laser.cholera 0.13.0__tar.gz

laser_cholera-0.13.0/AUTHORS.rst

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+
+Authors
+=======
+
+* Christopher Lorton - https://www.idmod.org
+* John Giles - https://www.idmod.org

laser_cholera-0.13.0/CHANGELOG.rst

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+
+Changelog
+=========
+
+0.12.5 (unreleased)
+-------------------
+
+* Add src/laser/cholera/calc_log_likelihood_distributions.py: Python translation of calc_log_likelihood_distributions.R (Beta, Binomial, Gamma, NegBin, Normal, Poisson)
+* Rename src/laser/cholera/spring_likelihood.py → calc_model_likelihood.py
+* Add tests/test_calc_log_likelihood_negbin.py: Python translation of test_calc_log_likelihood_negbin.R; update import to calc_log_likelihood_distributions
+* Add tests/test_calc_model_likelihood.py: Python translation of test_calc_model_likelihood.R
+* Add tests/test_calc_model_likelihood_extreme.py: Python translation of test_calc_model_likelihood_extreme.R
+* Add tests/test_calc_model_likelihood_reference.py: Python translation of test_calc_model_likelihood_reference.R
+* Add tests/test_compute_wis_parametric_row.py: Python translation of test_compute_wis_parametric_row.R
+* Add tests/test_ll_cumulative_progressive_nb.py: Python translation of test_ll_cumulative_progressive_nb.R
+* Add tests/test_nb_size_from_obs_weighted.py: Python translation of test_nb_size_from_obs_weighted.R
+* Update src/laser/cholera/calc_model_likelihood.py: replace the ``config`` dict argument on ``calc_model_likelihood`` with explicit ``epidemic_peaks`` (DataFrame with ``iso_code``, ``peak_date``, ``loc_idx`` columns), ``date_start``, and ``date_stop`` kwargs.
+* Update src/laser/cholera/metapop/params.py: ingestion of ``epidemic_peaks`` now asserts each ``iso_code`` is in ``location_name`` and appends a ``loc_idx`` column mapping each row to its simulation location index.
+* Remove HDF5 config-parameter loading from src/laser/cholera/metapop/params.py (``load_hdf5_parameters``, ``load_compressed_hdf5_parameters``, ``load_hdf5`` and the ``.h5``/``.hdf``/``.hdf5`` entries in ``get_parameters`` dispatch). HDF5 *output* via ``recorder.py`` is unaffected, as is the ``hdf5_output`` flag in ``utils.py``. Add a parametrized regression test in tests/test_params.py confirming HDF5 suffixes are now rejected by ``get_parameters``.
+* Add tests/test_recorder.py: 20-test coverage of ``Recorder`` — init/model identity, ``check()`` warn-on-missing for ``people``/``patches``, per-tick gating in ``__call__`` (final-tick timing, ``hdf5_output`` + ``return`` quadrants), ``outdir`` routing, ``compress`` → ``.h5.gz``, low-level ``save_hdf5_parameters`` / ``save_compressed_hdf5_parameters`` (groups, datasets, underscore + method filtering, ``AttributeError`` on missing frames), and an end-to-end happy-path round-trip.
+* Update tests/test_params.py: add tests covering ``epidemic_peaks`` ingestion (list-of-dicts and dict-of-lists → DataFrame, optional/absent case, ``loc_idx`` mapping correctness, unknown-ISO ``AssertionError``) and ``validate_parameters`` enforcement of ``iso_code`` and ``peak_date`` columns.
+* Fix latent bug in src/laser/cholera/metapop/utils.py: ``override_helper`` mapped ``date_start`` / ``date_stop`` to ``partial(datetime.strptime, format="%Y-%m-%d")``, which raises ``TypeError`` because ``datetime.strptime`` is a C function that rejects keyword arguments. Replaced with a positional-args wrapper.
+* Test-coverage push to ≥90% across five files: ``calc_log_likelihood_distributions.py`` 91.7%, ``calc_model_likelihood.py`` 91.5%, ``metapop/analyzer.py`` 100%, ``metapop/utils.py`` 100%, ``metapop/vaccinated.py`` 98.0%. New test files: ``tests/test_analyzer.py``, ``tests/test_calc_log_likelihood_{beta,binomial,gamma,normal,poisson,verbose}.py``. Extended files: ``tests/test_metapop_utils.py`` (new ``TestOverrideHelper`` class + single-location ``get_pi`` test), ``tests/test_vaccinated.py`` (2 dose-clamp branch tests), ``tests/test_calc_model_likelihood.py`` (new ``TestLegacyPeakHelpers`` and ``TestCalcModelLikelihoodCoverage`` classes covering legacy multi-peak helpers, peak shape-term dispatch, weekly-cadence detection, weights-validation paths, NB dispersion fallback, and the non-finite per-location safety net).
