lint

Author: samcraftt

server_api/chatbot/file_summaries/App.md

@@ -15,11 +15,13 @@ App
 ## Components
 
 ### `CacheBootstrapper`
+
 - Runs `resetFileState()` from `AppContext` on mount
 - Clears local cache (files, fileList, etc.) before rendering children
 - Renders nothing until cache is cleared; then renders main content
 
 ### `MainContent`
+
 - Renders `Views` component (main application layout with tabs)
 
 ## Contexts

server_api/chatbot/file_summaries/api.md

@@ -9,33 +9,41 @@ Central API client for the PyTC Client frontend. Exposes functions for all backe
 ## Exports
 
 ### `apiClient`
+
 Axios instance with base URL, `withCredentials: true`. Used for general requests (e.g. `/files`, `/files/upload`).
 
 ### Visualization
+
 - **`getNeuroglancerViewer(image, label, scales)`** — Launches Neuroglancer viewer. Accepts file objects or path strings. Uses FormData for browser uploads.
 
 ### File Checks
+
 - **`checkFile(file)`** — POST to `/check_files` to detect if file is likely a label (heuristic).
 
 ### Generic
+
 - **`makeApiRequest(url, method, data)`** — HTTP request helper with JSON Content-Type.
 
 ### Model Training
+
 - **`startModelTraining(trainingConfig, logPath, outputPath)`** — Injects OUTPUT_PATH into YAML config and POSTs to `/start_model_training`
 - **`stopModelTraining()`**
 - **`getTrainingStatus()`**
 - **`getTensorboardURL()`**
 
 ### Model Inference
+
 - **`startModelInference(inferenceConfig, outputPath, checkpointPath)`** — Injects OUTPUT_PATH into YAML, sets NUM_GPUS=1, POSTs to `/start_model_inference`
 - **`stopModelInference()`**
 - **`getInferenceStatus()`**
 
 ### Chatbot
+
 - **`queryChatBot(query)`** — POST to `/chat/query`
 - **`clearChat()`** — POST to `/chat/clear`
 
 ### Config Presets
+
 - **`getConfigPresets()`** — GET `/pytc/configs`
 - **`getConfigPresetContent(path)`** — GET `/pytc/config`
 - **`getModelArchitectures()`** — GET `/pytc/architectures`

server_api/chatbot/file_summaries/components/YamlFileEditor.md

@@ -9,13 +9,15 @@ Advanced YAML configuration editor with structured controls (switches, selects,
 ## Sections (CONTROL_SECTIONS)
 
 ### Training
+
 - Common training knobs: Optimizer, LR scheduler, learning rate, batch size, iterations, save/validation intervals
 - System: Distributed, Parallel mode, Debug mode
 - Model: Block type, Backbone, Normalization, Activation, Pooling, Mixed precision, Aux output
 - Dataset: 2D dataset, Load 2D slices, Isotropic, Drop channels, Reduce labels, Ensure min size, Pad mode
 - Solver (advanced): Weight decay, Momentum, Clip gradients
 
 ### Inference
+
 - Common: Batch size, Augmentations, Blending, Eval mode
 - Advanced: Run singly, Unpad output, Augment mode, Test count
 

server_api/chatbot/file_summaries/contexts/YamlContext.md

@@ -5,10 +5,12 @@ Context for YAML-related UI state (GPUs, batch size, etc.). Used by `YamlFileUpl
 ## State
 
 ### Training
+
 - `numGPUs`, `numCPUs`
 - `solverSamplesPerBatch`, `learningRate`
 
 ### Inference
+
 - `inferenceSamplesPerBatch`, `augNum`
 
 ## YamlContextWrapper

server_api/chatbot/file_summaries/main.md

@@ -18,12 +18,14 @@ FastAPI server that powers the PyTC Client application. Provides API endpoints f
 ## Key Endpoints
 
 ### Health & Config
+
 - `GET /health` — Server status check
 - `GET /pytc/configs` — List PyTorch Connectomics config presets (YAML)
 - `GET /pytc/config?path=...` — Get config file content
 - `GET /pytc/architectures` — List model architectures from build.py
 
 ### Model Training & Inference
+
 - `POST /start_model_training` — Proxy to PyTC server (localhost:4243)
 - `POST /stop_model_training` — Stop training
 - `GET /training_status` — Training status polling
@@ -32,12 +34,15 @@ FastAPI server that powers the PyTC Client application. Provides API endpoints f
 - `GET /get_tensorboard_url` — Returns TensorBoard URL (default: localhost:6006)
 
 ### Visualization
+
 - `POST /neuroglancer` — Create Neuroglancer viewer for image/label volumes. Accepts JSON or multipart/form-data with image, label, scales.
 
 ### Data & Files
+
 - `POST /check_files` — Heuristic check if file is a label (integer type, low unique values, or binary)
 
 ### Chatbot (RAG)
+
 - `POST /chat/query` — Chat query (requires chatbot configured)
 - `POST /chat/clear` — Clear chat history
 - `GET /chat/status` — Check if chatbot is configured

server_api/chatbot/update_faiss.py

@@ -1,16 +1,16 @@
-'''
+"""
 How to update faiss_index:
     1. Delete the existing server_api/chatbot/file_summaries directory
     2. Paste the following prompt into Cursor (or any AI IDE, in agent mode):
 
-        Create markdown files summarizing server_api/main.py and each file in client/src/*/** (including files in nested directories), 
+        Create markdown files summarizing server_api/main.py and each file in client/src/*/** (including files in nested directories),
         but don't create markdown files for index.js, utils.js, or any CSS files.
         These markdown files will serve as the knowledge base for a RAG chatbot that helps end users navigate the frontend client.
         Put these markdown files in a new server_api/chatbot/file_summaries directory.
 
     3. Run this script:
         python server_api/chatbot/update_faiss.py
-'''
+"""
 
 from pathlib import Path
 from langchain_core.documents import Document
@@ -30,7 +30,9 @@
             metadata={"source": str(relative_path)},
         )
     )
-embeddings = OllamaEmbeddings(model="mistral:latest", base_url="http://cscigpu08.bc.edu:11434")
+embeddings = OllamaEmbeddings(
+    model="mistral:latest", base_url="http://cscigpu08.bc.edu:11434"
+)
 vectorstore = FAISS.from_documents(documents, embeddings)
 faiss_directory.mkdir(parents=True, exist_ok=True)
 vectorstore.save_local(str(faiss_directory))