chATLAS_Chains 0.1.3__py3-none-any.whl

chatlas_chains-0.1.3.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
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chatlas_chains-0.1.3.dist-info/top_level.txt

@@ -0,0 +1,3 @@
+benchmark
+chATLAS_Chains
+tests

tests/conftest.py

@@ -0,0 +1,274 @@
+"""
+Some elements of a chain require a LangChainVectorStore object with a running PG server to connect to locally.
+This
+
+**NOTE** If running tests on lxplus can just connect to CERN dbod and
+update the TEST_DB_CONFIG to be correct for your server
+
+Pytest fixtures to:
+- Creates a test_db environment for testing the postgresql
+- Creates fake twiki documents to write to the db with
+- Populates the vectorstore with these documents
+"""
+
+import os
+import tempfile
+from pathlib import Path
+
+import psycopg2
+import pytest
+
+from chATLAS_Embed import (
+    PostgresParentChildVectorStore,
+    RecursiveTextSplitter,
+    syncedTwikiVectorStoreCreator,
+)
+from chATLAS_Embed.EmbeddingModels import SentenceTransformerEmbedding
+
+# Database configuration for testing
+TEST_DB_CONFIG = {
+    "host": "localhost",
+    "port": 5432,
+    "user": "postgres",
+    "password": "password",
+    "database": "chatlas_test_db",
+}
+
+
+@pytest.fixture(scope="session")
+def test_db():
+    """Create a test database and clean it up after tests"""
+    # Connect to default postgres database to create test database
+    conn = psycopg2.connect(
+        host=TEST_DB_CONFIG["host"],
+        port=TEST_DB_CONFIG["port"],
+        user=TEST_DB_CONFIG["user"],
+        password=TEST_DB_CONFIG["password"],
+        database="postgres",
+    )
+    conn.autocommit = True
+    cursor = conn.cursor()
+
+    # Drop test database if it exists and create new one
+    cursor.execute(f"DROP DATABASE IF EXISTS {TEST_DB_CONFIG['database']}")
+    cursor.execute(f"CREATE DATABASE {TEST_DB_CONFIG['database']}")
+
+    cursor.close()
+    conn.close()
+
+    # Return connection string for the test database
+    connection_string = f"postgresql://{TEST_DB_CONFIG['user']}:{TEST_DB_CONFIG['password']}@{TEST_DB_CONFIG['host']}:{TEST_DB_CONFIG['port']}/{TEST_DB_CONFIG['database']}"
+
+    yield connection_string
+
+    # Cleanup: Drop test database after all tests
+    try:
+        # Reconnect to the postgres database
+        conn = psycopg2.connect(
+            host=TEST_DB_CONFIG["host"],
+            port=TEST_DB_CONFIG["port"],
+            user=TEST_DB_CONFIG["user"],
+            password=TEST_DB_CONFIG["password"],
+            database="postgres",
+        )
+        conn.autocommit = True
+        cursor = conn.cursor()
+
+        # Disconnect any other sessions connected to the test database
+        cursor.execute(f"""
+            SELECT pg_terminate_backend(pid)
+            FROM pg_stat_activity
+            WHERE datname = '{TEST_DB_CONFIG["database"]}'
+            AND pid <> pg_backend_pid();
+        """)
+
+        # Now drop the database
+        cursor.execute(f"DROP DATABASE IF EXISTS {TEST_DB_CONFIG['database']}")
+        cursor.close()
+        conn.close()
+
+    except psycopg2.errors.ObjectInUse:
+        print(f"Database {TEST_DB_CONFIG['database']} is still in use, skipping drop.")
+
+
+@pytest.fixture(scope="session")
+def embedding_model():
+    """Initialize the real embedding model"""
+    return SentenceTransformerEmbedding(model_name="sentence-transformers/all-MiniLM-L6-v2")
+
+
+@pytest.fixture(scope="session")
+def test_docs():
+    """Create temporary test documents"""
+    temp_dir = tempfile.mkdtemp()
+    docs = []
+
+    # Create sample TWiki documents
+    test_contents = [
+        {
+            "filename": "ADCPlotOperations.txt",
+            "content": """%META:TOPICINFO{author="BaseUserMapping_333" date="1416477899" format="1.1" version="1.369"}%
+%META:TOPICPARENT{name="ADCOperationsDailyReports"}%
+%STARTINCLUDE%
+The ATLAS Experiment is one of the largest particle physics experiments at CERN.
+It is designed to study particle collisions at the Large Hadron Collider.
+The detector is 46 meters long and weighs about 7,000 tonnes.
+ATLAS is one of two general-purpose detectors at the Large Hadron Collider (LHC). It investigates a wide range of physics,
+from the Higgs boson to extra dimensions and particles that could make up dark matter.
+Although it has the same scientific goals as the CMS experiment, it uses different technical solutions and a different magnet-system design.
+Beams of particles from the LHC collide at the centre of the ATLAS detector making collision debris in the form of new particles,
