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steven-murraysteven-murray
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Merge pull request #121 from HERA-Team/modernize-build
maint: modernize build to use uv and ruff
2 parents 7d6aa4f + f6f93ee commit 543980c

31 files changed

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‎.github/workflows/run_notebooks.yaml‎

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with:
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python-version: "3.13"
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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with:
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enable-cache: true
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- name: Install
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run: |
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echo $(which pip)
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pip install .[test] papermill jupyter ipykernel
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uv sync --group doctests --locked
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- name: Install ipykernel
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run: python -m ipykernel install --user --name matvis --display-name "matvis"
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run: uv run python -m ipykernel install --user --name matvis --display-name "matvis"
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- name: Run Notebooks
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run: |
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papermill -k matvis docs/tutorials/matvis_tutorial.ipynb tmp.ipynb
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uv run papermill -k matvis docs/tutorials/matvis_tutorial.ipynb tmp.ipynb

‎.github/workflows/test_suite.yaml‎

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# - uses: FedericoCarboni/setup-ffmpeg@v2
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- name: Setup Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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with:
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enable-cache: true
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- name: Install
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run: |
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pip install .[test]
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uv sync --dev --locked
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- name: Run Tests
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run: |
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python -m pytest --ignore tests/test_plot.py --cov=matvis --cov-config=.coveragerc --cov-report xml:./coverage.xml --durations=25 --log-cli-level=${{ env.LOG_LEVEL}}
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uv run --no-sync pytest --ignore tests/test_plot.py --cov=matvis --cov-config=.coveragerc --cov-report xml:./coverage.xml --durations=25 --log-cli-level=${{ env.LOG_LEVEL }}
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- name: Upload coverage report
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uses: codecov/codecov-action@v4
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with:
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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with:
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enable-cache: true
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- name: Install
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run: |
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echo $(whoami)
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source ~/.bashrc
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micromamba activate testenv
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echo $(which pip)
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python -m pip install --upgrade pip
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python -m pip install .[test,gpu]
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python -m pip install --group dev .[gpu]
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- name: Run Tests
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run: |

‎.gitignore‎

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*.py[cod]
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*.so
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*.cfg
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!.isort.cfg
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!setup.cfg
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*.orig
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*.log
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*.pot

‎.isort.cfg‎

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This file was deleted.

‎.pre-commit-config.yaml‎

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- id: mixed-line-ending
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args: ['--fix=no']
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- repo: https://github.com/PyCQA/flake8
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rev: 7.3.0
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.15.12
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hooks:
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- id: flake8
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additional_dependencies:
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- flake8-docstrings
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- flake8-builtins
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- flake8-rst-docstrings
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- flake8-rst
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- flake8-markdown
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- flake8-bugbear
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- flake8-comprehensions
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- flake8-print
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- repo: https://github.com/psf/black-pre-commit-mirror
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rev: 26.3.1
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hooks:
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- id: black
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- id: ruff-check
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types_or: [python, pyi]
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args: [--fix]
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- id: ruff-format
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types_or: [python, pyi]
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- repo: https://github.com/pre-commit/pygrep-hooks
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rev: v1.10.0
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hooks:
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- id: rst-backticks
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- repo: https://github.com/PyCQA/isort
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rev: 9.0.0a3
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hooks:
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- id: isort
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- repo: https://github.com/asottile/pyupgrade
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rev: v3.21.2
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hooks:
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- id: pyupgrade
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args: [--py39-plus]
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- repo: https://github.com/asottile/setup-cfg-fmt
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rev: v3.2.0
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hooks:
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- id: setup-cfg-fmt

‎.readthedocs.yml‎

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# Required
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version: 2
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/conf.py
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# conda:
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# environment: docs/environment.yaml
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build:
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os: ubuntu-22.04
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os: ubuntu-lts-latest
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tools:
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python: "3.11"
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python: "3.13"
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python:
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install:
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- method: pip
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path: .
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extra_requirements:
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- method: uv
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command: sync
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groups:
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- docs

