merge changes from code-graph

cognee/infrastructure/llm/prompts/patch_gen_instructions.txt

@@ -1,3 +1,2 @@
-I need you to solve this issue by looking at the provided edges retrieved from a knowledge graph and 
-generate a single patch file that I can apply directly to this repository using git apply. 
+I need you to solve this issue by generating a single patch file that I can apply directly to this repository using git apply.
 Please respond with a single patch file in the following format.

cognee/infrastructure/llm/prompts/patch_gen_kg_instructions.txt

@@ -0,0 +1,3 @@
+I need you to solve this issue by looking at the provided knowledge graph and 
+generating a single patch file that I can apply directly to this repository using git apply. 
+Please respond with a single patch file in the following format.

evals/EC2_README.md

@@ -0,0 +1,64 @@
+## Creating the EC2 Instance
+
+Create an EC2 Instance with the 
+
+`Ubuntu Image`
+
+Many instance types will work, we used:
+
+`m7a.2xlarge` # more than 8 parallel processes doesn't seem to speed up overall process. Maybe to do with docker parallelism?
+
+DON'T FORGET TO ADD
+
+`500 GB storage`
+
+Or the evaluation run will run out of space
+
+Add a key pair login where you have access to the corresponding key file (*.pem)
+
+## Accessing your instance and setup
+
+To ssh into the instance, you have to save your key pair file (*.pem) to an appropriate location, such as ~/.aws. After launching the instance, you can access the Instance Summary, and retrieve "Public IPv4 DNS" address. Then run
+
+`ssh -i PATH_TO_KEY ubuntu@IPv4ADDRESS`
+
+to gain command line access to the instance.
+
+To copy your current state of cognee, go to the folder that contains "cognee" on your local machine, zip it to cognee.zip and run:
+
+`zip -r cognee.zip cognee`
+`scp -i PATH_TO_KEY cognee.zip ubuntu@IPv4ADDRESS:cognee.zip`
+
+And unzip cognee.zip in your SSH session:
+
+`sudo apt install unzip`
+`unzip cognee.zip`
+
+Then run:
+`cd cognee`
+`source evals/cloud/setup_ubuntu_instance.sh`
+
+`sudo usermod -aG docker $USER`
+
+disconnect, and reconnect. 
+
+Confirm that `ubuntu` has been added to the docker user group with
+
+`groups | grep docker`
+
+## Running SWE-bench
+
+Then enter a `screen` and activate the virtual env
+
+`screen`
+`source venv/bin/activate`
+
+then, from cognee, you can run swe_bench:
+
+`cd cognee`
+
+`python evals/eval_swe_bench.py --cognee_off --max_workers=N_CPUS`
+
+Building the environment images should take roughly 17 minutes
+
+If the virtual env wasn't set up correctly for some reason, just run the last few lines of `setup_ubuntu_instance.sh` manually

evals/cloud/setup_ubuntu_instance.sh

@@ -0,0 +1,33 @@
+sudo apt-get update -y
+sudo apt-get install -y ca-certificates curl
+sudo install -m 0755 -d /etc/apt/keyrings
+sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
+sudo chmod a+r /etc/apt/keyrings/docker.asc
+
+# Add the repository to Apt sources:
+echo \
+"deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
+ $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
+sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
+sudo apt-get update -y
+
+sudo apt-get install -y docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
+
+sudo docker run hello-world
+
+sudo apt install -y unzip
+
+sudo apt-get install -y python3-virtualenv
+
+sudo add-apt-repository -y ppa:deadsnakes/ppa
+
+sudo apt update -y
+
+sudo apt install -y python3.11
+
+virtualenv venv --python=python3.11
+
+source venv/bin/activate
+pip install poetry
+poetry install
+pip install swebench transformers sentencepiece datasets tiktoken protobuf

evals/eval_swe_bench.py

@@ -1,6 +1,7 @@
 import argparse
 import json
 import subprocess
+import sys
 from pathlib import Path
 
 from datasets import Dataset
@@ -13,6 +14,25 @@ from cognee.api.v1.search import SearchType
 from cognee.infrastructure.databases.graph import get_graph_engine
 from cognee.infrastructure.llm.get_llm_client import get_llm_client
 from cognee.infrastructure.llm.prompts import read_query_prompt
+from evals.eval_utils import download_instances
+
+
+def check_install_package(package_name):
+    """
+    Check if a pip package is installed and install it if not.
+    Returns True if package is/was installed successfully, False otherwise.
+    """
+    try:
+        __import__(package_name)
+        return True
+    except ImportError:
+        try:
+            subprocess.check_call(
+                [sys.executable, "-m", "pip", "install", package_name]
+            )
+            return True
+        except subprocess.CalledProcessError:
+            return False
 from cognee.modules.pipelines import Task, run_tasks
 from cognee.modules.retrieval.brute_force_triplet_search import \
     brute_force_triplet_search
@@ -39,7 +59,8 @@ def retrieved_edges_to_string(retrieved_edges):
         edge_strings.append(edge_str)
     return "\n".join(edge_strings)  
 