+which fly out from the collision point in all directions. Six different detecting subsystems arranged in layers around the collision point record the paths,
+momentum, and energy of the particles, allowing them to be individually identified. A huge magnet system bends the paths of charged particles so that their momenta can be measured.
+
+The interactions in the ATLAS detectors create an enormous flow of data. To digest the data, ATLAS uses an advanced
+“trigger” system to tell the detector which events to record and which to ignore. Complex data-acquisition and
+computing systems are then used to analyse the collision events recorded. At 46 m long, 25 m high and 25 m wide,
+the 7000-tonne ATLAS detector is the largest volume particle detector ever constructed. It sits in a cavern 100 m
+below ground near the main CERN site, close to the village of Meyrin in Switzerland.
+
+below ground near the main CERN site, close to the village of Meyrin in Switzerland.
+below ground near the main CERN site, close to the village of Meyrin in Switzerland.
+below ground near the main CERN site, close to the village of Meyrin in Switzerland.
+below ground near the main CERN site, close to the village of Meyrin in Switzerland.
+below ground near the main CERN site, close to the village of Meyrin in Switzerland.
+
+More than 5500 scientists from 245 institutes in 42 countries work on the ATLAS experiment (March 2022).
+For the latest information, see here.
+%STOPINCLUDE%
+Extra other info which should not be included.
+""",
+        },
+        {
+            "filename": "Higgs_Boson.txt",
+            "content": """%META:TOPICINFO{author="wikipedia" date="1736878918" format="1.1" version="1.3"}%
+%META:TOPICPARENT{name="HiggsToTauTauToHH2012Winter"}%
+
+%STARTINCLUDE%
+TWiki https://twiki.cern.ch/twiki/bin/view/Main/WebHome
+Atlas Web https://twiki.cern.ch/twiki/bin/view/Atlas/WebHome
+AtlasUpgrade https://twiki.cern.ch/twiki/bin/view/Atlas/AtlasUpgrade
+UpgradeProjectOffice https://twiki.cern.ch/twiki/bin/view/Atlas/UpgradeProjectOffice
+UpgradeProjectOfficeCAD https://twiki.cern.ch/twiki/bin/view/Atlas/UpgradeProjectOfficeCAD
+3DDataExchangeProcess https://twiki.cern.ch/twiki/bin/view/Atlas/3DDataExchangeProcess
+-----HEADERS-----
+h1: 3D Data exchange between ATLAS TC and collaboration institutes
+
+-----TEXT-----
+The Higgs boson was discovered by the ATLAS and CMS experiments in 2012.
+This discovery confirmed the existence of the Higgs field, which gives particles their mass.
+Peter Higgs and François Englert won the Nobel Prize in Physics for this theoretical prediction.
+The Higgs boson, sometimes called the Higgs particle, is an elementary particle in the Standard Model of particle
+physics produced by the quantum excitation of the Higgs field, one of the fields in particle physics theory.
+In the Standard Model, the Higgs particle is a massive scalar boson with zero spin, even (positive) parity,
+no electric charge, and no colour charge that couples to (interacts with) mass. It is also very unstable,
+decaying into other particles almost immediately upon generation.
+The Higgs field is a scalar field with two neutral and two electrically charged components that form a complex doublet
+of the weak isospin SU(2) symmetry. Its "Sombrero potential" leads it to take a nonzero value everywhere
+(including otherwise empty space), which breaks the weak isospin symmetry of the electroweak interaction and,
+via the Higgs mechanism, gives a rest mass to all massive elementary particles of the Standard Model,
+including the Higgs boson itself. The existence of the Higgs field became the last unverified part of the Standard
+Model of particle physics, and for several decades was considered "the central problem in particle physics"
+The Higgs boson, sometimes called the Higgs particle, is an elementary particle in the Standard Model of
+particle physics produced by the quantum excitation of the Higgs field, one of the fields in particle physics theory.
+As a layman I would now say… I think we have it.
+
+“It” was the Higgs boson, the almost-mythical entity that had put particle physics in the global spotlight,
+and the man proclaiming to be a mere layman was none other than CERN’s Director-General, Rolf Heuer.
+Heuer spoke in the Laboratory’s main auditorium on 4 July 2012, moments after the CMS and ATLAS collaborations
+at the Large Hadron Collider announced the discovery of a new elementary particle, which we now know is a Higgs boson.
+Applause reverberated in Geneva from as far away as Melbourne, Australia, where delegates of the International