+
+0.10.1 (2026-01-16)
+-------------------
+
+* Add tests for new IFR implementation
+
+0.10.0 (2026-01-15)
+-------------------
+
+* New IFR model (Infection Fatality Ratio)
+* Update observation process with rho and chi based on infectious prevalence and diagnostic rates
+* Update default_parameters.json and LICENSE copyright dates
+* Test fixes for NumPy scalar serialization
+* Remove MacOS x86_64 from test matrix
+* Linter issues and GitHub runner fixes
+
+0.9.1 (2025-10-02)
+------------------
+
+* Fix typo infective -> ineffective
+* Add checks against populations going negative
+* Expose new_symptomatic
+* Only print if verbose is True in parameters
+* Skip likelihood check unless "calc_likelihood" is in parameters
+* Address linter issues
+* Bugfix for parameter constraints (alphas)
+
+0.9.0 (2025-08-19)
+------------------
+
+* Support single location configuration
+
+0.8.0 (2025-07-24)
+------------------
+
+* Spatial hazard computation fix (don't transpose pi_ij in model.results)
+
+0.7.11 (2025-07-11)
+-------------------
+
+* Trim and transpose for convenience in MOSAIC
+
+0.7.10 (2025-07-10)
+-------------------
+
+* Fix bug in double counting Vxinf
+* Fix bug in suitability to decay calculations
+* Update default parameters
+* Fix indexing for human daily seasonality
+
+0.7.9 (2025-06-06)
+------------------
+
+* Rename beta_env to beta_jt_env
+* Rename beta_j_seasonality to beta_jt_human and use directly in spatial hazard calculation
+* Update pre-commit
+* Fix handling of pi_ij matrix math
+* Track vaccine doses delivered
+* Births should be Poisson rather than binomial
+* Rename estimated to simulated for clarity
+* Switch from 'agents' to 'people' terminology
+* Fix coupling calculation for denominator == 0
+
+0.7.8 (2025-05-16)
+------------------
+
+* Likelihood cleanup for NaNs and all zeros
+
+0.7.7 (2025-05-13)
+------------------
+
+* Calculate log likelihood at end of simulation
+
+0.7.6 (2025-05-13)
+------------------
+
+* Fix logging setup and np.var() usage
+
+0.7.5 (2025-05-13)
+------------------
+
+* Add Python implementation of R tests for likelihood functions
+
+0.7.4 (2025-05-07)
+------------------
+
+* Fix up reading JSON files back into memory (handle actual NaN vs "NA" or "NaN")
+* Record incidence (total and per source)
+* Adding likelihood functions
+* Adding likelihood function tests
+* More consistent variable names
+
+0.7.3 (2025-04-30)
+------------------
+
+* Gate file output on hdf5_output and "return" config parameters
+* Clean up console output with logging infrastructure
+* Add "quiet" parameter to suppress console progress bar (defaults to False for CLI, True for programmatic interface)
+* Update GHA to run tests on push to main
+* Support params from R (numeric values come in as doubles, but we need an integer for p)
+
+0.7.2 (2025-04-24)
+------------------
+
+* Support for passing dict to get_parameters()
+* Tests for run_model() function
+* Additional tests for tracking vital statistics (births, non-disease deaths, disease deaths)
+
+0.7.1 (2025-04-24)
+------------------
+
+* Minor version bump
+
+0.7.0 (2025-04-23)
+------------------
+
+* Initial alpha release
+* Support passing parameter dictionary to run_model()
+* Fix mapping of environmental suitability (psi_jt) to decay parameter (delta_jt)
+* Update default_parameters.json with matrices
+* Update parameter loading for matrices
+* Clean up plotting and fix seasonality phase
+* Handle command line parameter overrides
+* Enable parameter overrides correctly
+* Allow test parameter sets to skip validation
+* Pin numpy, numba, and llvmlite versions
+* Remove subpackages
+* Update laser-core dependency
+* Return model from run_model()
+* Require Numba that supports NumPy>=2.0
+* Update shedding to environment based on theta_j
+* Updated parameters including switch from delta_min/delta_max to decay_days_fast/decay_days_slow
+* Use decay_shape_1 and decay_shape_2 to parameterize scipy.stats.beta.cdf
+* Add version bump, build, and release GHA
+* Metapop implementation work-in-progress commits
+
+0.0.0 (2024-09-30)
+------------------
+
+* First release on PyPI

