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‎.bumpversion.cfg‎

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[bumpversion]
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current_version = 0.0.1
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commit = True
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tag = True
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files = pyproject.toml saezlab_core/_metadata.py
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parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
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serialize = {major}.{minor}.{patch}

‎.codecov.yaml‎

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# Based on pydata/xarray
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codecov:
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require_ci_to_pass: no
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coverage:
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status:
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project:
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default:
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# Require 1% coverage, i.e., always succeed
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target: 1
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patch: false
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changes: false
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comment:
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layout: diff, flags, files
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behavior: once
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require_base: no

‎.coveragerc‎

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[paths]
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source =
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project_name
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*/site-packages/saezlab_core
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[run]
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branch = true
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parallel = true
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source = saezlab_core
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omit = */__init__.py
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[report]
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exclude_lines =
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\#.*pragma:\s*no.?cover
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if __name__ == .__main__.
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^\s*raise AssertionError\b
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^\s*raise NotImplementedError\b
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^\s*return NotImplemented\b
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show_missing = true
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precision = 2

‎.cruft.json‎

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{
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"template": "https://github.com/saezlab/python-project.git",
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"commit": "9994d74de08e6c13ae1c82fd47675347f1e3a79f",
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"checkout": "master",
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"context": {
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"cookiecutter": {
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"project_name": "saezlab_core",
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"project_slug": "saezlab_core",
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"package_name": "saezlab_core",
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"short_description": "This is session handler, configuration and logging handler for Saezlab packages and applications.",
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"readme": "This is session handler, configuration and logging handler for Saezlab packages and applications.",
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"author_full_name": "Edwin Carreño",
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"author_email": "ecarrenolozano@gmail.com",
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"github_organization": "saezlab",
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"project_repo": "https://github.com/saezlab/saezlab_core",
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"license": "MIT License",
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"_license": {
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"MIT License": {
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"license_short": "MIT",
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"license_classifiers": "MIT License",
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"license_spdx": "MIT"
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},
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"BSD 2-Clause License": {
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"license_short": "BSD-2-Clause",
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"license_classifiers": "BSD License",
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"license_spdx": "BSD-2-Clause"
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},
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"BSD 3-Clause License": {
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"license_short": "BSD-3-Clause",
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"license_classifiers": "BSD License",
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"license_spdx": "BSD-3-Clause"
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},
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"Apache License Version 2.0": {
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"license_short": "Apache-2.0",
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"license_classifiers": "Apache Software License",
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"license_spdx": "Apache-2.0"
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},
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"GNU General Public License Version 3": {
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"license_short": "GPL-3.0-or-later",
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"license_classifiers": "GNU General Public License v3 (GPLv3)",
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"license_spdx": "GPL-3.0-or-later"
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},
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"GNU Lesser General Public License Version 3": {
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"license_short": "LGPL-3.0-or-later",
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"license_classifiers": "GNU Lesser General Public License v3 (LGPLv3)",
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"license_spdx": "LGPL-3.0-or-later"
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},
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"ISC License": {
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"license_short": "ISC",
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"license_classifiers": "ISC License (ISCL)",
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"license_spdx": "ISC"
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},
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"Unlicense": {
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"license_short": "Unlicense",
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"license_classifiers": "The Unlicense (Unlicense)",
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"license_spdx": "Unlicense"
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}
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},
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"python_version": "3.10",
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"copyright_holder": "Heidelberg University Hospital",
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"__year": "2025",
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"_extensions": [
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"cookiecutter.extensions.TimeExtension"
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],
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"_copy_without_render": [
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".github/workflows/*.yml",
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".github/workflows/**.yaml",
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".github/actions/*"
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],
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"_template": "https://github.com/saezlab/python-project.git",
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"_commit": "9994d74de08e6c13ae1c82fd47675347f1e3a79f"
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}
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},
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"directory": null
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}

‎.editorconfig‎

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root = true
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[*]
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indent_style = space
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indent_size = 4
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end_of_line = lf
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charset = utf-8
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trim_trailing_whitespace = true
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insert_final_newline = true
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[Makefile]
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indent_style = tab

‎.github/actions/setup/action.yml‎

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name: Setup Python and Install Dependencies
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description: Sets up Python and installs dependencies using uv
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runs:
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using: composite
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steps:
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- uses: actions/setup-python@v5
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with:
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python-version: ${{ inputs.python-version }}
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- name: Install uv
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shell: bash
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run: curl -LsSf https://astral.sh/uv/install.sh | sh
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- name: Create virtualenv and install dependencies
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shell: bash
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run: |
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uv venv .venv
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source .venv/bin/activate
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uv pip install ".[dev,tests,docs]"
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inputs:
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python-version:
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required: true
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description: Python version to use in the matrix.

‎.github/workflows/ci-docs.yml‎

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name: Build MkDocs documentation
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on:
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push:
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branches: [main, master]
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permissions:
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contents: write
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jobs:
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build-documentation:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Configure Git Credentials
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run: |
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git config user.name github-actions[bot]
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git config user.email 41898282+github-actions[bot]@users.noreply.github.com
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- uses: ./.github/actions/setup
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with:
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python-version: '3.12'
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- name: configure mkdocs-material cache
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uses: actions/cache@v4
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with:
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key: mkdocs-material-${{ github.run_id }}
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path: .cache
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restore-keys: |
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mkdocs-material-
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- name: Build documentation with mkdocs
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run: .venv/bin/mkdocs gh-deploy --force

‎.github/workflows/ci-linting.yml‎

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name: Linting
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on: [push, pull_request]
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jobs:
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linting:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: ./.github/actions/setup
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with:
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python-version: '3.13'
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- name: Run Ruff (lint + formatting + import order)
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run: .venv/bin/ruff check .
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- name: Run Ruff format check (like Black)
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run: .venv/bin/ruff format --check .

‎.github/workflows/ci-security.yml‎

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name: Security Scan
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on: [push, pull_request]
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jobs:
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security-check:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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- name: Install Bandit
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run: pip install bandit
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- name: Run Bandit
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run: bandit -r . --exclude venv,.venv,.tox --skip B101

‎.github/workflows/ci-testing-unit.yml‎

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name: CI testing [unit testing]
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on: [push, pull_request]
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jobs:
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lint:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: ./.github/actions/setup
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with:
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python-version: '3.13'
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- name: Run Ruff (lint + formatting + import order)
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run: .venv/bin/ruff check .
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- name: Run Ruff format check (like Black)
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run: .venv/bin/ruff format --check .
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.10', '3.11', '3.12', '3.13']
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steps:
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- uses: actions/checkout@v4
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- uses: ./.github/actions/setup
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with:
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python-version: ${{ matrix.python-version }}
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- name: Run tests with coverage
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run: |
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source .venv/bin/activate
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pytest --cov=omnigraph tests/
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- name: Upload coverage report
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uses: actions/upload-artifact@v4
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with:
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name: coverage-report
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path: .coverage*

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