Merge branch 'main' of https://github.com/EuniAI/Prometheus into issueTesting

Author: Wes1eyyy

.coveragerc

@@ -0,0 +1,3 @@
+[run]
+omit =
+    prometheus/script/*

.github/workflows/pytest_and_coverage.yml

@@ -14,6 +14,11 @@ jobs:
       # Logging
       PROMETHEUS_LOGGING_LEVEL: DEBUG
 
+      # General settings
+      PROMETHEUS_ENVIRONMENT: local
+      PROMETHEUS_BACKEND_CORS_ORIGINS: "[\"*\"]"
+      PROMETHEUS_ENABLE_AUTHENTICATION: false
+
       # Neo4j settings
       PROMETHEUS_NEO4J_URI: bolt://localhost:7687
       PROMETHEUS_NEO4J_USERNAME: neo4j
@@ -38,16 +43,23 @@ jobs:
       PROMETHEUS_OPENAI_FORMAT_BASE_URL: https://api.openai.com/v1/chat/completions
 
       # Model settings
-      PROMETHEUS_MAX_INPUT_TOKENS: 64000
-      PROMETHEUS_TEMPERATURE: 0.3
-      PROMETHEUS_MAX_OUTPUT_TOKENS: 15000
+      PROMETHEUS_ADVANCED_MODEL_MAX_INPUT_TOKENS: 64000
+      PROMETHEUS_ADVANCED_MODEL_TEMPERATURE: 0.3
+      PROMETHEUS_ADVANCED_MODEL_MAX_OUTPUT_TOKENS: 15000
+
+      PROMETHEUS_BASE_MODEL_MAX_INPUT_TOKENS: 64000
+      PROMETHEUS_BASE_MODEL_TEMPERATURE: 0.3
+      PROMETHEUS_BASE_MODEL_MAX_OUTPUT_TOKENS: 15000
 
       # GitHub settings
       PROMETHEUS_GITHUB_ACCESS_TOKEN: github_access_token
 
       # DATABASE settings
       PROMETHEUS_DATABASE_URL: postgresql://postgres:password@localhost:5432/postgres?sslmode=disable
 
+      # JWT settings
+      PROMETHEUS_JWT_SECRET_KEY: your_jwt_secret_key
+
     steps:
       - name: Check out code
         uses: actions/checkout@v4

README.md

@@ -9,7 +9,8 @@
 <div align="center">
   <a href="https://github.com/Pantheon-temple/Prometheus/graphs/contributors"><img src="https://img.shields.io/github/contributors/Pantheon-temple/Prometheus?style=for-the-badge&color=blue" alt="Contributors"></a>
   <a href="https://github.com/Pantheon-temple/Prometheus/stargazers"><img src="https://img.shields.io/github/stars/Pantheon-temple/Prometheus?style=for-the-badge&color=blue" alt="Stargazers"></a>
-  <a href="https://github.com/Pantheon-temple/Prometheus/blob/main/LICENSE"><img src="https://img.shields.io/github/license/Pantheon-temple/Prometheus?style=for-the-badge&color=blue" alt="MIT License"></a>
+  <a href="https://github.com/Pantheon-temple/Prometheus/blob/main/LICENSE"><img src="https://img.shields.io/github/license/Pantheon-temple/Prometheus?style=for-the-badge&color=blue" alt="APACHE-2.0 License"></a>
+  <a href="https://www.arxiv.org/abs/2507.19942"><img src="https://img.shields.io/badge/Paper-arXiv-red?style=for-the-badge&logo=arxiv" alt="Paper"></a>
   <br/>
     <a href="https://github.com/Pantheon-temple/Prometheus/blob/main/CREDITS.md"><img src="https://img.shields.io/badge/Project-Credits-blue?style=for-the-badge&color=FFE165&logo=github&logoColor=white" alt="Credits"></a>
   <br/>
@@ -36,11 +37,22 @@ governed by a state machine to ensure code quality through automated reviews, bu
 ## 📊 Evaluation Results on SWE-bench Lite
 
 <div align="center">
-  <img src="./docs/static/images/barChart.png" alt="SWE-bench Lite Result" width="800"/>
+  <img src="./docs/static/images/comparison_deepseek_July08.png" alt="SWE-bench Lite Result" width="800"/>
   <p><em>Success Rate Comparison across popular agents. Prometheus achieves 28.67%.</em></p>
 </div>
 
 
+```bibtex
+@misc{Prometheus-code-agent-2025,
+      title={Prometheus: Unified Knowledge Graphs for Issue Resolution in Multilingual Codebases}, 
+      author={Zimin Chen and Yue Pan and Siyu Lu and Jiayi Xu and Claire Le Goues and Martin Monperrus and He Ye},
+      year={2025},
+      eprint={2507.19942},
+      archivePrefix={arXiv},
+      primaryClass={cs.SE},
+      url={https://arxiv.org/abs/2507.19942}, 
+}
+```
 
