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Feature/deploy (#4)
* Init CI/CD * Replaced mypy with ty type checker, added JSON test exclusions, fixed type hints and code style. * Added jinja2 and tqdm dependencies, pandas dev dependency, improved test skip handling for LMOD and UGE. * Updated shell import to hpc_funcs, removed test_status.py, added UGE skip check. * Removed Development Status classifier from pyproject.toml. * Removed empty test_slurm.py file. * Removed code-quality workflow, simplified publish workflow with make targets. * Updated ty pre-commit hook to use system language. * Updated format check to use activated virtual environment.
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‎.github/workflows/publish.yml‎

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name: Publish to PyPI
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on:
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release:
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types: [published]
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jobs:
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deploy:
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name: Build & Publish
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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: Set up Python
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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 build dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build twine
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- name: Build package
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run: make build
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- name: Check distribution
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run: make test-dist
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- name: Publish to PyPI
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env:
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TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
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TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
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run: make upload

‎.github/workflows/test.yml‎

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name: Test
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on:
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push:
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branches:
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- '**'
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pull_request:
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branches: [main]
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jobs:
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test:
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name: Test Python ${{ matrix.python-version }}
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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strategy:
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matrix:
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python-version: ['3.11', '3.12', '3.13']
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steps:
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- uses: actions/checkout@v4
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- uses: astral-sh/setup-uv@v7
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with:
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python-version: ${{ matrix.python-version }}
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- name: Create environment
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run: make env python-version=${{ matrix.python-version }}
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- name: Run tests
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run: source ./env/bin/activate && make test python=python
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- name: Check format and types
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run: source ./env/bin/activate && make format
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- name: Build package
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run: source ./env/bin/activate && make build
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- name: Check distribution
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run: source ./env/bin/activate && make test-dist
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- name: Test installation from wheel
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run: |
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pip install dist/*.whl
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python -c "import hpc_funcs; print(hpc_funcs.__version__)"

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v3.4.0
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rev: v5.0.0
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hooks:
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- id: trailing-whitespace
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exclude: ^tests/resources/
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- id: end-of-file-fixer
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exclude: ^tests/resources/
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- id: check-yaml
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args: ["--unsafe"]
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- id: check-added-large-files
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- id: check-ast
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- id: check-json
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exclude: ^tests/resources/uge/qstat_jobinfo_(array|error)\.json$
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- id: debug-statements
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- id: detect-aws-credentials
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args: [--allow-missing-credentials]
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- id: check-added-large-files
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args: ['--maxkb=3000']
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- repo: https://github.com/myint/autoflake
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rev: v2.3.1
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hooks:
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- id: autoflake
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name: Removes unused variables
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args:
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- --in-place
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- --remove-all-unused-imports
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- --expand-star-imports
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- --ignore-init-module-imports
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- repo: https://github.com/pre-commit/mirrors-isort
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rev: v5.10.1
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hooks:
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- id: isort
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name: Sorts imports
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args: [
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# Align isort with black formatting
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"--multi-line=3",
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"--trailing-comma",
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"--force-grid-wrap=0",
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"--use-parentheses",
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"--line-width=99",
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]
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- repo: https://github.com/psf/black
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rev: 24.10.0
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.11.6
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hooks:
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- id: black
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name: Fixes formatting
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language_version: python3
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args: ["--line-length=99"]
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- repo: https://github.com/pycqa/flake8
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rev: 7.1.1
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hooks:
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- id: flake8
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name: Checks pep8 style
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args: [
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"--max-line-length=99",
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# Ignore imports in init files
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"--per-file-ignores=*/__init__.py:F401,setup.py:E121",
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# ignore long comments (E501), as long lines are formatted by black
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# ignore Whitespace before ':' (E203)
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# ignore Line break occurred before a binary operator (W503)
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"--ignore=E501,E203,W503",
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]
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# - repo: https://github.com/pre-commit/mirrors-mypy
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# rev: v0.782
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# hooks:
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# - id: mypy
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# args: [--ignore-missing-imports]
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- id: ruff
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args: [--fix]
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- id: ruff-format
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- repo: local
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hooks:
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- id: mypy
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- id: ty
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name: Static type checking
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entry: mypy
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files: \.py$
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language: python
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entry: ty check
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files: ^src/.*\.py$
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language: system
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- id: jupyisort
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name: Sorts ipynb imports
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entry: jupytext --pipe-fmt ".py" --pipe "isort - --multi-line=3 --trailing-comma --force-grid-wrap=0 --use-parentheses --line-width=99" --sync
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entry: jupytext --pipe-fmt ".py" --pipe "ruff check --select I --fix -" --sync
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files: \.ipynb$
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language: python
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- id: jupyblack
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- id: jupyformat
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name: Fixes ipynb format
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entry: jupytext --pipe-fmt ".py" --pipe "black - --line-length=99" --sync
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entry: jupytext --pipe-fmt ".py" --pipe "ruff format -" --sync
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files: \.ipynb$
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language: python
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‎Makefile‎

