astro-brutus 1.1.0__tar.gz

astro_brutus-1.1.0/AUTHORS.md

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+# Authors
+
+- [Josh Speagle](https://github.com/joshspeagle)
+
+Contributors:
+
+- [Gus Beane](https://github.com/gusbeane)
+- [Catherine Zucker](https://github.com/catherinezucker)
+- [Phil Cargile](https://github.com/pacargile)
+- [Greg Green](https://github.com/gregreen)
+- [Ben Johnson](https://github.com/bd-j)
+- [Eddie Schlafly](https://github.com/schlafly)

astro_brutus-1.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [1.1.0] - 2026-05-29
+
+Maintenance and polish release: verified bug fixes (several affecting numerical
+output on specific paths), documentation accuracy, test-suite hygiene, and
+release-process improvements. All fixes ship with regression tests.
+
+### Fixed
+
+- **`FastNN.encode` silent mis-scaling for 6-sample batches** *(affects output)*:
+  a 2-D input of shape `(6 params, 6 samples)` broadcast against the parameter
+  bounds without error and normalized along the wrong axis, producing silently
+  corrupted SEDs/bolometric corrections only when exactly 6 valid samples were
+  evaluated (reached via `StellarPop` synthesis). Now dispatches on input
+  dimensionality explicitly.
+- **`los_dust` kernels collapsing per-object cloud means** *(affects output)*:
+  `kernel_gauss`/`kernel_lorentz`/`kernel_tophat` collapsed an array-valued mean
+  to a scalar, so line-of-sight fits using a reddening template (`template_reds`,
+  `additive_foreground`) evaluated every object against object 0's cloud mean.
+  Means are now kept broadcastable. The default uniform-cloud path is unchanged.
+- **Binary companions no longer discard a valid primary SED** *(affects binary
+  grid generation)*: `StarEvolTrack.get_seds` returned an all-NaN combined SED
+  (dropping the valid primary) when the secondary's age could not be matched to
+  the unrealistically tight default tolerance. The default `tol` is relaxed
+  `1e-6 -> 1e-2` dex and a primary-only fallback is used when the companion does
+  not converge. *Regenerate binary (smf>0) grids to benefit; single-star fitting
+  and the shipped default grids are unaffected.*
+- `load_offsets` no longer crashes on a single-filter offsets file.
+- `logp_imf` no longer raises `ZeroDivisionError` for a power-law slope of
+  exactly 1.0 (flat-in-log); uses the logarithmic mass integral.
+- `_fetch` (data download) removes a stale/broken symlink before re-linking and
+  falls back to a file copy on filesystems without symlink support.
+- `BruteForce.logpost_grid` floors the Monte-Carlo sample count at 1 (a very
+  small `mem_lim` could drive it to 0 and crash).
+- `BruteForce.loglike_grid` guards the dimensional-prior `log(Ndim)` term and
+  fails fast with a clear error on a fully-masked object (was an opaque
+  `ZeroDivisionError` deep in the optimizer).
+- `cornerplot` no longer mutates a caller-supplied `labels` list in place.
+- `dist_vs_red` uses `interpolation="none"` so binned PDF images show raw bins;
+  fixed a no-op smoothing guard in `hist2d`.
+- Removed a dead `from scipy import polyfit` import (`scipy` has no top-level
+  `polyfit`; the code always used `numpy.polyfit`).
+
+### Changed
+
+- **Python support**: dropped end-of-life Python 3.8 (`requires-python>=3.9`);
+  added 3.13 to the classifiers and tooling targets.
+- **Dependencies**: raised the `numba` floor to `>=0.59.0` (the old 0.53 floor
+  predates `numpy>=1.22`/2.x support); `numpy` remains uncapped (the code is
+  numpy-2.0 clean, verified on 2.2).
