Add ChromaDB Support. #27

PatrykWyzgowski · 2024-09-20T12:16:12Z

Add ChromaDB Support.

github-actions · 2024-09-20T12:24:08Z

🧪 Test coverage: 92.60%

Code Coverage Summary

Filename                                                                                                Stmts    Miss  Cover    Missing
----------------------------------------------------------------------------------------------------  -------  ------  -------  --------------------------------
packages/ragbits-core/src/ragbits/core/__init__.py                                                          0       0  100.00%
packages/ragbits-core/src/ragbits/core/embeddings/__init__.py                                               0       0  100.00%
packages/ragbits-core/src/ragbits/core/embeddings/base.py                                                   4       0  100.00%
packages/ragbits-core/src/ragbits/core/llms/__init__.py                                                     4       0  100.00%
packages/ragbits-core/src/ragbits/core/llms/base.py                                                        33       4  87.88%   33, 52, 88, 97
packages/ragbits-core/src/ragbits/core/llms/litellm.py                                                     25       4  84.00%   8-9, 54, 85
packages/ragbits-core/src/ragbits/core/llms/local.py                                                       24      10  58.33%   8-9, 42-47, 57, 70-71
packages/ragbits-core/src/ragbits/core/llms/types.py                                                        8       2  75.00%   24, 28
packages/ragbits-core/src/ragbits/core/llms/clients/__init__.py                                             4       0  100.00%
packages/ragbits-core/src/ragbits/core/llms/clients/base.py                                                23       0  100.00%
packages/ragbits-core/src/ragbits/core/llms/clients/exceptions.py                                          14       6  57.14%   7-8, 17, 26-27, 36
packages/ragbits-core/src/ragbits/core/llms/clients/litellm.py                                             50      10  80.00%   10-11, 70, 108, 122-127
packages/ragbits-core/src/ragbits/core/llms/clients/local.py                                               37      12  67.57%   11-12, 62-70, 92-103
packages/ragbits-core/src/ragbits/core/prompt/__init__.py                                                   2       0  100.00%
packages/ragbits-core/src/ragbits/core/prompt/base.py                                                      18       0  100.00%
packages/ragbits-core/src/ragbits/core/prompt/parsers.py                                                   34       0  100.00%
packages/ragbits-core/src/ragbits/core/prompt/prompt.py                                                    96       2  97.92%   103, 107
packages/ragbits-core/tests/unit/__init__.py                                                                0       0  100.00%
packages/ragbits-core/tests/unit/llms/__init__.py                                                           0       0  100.00%
packages/ragbits-core/tests/unit/llms/test_litellm.py                                                      63       0  100.00%
packages/ragbits-core/tests/unit/prompts/__init__.py                                                        0       0  100.00%
packages/ragbits-core/tests/unit/prompts/test_parsers.py                                                   65       0  100.00%
packages/ragbits-core/tests/unit/prompts/test_prompt.py                                                    81       0  100.00%
packages/ragbits-dev-kit/src/ragbits/dev_kit/__init__.py                                                    0       0  100.00%
packages/ragbits-dev-kit/src/ragbits/dev_kit/prompt_lab/__init__.py                                         0       0  100.00%
packages/ragbits-dev-kit/src/ragbits/dev_kit/prompt_lab/discovery/__init__.py                               2       0  100.00%
packages/ragbits-dev-kit/src/ragbits/dev_kit/prompt_lab/discovery/prompt_discovery.py                      38       1  97.37%   62
packages/ragbits-dev-kit/tests/unit/discovery/prompt_classes_for_tests.py                                  27       0  100.00%
packages/ragbits-dev-kit/tests/unit/discovery/test_prompt_discovery.py                                     25       0  100.00%
packages/ragbits-dev-kit/tests/unit/discovery/ragbits_tests_pkg_with_prompts/__init__.py                    2       0  100.00%
packages/ragbits-dev-kit/tests/unit/discovery/ragbits_tests_pkg_with_prompts/prompts/__init__.py            3       0  100.00%
packages/ragbits-dev-kit/tests/unit/discovery/ragbits_tests_pkg_with_prompts/prompts/temp_prompt1.py       14       0  100.00%
packages/ragbits-dev-kit/tests/unit/discovery/ragbits_tests_pkg_with_prompts/prompts/temp_prompt2.py       14       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/__init__.py                                    2       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/_main.py                                      34       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/documents/__init__.py                          0       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/documents/document.py                         55       3  94.55%   52, 95, 124
packages/ragbits-document-search/src/ragbits/document_search/documents/element.py                          30       1  96.67%   34
packages/ragbits-document-search/src/ragbits/document_search/documents/sources.py                          45       8  82.22%   13-14, 58, 87, 106, 109, 120-121
packages/ragbits-document-search/src/ragbits/document_search/ingestion/__init__.py                          0       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/ingestion/document_processor.py               21       1  95.24%   80
packages/ragbits-document-search/src/ragbits/document_search/ingestion/providers/__init__.py                0       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/ingestion/providers/base.py                   14       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/ingestion/providers/dummy.py                  11       1  90.91%   29
packages/ragbits-document-search/src/ragbits/document_search/ingestion/providers/unstructured.py           26       4  84.62%   79-89, 93
packages/ragbits-document-search/src/ragbits/document_search/retrieval/__init__.py                          0       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/retrieval/rephrasers/__init__.py               0       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/retrieval/rephrasers/base.py                   5       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/retrieval/rephrasers/noop.py                   5       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/retrieval/rerankers/__init__.py                0       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/retrieval/rerankers/base.py                    6       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/retrieval/rerankers/noop.py                    7       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/vector_store/__init__.py                       0       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/vector_store/base.py                          12       0  100.00%
packages/ragbits-document-search/src/ragbits/document_search/vector_store/chromadb_store.py                75       3  96.00%   10-11, 133
packages/ragbits-document-search/src/ragbits/document_search/vector_store/in_memory.py                     18       0  100.00%
packages/ragbits-document-search/tests/__init__.py                                                          0       0  100.00%
packages/ragbits-document-search/tests/helpers.py                                                           3       0  100.00%
packages/ragbits-document-search/tests/integration/__init__.py                                              0       0  100.00%
packages/ragbits-document-search/tests/integration/test_unstructured.py                                    38      24  36.84%   22-29, 37-43, 51-57, 65-72
packages/ragbits-document-search/tests/unit/__init__.py                                                     0       0  100.00%
packages/ragbits-document-search/tests/unit/test_chromadb_store.py                                         88       1  98.86%   34
packages/ragbits-document-search/tests/unit/test_document_processor.py                                     11       0  100.00%
packages/ragbits-document-search/tests/unit/test_document_search.py                                        14       0  100.00%
packages/ragbits-document-search/tests/unit/test_documents.py                                              13       0  100.00%
packages/ragbits-document-search/tests/unit/test_elements.py                                               15       0  100.00%
packages/ragbits-document-search/tests/unit/test_gcs_source.py                                             14       0  100.00%
packages/ragbits-document-search/tests/unit/test_providers.py                                              22       0  100.00%
packages/ragbits-document-search/tests/unit/test_simple_vector_store.py                                    16       0  100.00%
TOTAL                                                                                                    1310      97  92.60%