 ## ⚙️ Quick Start
 
@@ -54,18 +66,34 @@ governed by a state machine to ensure code quality through automated reviews, bu
 
 ### 📦 Setup
 
-1. Clone the repository:
+1. #### Clone the repository:
    ```bash
    git clone https://github.com/Pantheon-temple/Prometheus.git
    cd Prometheus
    ```
 
-2. Copy the `example.env` file to `.env` and update it with your API keys and other required configurations:
+2. #### Copy the `example.env` file to `.env` and update it with your API keys and other required configurations:
+
    ```bash
    mv example.env .env
    ```
 
-3. Start the services using Docker Compose:
+   > You need to provide a secure `JWT_SECRET_KEY` in the `.env` file.
+   > You can generate a strong key by running the following command:
+
+   ```bash
+   python -m prometheus.script.generate_jwt_token
+   ```
+
+   This will print a secure token you can copy and paste into your `.env` file
+
+3. #### Create the working directory to store logs and cloned repositories:
+
+   ```bash
+   mkdir working_dir
+   ```
+
+4. #### Start the services using Docker Compose:
 
     - **Linux (includes PostgreSQL)**:
       ```bash
@@ -82,10 +110,27 @@ governed by a state machine to ensure code quality through automated reviews, bu
       docker-compose -f docker-compose.win_mac.yml up --build
       ```
 
-4. Access Prometheus:
-    - Service: [http://localhost:9002](http://localhost:9002)
+5. #### Access Prometheus:
+    - Service: [http://localhost:9002/v1.2](http://localhost:9002/v1.2)
     - OpenAPI Docs: [http://localhost:9002/docs](http://localhost:9002/docs)
 
+6. #### Upload Your Codebase:
+
+   You can upload a GitHub repository to Prometheus using the following API endpoint:
+
+   - **Endpoint:** `POST /repository/upload/`
+     - **Request Body:** JSON object matching the `UploadRepositoryRequest` schema (see [API Documents](http://127.0.0.1:9002/docs#/repository/repository-upload_github_repository))
+
+   This will clone the specified repository (defaulting to the latest commit on the main branch) into Prometheus.
+
+7. #### 📝 Answer Repository Issues
+
+   You can ask Prometheus to analyze and answer a specific issue in your codebase using the `/issue/answer/` API endpoint.
+   
+   - **Endpoint:** `POST /issue/answer/`
+     - **Request Body:** JSON object matching the `IssueRequest` schema (see [API Documents](http://127.0.0.1:9002/docs#/issue/issue-answer_issue))
+     - **Response:** Returns the generated patch, test/build results, and a summary response.
+
 ---
 
 ## 🗄️ Database Setup
@@ -126,39 +171,6 @@ Verify Neo4J at: [http://localhost:7474](http://localhost:7474)
 
 ---
 
-## ⚙️ Configuration
-
-Set the following variables in your `.env` file:
-
-### 🔹 Neo4j
-
-* `PROMETHEUS_NEO4J_URI`
-* `PROMETHEUS_NEO4J_USERNAME`
-* `PROMETHEUS_NEO4J_PASSWORD`
-
-### 🔹 LLM Models
-
-* `PROMETHEUS_ADVANCED_MODEL`
-* `PROMETHEUS_BASE_MODEL`
-* API Keys:
-
-    * `PROMETHEUS_OPENAI_FORMAT_API_KEY`
-    * `PROMETHEUS_ANTHROPIC_API_KEY`
-    * `PROMETHEUS_GEMINI_API_KEY`
-* Base URL for LLMs:
-
-    * `PROMETHEUS_OPENAI_FORMAT_BASE_URL`
-
-### 🔹 Other Settings
-
-* `PROMETHEUS_WORKING_DIRECTORY`
-* `PROMETHEUS_GITHUB_ACCESS_TOKEN`