laser_cholera-0.13.0/CONTRIBUTING.rst

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+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+Bug reports
+===========
+
+When `reporting a bug <https://github.com/InstituteforDiseaseModeling/laser-cholera/issues>`_ please include:
+
+    * Your operating system name and version.
+    * Any details about your local setup that might be helpful in troubleshooting.
+    * Detailed steps to reproduce the bug.
+
+Documentation improvements
+==========================
+
+LASER Cholera could always use more documentation, whether as part of the
+official LASER Cholera docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Feature requests and feedback
+=============================
+
+The best way to send feedback is to file an issue at https://github.com/InstituteforDiseaseModeling/laser-cholera/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that code contributions are welcome :)
+
+Development
+===========
+
+To set up `laser-cholera` for local development:
+
+1. Fork `laser-cholera <https://github.com/InstituteforDiseaseModeling/laser-cholera>`_
+   (look for the "Fork" button).
+2. Clone your fork locally::
+
+    git clone git@github.com:YOURGITHUBNAME/laser-cholera.git
+
+3. Create a branch for local development::
+
+    git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+4. When you're done making changes run all the checks and docs builder with one command::
+
+    tox
+
+5. Commit your changes and push your branch to GitHub::
+
+    git add .
+    git commit -m "Your detailed description of your changes."
+    git push origin name-of-your-bugfix-or-feature
+
+6. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+If you need some code review or feedback while you're developing the code just make the pull request.
+
+For merging, you should:
+
+1. Include passing tests (run ``tox``).
+2. Update documentation when there's new API, functionality etc.
+3. Add a note to ``CHANGELOG.rst`` about the changes.
+4. Add yourself to ``AUTHORS.rst``.
+
+Tips
+----
+
+To run a subset of tests::
+
+    tox -e envname -- pytest -k test_myfeature
+
+To run all the test environments in *parallel*::
+
+    tox -p auto

laser_cholera-0.13.0/LICENSE

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+MIT License
+
+Copyright (c) 2024-2026, Bill & Melinda Gates Foundation
+
+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 (including the next paragraph) 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.