+Conference on High Energy Physics were connected via video-conference.higgsjuly4,seminar,Milestones,
+Higgs Boson Discovery,360
+4 July 2012: A packed auditorium at CERN listens keenly to the announcement from CMS and ATLAS (Image: Maximilien Brice/CERN)
+So what exactly is so special about this particle?“Easy! It is the first and only elementary scalar
+particle we have observed,” grins Rebeca Gonzalez Suarez, who, as a doctoral student, was involved in
+the CMS search for the Higgs boson. Easy for a physicist,
+%STOPINCLUDE%
+Extra text that should be ignored
+            """,
+        },
+        {
+            "filename": "LHC.txt",
+            "content": """%META:TOPICINFO{author="google" date="1328618061" format="1.1" version="1.3"}%
+%META:TOPICPARENT{name="LHC"}%
+
+%STARTINCLUDE%
+-----PARENT STRUCTURE----
+TWiki https://twiki.cern.ch/twiki/bin/view/Main/WebHome
+Atlas Web https://twiki.cern.ch/twiki/bin/view/Atlas/WebHome
+AtlasUpgrade https://twiki.cern.ch/twiki/bin/view/Atlas/AtlasUpgrade
+UpgradeProjectOffice https://twiki.cern.ch/twiki/bin/view/Atlas/UpgradeProjectOffice
+UpgradeProjectOfficeCAD https://twiki.cern.ch/twiki/bin/view/Atlas/UpgradeProjectOfficeCAD
+-----HEADERS-----
+h1: 3D Data exchange between ATLAS TC and collaboration institutes
+
+-----TEXT-----
+The Large Hadron Collider (LHC) is the world's largest particle accelerator.
+It consists of a 27-kilometer ring of superconducting magnets.
+The LHC can collide protons at energies up to 13 TeV.
+Inside the accelerator, two high-energy particle beams travel at close to the speed of light before they
+are made to collide. The beams travel in opposite directions in separate beam pipes – two tubes kept at
+ultrahigh vacuum. They are guided around the accelerator ring by a strong magnetic field maintained by
+superconducting electromagnets. The electromagnets are built from coils of special electric cable that
+operates in a superconducting state, efficiently conducting electricity without resistance or loss of energy.
+This requires chilling the magnets to ‑271.3°C – a temperature colder than outer space. For this reason,
+much of the accelerator is connected to a distribution system of liquid helium, which cools the magnets,
+as well as to other supply services.
+
+LHC stands for Large Hadron Collider, the world's largest and most powerful particle accelerator. It's located in a tunnel at CERN, the European Organization for Nuclear Research, on the Swiss-French border.
+How it works
+The LHC is a 27-kilometer ring of superconducting magnets that accelerate particles.
+Beams of particles collide at four locations around the ring.
+The collisions produce tiny fireballs that are hotter than the core of the sun.
+What it's used for
+The LHC has helped scientists discover the Higgs boson, a particle that gives mass to other particles.
+The LHC may also help scientists understand why there is an imbalance of matter and antimatter in the universe.
+Safety
+The LHC Safety Assessment Group (LSAG) has concluded that the LHC collisions are not dangerous.
+The LSAG's conclusions have been endorsed by CERN's Scientific Policy Committee.
+History
+The LHC was built between 1998 and 2008 with the help of over 10,000 scientists from hundreds of universities and laboratories.
+It first started up on September 10, 2008.
+%STOPINCLUDE%
+       """,
+        },
+    ]
+
+    for doc in test_contents:
+        doc_path = Path(temp_dir) / doc["filename"]
+        with open(doc_path, "w", encoding="UTF-8") as f:
+            f.write(doc["content"])
+        docs.append(doc_path)
+
+    yield Path(temp_dir)
+
+    # Cleanup temporary files
+    for doc in docs:
+        os.remove(doc)
+    os.rmdir(temp_dir)
+
+
+@pytest.fixture(scope="session")
+def vector_store(test_db, embedding_model):
+    """Initialize the vector store with test database"""
+    return PostgresParentChildVectorStore(connection_string=test_db, embedding_model=embedding_model)
+
+
+@pytest.fixture(scope="session")
+def populated_vector_store(vector_store, test_docs):
+    """Populate the vector store with test documents"""
+    parent_splitter = RecursiveTextSplitter(chunk_size=2048, chunk_overlap=24)
+    child_splitter = RecursiveTextSplitter(chunk_size=256, chunk_overlap=24)
+
+    twiki_creator = syncedTwikiVectorStoreCreator(
+        vector_store=vector_store,
+        child_splitter=child_splitter,
+        parent_splitter=parent_splitter,
+        output_dir=Path("./test_output"),
+    )
+
+    twiki_creator.create_update_vectorstore(input_path=test_docs, update=True, verbose=True)
+
+    yield vector_store
+
+    del vector_store

