mhmdaskari · mhmdaskari · May 23, 2026 · May 23, 2026
diff --git a/.gitattributes b/.gitattributes
@@ -1 +1,4 @@
 data/processed/*.npy filter=lfs diff=lfs merge=lfs -text
+
+# Keep notebooks available in the repository without counting them in GitHub's language bar.
+*.ipynb -linguist-detectable
diff --git a/docs/api.md b/docs/api.md
diff --git a/docs/api/augmentation.md b/docs/api/augmentation.md
@@ -0,0 +1,6 @@
+# GAN Augmentation
+
+::: eegclassify.augmentation
+    options:
+      show_root_heading: false
+
diff --git a/docs/api/bci2a.md b/docs/api/bci2a.md
@@ -0,0 +1,6 @@
+# BCI IV-2a Conversion
+
+::: eegclassify.bci2a
+    options:
+      show_root_heading: false
+
diff --git a/docs/api/cli.md b/docs/api/cli.md
@@ -0,0 +1,6 @@
+# Command Line Interface
+
+::: eegclassify.cli
+    options:
+      show_root_heading: false
+
diff --git a/docs/api/config.md b/docs/api/config.md
@@ -0,0 +1,6 @@
+# Configuration
+
+::: eegclassify.config
+    options:
+      show_root_heading: false
+
diff --git a/docs/api/constants.md b/docs/api/constants.md
@@ -0,0 +1,6 @@
+# Constants
+
+::: eegclassify.constants
+    options:
+      show_root_heading: false
+
diff --git a/docs/api/data.md b/docs/api/data.md
@@ -0,0 +1,6 @@
+# Data Loading And Comparison
+
+::: eegclassify.data
+    options:
+      show_root_heading: false
+
diff --git a/docs/api/index.md b/docs/api/index.md
@@ -0,0 +1,14 @@
+# API Reference
+
+The API reference is organized around the main EEG classification workflow: configure an experiment, prepare data, optionally augment training samples, train framework-specific models, and inspect results.
+
+- [Configuration](config.md)
+- [Data Loading And Comparison](data.md)
+- [Preprocessing](preprocessing.md)
+- [BCI IV-2a Conversion](bci2a.md)
+- [GAN Augmentation](augmentation.md)
+- [Model APIs](models/index.md)
+- [Plotting](plotting.md)
+- [Command Line Interface](cli.md)
+- [Constants](constants.md)
+
diff --git a/docs/api/models/index.md b/docs/api/models/index.md
@@ -0,0 +1,8 @@
+# Model APIs
+
+The framework modules expose matching classifier families for TensorFlow/Keras, PyTorch, and JAX/Flax, along with the reusable GAN augmentation path used by the training workflow.
+
+- [TensorFlow Models](tensorflow.md)
+- [PyTorch Models](pytorch.md)
+- [JAX Models](jax.md)
+
diff --git a/docs/api/models/jax.md b/docs/api/models/jax.md
@@ -0,0 +1,6 @@
+# JAX Models
+
+::: eegclassify.models.jax
+    options:
+      show_root_heading: false
+
diff --git a/docs/api/models/pytorch.md b/docs/api/models/pytorch.md
@@ -0,0 +1,6 @@
+# PyTorch Models
+
+::: eegclassify.models.pytorch
+    options:
+      show_root_heading: false
+
diff --git a/docs/api/models/tensorflow.md b/docs/api/models/tensorflow.md
@@ -0,0 +1,6 @@
+# TensorFlow Models
+
+::: eegclassify.models.tensorflow
+    options:
+      show_root_heading: false
+
diff --git a/docs/api/plotting.md b/docs/api/plotting.md
@@ -0,0 +1,6 @@
+# Plotting
+
+::: eegclassify.plotting
+    options:
+      show_root_heading: false
+
diff --git a/docs/api/preprocessing.md b/docs/api/preprocessing.md
@@ -0,0 +1,6 @@
+# Preprocessing
+
+::: eegclassify.preprocessing
+    options:
+      show_root_heading: false
+
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -46,7 +46,22 @@ nav:
   - Data: data.md
   - Reproduce Results: reproduce.md
   - Results: results.md
-  - API: api.md
+  - API Reference:
+      - Overview: api/index.md
+      - Configuration: api/config.md
+      - Data:
+          - Loading And Comparison: api/data.md
+          - Preprocessing: api/preprocessing.md
+          - BCI IV-2a Conversion: api/bci2a.md
+          - GAN Augmentation: api/augmentation.md
+      - Models:
+          - Overview: api/models/index.md
+          - TensorFlow: api/models/tensorflow.md
+          - PyTorch: api/models/pytorch.md
+          - JAX: api/models/jax.md
+      - Plotting: api/plotting.md
+      - Command Line Interface: api/cli.md
+      - Constants: api/constants.md
 
 watch:
   - src