-* `PROMETHEUS_KNOWLEDGE_GRAPH_MAX_AST_DEPTH`
-* `PROMETHEUS_NEO4J_BATCH_SIZE`
-* `PROMETHEUS_POSTGRES_URL`
-
----
-
 ## 🧪 Development
 
 ### Requirements

docker-compose.win_mac.yml

@@ -36,6 +36,11 @@ services:
       # Logging
       - PROMETHEUS_LOGGING_LEVEL=${PROMETHEUS_LOGGING_LEVEL}
 
+      # General settings
+      - PROMETHEUS_ENVIRONMENT=${PROMETHEUS_ENVIRONMENT}
+      - PROMETHEUS_BACKEND_CORS_ORIGINS=${PROMETHEUS_BACKEND_CORS_ORIGINS}
+      - PROMETHEUS_ENABLE_AUTHENTICATION=${PROMETHEUS_ENABLE_AUTHENTICATION}
+
       # Neo4j settings
       - PROMETHEUS_NEO4J_URI=${PROMETHEUS_NEO4J_URI}
       - PROMETHEUS_NEO4J_USERNAME=${PROMETHEUS_NEO4J_USERNAME}
@@ -60,15 +65,19 @@ services:
       - PROMETHEUS_OPENAI_FORMAT_BASE_URL=${PROMETHEUS_OPENAI_FORMAT_BASE_URL}
 
       # Model settings
-      - PROMETHEUS_MAX_INPUT_TOKENS=${PROMETHEUS_MAX_INPUT_TOKENS}
-      - PROMETHEUS_MAX_OUTPUT_TOKENS=${PROMETHEUS_MAX_OUTPUT_TOKENS}
-      - PROMETHEUS_TEMPERATURE=${PROMETHEUS_TEMPERATURE}
+      - PROMETHEUS_ADVANCED_MODEL_MAX_INPUT_TOKENS=${PROMETHEUS_ADVANCED_MODEL_MAX_INPUT_TOKENS}
+      - PROMETHEUS_ADVANCED_MODEL_MAX_OUTPUT_TOKENS=${PROMETHEUS_ADVANCED_MODEL_MAX_OUTPUT_TOKENS}
+      - PROMETHEUS_ADVANCED_MODEL_TEMPERATURE=${PROMETHEUS_ADVANCED_MODEL_TEMPERATURE}
 
-      # GitHub settings
-      - PROMETHEUS_GITHUB_ACCESS_TOKEN=${PROMETHEUS_GITHUB_ACCESS_TOKEN}
+      - PROMETHEUS_BASE_MODEL_MAX_INPUT_TOKENS=${PROMETHEUS_BASE_MODEL_MAX_INPUT_TOKENS}
+      - PROMETHEUS_BASE_MODEL_MAX_OUTPUT_TOKENS=${PROMETHEUS_BASE_MODEL_MAX_OUTPUT_TOKENS}
+      - PROMETHEUS_BASE_MODEL_TEMPERATURE=${PROMETHEUS_BASE_MODEL_TEMPERATURE}
 
       # Database settings
       - PROMETHEUS_DATABASE_URL=${PROMETHEUS_DATABASE_URL}
+
+      # JWT settings
+      - PROMETHEUS_JWT_SECRET_KEY=${PROMETHEUS_JWT_SECRET_KEY}
     networks:
       - prometheus_network
     volumes:

docker-compose.yml

@@ -57,6 +57,11 @@ services:
       # Logging
       - PROMETHEUS_LOGGING_LEVEL=${PROMETHEUS_LOGGING_LEVEL}
 
+      # General settings
+      - PROMETHEUS_ENVIRONMENT=${PROMETHEUS_ENVIRONMENT}
+      - PROMETHEUS_BACKEND_CORS_ORIGINS=${PROMETHEUS_BACKEND_CORS_ORIGINS}
+      - PROMETHEUS_ENABLE_AUTHENTICATION=${PROMETHEUS_ENABLE_AUTHENTICATION}
+
       # Neo4j settings
       - PROMETHEUS_NEO4J_URI=${PROMETHEUS_NEO4J_URI}
       - PROMETHEUS_NEO4J_USERNAME=${PROMETHEUS_NEO4J_USERNAME}
@@ -81,15 +86,19 @@ services:
       - PROMETHEUS_OPENAI_FORMAT_BASE_URL=${PROMETHEUS_OPENAI_FORMAT_BASE_URL}
 
       # Model settings
-      - PROMETHEUS_MAX_INPUT_TOKENS=${PROMETHEUS_MAX_INPUT_TOKENS}
-      - PROMETHEUS_MAX_OUTPUT_TOKENS=${PROMETHEUS_MAX_OUTPUT_TOKENS}
-      - PROMETHEUS_TEMPERATURE=${PROMETHEUS_TEMPERATURE}
+      - PROMETHEUS_ADVANCED_MODEL_MAX_INPUT_TOKENS=${PROMETHEUS_ADVANCED_MODEL_MAX_INPUT_TOKENS}
+      - PROMETHEUS_ADVANCED_MODEL_MAX_OUTPUT_TOKENS=${PROMETHEUS_ADVANCED_MODEL_MAX_OUTPUT_TOKENS}
+      - PROMETHEUS_ADVANCED_MODEL_TEMPERATURE=${PROMETHEUS_ADVANCED_MODEL_TEMPERATURE}
 
-      # GitHub settings
-      - PROMETHEUS_GITHUB_ACCESS_TOKEN=${PROMETHEUS_GITHUB_ACCESS_TOKEN}
+      - PROMETHEUS_BASE_MODEL_MAX_INPUT_TOKENS=${PROMETHEUS_BASE_MODEL_MAX_INPUT_TOKENS}
