From 9093daf41ab877608c8ec77724a05330d6d5986a Mon Sep 17 00:00:00 2001 From: Graham Hukill Date: Fri, 1 May 2026 10:07:40 -0400 Subject: [PATCH 1/2] Update TDA to version 5 Why these changes are being introduced: The timdex-dataset-api (TDA) library recently had a major version bump to account for a refactor that puts Records and Embeddings on more equal footing. This resulted in records read methods moving from TIMDEXDataset to TIMDEXDataset.records. Additionally, the dataset was minorly restructured physically and logically, requiring a metadata rebuild. How this addresses that need: * Updates to TDA v5 * All records reading is updated to use td.records.read*() * All embeddings writing remains the same as td.embeddings.write() Side effects of this change: * None Relevant ticket(s): * https://mitlibraries.atlassian.net/browse/USE-530 --- embeddings/cli.py | 4 +- tests/conftest.py | 5 +- tests/test_cli.py | 2 +- uv.lock | 1627 ++++++++++++++++++++++++--------------------- 4 files changed, 882 insertions(+), 756 deletions(-) diff --git a/embeddings/cli.py b/embeddings/cli.py index cb2c6cf..a503977 100644 --- a/embeddings/cli.py +++ b/embeddings/cli.py @@ -281,7 +281,7 @@ def create_embeddings( # get ETL run records if run_id: - timdex_records = timdex_dataset.read_dicts_iter( + timdex_records = timdex_dataset.records.read_dicts_iter( table="records", columns=[ "timdex_record_id", @@ -297,7 +297,7 @@ def create_embeddings( # get current records for a source else: - timdex_records = timdex_dataset.read_dicts_iter( + timdex_records = timdex_dataset.records.read_dicts_iter( table="current_records", columns=[ "timdex_record_id", diff --git a/tests/conftest.py b/tests/conftest.py index 73a8e2e..854387a 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -7,8 +7,7 @@ import pytest from click.testing import CliRunner -from timdex_dataset_api import TIMDEXDataset -from timdex_dataset_api.record import DatasetRecord +from timdex_dataset_api import DatasetRecord, TIMDEXDataset from embeddings.embedding import Embedding, EmbeddingInput from embeddings.models import registry @@ -160,7 +159,7 @@ def dataset_with_records(tmp_path) -> TIMDEXDataset: ) timdex_dataset = TIMDEXDataset(str(dataset_path)) - timdex_dataset.write(records) + timdex_dataset.records.write(records) timdex_dataset.metadata.rebuild_dataset_metadata() # reload and return dataset diff --git a/tests/test_cli.py b/tests/test_cli.py index 9147d4c..9947d7a 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -179,7 +179,7 @@ def 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-0400 Subject: [PATCH 2/2] Gentle Python project spec alignment Why these changes are being introduced: During the upgrade to TDA v5, there were some minor things out of alignment with the current python projects specification. How this addresses that need: * updates linting and formatting to use ruff format instead of black * moves pip-audit out of linting and into a dedicated make security target * documents the long-running CVE ignores in Makefile Side effects of this change: * ruff used for linting * pip-audit only fires on git push per new pre-commit hooks Relevant ticket(s): * https://mitlibraries.atlassian.net/browse/USE-530 --- .pre-commit-config.yaml | 25 ++++++------ Makefile | 42 +++++++++++--------- README.md | 4 +- embeddings/strategies/processor.py | 1 - pyproject.toml | 4 -- uv.lock | 63 ------------------------------ 6 files changed, 40 insertions(+), 99 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4d13446..e8b9d1e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,29 +1,30 @@ default_language_version: python: python3.12 + +default_stages: + - pre-push + repos: - repo: local hooks: - - id: black-apply - name: black-apply - entry: uv run black + - id: ruff-format + name: ruff-format + entry: uv run ruff format --diff language: system pass_filenames: true types: ["python"] + - id: mypy name: mypy entry: uv run mypy language: system pass_filenames: true types: ["python"] - exclude: "tests/" - - id: ruff-apply - name: ruff-apply - entry: uv run ruff check --fix + exclude: "(tests/|output/|migrations/)" + + - id: ruff-check + name: ruff-check + entry: uv run ruff check language: system pass_filenames: true types: ["python"] - - id: pip-audit - name: pip-audit - entry: uv run pip-audit --ignore-vuln CVE-2025-2953 --ignore-vuln CVE-2025-3730 - language: system - pass_filenames: false \ No newline at end of file diff --git a/Makefile b/Makefile index dcaeb1b..f126ff3 100644 --- a/Makefile +++ b/Makefile @@ -13,22 +13,26 @@ help: # Preview Makefile commands /^[-_[:alpha:]]+:.?