‎AGENTS.md‎

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# AGENTS
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## Scope
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- Keep changes tightly scoped to the requested task.
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- Do not rewrite scientific logic or numerical behavior unless the task explicitly requires it.
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- Avoid touching generated artifacts in `docs/_build/`, `build/`, or `src/matvis.egg-info/` unless explicitly asked.
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## Do
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- use uv run for all project tooling commands (pytest, ruff, etc.)
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- setup environment with uv sync; prefer uv sync --locked --all-extras --dev for CI parity
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- add type hints for all new parameters
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- write or update tests for every behavior change
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- add numpydoc-style docstrings for new public modules, classes, and functions
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- update docstrings whenever parameters are added or changed
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- prefer minimal, file-scoped checks before broad checks
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## Do not
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- do not edit CHANGELOG.rst unless explicitly asked
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- do not modify regression artifacts or data snapshots unless explicitly asked
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- do not run full test suites or expensive notebook/doc executions without approval
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- do not introduce API-breaking renames or default changes without explicit confirmation
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### Commands
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#### File-scoped quality checks (preferred)
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uv run ruff format path/to/file.py
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uv run ruff check --fix path/to/file.py
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#### Targeted tests (preferred)
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uv run pytest tests/path/to/test_file.py
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uv run pytest tests/path/to/test_file.py -k keyword
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#### Wider checks (ask first)
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uv run prek run -a
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uv run pytest
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### Safety and permissions
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Allowed without prompt:
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- read, list, and search files
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- edit source, tests, and docs text files relevant to the task
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- run file-scoped ruff checks
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- run one or a few targeted pytest files
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Ask first:
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- package or environment installs/upgrades
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- full-suite pytest runs
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- notebook execution across docs/examples
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- regenerating regression data
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- deleting files, chmod, git push
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### Testing expectations
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- bug fixes should include regression tests
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- use explicit numeric tolerances for floating-point comparisons
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- handle warnings intentionally (fix or filter in tests)
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### API docs
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- docs are built with sphinx and numpydoc
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- keep API docs indexed in docs/api.rst when adding new public objects
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### Process note
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- branch/release docs and workflows may differ historically; do not assume release branching strategy unless user specifies
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### PR checklist
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- formatting and lint checks pass
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- unit tests pass
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- tests added for new or changed behavior
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### When stuck
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- ask a clarifying question
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- propose a short plan with assumptions
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- provide a minimal draft patch with explicit unknowns
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### Test-first mode
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- for new features, write or update tests first, then code to green
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## GPU CI Constraints
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- Treat the self-hosted GPU runner as environment-sensitive infrastructure.
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- Keep the existing micromamba activation flow unless the user explicitly asks to replace it.
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- Prefer replacing `pip` usage with `uv` usage inside the existing GPU environment rather than redesigning the runner.

‎README.rst‎

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:target: https://badge.fury.io/py/vis-cpu
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.. image:: https://codecov.io/gh/hera-team/ matvis/branch/main/graph/badge.svg
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:target: https://codecov.io/gh/hera-team/ matvis
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.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
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:target: https://github.com/psf/black
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.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
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:target: https://github.com/astral-sh/ruff
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Fast matrix-based visibility simulator capable of running on CPU and GPU.

‎gpu-analysis.nvprof‎

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‎pyproject.toml‎

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[build-system]
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requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4"]
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requires = ["setuptools>=77", "setuptools_scm[toml]>=8"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "matvis"
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description = "Fast matrix-based visibility simulator with interface to CPU and GPU"
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readme = { file = "README.rst", content-type = "text/x-rst" }
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requires-python = ">=3.11"
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license = "MIT"
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license-files = ["LICENSE.txt"]
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authors = [{ name = "HERA-Team", email = "steven.g.murray@asu.edu" }]
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classifiers = [
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"Development Status :: 4 - Beta",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3 :: Only",
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]
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dynamic = ["version"]
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dependencies = [
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"astropy",
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"click",
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"docstring-parser",
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"line-profiler",
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"numpy>=2.0",
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"psutil",
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"pyuvdata>=3.2.0",
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"rich",
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"scipy",
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]
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[project.urls]
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Homepage = "https://github.com/hera-team/matvis"
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[project.scripts]
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matvis = "matvis.cli:main"
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[project.optional-dependencies]
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gpu = [
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"cupy",
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"jinja2",
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]
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profile = [
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"click",
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"line-profiler",
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"pyuvsim>=1.2.5",
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]
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[dependency-groups]
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docs = [
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"furo",
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"ipython",
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"nbsphinx",
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"numpydoc",
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"sphinx",
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]
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doctests = [
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"ipykernel>=7.2.0",
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"jupyter>=1.1.1",
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"matplotlib>=3.8.0",
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"papermill>=2.7.0",
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]
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test = [
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"astropy-healpix",
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"hypothesis",
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"ipython",
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"matplotlib",
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"pyradiosky",
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"pytest",
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"pytest-cov",
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"pytest-lazy-fixtures",
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"pyuvsim[sim]>=1.2.5",
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]
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dev = [
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{ include-group = "docs" },
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{ include-group = "test" },
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{ include-group = "doctests" },
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"prek",
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"ruff",
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]
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[tool.setuptools]
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include-package-data = true
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zip-safe = false
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[tool.setuptools.package-dir]
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"" = "src"
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[tool.setuptools.packages.find]
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where = ["src"]
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exclude = ["tests"]
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namespaces = true
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[tool.pytest.ini_options]
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addopts = ["--cov=matvis", "--cov-report=term-missing", "--verbose"]
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norecursedirs = ["dist", "build", ".tox"]
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testpaths = ["tests"]
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[tool.ruff]
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line-length = 88
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extend-exclude = [
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"build",
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"dist",
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".eggs",
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".tox",
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"docs/_build",
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"docs/conf.py",
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"src/matvis/data",
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]
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[tool.ruff.lint]
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select = ["A", "B", "C4", "C90", "D", "E", "F", "G", "I", "T20", "UP", "W"]
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ignore = ["B007", "D107", "D401", "D404", "E203", "E231", "E266", "E501", "F401", "F403", "G004"]
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per-file-ignores = { "src/matvis/cli.py" = ["T20"], "tests/*.py" = ["E402", "T20"] }
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[tool.ruff.lint.mccabe]
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max-complexity = 25
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[tool.ruff.lint.pydocstyle]
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convention = "numpy"
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[tool.ruff.format]
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docstring-code-format = true
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[tool.setuptools_scm]

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