diff --git a/.github/workflows/test-deploy.yml b/.github/workflows/test-deploy.yml new file mode 100644 index 0000000..b3f74c7 --- /dev/null +++ b/.github/workflows/test-deploy.yml @@ -0,0 +1,78 @@ +name: Build and Deploy to TestPyPI + +on: workflow_dispatch + +jobs: + build_wheels: + name: Build wheels for ${{ matrix.os }} + runs-on: ${{ matrix.os }} + strategy: + matrix: + # macos-15-intel is an Intel runner, macos-14 is Apple silicon + os: + [ + ubuntu-latest, + ubuntu-24.04-arm, + windows-latest, + windows-11-arm, + macos-15-intel, + macos-14, + ] + + steps: + - uses: actions/checkout@v6 + with: + persist-credentials: false + + - name: Build wheels + uses: pypa/cibuildwheel@v3.4.0 + with: + extras: "uv" + + - uses: actions/upload-artifact@v4 + with: + name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }} + path: ./wheelhouse/*.whl + + build_sdist: + name: Build Source Distribution + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v6 + with: + persist-credentials: false + + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b + with: + version: "0.11.20" + + - name: Build sdist + run: uvx --from build pyproject-build + - uses: actions/upload-artifact@v4 + with: + name: cibw-sdist + path: dist/*.tar.gz + + upload_pypi: + name: Publish to PyPI + needs: [build_wheels, build_sdist] + runs-on: ubuntu-latest + environment: + name: testpypi + url: https://test.pypi.org/p/respondpy/ + permissions: + id-token: write + steps: + - name: Download wheel artifacts + uses: actions/download-artifact@v5 + with: + path: dist + pattern: cibw-* + merge-multiple: true + + - name: Publish distributions to PyPI with attestations + uses: pypa/gh-action-pypi-publish@release/v1 + with: + packages-dir: dist + attestations: true diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml new file mode 100644 index 0000000..ef24c23 --- /dev/null +++ b/.github/workflows/testing.yml @@ -0,0 +1,95 @@ +name: Smoke Testing, Unit Testing, and Code Coverage + +on: + push: + branches: ["main"] + pull_request: + branches: ["main"] + +jobs: + smoke-testing: + runs-on: ${{ matrix.os }} + defaults: + run: + shell: ${{ matrix.shell }} + strategy: + matrix: + os: [ubuntu-latest, windows-latest, macos-latest] + include: + - os: ubuntu-latest + shell: bash + - os: windows-latest + shell: pwsh + - os: macos-latest + shell: bash + steps: + - name: Checkout + uses: actions/checkout@v6 + + - name: Install uv + uses: astral-sh/setup-uv@v7 + with: + version: "0.10.11" + + - name: Set up Python + uses: actions/setup-python@v6 + with: + python-version: "3.12" + + - name: Install dependencies + run: uv sync --group github + + - name: Run smoke tests + run: uv run pytest -m smoke + + unit-testing: + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v6 + + - name: Install uv + uses: astral-sh/setup-uv@v7 + with: + version: "0.10.11" + + - name: Set up Python + uses: actions/setup-python@v6 + with: + python-version: "3.12" + + - name: Install dependencies + run: uv sync --group github + + - name: Run tests + run: uv run pytest -m unit + + code-coverage: + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v6 + + - name: Install uv + uses: astral-sh/setup-uv@v7 + with: + version: "0.10.11" + + - name: Set up Python + uses: actions/setup-python@v6 + with: + python-version: "3.12" + + - name: Install dependencies + run: uv sync --group github + + - name: Run tests with coverage + run: uv run pytest --cov=respondpy --cov-report=term-missing --cov-report=xml tests + + - name: Upload coverage to Codecov + uses: codecov/codecov-action@v5 + with: + token: ${{ secrets.CODECOV_TOKEN }} + slug: SyndemicsLab/respondpy diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml deleted file mode 100644 index 239420a..0000000 --- a/.github/workflows/tests.