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.PHONY: update-format format test test-dist build types upload cov
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.PHONY: update-format format check test test-dist build types upload cov clean clean-env
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package=hpc_funcs
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version_file1=./src/hpc_funcs/version.py
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env_uv:
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uv venv ${env}
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uv pip install -r requirements.txt --python ${env}/bin/python
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uv pip install -e . --python ${env}/bin/python
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uv pip install -e .[dev] --python ${env}/bin/python
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${python} -m pre_commit install
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env_conda:
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conda env create -f ./environment.yml -p ${env} --quiet
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${python} -m pre_commit install
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${python} -m pip install -e .
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## Development
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update-format:
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format:
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${python} -m pre_commit run --all-files
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check: format types
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test:
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${python} -m pytest ./tests
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rm -rf *.whl
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rm -rf ./build/ ./__pycache__/
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rm -rf ./dist/
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clean-env:
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rm -rf ./${env}/
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rm -f .git/hooks/pre-commit

‎pyproject.toml‎

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[build-system]
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requires = ["setuptools", "setuptools-scm"]
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requires = ["setuptools>=61.0"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "hpce_utils"
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name = "hpc_funcs"
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dynamic = ["version"]
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authors = []
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description = "HPC utility functions"
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readme = "README.md"
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license = {text = "MIT"}
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requires-python = ">=3.11"
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classifiers = [
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Programming Language :: Python :: 3.13",
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]
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dependencies = [
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"jinja2",
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"tqdm",
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]
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[project.optional-dependencies]
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dev = [
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"ruff",
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"ty",
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"pip",
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"pre-commit",
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"pytest",
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"pytest-cov",
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"pandas",
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"twine",
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"build",
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"monkeytype",
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]
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[tool.setuptools.dynamic]
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version = {attr = "hpce_utils.version.VERSION"}
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version = {attr = "hpc_funcs.version.__version__"}
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[options.packages.find]
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where="src"
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[tool.setuptools.packages.find]
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where = ["src"]
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[tool.setuptools.package-data]
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"*" = ["*.jinja"]
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"*" = ["*.jinja", "py.typed"]
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[tool.ruff]
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line-length = 99
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target-version = "py311"
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exclude = [
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".git",
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".github",
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"__pycache__",
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"build",
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"dist",
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"*.egg-info",
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"env",
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]
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[tool.ruff.lint]
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select = [
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"E", # pycodestyle errors
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"F", # pyflakes
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"I", # isort (import sorting)
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"UP", # pyupgrade (modern Python syntax)
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"B", # flake8-bugbear
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"C4", # flake8-comprehensions
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"SIM", # flake8-simplify
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]
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[tool.ruff.lint.isort]
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known-first-party = ["hpc_funcs"]
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[tool.ruff.lint.per-file-ignores]
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"tests/*" = ["B017", "B023", "E501"]
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"*/__init__.py" = ["F401"]
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[tool.ty]
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# Type checking with ty (Astral's extremely fast Python type checker)
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[tool.ty.environment]
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python-version = "3.11"
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[tool.ty.src]
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exclude = ["tests/"]
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[tool.ty.rules]
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# Ignore unresolved imports since pre-commit env doesn't have all packages
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unresolved-import = "ignore"
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[tool.pytest.ini_options]
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testpaths = ["tests"]
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log_cli = true
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log_cli_level = "DEBUG"

‎setup.py‎

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