Diff against main

Filename                                                                                       Stmts    Miss  Cover
-------------------------------------------------------------------------------------------  -------  ------  -------
packages/ragbits-document-search/src/ragbits/document_search/vector_store/chromadb_store.py      +75      +3  +96.00%
packages/ragbits-document-search/tests/unit/test_chromadb_store.py                               +88      +1  +98.86%
TOTAL                                                                                           +163      +4  +0.71%

Results for commit: 25275d1

Minimum allowed coverage is 60%

♻️ This comment has been updated with latest results

github-actions · 2024-09-20T12:35:57Z

Trivy scanning results.

.venv/lib/python3.10/site-packages/PyJWT-2.9.0.dist-info/METADATA (secrets)

Total: 1 (MEDIUM: 1, HIGH: 0, CRITICAL: 0)

MEDIUM: JWT (jwt-token)
════════════════════════════════════════
JWT token
────────────────────────────────────────
.venv/lib/python3.10/site-packages/PyJWT-2.9.0.dist-info/METADATA:80
────────────────────────────────────────
78 >>> encoded = jwt.encode({"some": "payload"}, "secret", algorithm="HS256")
79 >>> print(encoded)
80 [ *********************************************************************************************************
81 >>> jwt.decode(encoded, "secret", algorithms=["HS256"])
────────────────────────────────────────

.venv/lib/python3.10/site-packages/litellm/proxy/_types.py (secrets)

Total: 1 (MEDIUM: 1, HIGH: 0, CRITICAL: 0)

MEDIUM: Slack (slack-web-hook)
════════════════════════════════════════
Slack Webhook
────────────────────────────────────────
.venv/lib/python3.10/site-packages/litellm/proxy/_types.py:1287
────────────────────────────────────────
1285 alert_to_webhook_url: Optional[Dict] = Field(
1286 None,
1287 [ description="Mapping of alert type to webhook url. e.g. alert_to_webhook_url: {'budget_alerts': '*****************************************************************************'}",
1288 )
────────────────────────────────────────

packages/ragbits-document-search/examples/chromadb_example.py

mhordynski · 2024-09-23T07:20:25Z

packages/ragbits-document-search/src/ragbits/document_search/vector_store/chromadb_store.py

+from ragbits.document_search.vector_store.in_memory import InMemoryVectorStore, VectorDBEntry
+
+
+class ChromaDBStore(InMemoryVectorStore):


Why it derives from InMemoryVectorStory? It should be VectorStore base class.