*#/ { printf " %-15s%s\n", $$1, $$2 }' $(MAKEFILE_LIST) # ensure OS binaries aren't called if naming conflict with Make recipes -.PHONY: help venv install update test coveralls lint black mypy ruff safety lint-apply black-apply ruff-apply check-arch dist-dev publish-dev docker-clean +.PHONY: help venv install update test coveralls lint ruff-format mypy ruff lint-fix security validate-arch ensure-builder dist-dev-gpu dist-dev-cpu dist-dev-all publish-dev-gpu publish-dev-cpu publish-dev-all docker-clean ############################################## # Python Environment and Dependency commands ############################################## -install: .venv .git/hooks/pre-commit # Install Python dependencies and create virtual environment if not exists +install: .venv .git/hooks/pre-commit .git/hooks/pre-push # Install Python dependencies and create virtual environment if not exists uv sync --group dev --group local .venv: # Creates virtual environment if not found @echo "Creating virtual environment at .venv..." uv venv .venv -.git/hooks/pre-commit: # Sets up pre-commit hook if not setup - @echo "Installing pre-commit hooks..." - uv run pre-commit install +.git/hooks/pre-commit: # Sets up pre-commit commit hooks if not setup + @echo "Installing pre-commit commit hooks..." + uv run pre-commit install --hook-type pre-commit + +.git/hooks/pre-push: # Sets up pre-commit push hooks if not setup + @echo "Installing pre-commit push hooks..." + uv run pre-commit install --hook-type pre-push venv: .venv # Create the Python virtual environment @@ -48,13 +52,13 @@ coveralls: test # Write coverage data to an LCOV report uv run coverage lcov -o ./coverage/lcov.info #################################### -# Code quality and safety commands +# Code linting, formatting, and security #################################### -lint: black mypy ruff safety # Run linters +lint: ruff-format mypy ruff # Run linting, alerts only, no code changes -black: # Run 'black' linter and print a preview of suggested changes - uv run black --check --diff . +ruff-format: # Run 'ruff format' and print a preview of suggested changes + uv run ruff format --diff . mypy: # Run 'mypy' linter uv run mypy . @@ -62,17 +66,19 @@ mypy: # Run 'mypy' linter ruff: # Run 'ruff' linter and print a preview of errors uv run ruff check . -safety: # Check for security vulnerabilities - uv run pip-audit --ignore-vuln CVE-2025-2953 --ignore-vuln CVE-2025-3730 - -lint-apply: black-apply ruff-apply # Apply changes with 'black' and resolve 'fixable errors' with 'ruff' - -black-apply: # Apply changes with 'black' - uv run black . - -ruff-apply: # Resolve 'fixable errors' with 'ruff' +lint-fix: # Run linting, auto fix behaviors where supported + uv run ruff format . uv run ruff check --fix . +# CVE-2025-2953 = torch 2.6; acceptable risk, keeping until we move away from torch 2.6 +# CVE-2025-3730 = torch 2.6; acceptable risk, keeping until we move away from torch 2.6 +# CVE-2026-1839 = transformers 4.57; acceptable risk, keeping until we move to transformers 5.x +security: # Check for security vulnerabilities + uv run pip-audit \ + --ignore-vuln CVE-2025-2953 \ + --ignore-vuln CVE-2025-3730 \ + --ignore-vuln CVE-2026-1839 + #################################### # Developer Build and Deploy Commands for Dev environment in AWS diff --git a/README.md b/README.md index 33bbe59..702b5be 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,9 @@ A CLI application for creating embeddings for TIMDEX. - To update dependencies: `make update` - To run unit tests: `make test` - To lint the repo: `make lint` -- To run the app: `embeddings --help` +- To apply formatting and fixable lint errors: `make lint-fix` +- To run security checks: `make security` +- To run the app: `uv run embeddings --help` - see below for more details about running the CLI with `.env` files and arguments ### Building Docker Images diff --git a/embeddings/strategies/processor.py b/embeddings/strategies/processor.py index a5131c5..c541145 100644 --- a/embeddings/strategies/processor.py +++ b/embeddings/strategies/processor.py @@ -31,7 +31,6 @@ def create_embedding_inputs( # loop through records and apply all strategies, yielding an EmbeddingInput for each for timdex_dataset_record in timdex_dataset_records: - # decode and parse the TIMDEX JSON record once for all requested strategies transformed_record_raw = timdex_dataset_record["transformed_record"] timdex_record = json.loads( diff --git a/pyproject.toml b/pyproject.toml index b2c92f2..7d94eff 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,6 @@ dependencies = [ [dependency-groups] dev = [ - 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