laser_cholera-0.13.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: laser.cholera
+Version: 0.13.0
+Summary: LASIK - LASER based SImulation of Kolera
+Keywords: cholera,simulation,laser,spatial modeling
+Author: Christopher Lorton, John Giles
+Author-email: Christopher Lorton <christopher.lorton@gatesfoundation.org>, John Giles <john.giles@gatesfoundation.org>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+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: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Requires-Dist: laser-core~=1.0
+Requires-Dist: geopandas>=1.1.2
+Requires-Dist: h5py
+Requires-Dist: scipy
+Requires-Dist: tqdm
+Requires-Dist: pytest>=9.0.3 ; extra == 'dev'
+Requires-Dist: build ; extra == 'dev'
+Requires-Dist: uv ; extra == 'dev'
+Requires-Dist: jupyter ; extra == 'nb'
+Requires-Dist: nbconvert>=7.17.1 ; extra == 'nb'
+Requires-Dist: nbformat ; extra == 'nb'
+Requires-Dist: ipykernel ; extra == 'nb'
+Maintainer: Christopher Lorton
+Maintainer-email: Christopher Lorton <christopher.lorton@gatesfoundation.org>
+Requires-Python: >=3.10
+Project-URL: Homepage, https://example.com
+Project-URL: Documentation, https://laser-cholera.readthedocs.io/en/latest/
+Project-URL: Repository, https://github.com/InstituteforDiseaseModeling/laser-cholera.git
+Project-URL: Issues, https://github.com/InstituteforDiseaseModeling/laser-cholera/issues
+Project-URL: Changelog, https://github.com/InstituteforDiseaseModeling/laser-cholera/blob/master/CHANGELOG.md
+Provides-Extra: dev
+Provides-Extra: nb
+Description-Content-Type: text/markdown
+
+# LASIK - LASER based SImulation of Kolera
+
+-----
+
+[![documentation](https://readthedocs.org/projects/laser-cholera/badge/?style=flat)](https://docs.idmod.org/projects/laser-cholera/en/latest/)
+
+![tests](https://github.com/InstituteforDiseaseModeling/laser-cholera/actions/workflows/github-actions.yml/badge.svg)
+
+[![package](https://img.shields.io/pypi/v/laser-cholera.svg)](https://pypi.org/project/laser-cholera/)
+![wheel](https://img.shields.io/pypi/wheel/laser-cholera.svg)
+![python versions](https://img.shields.io/pypi/pyversions/laser-cholera)
+![implementation](https://img.shields.io/pypi/implementation/laser-cholera.svg)
+![license](https://img.shields.io/pypi/l/laser-cholera.svg)
+
+![commits since v0.13.0](https://img.shields.io/github/commits-since/InstituteforDiseaseModeling/laser-cholera/v0.13.0.svg)
+
+-----
+
+- `uv` package and project manager: `python3 -m pip install uv`
+  - `uv python install 3.10 3.11 3.12 3.13 3.14`
+  - in the `laser-cholera` directory:
+  - `uv venv` optionally specify `--python #` to use a particular versin of Python in the virtual environment
+  - `uv pip install -e .`

laser_cholera-0.13.0/README.md

@@ -0,0 +1,23 @@
+# LASIK - LASER based SImulation of Kolera
+
+-----
+
+[![documentation](https://readthedocs.org/projects/laser-cholera/badge/?style=flat)](https://docs.idmod.org/projects/laser-cholera/en/latest/)
+
+![tests](https://github.com/InstituteforDiseaseModeling/laser-cholera/actions/workflows/github-actions.yml/badge.svg)
+
+[![package](https://img.shields.io/pypi/v/laser-cholera.svg)](https://pypi.org/project/laser-cholera/)
+![wheel](https://img.shields.io/pypi/wheel/laser-cholera.svg)
+![python versions](https://img.shields.io/pypi/pyversions/laser-cholera)
+![implementation](https://img.shields.io/pypi/implementation/laser-cholera.svg)
+![license](https://img.shields.io/pypi/l/laser-cholera.svg)
+
+![commits since v0.13.0](https://img.shields.io/github/commits-since/InstituteforDiseaseModeling/laser-cholera/v0.13.0.svg)
+
+-----
+
+- `uv` package and project manager: `python3 -m pip install uv`
+  - `uv python install 3.10 3.11 3.12 3.13 3.14`
+  - in the `laser-cholera` directory:
+  - `uv venv` optionally specify `--python #` to use a particular versin of Python in the virtual environment
+  - `uv pip install -e .`