tests/test_chains.py

@@ -0,0 +1,54 @@
+"""
+Unit tests for basic_retrieval_chain
+
+These**NOTE** These require a running postgres database with a populated vector store.
+
+The fixtures used for the tests are defined in conftest.py and are automatically gathered by pytest
+"""
+
+import pytest
+from langchain_core.runnables import RunnableSequence
+from pydantic import ValidationError
+
+from chATLAS_Chains.chains.basic import basic_retrieval_chain
+from chATLAS_Chains.prompt.starters import CHAT_PROMPT_TEMPLATE
+
+
+def test_basic_retrieval_chain_returns_runnablesequence(populated_vector_store):
+    """
+    Test the search_runnable function with a populated vector store.
+    """
+
+    chain = basic_retrieval_chain(
+        prompt=CHAT_PROMPT_TEMPLATE, vectorstore=populated_vector_store, model_name="gpt-4o-mini"
+    )
+
+    assert isinstance(chain, RunnableSequence)
+
+
+@pytest.fixture
+def vectorstores_list(populated_vector_store):
+    return [populated_vector_store for _ in range(3)]
+
+
+def test_search_runnable_returns_runnablesequence_with_list_of_vectorstores(vectorstores_list):
+    chain = basic_retrieval_chain(prompt=CHAT_PROMPT_TEMPLATE, vectorstore=vectorstores_list, model_name="gpt-4o-mini")
+    print(type(chain))
+    assert isinstance(chain, RunnableSequence)
+
+
+def test_search_runnable_error_on_invalid_input():
+    with pytest.raises(ValidationError):
+        basic_retrieval_chain(prompt=CHAT_PROMPT_TEMPLATE, vectorstore="not a vectorstore", model_name="gpt-4o-mini")
+
+
+def test_search_runnable_returns_docs_and_answer(populated_vector_store):
+    chain = basic_retrieval_chain(
+        prompt=CHAT_PROMPT_TEMPLATE, vectorstore=populated_vector_store, model_name="gpt-4o-mini"
+    )
+    output = chain.invoke("What is the Higgs boson?")
+
+    assert "docs" in output
+    assert "answer" in output
+
+    assert isinstance(output["docs"], list)

