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Update small_variants.py#23

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rhshah merged 20 commits into
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filter_duplicates_set_to_true
Sep 4, 2025
Merged

Update small_variants.py#23
rhshah merged 20 commits into
developfrom
filter_duplicates_set_to_true

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@rhshah rhshah commented May 13, 2025

Making filter duplicates by default as true

Making filter duplicates by default as true
Updated GitHub Actions workflow for Docker publishing to use improved metadata extraction, caching, and vulnerability scanning. Refactored Dockerfile to use multi-stage builds, non-root user, and health checks. Improved generate_gbcms_cmd in small_variants.py for better argument validation, output handling, and command construction.
Expanded the GitHub Actions workflow to support multiple Python versions, improved caching for pip and tox, added code style checks, and introduced a dedicated lint job using pre-commit. The workflow now runs tests across Python 3.7–3.10, uploads coverage for 3.8, and enforces code quality standards.
Removed the matrix strategy from the GitHub Actions workflow to run tests exclusively on Python 3.8 and Ubuntu. Updated cache keys and steps to reflect the single environment, streamlining CI and reducing complexity.
Replaces legacy setup.py, Makefile, tox.ini, MANIFEST.in, and Travis CI with pyproject.toml and modernizes CI/CD using GitHub Actions for validation, Docker, and PyPI publishing. Updates Dockerfile for improved reproducibility and caching, switches dependency management to requirements.in/requirements.txt, and refactors development dependencies. This streamlines packaging, testing, and deployment workflows.
Introduces .pre-commit-config.yaml with hooks for code style, linting, and type checking. Updates GitHub Actions workflow to install pre-commit, set up hooks, and run checks automatically during validation.
Simplifies uv installation and usage in the GitHub Actions workflow by updating the install command and PATH handling. Directly uses 'uv' for package and pre-commit installation, improving readability and maintainability.
The GitHub Actions workflow now creates and activates a uv-managed virtual environment before installing dependencies. Also fixed a typo in the pyproject.toml description string.
The GitHub Actions workflow now explicitly creates the virtual environment with Python 3.8 and uses pip for package installation and pre-commit setup. The pyproject.toml adds Python 3.9 and 3.10 to classifiers and bumps the package version to 0.3.9.
Replaces 'uv venv' with 'python -m venv' for environment creation and ensures pip, setuptools, and wheel are upgraded before installing build tools. This improves compatibility and reliability of the CI setup.
Updated GitHub Actions workflow to ensure the Python virtual environment is activated before running dependency installation, pre-commit checks, security scans, package builds, and code style checks. This improves environment consistency and reliability across workflow steps.
Deleted .pre-commit-config.yaml and setup.cfg, and removed pre-commit and related linting steps from the GitHub Actions workflow. The CI workflow is now focused on validation and code style checks, streamlining the process and removing unused configuration files.
The CI workflow now runs pytest on the tests directory instead of performing code style and type checks with black, flake8, isort, and mypy.
Updated version to 0.3.9 across package files. Refactored code for consistent use of double quotes, improved formatting, and enhanced readability in multiple modules. Made minor logic and style improvements in command generation, dataframe creation, and test files for better maintainability.
Bump minimum supported Python version from 3.8 to 3.9 across workflows, Dockerfile, documentation, and configuration files. Update CONTRIBUTING guidelines and pyproject.toml to reflect support for Python 3.9, 3.10, and 3.11. Adjust requirements.txt header to match new Python version.
Updated version numbers in __init__.py files and pyproject.toml to 0.3.10 for a new release.
@rhshah rhshah self-assigned this Sep 4, 2025
Modified the test job condition to handle cases where github.event.head_commit is null, preventing errors when the event does not include a head commit.
@rhshah rhshah requested a review from buehlere September 4, 2025 21:39
@rhshah rhshah merged commit 5e29129 into develop Sep 4, 2025
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@rhshah rhshah deleted the filter_duplicates_set_to_true branch September 4, 2025 21:50
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Deprecate Python 3.7 support Push to Pypi remove generic counting for STD bam files

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