laser_cholera-0.13.0/README.rst

@@ -0,0 +1,97 @@
+========
+Overview
+========
+
+.. start-badges
+
+.. list-table::
+    :stub-columns: 1
+
+    * - docs
+      - |docs|
+    * - tests
+      - |github-actions| |codecov|
+    * - package
+      - |version| |wheel| |supported-versions| |supported-implementations| |commits-since|
+.. |docs| image:: https://readthedocs.org/projects/laser-cholera/badge/?style=flat
+    :target: https://laser-cholera.readthedocs.io/en/latest/
+    :alt: Documentation Status
+
+.. |github-actions| image:: https://github.com/InstituteforDiseaseModeling/laser-cholera/actions/workflows/github-actions.yml/badge.svg
+    :alt: GitHub Actions Build Status
+    :target: https://github.com/InstituteforDiseaseModeling/laser-cholera/actions
+
+.. |codecov| image:: https://codecov.io/gh/InstituteforDiseaseModeling/laser-cholera/branch/main/graphs/badge.svg?branch=main
+    :alt: Coverage Status
+    :target: https://app.codecov.io/github/InstituteforDiseaseModeling/laser-cholera
+
+.. |version| image:: https://img.shields.io/pypi/v/laser-cholera.svg
+    :alt: PyPI Package latest release
+    :target: https://test.pypi.org/project/laser-cholera/
+
+.. |wheel| image:: https://img.shields.io/pypi/wheel/laser-cholera.svg
+    :alt: PyPI Wheel
+    :target: https://test.pypi.org/project/laser-cholera/
+
+.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/laser-cholera.svg
+    :alt: Supported versions
+    :target: https://test.pypi.org/project/laser-cholera/
+
+.. |supported-implementations| image:: https://img.shields.io/pypi/implementation/laser-cholera.svg
+    :alt: Supported implementations
+    :target: https://test.pypi.org/project/laser-cholera/
+
+.. |commits-since| image:: https://img.shields.io/github/commits-since/InstituteforDiseaseModeling/laser-cholera/v0.13.0.svg
+    :alt: Commits since latest release
+    :target: https://github.com/InstituteforDiseaseModeling/laser-cholera/compare/v0.13.0...main
+
+
+
+.. end-badges
+
+LASIK - LASER based SImulation of Kolera
+
+* Free software: MIT license
+
+Installation
+============
+
+::
+
+    pip install laser-cholera
+
+You can also install the in-development version with::
+
+    pip install https://github.com/InstituteforDiseaseModeling/laser-cholera/archive/main.zip
+
+
+Documentation
+=============
+
+
+https://laser-cholera.readthedocs.io/en/latest/
+
+
+Development
+===========
+
+To run all the tests run::
+
+    tox
+
+Note, to combine the coverage data from all the tox environments run:
+
+.. list-table::
+    :widths: 10 90
+    :stub-columns: 1
+
+    - - Windows
+      - ::
+
+            set PYTEST_ADDOPTS=--cov-append
+            tox
+
+    - - Other
+      - ::
+
+            PYTEST_ADDOPTS=--cov-append tox