+- **Documentation engine**: standardized on a single NumPy-docstring processor
+  (`napoleon`); removed the redundant `numpydoc` extension. The docs now build
+  with zero warnings.
+- **Tutorials**: standardized on the committed `Orion_l209.1_b-19.9` example
+  field; replaced chi2/Nbands quality cuts with goodness-of-fit p-values.
+
+### Documentation
+
+- Corrected numerous stale code examples across the docs and docstrings to match
+  the real API (`StarGrid(models, labels)`, `get_seds` 3-tuple in magnitudes,
+  `magnitude(flux, err)`, `sample_multivariate_normal(size=)`, the prior call
+  signatures, `samps_dred`, the data cache path/env var, real filter names, and
+  the maggies flux convention).
+- Added `summary_plot` to the API reference; documented `BruteForce.fit`'s
+  performance/accuracy parameters (`max_models`, `precision_shrinkage`,
+  `subsample_mode`, `R_solar`, `Z_solar`); reframed fit-quality guidance around
+  the p-value methodology.
+
+### Testing & packaging
+
+- Added regression tests covering every fix above; reconciled the `conftest`
+  coverage guidance with what CI actually runs
+  (`NUMBA_DISABLE_JIT=1 pytest --cov`); the default `pytest` run no longer
+  enables coverage (which crashed on some WSL/DrvFs paths).
+- Added a tag-triggered PyPI publish workflow (Trusted Publishing); fixed the
+  stale `MANIFEST.in` data-file path.
+
+## [1.0.0] - 2025-12-08
+
+First stable release of brutus following code verification, testing, and documentation improvements.
+
+### Added
+
+- **Documentation**: Scientific background pages, user guides, API documentation with examples, and ReadTheDocs hosting
+- **Testing**: 92% code coverage, 606 tests, GitHub Actions CI/CD with Codecov integration
+- **Code verification**: All functions verified for correctness; fixed IMF normalization bug, StarGrid distance reference, and other issues
+
+### Changed
+
+- Development status updated to Production/Stable
+- Added `tqdm` as formal dependency
+- Enforced Black formatting across codebase
+
+## [0.9.0] - 2024-08-28
+
+Major refactoring to improve usability and maintainability while preserving scientific functionality.
+
+### Added
+
+- **Modern packaging**: Migrated to `pyproject.toml` with black, isort, flake8, mypy
+- **Testing**: pytest framework with 100+ tests, coverage reporting, multi-platform CI
+- **Modular architecture**: Split into `brutus.core`, `brutus.analysis`, `brutus.plotting`, `brutus.dust`, `brutus.utils`, `brutus.data`, `brutus.priors`
+- **Performance**: Numba JIT compilation, vectorized operations, improved caching
+
+### Changed
+
+- Minimum Python version: 3.8+ (dropped Python 2.7)
+- Split large modules (`utils.py`, `plotting.py`) into focused submodules
+- Updated all dependencies to modern versions
+
+### Fixed
+
+- Windows/WSL compatibility documentation
+- Circular imports and module loading issues
+- Infinite loop bug in `hist2d` function
+
+### Migration
+
+Update imports:
+
+```python
+# Old
+from brutus.seds import Isochrone
+from brutus.fitting import BruteForce
+
+# New
+from brutus import Isochrone, BruteForce
+# or
+from brutus.core import Isochrone
+from brutus.analysis import BruteForce
+```
+
+All scientific algorithms, file formats, and core APIs remain unchanged.
+
+## [0.8.3] - Previous Release
+
+Final release using old project structure and Python 2 compatibility.
+
+Features: individual star fitting, cluster modeling, 3D dust mapping, MIST support, neural network SED prediction.
+
+---
+
+For migration questions or bug reports, see the [issue tracker](https://github.com/joshspeagle/brutus/issues).