Consider it done.

packages/ragbits-document-search/src/ragbits/document_search/vector_store/chromadb_store.py

akonarski-ds · 2024-09-23T07:13:04Z

packages/ragbits-document-search/tests/unit/test_chromadb_store.py

+
+
+def test_is_json_valid_string(mock_chromadb_store):
+    # Arrange


Really nice that you used AAA formatting for this test, could you also apply it to others ? Also, IMO comments are not necessary, only newlines for readability are useful.

@akonarski-ds it was covered in separate pull request.

packages/ragbits-document-search/tests/unit/test_chromadb_store.py

packages/ragbits-document-search/src/ragbits/document_search/vector_store/chromadb_store.py

…it function.

PatrykWyzgowski added 8 commits September 20, 2024 14:13

Added chromadb as optional dependency. Staging previous implementation.

7220ea2

Adding and example and adjusting to current VectorStore API.

71d7b34

Switching to Elements API.

4ff9c17

Adding unit tests and fixing the code tested by them.

f7d83ab

Increasing coverage with unit tests.

4a503ef

Covering 96% of the ChromaDBStore with tests.

6c9c8bb

Applying pre-commit.

717052d

Covered all pylint errors and warnings.

4f2fbfe

PatrykWyzgowski requested a review from micpst September 20, 2024 12:16

PatrykWyzgowski added 2 commits September 20, 2024 14:17

Merge branch 'main' into pw/add-chromadb-support

1d373de

Fixing pyproject.toml issues.

068b6fa

PatrykWyzgowski self-assigned this Sep 20, 2024

PatrykWyzgowski requested review from akotyla and micpst and removed request for micpst and akotyla September 20, 2024 12:24

mhordynski reviewed Sep 23, 2024

View reviewed changes

packages/ragbits-document-search/examples/chromadb_example.py Outdated Show resolved Hide resolved

mhordynski reviewed Sep 23, 2024

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akonarski-ds reviewed Sep 23, 2024

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mhordynski reviewed Sep 23, 2024

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packages/ragbits-document-search/src/ragbits/document_search/vector_store/chromadb_store.py Outdated Show resolved Hide resolved

mhordynski linked an issue Sep 23, 2024 that may be closed by this pull request

feat(document-search): add chromadb support #4

Closed

PatrykWyzgowski added 3 commits September 25, 2024 09:54

Applying review feedback.

b401594

Fixed pre-commit warning and errors.

0610aa1

feat(document-search): add chromadb support

6a942a1

PatrykWyzgowski force-pushed the pw/add-chromadb-support branch from cf88e79 to 6a942a1 Compare September 25, 2024 08:49

PatrykWyzgowski added 2 commits September 25, 2024 11:00

fix(document_search): fix test after moving private method call to in…

8096f1f

…it function.

fix(document-search): add chroma-hnswlib to libraries whitelist

25275d1

PatrykWyzgowski merged commit 7833615 into main Sep 25, 2024
3 checks passed

mhordynski deleted the pw/add-chromadb-support branch November 21, 2024 21:54

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Add ChromaDB Support. #27

Add ChromaDB Support. #27

PatrykWyzgowski commented Sep 20, 2024

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PatrykWyzgowski Sep 25, 2024

akonarski-ds Sep 23, 2024

PatrykWyzgowski Sep 25, 2024 •

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		from ragbits.document_search.vector_store.in_memory import InMemoryVectorStore, VectorDBEntry


		class ChromaDBStore(InMemoryVectorStore):



		def test_is_json_valid_string(mock_chromadb_store):
		# Arrange

Add ChromaDB Support. #27

Add ChromaDB Support. #27

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PatrykWyzgowski commented Sep 20, 2024

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.venv/lib/python3.10/site-packages/PyJWT-2.9.0.dist-info/METADATA (secrets)

.venv/lib/python3.10/site-packages/litellm/proxy/_types.py (secrets)

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