laser_cholera-0.13.0/pyproject.toml

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+[build-system]
+requires = ["uv_build>=0.10.0,<0.12.0"]
+build-backend = "uv_build"
+
+[project]
+name = "laser.cholera"
+version = "0.13.0"
+authors = [
+  { name="Christopher Lorton", email="christopher.lorton@gatesfoundation.org" },
+  { name="John Giles", email="john.giles@gatesfoundation.org" },
+]
+maintainers = [
+  { name="Christopher Lorton", email="christopher.lorton@gatesfoundation.org" },
+]
+description = "LASIK - LASER based SImulation of Kolera"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+requires-python = ">=3.10"
+keywords = ["cholera", "simulation", "laser", "spatial modeling"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    # "Programming Language :: Python :: 3.15",   # Not until Numba supports it
+    "Programming Language :: Python :: Implementation :: CPython",
+]
+dependencies = [
+    "laser-core~=1.0",
+    "geopandas>=1.1.2",
+    "h5py",
+    "scipy",
+    "tqdm",
+]
+
+[project.optional-dependencies]
+"dev" = ["pytest>=9.0.3", "build", "uv"]
+# "docs" = ["sphinx", "sphinx-rtd-theme"]
+"nb" = ["jupyter", "nbconvert>=7.17.1", "nbformat", "ipykernel"]
+
+[project.urls]
+Homepage = "https://example.com"
+Documentation = "https://laser-cholera.readthedocs.io/en/latest/"
+Repository = "https://github.com/InstituteforDiseaseModeling/laser-cholera.git"
+Issues = "https://github.com/InstituteforDiseaseModeling/laser-cholera/issues"
+Changelog = "https://github.com/InstituteforDiseaseModeling/laser-cholera/blob/master/CHANGELOG.md"
+
+[project.scripts]
+metapop = "laser.cholera.metapop.model:cli_run"
+
+[tool.uv.build-backend]
+module-name = [ "laser.cholera" ]
+source-include = [
+    "AUTHORS.rst", "CHANGELOG.rst", "CONTRIBUTING.rst", "README.rst",
+    "src/laser/cholera/metapop/data/default_parameters.*",
+    "src/laser/cholera/metapop/data/demographics_africa_2000_2023.csv",
+    "src/laser/cholera/metapop/data/mosaic_countries*",
+    "tests/test*py"
+    ]
+
+[tool.ruff]
+extend-exclude = ["static", "ci/templates"]
+line-length = 150
+src = ["src", "tests"]
+target-version = "py39"
+
+[tool.ruff.lint.per-file-ignores]
+"ci/*" = ["S"]
+
+[tool.ruff.lint]
+select = [
+    "B", # flake8-bugbear
+    "C4", # flake8-comprehensions
+    "DTZ", # flake8-datetimez
+    "E", # pycodestyle errors
+    "EXE", # flake8-executable
+    "F", # pyflakes
+    "I", # isort
+    "INT", # flake8-gettext
+    "PIE", # flake8-pie
+    "PLC", # pylint convention
+    "PLE", # pylint errors
+    "PT", # flake8-pytest-style
+    "PTH", # flake8-use-pathlib
+    "RSE", # flake8-raise
+    "RUF", # ruff-specific rules
+    "S", # flake8-bandit
+    "UP", # pyupgrade
+    "W", # pycodestyle warnings
+]
+ignore = [
+    "RUF001", # ruff-specific rules ambiguous-unicode-character-string
+    "RUF002", # ruff-specific rules ambiguous minus sign
+    "S101", # flake8-bandit assert
+    "S308", # flake8-bandit suspicious-mark-safe-usage
+    "S603", # flake8-bandit subprocess-without-shell-equals-true
+    "S607", # flake8-bandit start-process-with-partial-path
+    "E501", # pycodestyle line-too-long
+    "DTZ001", # flake8-datetimez call datetime without tzinfo
+]
+
+[tool.ruff.lint.flake8-pytest-style]
+fixture-parentheses = false
+mark-parentheses = false
+
+[tool.ruff.lint.isort]
+forced-separate = ["conftest"]
+force-single-line = true
+
+[tool.ruff.format]
+quote-style = "double"
+
+
+[tool.bumpversion]
+current_version = "0.13.0"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+tag = true
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+
+[[tool.bumpversion.files]]
+filename = "README.md"
+search = "since v{current_version}"
+replace = "since v{new_version}"
+
+[[tool.bumpversion.files]]
+filename = "README.md"
+search = "/v{current_version}.svg"
+replace = "/v{new_version}.svg"
+
+[[tool.bumpversion.files]]
+filename = "README.rst"
+search = "/v{current_version}.svg"
+replace = "/v{new_version}.svg"
+
+[[tool.bumpversion.files]]
+filename = "README.rst"
+search = "/v{current_version}...main"
+replace = "/v{new_version}...main"
+
+[[tool.bumpversion.files]]
+filename = "docs/conf.py"
+search = 'version = release = "{current_version}"'
+replace = 'version = release = "{new_version}"'
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = 'version = "{current_version}"'
+replace = 'version = "{new_version}"'

laser_cholera-0.13.0/src/laser/cholera/__init__.py

@@ -0,0 +1,12 @@
+from importlib.metadata import version
+
+__version__ = version("laser.cholera")
+
+from .core import compute
+from .iso_codes import iso_codes
+
+__all__ = [
+    "__version__",
+    "compute",
+    "iso_codes",
+]