astro_brutus-1.1.0/LICENSE

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+# MIT License
+
+Copyright (c) 2018 Josh Speagle
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

astro_brutus-1.1.0/MANIFEST.in

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+# Include package metadata and documentation
+include LICENSE
+include README.md
+include AUTHORS.md
+include CHANGELOG.md
+include pyproject.toml
+
+# Include data files
+include src/brutus/priors/PSMrLF_lnprior.dat
+
+# Include package data recursively
+recursive-include src/brutus *.dat *.txt *.h5
+
+# Exclude development and build files
+exclude setup.py.old
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+recursive-exclude * *~
+recursive-exclude * .git*
+exclude .gitignore
+
+# Exclude test files from distribution
+recursive-exclude tests *
+exclude tox.ini
+exclude .travis.yml
+exclude .github

astro_brutus-1.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: astro-brutus
+Version: 1.1.0
+Summary: Brute-force Bayesian inference for photometric distances, reddenings, and stellar properties
+Author-email: Joshua S Speagle <j.speagle@utoronto.ca>
+Maintainer-email: Joshua S Speagle <j.speagle@utoronto.ca>
+License: MIT
+Project-URL: Homepage, https://github.com/joshspeagle/brutus
+Project-URL: Repository, https://github.com/joshspeagle/brutus
+Project-URL: Documentation, https://brutus.readthedocs.io
+Project-URL: Bug Tracker, https://github.com/joshspeagle/brutus/issues
+Keywords: brute force,photometry,bayesian,stellar,star,cluster,isochrone,dust,reddening,parallax,distance,template fitting
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Intended Audience :: Science/Research
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS.md
+Requires-Dist: numpy>=1.19
+Requires-Dist: scipy>=1.6.0
+Requires-Dist: matplotlib>=3.3.0
+Requires-Dist: h5py>=3.0.0
+Requires-Dist: healpy>=1.14.0
+Requires-Dist: numba>=0.59.0
+Requires-Dist: pooch>=1.4.0
+Requires-Dist: tqdm>=4.50.0
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0; extra == "dev"
+Requires-Dist: pytest-cov>=2.10; extra == "dev"
+Requires-Dist: black>=21.0; extra == "dev"
+Requires-Dist: flake8>=3.8; extra == "dev"
+Requires-Dist: isort>=5.0; extra == "dev"
+Requires-Dist: mypy>=0.900; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=6.0; extra == "docs"
+Requires-Dist: sphinx-book-theme>=1.0.0; extra == "docs"
+Requires-Dist: sphinx-design>=0.5.0; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5.0; extra == "docs"
+Requires-Dist: numpydoc>=1.1; extra == "docs"
+Requires-Dist: jupyter>=1.0; extra == "docs"
+Requires-Dist: myst-nb>=1.0; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest>=6.0; extra == "test"
+Requires-Dist: pytest-cov>=2.10; extra == "test"
+Requires-Dist: numpy; extra == "test"
+Requires-Dist: scipy; extra == "test"
+Requires-Dist: matplotlib; extra == "test"
+Dynamic: license-file
+
+# brutus
+
+*Et tu, Brute?*
+
+![brutus logo](https://github.com/joshspeagle/brutus/blob/master/brutus_logo.png?raw=true)
+
+[![Tests](https://github.com/joshspeagle/brutus/workflows/Tests/badge.svg)](https://github.com/joshspeagle/brutus/actions)
+[![Coverage](https://codecov.io/gh/joshspeagle/brutus/branch/master/graph/badge.svg)](https://codecov.io/gh/joshspeagle/brutus)
+[![Documentation Status](https://readthedocs.org/projects/brutus/badge/?version=latest)](https://brutus.readthedocs.io/en/latest/?badge=latest)
+[![PyPI](https://img.shields.io/pypi/v/astro-brutus.svg)](https://pypi.org/project/astro-brutus/)
+[![arXiv](https://img.shields.io/badge/arXiv-2503.02227-b31b1b.svg)](https://arxiv.org/abs/2503.02227)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+`brutus` is a Python package for Bayesian inference of stellar properties, distances, and extinctions from photometry. It supports individual star fitting, cluster analysis, and 3D dust mapping.
+
+**Documentation**: [brutus.readthedocs.io](https://brutus.readthedocs.io)
+
+## Installation
+
+```bash
+pip install astro-brutus
+```
+
+Requires Python 3.9+ on Linux, macOS, or Windows with WSL.
+
+**Windows users**: Due to the `healpy` dependency, brutus requires WSL (Windows Subsystem for Linux) on Windows.
+
+### Development Install
+
+```bash
+git clone https://github.com/joshspeagle/brutus.git
+cd brutus
+pip install -e ".[dev]"
+```
+
+## Data Files
+
+Download required stellar models and dust maps:
+
+```python
+from brutus import fetch_grids, fetch_isos, fetch_dustmaps
+
+fetch_grids()      # MIST stellar grids
+fetch_isos()       # MIST isochrones
+fetch_dustmaps()   # 3D dust maps
+```
+
+Data files are also available from the [Harvard Dataverse](https://dataverse.harvard.edu/dataverse/astro-brutus).
+
+## Citation
+
+If you use `brutus`, please cite [Speagle et al. (2025)](https://arxiv.org/abs/2503.02227).
+
+## License
+
+MIT License. See [LICENSE](LICENSE) for details.
+
+## Contact
+
+- Author: Joshua S. Speagle (<j.speagle@utoronto.ca>)
+- Issues: [GitHub Issues](https://github.com/joshspeagle/brutus/issues)
+
+## Acknowledgments
+
+`brutus` uses [MIST](http://waps.cfa.harvard.edu/MIST/) stellar evolution models and [Bayestar](https://argonaut.skymaps.info/) dust maps. We thank the developers for making their data publicly available.

