diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7fe4a47..efada36 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,15 +1,28 @@ name: CI on: - push: - branches: [ main ] pull_request: + types: [ opened, synchronize, reopened, ready_for_review ] branches: [ main ] jobs: build: name: Build and Test runs-on: ubuntu-latest + if: ${{ !github.event.pull_request.draft }} + services: + neo4j: + image: neo4j:5 + ports: + - 7687:7687 # Bolt port + - 7474:7474 # HTTP port + env: + NEO4J_AUTH: neo4j:${{ secrets.NEO4J_PASSWORD }} + options: >- + --health-cmd="curl -f http://localhost:7474 || exit 1" + --health-interval=10s + --health-timeout=5s + --health-retries=5 strategy: matrix: @@ -32,4 +45,8 @@ jobs: run: poetry run pre-commit run --all-files --show-diff-on-failure - name: Run tests + env: + NEO4J_URI: bolt://localhost:7687 + NEO4J_USER: neo4j + NEO4J_PASSWORD: ${{ secrets.NEO4J_PASSWORD }} run: poetry run pytest diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 92295d5..26eea7a 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -1,17 +1,14 @@ name: "CodeQL" on: - push: - branches: [ main ] pull_request: branches: [ main ] - schedule: - - cron: '35 6 * * 3' # Runs at 06:35 every Wednesday jobs: analyze: name: Analyze runs-on: ubuntu-latest + if: ${{ !github.event.pull_request.draft }} permissions: actions: read diff --git a/.gitignore b/.gitignore index a9aabee..41c6cbb 100644 --- a/.gitignore +++ b/.gitignore @@ -164,3 +164,4 @@ cython_debug/ .idea/Concord.iml .idea/modules.xml .idea/vcs.xml +/.idea/developer-tools.xml diff --git a/.idea/misc.xml b/.idea/misc.xml index f8b3cd4..af88c4c 100644 --- a/.idea/misc.xml +++ b/.idea/misc.xml @@ -1,9 +1,7 @@ - - + \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2b9afce..5108344 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,19 +1,20 @@ repos: - repo: local hooks: - - id: black - name: black - entry: poetry run black + - id: yapf + name: yapf + entry: poetry run yapf language: system - types: [ python ] - args: [ --check, --diff ] + pass_filenames: false + args: [ "-i", "-r", "concord/", "tests/" ] - id: flake8 name: flake8 entry: poetry run flake8 language: system - types: [ python ] + pass_filenames: false + args: [ "concord/", "tests/" ] - id: pytest name: pytest entry: poetry run pytest language: system - pass_filenames: false + pass_filenames: false \ No newline at end of file diff --git a/README.md b/README.md index e93dd8a..3aedda4 100644 --- a/README.md +++ b/README.md @@ -1 +1,149 @@ # Concord + +Concord is a Python project that leverages FastAPI, Neo4j, and BERTopic for advanced text analysis. It provides a +platform for analyzing and visualizing text data using state-of-the-art machine learning techniques. + +## Table of Contents + +- [Prerequisites](#prerequisites) +- [Installation](#installation) + - [Clone the Repository](#clone-the-repository) + - [Set Up Dependencies](#set-up-dependencies) + - [Debian-based Systems](#debian-based-systems) + - [Windows](#windows) +- [Running the Application](#running-the-application) + - [Start Docker Containers](#start-docker-containers) + - [Run Pre-commit Hooks and Tests](#run-pre-commit-hooks-and-tests) +- [Contributing](#contributing) +- [License](#license) + +## Prerequisites + +- **Python 3.12+** +- **Poetry** for dependency management +- **Docker** and **Docker Compose** +- **Git** + +## Installation + +### Clone the Repository + +```bash +git clone https://github.com/yourusername/concord.git +cd concord +``` + +### Set Up Dependencies + +#### Debian-based Systems + +1. **Update Package Lists** + + ```bash + sudo apt update + ``` + +2. **Install Required Packages** + + ```bash + sudo apt install -y software-properties-common