `chebai_proteins` (from another repo like `python-chebai-proteins/`) unless you add it to `PYTHONPATH`.
+
+
+### How Python Finds Modules
+
+Python looks for imports in this order:
+
+1. Current directory
+2. Standard library
+3. Paths in `PYTHONPATH`
+4. Installed packages (`site-packages`)
+
+You can inspect the full search paths:
+
+```bash
+python -c "import sys; print(sys.path)"
+```
+
+
+
+### ✅ Setting `PYTHONPATH`
+
+#### 🐧 Linux / macOS
+
+```bash
+export PYTHONPATH=/path/to/python-chebai-graph
+echo $PYTHONPATH
+```
+
+#### 🪟 Windows CMD
+
+```cmd
+set PYTHONPATH=C:\path\to\python-chebai-graph
+echo %PYTHONPATH%
+```
+
+> 💡 Note: This is temporary for your terminal session. To make it permanent, add it to your system environment variables.