astro_brutus-1.1.0/README.md

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+# brutus
+
+*Et tu, Brute?*
+
+![brutus logo](https://github.com/joshspeagle/brutus/blob/master/brutus_logo.png?raw=true)
+
+[![Tests](https://github.com/joshspeagle/brutus/workflows/Tests/badge.svg)](https://github.com/joshspeagle/brutus/actions)
+[![Coverage](https://codecov.io/gh/joshspeagle/brutus/branch/master/graph/badge.svg)](https://codecov.io/gh/joshspeagle/brutus)
+[![Documentation Status](https://readthedocs.org/projects/brutus/badge/?version=latest)](https://brutus.readthedocs.io/en/latest/?badge=latest)
+[![PyPI](https://img.shields.io/pypi/v/astro-brutus.svg)](https://pypi.org/project/astro-brutus/)
+[![arXiv](https://img.shields.io/badge/arXiv-2503.02227-b31b1b.svg)](https://arxiv.org/abs/2503.02227)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+`brutus` is a Python package for Bayesian inference of stellar properties, distances, and extinctions from photometry. It supports individual star fitting, cluster analysis, and 3D dust mapping.
+
+**Documentation**: [brutus.readthedocs.io](https://brutus.readthedocs.io)
+
+## Installation
+
+```bash
+pip install astro-brutus
+```
+
+Requires Python 3.9+ on Linux, macOS, or Windows with WSL.
+
+**Windows users**: Due to the `healpy` dependency, brutus requires WSL (Windows Subsystem for Linux) on Windows.
+
+### Development Install
+
+```bash
+git clone https://github.com/joshspeagle/brutus.git
+cd brutus
+pip install -e ".[dev]"
+```
+
+## Data Files
+
+Download required stellar models and dust maps:
+
+```python
+from brutus import fetch_grids, fetch_isos, fetch_dustmaps
+
+fetch_grids()      # MIST stellar grids
+fetch_isos()       # MIST isochrones
+fetch_dustmaps()   # 3D dust maps
+```
+
+Data files are also available from the [Harvard Dataverse](https://dataverse.harvard.edu/dataverse/astro-brutus).
+
+## Citation
+
+If you use `brutus`, please cite [Speagle et al. (2025)](https://arxiv.org/abs/2503.02227).
+
+## License
+
+MIT License. See [LICENSE](LICENSE) for details.
+
+## Contact
+
+- Author: Joshua S. Speagle (<j.speagle@utoronto.ca>)
+- Issues: [GitHub Issues](https://github.com/joshspeagle/brutus/issues)
+
+## Acknowledgments
+
+`brutus` uses [MIST](http://waps.cfa.harvard.edu/MIST/) stellar evolution models and [Bayestar](https://argonaut.skymaps.info/) dust maps. We thank the developers for making their data publicly available.