curl git + ``` + +3. **Install Python 3.12** + + Add the Deadsnakes PPA and install Python 3.12: + + ```bash + sudo add-apt-repository ppa:deadsnakes/ppa + sudo apt update + sudo apt install -y python3.12 python3.12-venv python3.12-dev + ``` + +4. **Install Poetry** + + ```bash + curl -sSL https://install.python-poetry.org | python3 - + echo 'export PATH="$HOME/.local/bin:$PATH"' >> ~/.bashrc + source ~/.bashrc + ``` + +5. **Install Docker and Docker Compose** + + ```bash + sudo apt install -y docker.io docker-compose + sudo systemctl start docker + sudo systemctl enable docker + sudo usermod -aG docker $USER + ``` + + Log out and log back in for the group changes to take effect. + +6. **Install Project Dependencies** + + ```bash + poetry install + poetry run pre-commit install + ``` + +#### Windows + +1. **Install Python 3.12** + + Download and install Python 3.12 from the [official website](https://www.python.org/downloads/windows/). During + installation, make sure to check the box **"Add Python to PATH"**. + +2. **Install Git** + + Download and install Git from the [official website](https://git-scm.com/download/win). + +3. **Install Poetry** + + Open Command Prompt or PowerShell and run: + + ```powershell + (Invoke-WebRequest -Uri https://install.python-poetry.org -UseBasicParsing).Content | python - + ``` + + Add Poetry to your PATH by adding the following line to your PowerShell profile: + + ```powershell + $env:Path += ";$env:APPDATA\Python\Scripts" + ``` + +4. **Install Docker Desktop** + + Download and install Docker Desktop from the [official website](https://www.docker.com/products/docker-desktop). + Ensure that it is running before proceeding. + +5. **Install Project Dependencies** + + ```powershell + poetry install + poetry run pre-commit install + ``` + +## Running the Application + +### Start Docker Containers + +Set up a temporary Neo4j database: + +```bash +docker-compose up -d +``` + +> **Note:** On Windows, ensure Docker Desktop is running and has sufficient resources allocated. + +### Run Pre-commit Hooks and Tests + +```bash +poetry run pre-commit run -a +``` + +## Contributing + +Contributions are welcome! Please open an issue or submit a pull request for any improvements or suggestions. + +## License + +This project is licensed under the [MIT License](LICENSE). \ No newline at end of file diff --git a/concord/bert/__init__.py b/concord/bert/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/concord/bert/bert.py b/concord/bert/bert.py new file mode 100644 index 0000000..4976d49 --- /dev/null +++ b/concord/bert/bert.py @@ -0,0 +1,44 @@ +# bert.py + +import os + +import joblib +from bertopic import BERTopic +from sentence_transformers import SentenceTransformer + + +def initialize_model(): + """ + Initialize the BERTopic model. + You can customize the model with different parameters as needed. + """ + # Using a specific embedding model for better performance + embedding_model = SentenceTransformer("all-mpnet-base-v2") + + topic_model = BERTopic( + embedding_model=embedding_model, + verbose=True, + # You can add more parameters here + ) + return topic_model + + +def save_model(model, path): + """ + Save the BERTopic model to disk. + """ + joblib.dump(model, path) + print(f"Model saved to {path}") + + +def load_model(path): + """ + Load the BERTopic model from disk. + """ + if os.path.exists(path): + model = joblib.load(path) + print(f"Model loaded from {path}") + return model + else: + print(f"No existing model found at {path}. Initializing a new model.") + return None diff --git a/concord/concord.py b/concord/concord.py new file mode 100644 index 0000000..a126d65 --- /dev/null +++ b/concord/concord.py @@ -0,0 +1,84 @@ +# concord.py + +from bertopic import BERTopic +from sklearn.datasets import fetch_20newsgroups + +from bert.bert import load_model, save_model + +# Configuration +MODEL_SAVE_PATH = "bertopic_model.pkl" +INITIAL_BATCH_SIZE = 100 # Number of documents in the initial batch +BATCH_SIZE = 50 # Number of documents per new batch +TOTAL_BATCHES = 10 # Total number of batches to simulate + + +def load_data(batch_number, batch_size): + """ + Simulate loading a batch of data. + For demonstration, we're using the 20 Newsgroups dataset. + In a real-world scenario, replace this with your data loading mechanism. + """ + newsgroups = fetch_20newsgroups(subset="all", + remove=("headers", "footers", "quotes")) + start = batch_number * batch_size + end = start + batch_size + if start >= len(newsgroups.data): + return [] + return newsgroups.data[start:end] + + +def setup(): + # Load existing model or initialize a new one + topic_model = load_model(MODEL_SAVE_PATH) + + # Initialize data storage + all_documents = [] + + if topic_model is None: + # Initial batch + print("Processing initial batch...") + initial_batch = load_data(batch_number=0, + batch_size=INITIAL_BATCH_SIZE) + all_documents.extend(initial_batch) + + # Fit the model with the initial batch + topic_model = BERTopic() + topics, probs = topic_model.fit_transform(all_documents) + + # Save the model + save_model(topic_model, MODEL_SAVE_PATH) + else: + # If model exists, load existing documents if stored + # For simplicity, we're not storing all_documents. In a real application, consider storing them. + print("Existing model loaded. Starting incremental updates...") + # Optionally, load existing documents from a file or database + # all_documents = load_existing_documents() + + # Simulate incremental updates with new batches + for batch_num in range(1, TOTAL_BATCHES + 1): + print(f"\nProcessing batch {batch_num}...") + new_batch = load_data(batch_number=batch_num, batch_size=BATCH_SIZE) + + if not new_batch: + print("No more data to process.") + break + + all_documents.extend(new_batch) + + # Refit the model with all documents (existing + new) + print("Refitting the BERTopic model with the updated dataset...") + topic_model = BERTopic() + topics, probs = topic_model.fit_transform(all_documents) + + # Optionally, analyze topics + print( + f"Number of topics after batch {batch_num}: {len(set(topics)) - (1 if -1 in topics else 0)}" + ) + + # Save the updated model + save_model(topic_model, MODEL_SAVE_PATH) + + # Optional: Integrate with Neo4j to store/update topics + # store_topics_in_neo4j(topic_model, batch_num) + + print("\nTopic modeling completed.") diff --git a/concord/fast_api.py b/concord/fast_api.py new file mode 100644 index 0000000..b6b5603 --- /dev/null +++ b/concord/fast_api.py @@ -0,0 +1,10 @@ +# fast_api.py + +from fastapi import FastAPI + +app = FastAPI(title="Concord API", version="1.0") + + +@app.get("/") +def read_root(): + return {"message": "Welcome to Concord API"} diff --git a/concord/graph/__init__.py b/concord/graph/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/concord/graph/graph.py b/concord/graph/graph.py new file mode 100644 index 0000000..fa09ccf --- /dev/null +++ b/concord/graph/graph.py @@ -0,0 +1,37 @@ +# graph.py +import os + +from neo4j import GraphDatabase + + +# Initialize Neo4j driver +def initialize_neo4j(): + # Get uri username and password from ENV + user = os.environ.get("NEO4J_USERNAME") + password = os.environ.get("NEO4J_PASSWORD") + uri = os.environ.get("NEO4J_URI") + + return GraphDatabase.driver(uri, auth=(user, password)) + + +# Function to store topics in Neo4j +def store_topics_in_neo4j(model, batch_num): + """ + Store topics and their