Merge pull request #59 from SELab-3-2026/docfix

Finalizing docs

README.md

@@ -45,6 +45,9 @@ For detailed instructions on how to use the project, please refer to the **[API
 3. **Simulate a trained model:**
    See [Simulation & Evaluation](docs/api/simulation.md).
 
+4. **Compare fault tolerance of models:**
+   See [Checkpoint & Model Evaluation](docs/api/evaluation.md)
+
 ## HPC
 
 See **[docs/HPC.md](docs/HPC.md)** for the full guide, including environment setup, cluster selection, interactive debugging, and job submission.

docs/README.md

@@ -1,6 +1,6 @@
 # Documentation
 
-## Design & architecture ([`/design`](./design/))
+## Design & architecture (`/design`)
 
 If you are interested in the "why did you do it like this?"
 
@@ -11,7 +11,7 @@ If you are interested in the "why did you do it like this?"
 - [Learning algorithm](./design/learning_algorithm.md): RL techniques, i.e. PPO.
 - [Reward function](./design/learning_algorithm.md): Goals, fitness tracking, and reward structures.
 
-## API reference ([`/api`](./api/))
+## API reference (`/api`)
 
 If you are interested in the "how do I use it?"
 
@@ -19,3 +19,5 @@ If you are interested in the "how do I use it?"
 - [Tracking & Monitoring](./api/tracking.md): Setting up WandB and TensorBoard to monitor runs.
 - [Simulation](./api/simulation.md): Visualizing and evaluating models.
 - [Environment](./api/environment.md): MuJoCo environment interaction and configuration.
+- [Analysis](./api/analysis.md): Comparing checkpoints and generating plots.
+- [Evaluation](./api/evaluation.md): Evaluating checkpoints and comparing fault tolerance.

docs/api/evaluation.md

@@ -15,7 +15,7 @@ python scripts/train.py evaluation.evaluate_checkpoints=true evaluation.eval_max
 
 Results are saved to `runs/<run_dir>/metrics/checkpoint_evaluation.csv` and synced to Weights & Biases if enabled.
 
-## Cross-Model & Defect Tolerance Analysis
+## Cross-Model & Fault Tolerance Analysis
 
 To measure how well different controllers handle damage (amputations), use `scripts/compare_models.py`. This script performs a grid search over models x morphologies.