-async def generate_patch_with_cognee(instance):
+async def generate_patch_with_cognee(instance, llm_client, search_type=SearchType.CHUNKS):
+
     await cognee.prune.prune_data()
     await cognee.prune.prune_system()
 
@@ -69,7 +90,7 @@ async def generate_patch_with_cognee(instance):
     await render_graph(None, include_labels = True, include_nodes = True)
 
     problem_statement = instance['problem_statement']
-    instructions = read_query_prompt("patch_gen_instructions.txt")
+    instructions = read_query_prompt("patch_gen_kg_instructions.txt")
 
     retrieved_edges = await brute_force_triplet_search(problem_statement, top_k = 3)
     
@@ -93,20 +114,20 @@ async def generate_patch_with_cognee(instance):
     return answer_prediction
 
 
-async def generate_patch_without_cognee(instance):
-    problem_statement = instance['problem_statement']
-    prompt = instance["text"]
+async def generate_patch_without_cognee(instance, llm_client):
+    instructions = read_query_prompt("patch_gen_instructions.txt")
 
-    llm_client = get_llm_client()
     answer_prediction = await llm_client.acreate_structured_output(
-        text_input=problem_statement,
-        system_prompt=prompt,
+        text_input=instance["text"],
+        system_prompt=instructions,
         response_model=str,
     )
     return answer_prediction
 
 
 async def get_preds(dataset, with_cognee=True):
+    llm_client = get_llm_client()
+
     if with_cognee:
         model_name = "with_cognee"
         pred_func = generate_patch_with_cognee
@@ -114,14 +135,21 @@ async def get_preds(dataset, with_cognee=True):
         model_name = "without_cognee"
         pred_func = generate_patch_without_cognee
 
+    futures = [
+        (instance["instance_id"], pred_func(instance, llm_client))
+        for instance in dataset
+    ]
+    model_patches = await asyncio.gather(*[x[1] for x in futures])
 
-    for instance in dataset:
-        await pred_func(instance)
+    preds = [
+        {
+            "instance_id": instance_id,
+            "model_patch": model_patch,
+            "model_name_or_path": model_name,
+        }
+        for (instance_id, _), model_patch in zip(futures, model_patches)
+    ]
 
-    preds = [{"instance_id": instance["instance_id"],
-              "model_patch": await pred_func(instance),
-              "model_name_or_path": model_name} for instance in dataset]
-  
     return preds
 
 
@@ -129,8 +157,12 @@ async def main():
     parser = argparse.ArgumentParser(
         description="Run LLM predictions on SWE-bench dataset")
     parser.add_argument('--cognee_off', action='store_true')
+    parser.add_argument("--max_workers", type=int, required=True)
     args = parser.parse_args()
 
+    for dependency in ["transformers", "sentencepiece", "swebench"]:
+        check_install_package(dependency)
+
     if args.cognee_off:
         dataset_name = 'princeton-nlp/SWE-bench_Lite_bm25_13K'
         dataset = load_swebench_dataset(dataset_name, split='test')
@@ -153,12 +185,25 @@ async def main():
         with open(predictions_path, "w") as file:
             json.dump(preds, file)
 
-    subprocess.run(["python", "-m", "swebench.harness.run_evaluation",
-                    "--dataset_name", dataset_name,
-                    "--split", "test",
-                    "--predictions_path",  predictions_path,
-                    "--max_workers", "1",
-                    "--run_id", "test_run"])
+
+    subprocess.run(
+        [
+            "python",
+            "-m",
+            "swebench.harness.run_evaluation",
+            "--dataset_name",
+            dataset_name,
+            "--split",
+            "test",
+            "--predictions_path",
+            predictions_path,
+            "--max_workers",
+            str(args.max_workers),
+            "--run_id",
+            "test_run",
+        ]
+    )
+
 
 if __name__ == "__main__":
     import asyncio