+      - PROMETHEUS_BASE_MODEL_MAX_OUTPUT_TOKENS=${PROMETHEUS_BASE_MODEL_MAX_OUTPUT_TOKENS}
+      - PROMETHEUS_BASE_MODEL_TEMPERATURE=${PROMETHEUS_BASE_MODEL_TEMPERATURE}
 
       # Database settings
       - PROMETHEUS_DATABASE_URL=${PROMETHEUS_DATABASE_URL}
+
+      # JWT settings
+      - PROMETHEUS_JWT_SECRET_KEY=${PROMETHEUS_JWT_SECRET_KEY}
     volumes:
       - .:/app
       - /var/run/docker.sock:/var/run/docker.sock

docs/Evaluation-log.md

@@ -1,5 +1,7 @@
 ## This log tracks our evaluation results and associated costs.
 
-| Date       | Version  | Dataset      |  #Instance  | Model         |Resolved Rate  |  API Cost |    Notes |
-|------------|----------|--------------|------------|----------------|-------------- |---------- |---------- |
-| 2025-07-08 | v1.0     |SWE-Bench Lite|  300       |  DeepSeek V3   | 28.67%        | $80.05    |    -      |
+| Date       | Executed by | Version | Dataset                | #Instance | Model       | Resolved Rate | API Cost | Notes                              |
+|------------|-------------|---------|------------------------|-----------|-------------|---------------|----------|------------------------------------|
+| 2025-07-08 | Yue Pan     | v1.0    | SWE-Bench Lite         | 300       | DeepSeek V3 | 28.67%        | $70.05   | initial version                    |
+| 2025-07-18 | Yue Pan     | v1.0    | SWE-Bench Multilingual | 300       | DeepSeek V3 | 13.67%        | $113.6   | initial version                    |
+| 2025-07-31 | Yue Pan     | v1.1    | SWE-Bench Lite         | 300       | GPT-4o      | 30.00%        | $1569.73 | context retrieval improved version |

docs/static/images/comparison_deepseek_July08.png

@@ -1,14 +1,20 @@
 # Logging
 PROMETHEUS_LOGGING_LEVEL=DEBUG
 
+# General settings
+PROMETHEUS_ENVIRONMENT=local
+PROMETHEUS_BACKEND_CORS_ORIGINS=["*"]
+PROMETHEUS_ENABLE_AUTHENTICATION=false
+
+
 # Neo4j settings
-PROMETHEUS_NEO4J_URI=bolt://localhost:7687
+PROMETHEUS_NEO4J_URI=bolt://neo4j:7687
 PROMETHEUS_NEO4J_USERNAME=neo4j
 PROMETHEUS_NEO4J_PASSWORD=password
 PROMETHEUS_NEO4J_BATCH_SIZE=1000
 
 # Knowledge Graph settings
-PROMETHEUS_WORKING_DIRECTORY=/tmp/
+PROMETHEUS_WORKING_DIRECTORY=working_dir/
 PROMETHEUS_KNOWLEDGE_GRAPH_MAX_AST_DEPTH=3
 PROMETHEUS_KNOWLEDGE_GRAPH_CHUNK_SIZE=10000
 PROMETHEUS_KNOWLEDGE_GRAPH_CHUNK_OVERLAP=1000
@@ -25,12 +31,16 @@ PROMETHEUS_OPENAI_FORMAT_BASE_URL=https://api.openai.com/v1
 PROMETHEUS_OPENAI_FORMAT_API_KEY=your_api_key
 
 # Model settings
-PROMETHEUS_MAX_INPUT_TOKENS=64000
-PROMETHEUS_TEMPERATURE=0.3
-PROMETHEUS_MAX_OUTPUT_TOKENS=15000
+PROMETHEUS_ADVANCED_MODEL_MAX_INPUT_TOKENS=64000
+PROMETHEUS_ADVANCED_MODEL_TEMPERATURE=0.3
+PROMETHEUS_ADVANCED_MODEL_MAX_OUTPUT_TOKENS=15000
 
-# GitHub settings
-PROMETHEUS_GITHUB_ACCESS_TOKEN=github_access_token
+PROMETHEUS_BASE_MODEL_MAX_INPUT_TOKENS=64000
+PROMETHEUS_BASE_MODEL_TEMPERATURE=0.3
+PROMETHEUS_BASE_MODEL_MAX_OUTPUT_TOKENS=15000
 
 # Database settings
-PROMETHEUS_DATABASE_URL=postgresql://postgres:password@localhost:5432/postgres?sslmode=disable
+PROMETHEUS_DATABASE_URL=postgresql://postgres:password@postgres:5432/postgres?sslmode=disable
+
+# JWT settings
+PROMETHEUS_JWT_SECRET_KEY=your_jwt_secret_key