astro_brutus-1.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=64", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "astro-brutus"
+version = "1.1.0"
+description = "Brute-force Bayesian inference for photometric distances, reddenings, and stellar properties"
+readme = "README.md"
+license = {text = "MIT"}
+authors = [
+    {name = "Joshua S Speagle", email = "j.speagle@utoronto.ca"}
+]
+maintainers = [
+    {name = "Joshua S Speagle", email = "j.speagle@utoronto.ca"}
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "License :: OSI Approved :: MIT License",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Topic :: Scientific/Engineering :: Astronomy",
+    "Intended Audience :: Science/Research",
+]
+keywords = [
+    "brute force", "photometry", "bayesian", "stellar", "star",
+    "cluster", "isochrone", "dust", "reddening",
+    "parallax", "distance", "template fitting"
+]
+requires-python = ">=3.9"
+dependencies = [
+    "numpy>=1.19",
+    "scipy>=1.6.0",
+    "matplotlib>=3.3.0",
+    "h5py>=3.0.0",
+    "healpy>=1.14.0",
+    "numba>=0.59.0",
+    "pooch>=1.4.0",
+    "tqdm>=4.50.0",
+]
+# dynamic = ["version"]  # removed to avoid conflict with static 'version' field
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=6.0",
+    "pytest-cov>=2.10",
+    "black>=21.0",
+    "flake8>=3.8",
+    "isort>=5.0",
+    "mypy>=0.900",
+]
+docs = [
+    "sphinx>=6.0",
+    "sphinx-book-theme>=1.0.0",
+    "sphinx-design>=0.5.0",
+    "sphinx-copybutton>=0.5.0",
+    "numpydoc>=1.1",
+    "jupyter>=1.0",
+    "myst-nb>=1.0",
+]
+test = [
+    "pytest>=6.0",
+    "pytest-cov>=2.10",
+    "numpy",
+    "scipy",
+    "matplotlib",
+]
+
+[project.urls]
+Homepage = "https://github.com/joshspeagle/brutus"
+Repository = "https://github.com/joshspeagle/brutus"
+Documentation = "https://brutus.readthedocs.io"
+"Bug Tracker" = "https://github.com/joshspeagle/brutus/issues"
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"*" = ["*.dat", "*.txt", "*.md"]
+
+# Development tools configuration
+[tool.black]
+line-length = 88
+target-version = ['py39', 'py310', 'py311', 'py312', 'py313']
+include = '\.pyi?$'
+extend-exclude = '''
+/(
+    # directories
+    \.eggs
+    | \.git
+    | \.hg
+    | \.mypy_cache
+    | \.tox
+    | \.venv
+    | build
+    | dist
+)/
+'''
+
+[tool.isort]
+profile = "black"
+line_length = 88
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+ensure_newline_before_comments = true
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+# Coverage flags are intentionally NOT enabled by default. Writing the HTML
+# coverage report fails on some filesystems (notably WSL/DrvFs, with
+# "OSError: [Errno 22] Invalid argument" on htmlcov/*), which aborts every
+# pytest invocation including --collect-only. Default runs therefore omit
+# coverage; CI measures it explicitly (see .github/workflows/tests.yml):
+#   NUMBA_DISABLE_JIT=1 pytest tests/ --cov=brutus --cov-report=xml
+# For a local coverage report, run that command yourself.
+addopts = [
+    "--strict-markers",
+    "--strict-config",
+]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+markers = [
+    "slow: marks tests as slow-running (deselect with '-m \"not slow\"')",
+    "requires_data: marks tests that need downloaded model data (they skip if absent)",
+]
+filterwarnings = [
+    "error",
+    "ignore::UserWarning",
+    "ignore::DeprecationWarning",
+]
+# Note: Set NUMBA_DISABLE_JIT=1 environment variable for accurate coverage
+# of @jit/@njit decorated functions. Without this, numba-compiled functions
+# will show 0% coverage even if executed by tests.
+
+[tool.coverage.run]
+source = ["src/brutus"]
+omit = [
+    "*/tests/*",
+    "*/test_*",
+    "setup.py",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "if self.debug:",
+    "if settings.DEBUG",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if 0:",
+    'if __name__ == "__main__":',
+    'class .*\bProtocol\):',
+    '@(abc\.)?abstractmethod',
+]
+
+[tool.mypy]
+python_version = "3.9"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false  # Start lenient, tighten later
+disallow_incomplete_defs = false
+check_untyped_defs = true
+disallow_untyped_decorators = false
+no_implicit_optional = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_no_return = true
+warn_unreachable = true
+strict_equality = true

astro_brutus-1.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+