tests/test_llm.py

@@ -0,0 +1,81 @@
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from chATLAS_Chains.llm.model_selection import SUPPORTED_CHAT_MODELS, get_chat_model  # Replace with actual path
+
+
+@pytest.fixture
+def mock_env_key(monkeypatch):
+    monkeypatch.setenv("CHATLAS_OPENAI_KEY", "fake-api-key")
+
+
+@pytest.fixture
+def mock_model_class():
+    """Returns a MagicMock class that returns a mock instance when called."""
+    mock_instance = MagicMock(name="MockChatModelInstance")
+    mock_class = MagicMock(name="MockChatModelClass", return_value=mock_instance)
+    return mock_class
+
+
+def test_get_chat_model_valid_model_name(mock_env_key, mock_model_class):
+    with patch("importlib.import_module") as mock_import_module:
+        mock_import_module.return_value = MagicMock(ChatOpenAI=mock_model_class)
+
+        model = get_chat_model("gpt-4")
+
+        mock_import_module.assert_called_with("langchain_openai")
+        mock_model_class.assert_called_once_with(model_name="gpt-4", openai_api_key="fake-api-key")
+        assert model is mock_model_class.return_value
+
+
+def test_get_chat_model_unsupported_model_name_defaults(mock_env_key, mock_model_class):
+    with patch("importlib.import_module") as mock_import_module:
+        mock_import_module.return_value = MagicMock(ChatOpenAI=mock_model_class)
+
+        model = get_chat_model("unknown-model")
+
+        mock_model_class.assert_called_once_with(model_name="gpt-4o-mini", openai_api_key="fake-api-key")
+        assert model is mock_model_class.return_value
+
+
+def test_get_chat_model_missing_env_var(monkeypatch):
+    monkeypatch.delenv("CHATLAS_OPENAI_KEY", raising=False)
+
+    with pytest.raises(ValueError, match="CHATLAS_OPENAI_KEY not set in environment"):
+        get_chat_model("gpt-3.5-turbo")
+
+
+def test_get_chat_model_api_key_stripped(monkeypatch, mock_model_class):
+    monkeypatch.setenv("CHATLAS_OPENAI_KEY", "  api-key-with-spaces  ")
+
+    with patch("importlib.import_module") as mock_import_module:
+        mock_import_module.return_value = MagicMock(ChatOpenAI=mock_model_class)
+
+        get_chat_model("gpt-4")
+        mock_model_class.assert_called_once_with(model_name="gpt-4", openai_api_key="api-key-with-spaces")
+
+
+def test_get_chat_model_import_error(mock_env_key):
+    with patch("importlib.import_module", side_effect=ImportError("Module not found")):
+        with pytest.raises(ImportError, match="Module not found"):
+            get_chat_model("gpt-4")
+
+
+def test_get_chat_model_attribute_error(mock_env_key):
+    mock_library = MagicMock()
+    del mock_library.ChatOpenAI  # simulate missing attribute
+
+    with patch("importlib.import_module", return_value=mock_library):
+        with pytest.raises(AttributeError):
+            get_chat_model("gpt-4")
+
+
+def test_all_supported_models_resolve(mock_env_key, mock_model_class):
+    """Checks that all models in the supported list work correctly."""
+    with patch("importlib.import_module") as mock_import_module:
+        mock_import_module.return_value = MagicMock(ChatOpenAI=mock_model_class)
+
+        for model_name in SUPPORTED_CHAT_MODELS:
+            result = get_chat_model(model_name)
+            assert result is mock_model_class.return_value

tests/test_search.py

@@ -0,0 +1,48 @@
+"""
+Unit tests for search_runnable
+
+**NOTE** These require a running postgres database with a populated vector store.
+
+The fixtures used for the tests are defined in conftest.py and are automatically gathered by pytest
+
+"""
+
+import pytest
+from langchain_core.runnables import RunnableSequence
+from pydantic import ValidationError
+
+from chATLAS_Chains.search.basic import search_runnable
+
+
+def test_search_runnable_returns_runnablesequence(populated_vector_store):
+    """
+    Test the search_runnable function with a populated vector store.
+    """
+    print(type(populated_vector_store))
+    # Create a runnable for searching
+    searcher = search_runnable(vectorstore=populated_vector_store)
+
+    assert isinstance(searcher, RunnableSequence)
+
+
+@pytest.fixture
+def vectorstores_list(populated_vector_store):
+    return [populated_vector_store for _ in range(3)]
+
+
+def test_search_runnable_returns_runnablesequence_with_list_of_vectorstores(vectorstores_list):
+    runnable = search_runnable(vectorstores_list)
+    assert isinstance(runnable, RunnableSequence)
+
+
+def test_search_runnable_error_on_invalid_input():
+    with pytest.raises(ValidationError):
+        search_runnable("not_a_vectorstore")
+
+
+def test_search_runnable_returns_docs_and_questions(populated_vector_store):
+    searcher = search_runnable(vectorstore=populated_vector_store)
+    output = searcher.invoke("What is the Higgs boson?")
+
+    assert "docs" in output
+    assert "question" in output