relationships in Neo4j. + """ + driver = initialize_neo4j() + with driver.session() as session: + topics = model.get_topics() + for topic_num, words in topics.items(): + if topic_num == -1: + continue # -1 is usually the outlier/noise topic + # Create Topic node + session.run( + "MERGE (t:Topic {id: $id}) " + "SET t.keywords = $keywords, t.batch = $batch", + id=topic_num, + keywords=words, + batch=batch_num, + ) + driver.close() + print("Topics stored in Neo4j.") diff --git a/concord/main.py b/concord/main.py index f2f0af7..3f9d467 100644 --- a/concord/main.py +++ b/concord/main.py @@ -1,6 +1,28 @@ -def main(): - return +# main.py + +import threading +import time + +import uvicorn + +from fast_api import app as fastapi_app + + +def run_fastapi_server(): + uvicorn.run(fastapi_app, host="0.0.0.0", port=8000) if __name__ == "__main__": - main() + # Create threads for FastAPI servers + fastapi_thread = threading.Thread(target=run_fastapi_server, daemon=True) + + # Start the servers + fastapi_thread.start() + + print("Concord servers are running.") + + try: + while True: + time.sleep(86400) + except KeyboardInterrupt: + print("Shutting down servers...") diff --git a/docker-compose.yml b/docker-compose.yml new file mode 100644 index 0000000..d1ded95 --- /dev/null +++ b/docker-compose.yml @@ -0,0 +1,10 @@ +services: + neo4j: + image: neo4j:5.24.2 + container_name: neo4j-dev + ports: + - "7474:7474" # HTTP port for Neo4j Browser + - "7687:7687" # Bolt port for client connections + environment: + NEO4J_AUTH: ${NEO4J_AUTH} + restart: unless-stopped \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index 695471f..f776e14 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,48 +1,78 @@ # This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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a/pyproject.toml +++ b/pyproject.toml @@ -8,12 +8,19 @@ readme = "README.md" [tool.poetry.dependencies] python = "^3.12" +bertopic = "^0.16.4" +llvmlite = "0.43.0" +numba = "0.60" +neo4j = "^5.25.0" +fastapi = "^0.115.4" +uvicorn = "^0.32.0" [tool.poetry.group.dev.dependencies] pytest = "^8.3.3" flake8 = "^7.1.1" -black = "^24.10.0" pre-commit = "^4.0.1" +httpx = "^0.27.2" +yapf = "^0.40.2" [build-system] requires = ["poetry-core"] diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000..0f77bf8 --- /dev/null +++ b/setup.cfg @@ -0,0 +1,13 @@ +[flake8] +max-line-length = 120 +extend-ignore = E203, W503 +exclude = .git,__pycache__,build,dist,.venv + +[style] +based_on_style = pep8 +column_limit = 120 +blank_lines_around_top_level_definition = 2 +split_before_logical_operator = true +split_before_expression_after_opening_paren = true +split_before_first_argument = true +dedent_closing_brackets = true diff --git a/tests/test_fast_api.py b/tests/test_fast_api.py new file mode 100644 index 0000000..4094b99 --- /dev/null +++ b/tests/test_fast_api.py @@ -0,0 +1,23 @@ +# test_fast_api.py + +from fastapi.testclient import TestClient + +from concord.fast_api import app + +client = TestClient(app) + + +def test_root_endpoint_returns_welcome_message(): + response = client.get("/") + assert response.status_code == 200 + assert response.json() == {"message": "Welcome to Concord API"} + + +def test_root_endpoint_handles_get_method(): + response = client.get("/") + assert response.status_code == 200 + + +def test_root_endpoint_handles_post_method(): + response = client.post("/") + assert response.status_code == 405 diff --git a/tests/test_main.py b/tests/test_main.py deleted file mode 100644 index 1e8bfd2..0000000 --- a/tests/test_main.py +++ /dev/null @@ -1,7 +0,0 @@ -# tests/test_main.py - -from concord.main import main - - -def test_main(): - assert main() is None