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: Tests - -on: - push: - branches: - - main - - feature/** - pull_request: - branches: - - main - -jobs: - test: - runs-on: ubuntu-latest - - steps: - - name: Checkout - uses: actions/checkout@v6 - - - name: Install uv - uses: astral-sh/setup-uv@v7 - with: - version: "0.10.11" - - - name: Set up Python - uses: actions/setup-python@v6 - with: - python-version: "3.12" - - - name: Install dependencies - run: uv sync --group github - - - name: Run tests - run: uv run pytest --benchmark-disable --cov=respondpy --cov-report=term-missing --cov-report=xml tests - - - name: Upload coverage reports to Codecov - uses: codecov/codecov-action@v5 - with: - token: ${{ secrets.CODECOV_TOKEN }} - slug: SyndemicsLab/respondpy diff --git a/.gitignore b/.gitignore index cf609cd..d67e149 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,7 @@ .vscode None wheelhouse +_version.py # Byte-compiled / optimized / DLL files __pycache__/ diff --git a/CMakeLists.txt b/CMakeLists.txt index 06f457d..039d559 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -4,7 +4,7 @@ project(RESPONDPY LANGUAGES CXX) include(FetchContent) -set(CMAKE_CXX_STANDARD 17 CACHE STRING "The C++ standard to compile with, 17") +set(CMAKE_CXX_STANDARD 20 CACHE STRING "The C++ standard to compile with, 20") set(CMAKE_CXX_STANDARD_REQUIRED ON) set(CMAKE_CXX_EXTENSIONS OFF) @@ -62,7 +62,7 @@ set(SPDLOG_INSTALL ON) FetchContent_Declare( respond GIT_REPOSITORY https://github.com/SyndemicsLab/respond.git - GIT_TAG 6a134d60fefd54b00f433c4814f4c4bcb9eace9a + GIT_TAG dde215f20e921e0d52a9f749cd14e91c925b18ac OVERRIDE_FIND_PACKAGE ) set(RESPOND_BUILD_DOCS OFF) diff --git a/pyproject.toml b/pyproject.toml index 35ad74e..3dfb615 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,96 +1,103 @@ [build-system] -requires = ["scikit-build-core>=0.11", "pybind11"] +requires = ["scikit-build-core>=0.11", "pybind11", "numpy", "polars>=1.37.1"] build-backend = "scikit_build_core.build" [project] name = "respondpy" -version = "0.2.0" +version = "0.2.2" description = "The Syndemic Lab's RESPOND Simulation Python Extension Module." readme = "README.md" -requires-python = ">=3.10" +requires-python = ">=3.11" authors = [ { name = "Matthew Carroll", email = "Matthew.Carroll@bmc.org" }, { name = "Dimitri Baptiste", email = "Dimitri.Baptiste@bmc.org" }, ] -maintainers = [{ name = "Syndemics Lab", email = "Benjamin.Linas@bmc.org" }] -keywords = ["simulation", "Opioid Use Disorder", "Syndemics"] +maintainers = [ + { name = "Syndemics Lab", email = "Benjamin.Linas@bmc.org" } +] license = "AGPL-3.0-or-later" license-files = ["LICENSE.txt"] +keywords = ["simulation", "Opioid Use Disorder", "markov", "Syndemics"] +classifiers = [ + "Development Status :: 3 - Alpha", + "Intended Audience :: Science/Research", + "Operating System :: POSIX :: Linux", + "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", + "Topic :: Scientific/Engineering :: Medical Science Apps.", + "Typing :: Stubs Only" +] dependencies = [ "numpy", - "polars>=1.37.1", - "setuptools-scm>=10.0.5", + "polars>=1.37.1" ] [project.urls] -Homepage = "https://github.com/SyndemicsLab/respond" +Homepage = "https://syndemicslab.org" +Documentation = "https://syndemicslab.github.io/respond/" +Repository = "https://github.com/SyndemicsLab/respond.git" Issues = "https://github.com/SyndemicsLab/respond/issues" -[tool.scikit-build] -minimum-version = "build-system.requires" -metadata.version.provider = "scikit_build_core.metadata.setuptools_scm" -sdist.exclude = [] -logging.level = "INFO" -cmake.build-type = "Release" -messages.after-success = "{green}Wheel successfully built" -messages.after-failure = """ -{bold.red}Sorry{normal}, build failed. Your platform is {platform.platform}. -""" - [dependency-groups] -dev = [ - { include-group = "test" }, - "ipykernel", - "nbconvert", - "nox>=2026.2.9", - "polars>=1.37.1", - "pybind11-stubgen>=2.5.5", - "pylint>=4.0.5", - "pytest>=9.0.2", - "setuptools_scm", - "typer", - "uhi", -] docs = [ "ipython", "myst_parser>=0.13", "nbsphinx", - "numpy", "sphinx-book-theme>=0.0.33", "sphinx>=4.0", "sphinx_copybutton", ] -examples = [] +# hypothesis is slow on iOS, can fail health check +# pytest-xdist has no processes on iOS test = [ "cloudpickle", - "pytest-benchmark", + "pylint>=4.0.5", "pytest-cov>=7.0.0", - "pytest>=6.0", + "pytest>=9.0.2", "pytest-benchmark", - "numpy", - "hypothesis>=6.0; sys_platform != 'ios'", # slow on iOS, can fail health check - "pytest-xdist; sys_platform != 'ios'", # No processes on iOS + "nox>=2026.2.9", + "hypothesis>=6.0; sys_platform != 'ios'", + "pytest-xdist; sys_platform != 'ios'" ] github = [ { include-group = "test" }, - "setuptools_scm", "pytest-github-actions-annotate-failures" ] -benchmark = [ - { include-group = "test" }, - "polars>=1.37.1", +dev = [ + { include-group = "test" }, + { include-group = "docs" }, + "cibuildwheel>=2.15.0", ] +[tool.scikit-build] +build.verbose = true +logging.level = "INFO" +minimum-version = "build-system.requires" +cmake.version = ">=3.27.0" +ninja.version = ">=1.11" +sdist.exclude = [ + ".github/*", + "docs/*", + "benchmarks/*", +] +sdist.include = [ + "src/respondpy/_version.py" +] +cmake.build-type = "Release" +messages.after-success = "{green}Wheel successfully built" +messages.after-failure = """ +{bold.red}Sorry{normal}, build failed. Your platform is {platform.platform}. +""" + [[tool.scikit-build.generate]] -path = "respondpy/version.py" +path = "src/respondpy/_version.py" template = ''' -__version__ = version = "$version" +__version__ = version = "${version}" ''' - -[tool.setuptools_scm] - -[tool.uv.pip] -only-binary = ["numpy"] +location = "source" [[tool.uv.index]] name = "testpypi" @@ -98,112 +105,60 @@ url = "https://test.pypi.org/simple/" publish-url = "https://test.pypi.org/legacy/" explicit = true -[tool.pytest.ini_options] -minversion = "6.0" -junit_family = "xuint2" +[tool.pytest] +minversion = "9.0" +testpaths = ["tests"] addopts = [ "-ra", - "--strict-markers", - "--strict-config", - "--import-mode=importlib", + "--strict", + "--import-mode=importlib" ] filterwarnings = [ "error", "default:could not create cache path:pytest.PytestCacheWarning", ] -xfail_strict = true -testpaths = ["tests"] +log_level = "INFO" +markers = ["smoke", "unit", "benchmark"] required_plugins = ["pytest-benchmark"] -log_level = "DEBUG" -markers = [ - "smoke: Marks tests as smoke tests to respond import accuracy.", - "unit: Marks tests as unit tests to verify basic functionality.", - "benchmark: Marks benchmarks for end-to-end performance measurement." + +[tool.coverage.run] +omit = ["tests/*"] + +[tool.coverage.report] +exclude_also = [ + "raise AssertionError", + "raise NotImplementedError", + "if __name__ == '__main__'" ] +ignore_errors = true +# We only care about type checking the source code [tool.mypy] -python_version = 3.12 -files = ["src"] strict = true -enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"] -warn_unreachable = true - -[[tool.mypy.overrides]] -module = "tests.*" -disallow_untyped_defs = false -disallow_untyped_calls = false - -[[tool.mypy.overrides]] -module = ["typer"] ignore_missing_imports = true - -[tool.cibuildwheel] -build-frontend = "build[uv]" -test-groups = ["test"] -test-command = "python -m pytest -n auto --benchmark-disable tests" -test-sources = ["pyproject.toml", "tests"] -test-skip = [ - "cp310-win_arm64", - "cp31*-musllinux_*", # Threading test crashes - "cp313*", # polars-runtime-32 has issues with abi3 on 3.13 and above - "cp314*", - "pp*", # polars-runtime-32 unsupported on PyPy 3.11 (pp73) - "cp314*-ios_*", # No numpy wheels yet -] -enable = ["pypy"] -environment-pass = ["SETUPTOOLS_SCM_PRETEND_VERSION"] -environment.PIP_ONLY_BINARY = "numpy" -environment.PIP_PREFER_BINARY = "1" -environment.UV_ONLY_BINARY = "numpy" -environment.UV_PREFER_BINARY = "1" -environment.CMAKE_BUILD_PARALLEL_LEVEL = "3" - -[tool.cibuildwheel.pyodide] -build-frontend = {name = "build", args = ["--exports", "whole_archive"]} -test-command = "pytest --benchmark-disable tests" - -[tool.cibuildwheel.ios] -build-frontend = "build" -xbuild-tools = ["cmake", "ninja"] -test-command = "python -m pytest --benchmark-disable tests" -environment.PIP_EXTRA_INDEX_URL = "https://pypi.anaconda.org/beeware/simple/" - -[[tool.cibuildwheel.overrides]] -select = "pp310-macosx_arm64" -inherit.environment = "append" -environment.MACOSX_DEPLOYMENT_TARGET = "14.0" - -[[tool.cibuildwheel.overrides]] -select = ["gp*"] -inherit.environment = "append" -environment.UV_INDEX = "https://www.graalvm.org/python/wheels/" -environment.UV_INDEX_STRATEGY = "unsafe-best-match" -test-command = "pytest --benchmark-disable tests" - -[tool.coverage.run] -omit = [ - "src/respondpy/test.py", - "tests/*" -] +warn_unreachable = true +files = ["src/**/*.py", "src/**/*.pyi"] +exclude = ["src/respondpy/_version.py"] +enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"] [tool.pylint] py-version = "3.12" # Shim added to make sure pylint can find our modules since the pybind11 is messing with uv virtual environments. This just adds the src directory to the path before pylint runs but shouldn't impact any distribution details. init-hook = "import os,sys; sys.path.insert(0, os.path.join(os.getcwd(), 'src'))" ignore-patterns = ['.*\.pyi'] -ignore = "version.py" +ignore = "_version.py" extension-pkg-allow-list = ["respondpy._core"] reports.output-format = "colorized" similarities.ignore-imports = "yes" messages_control.disable = [ - "cyclic-import", # TODO: move files out of _internal + "cyclic-import", "fixme", "invalid-name", "line-too-long", "missing-class-docstring", "missing-function-docstring", "missing-module-docstring", - "c-extension-no-member", # C extensions mess with this + "c-extension-no-member", "protected-access", "too-few-public-methods", "too-many-arguments", @@ -251,25 +206,59 @@ ignore = [ "PT011", # pytest.raises too broad "PYI034", # We are returning Self, just generic ] -typing-modules = ["respondpy._compat.typing"] +typing-modules = ["respondpy._core"] isort.required-imports = ["from __future__ import annotations"] -exclude = ["extern/*"] - -[tool.ruff.lint.flake8-tidy-imports.banned-api] -"typing.Self".msg = "Use respondpy._compat.typing.Self instead." -"typing_extensions.Self".msg = "Use respondpy._compat.typing.Self instead." +exclude = ["tests/*"] [tool.ruff.lint.mccabe] max-complexity = 13 [tool.ruff.lint.per-file-ignores] "docs/*" = ["T20"] -"examples/*" = ["T20"] -"scripts/*" = ["T20"] "tests/*" = ["T20"] -"notebooks/*" = ["T20"] +"benchmarks/*" = ["T20"] "*.pyi" = ["F401", "TID251"] -"docs/conf.py" = ["ARG001"] -"src/respondpy/test.py" = ["PT"] "**.ipynb" = ["I002", "E731"] -"src/respondpy/_compat/**.py" = ["TID251"] + + +[tool.cibuildwheel] +# Configuration Details +## Note: We only build for Python 3.11 and above, and only for 64 bit architectures. We also skip PyPy, pyodide, android, iOS and graalPy builds. +build = [ + "cp311-*", + "cp312-*", + "cp313-*", + "cp314-*" +] +skip = [ + "*-win32", + "*-pyodide_*", + "*-android_*", + "*-ios_*", +] +archs = ["auto64"] +# Build Step Details +build-frontend = "build[uv]" +# Test Step Details +test-groups = ["test"] +test-sources = ["pyproject.toml", "tests"] +test-command = "python -m pytest tests" +test-skip = [ + "cp31*-musllinux_*", # Threading test crashes on musllinux + "cp313*", # polars-runtime-32 has issues with abi3 on 3.13 and above + "cp314*" # polars-runtime-32 has issues with abi3 on 3.13 and above +] +environment.PIP_PREFER_BINARY = "1" +environment.UV_PREFER_BINARY = "1" +environment.CMAKE_BUILD_PARALLEL_LEVEL = "4" + + +[[tool.cibuildwheel.overrides]] +select = ["cp3*-win_arm64"] +inherit.environment = "append" +test-command = "python -m pytest -n 1 --benchmark-disable tests" +environment.OMP_NUM_THREADS = "1" +environment.OPENBLAS_NUM_THREADS = "1" +environment.MKL_NUM_THREADS = "1" +environment.NUMEXPR_NUM_THREADS = "1" +environment.POLARS_MAX_THREADS = "1" diff --git a/src/register_model.cpp b/src/register_model.cpp index e5f8995..1a64b61 100644 --- a/src/register_model.cpp +++ b/src/register_model.cpp @@ -4,7 +4,7 @@ // Created Date: 2026-01-08 // // Author: Matthew Carroll // // ----- // -// Last Modified: 2026-02-12 // +// Last Modified: 2026-06-25 // // Modified By: Matthew Carroll // // ----- // // Copyright (c) 2026 Syndemics Lab at Boston Medical Center // @@ -22,7 +22,10 @@ void register_model(py::module &m) { py::class_(m, "Model") .def(py::init(&Model::Create), py::arg("name"), py::arg("log_name") = "console") - .def("set_state", &Model::SetState) + .def("set_state", + [](Model &m, const py::EigenDRef &vec) { + return m.SetState(vec); + }) .def("get_state", &Model::GetState) .def("run_transitions", &Model::RunTransitions) .def("add_transition", &Model::AddTransition) @@ -35,13 +38,11 @@ void register_model(py::module &m) { .def("create_default_histories", &Model::CreateDefaultHistories) .def("clear_histories", &Model::ClearHistories, "Clear all history records and reset history tracking state.") - .def("set_history_capture_interval", - &Model::SetHistoryCaptureInterval, + .def("set_history_capture_interval", &Model::SetHistoryCaptureInterval, py::arg("interval"), "Set the global history capture interval. Records every " "interval timesteps; values less than 1 default to full capture.") - .def("get_history_capture_interval", - &Model::GetHistoryCaptureInterval, + .def("get_history_capture_interval", &Model::GetHistoryCaptureInterval, "Get the active capture interval. A value of 1 means full " "capture.") .def("set_final_timestep", &Model::SetFinalTimestep, diff --git a/src/respondpy/__init__.py b/src/respondpy/__init__.py index 67ac460..103c55a 100644 --- a/src/respondpy/__init__.py +++ b/src/respondpy/__init__.py @@ -4,7 +4,7 @@ # Created Date: 2025-08-04 # # Author: Matthew Carroll # # ----- # -# Last Modified: 2026-06-10 # +# Last Modified: 2026-06-26 # # Modified By: Matthew Carroll # # ----- # # Copyright (c) 2025-2026 Syndemics Lab at Boston Medical Center # @@ -12,7 +12,7 @@ from __future__ import annotations -from .version import version as __version__ # pylint: disable=E0611,E0401 # type: ignore[reportMissingModuleSource] +from ._version import version as __version__ # pylint: disable=E0611,E0401 # type: ignore[reportMissingModuleSource] from . import data diff --git a/src/respondpy/_core/model.pyi b/src/respondpy/_core/model.pyi index e98d792..2e61ac5 100644 --- a/src/respondpy/_core/model.pyi +++ b/src/respondpy/_core/model.pyi @@ -4,7 +4,7 @@ # Created Date: 2026-02-09 # # Author: Matthew Carroll # # ----- # -# Last Modified: 2026-02-12 # +# Last Modified: 2026-06-25 # # Modified By: Matthew Carroll # # ----- # # Copyright (c) 2026 Syndemics Lab at Boston Medical Center # @@ -66,7 +66,7 @@ class Model: def set_histories(self, histories: collections.abc.Mapping[str, respondpy._core.history.History]) -> None: ... - def set_state(self, state: typing.Annotated[numpy.typing.ArrayLike, numpy.float64, "[m, 1]"]) -> None: + def set_state(self, state: numpy.typing.NDArray[numpy.float64]) -> None: ... def create_default_histories(self) -> None: diff --git a/src/respondpy/data/input.py b/src/respondpy/data/input.py index 1b22a85..381725d 100644 --- a/src/respondpy/data/input.py +++ b/src/respondpy/data/input.py @@ -4,7 +4,7 @@ # Created Date: 2026-06-05 # # Author: Matthew Carroll # # ----- # -# Last Modified: 2026-06-17 # +# Last Modified: 2026-06-25 # # Modified By: Matthew Carroll # # ----- # # Copyright (c) 2026 Syndemics Lab at Boston Medical Center # @@ -12,11 +12,12 @@ import sqlite3 from pathlib import Path -from typing import Literal +from typing import Literal, Annotated from operator import itemgetter from configparser import ConfigParser import numpy as np +import numpy.typing as npt import polars as pl from .database_helpers import sort_dataframes @@ -216,7 +217,7 @@ def _extract_values( lf: pl.LazyFrame, *, n: int = 64 # 16 interventions * 4 behaviors - ) -> np.ndarray: + ) -> Annotated[npt.NDArray[np.float64], "[m, 1] | [m, m]"]: """Convert extracted rows to a model-ready state vector or matrix. :param param: Parameter descriptor controlling output shape. @@ -360,6 +361,10 @@ def _get_parameter_filled( # External Functions + def get_intervention_id_maps(self) -> dict[int, str]: + """Return a map of intervention ids to names.""" + return dict(self._get_single_state_table(state="intervention")) + def get_interventions(self) -> list[str]: """Return ordered intervention names from the database.""" if self.interventions is None: @@ -369,6 +374,10 @@ def get_interventions(self) -> list[str]: )) return self.interventions + def get_behavior_id_maps(self) -> dict[int, str]: + """Return a map of behavior ids to names.""" + return dict(self._get_single_state_table(state="behavior")) + def get_behaviors(self) -> list[str]: """Return ordered behavior names from the database.""" if self.behaviors is None: diff --git a/src/respondpy/model.py b/src/respondpy/model.py index 1c2cd1a..19589a1 100644 --- a/src/respondpy/model.py +++ b/src/respondpy/model.py @@ -4,7 +4,7 @@ # Created Date: 2026-06-05 # # Author: Matthew Carroll # # ----- # -# Last Modified: 2026-06-09 # +# Last Modified: 2026-06-25 # # Modified By: Matthew Carroll # # ----- # # Copyright (c) 2026 Syndemics Lab at Boston Medical Center # @@ -41,7 +41,7 @@ def build_model( """ m = Model(name, log_name) init_pop = input_data.select_parameter( - Parameter(ParameterType.INITIAL_COHORT), cohort_id, time=1).squeeze() + Parameter(ParameterType.INITIAL_COHORT), cohort_id, time=1) m.set_state(init_pop) m = build_model_transitions(m, input_data, cohort_id) return m diff --git a/src/respondpy/version.pyi b/src/respondpy/version.pyi deleted file mode 100644 index 063cfe1..0000000 --- a/src/respondpy/version.pyi +++ /dev/null @@ -1,12 +0,0 @@ -################################################################################ -# File: version.pyi # -# Project: respondpy # -# Created Date: 2026-01-07 # -# Author: Matthew Carroll # -# ----- # -# Last Modified: 2026-01-07 # -# Modified By: Matthew Carroll # -# ----- # -# Copyright (c) 2026 Syndemics Lab at Boston Medical Center # -################################################################################ -version: str diff --git a/tests/test_data_input.py b/tests/test_data_input.py index f225a9d..a9b258e 100644 --- a/tests/test_data_input.py +++ b/tests/test_data_input.py @@ -4,7 +4,7 @@ # Created Date: 2026-06-10 # # Author: Matthew Carroll # # ----- # -# Last Modified: 2026-06-11 # +# Last Modified: 2026-06-25 # # Modified By: Matthew Carroll # # ----- # # Copyright (c) 2026 Syndemics Lab at Boston Medical Center # @@ -143,6 +143,23 @@ def test_get_behaviors(input_data): assert set(behaviors) == set(expected_behaviors) +@pytest.mark.unit +def test_get_interventions_id_maps(input_data): + interventions = input_data.get_intervention_id_maps() + expected_interventions = { + 1: 'no_treatment', 2: 'early_buprenorphine', 3: 'buprenorphine', 4: 'post_buprenorphine'} + assert isinstance(interventions, dict) + assert interventions == expected_interventions + + +@pytest.mark.unit +def test_get_behaviors_id_maps(input_data): + behaviors = input_data.get_behavior_id_maps() + expected_behaviors = {1: 'active_injection', 2: 'nonactive_injection'} + assert isinstance(behaviors, dict) + assert behaviors == expected_behaviors + + @pytest.mark.unit def test_get_cohorts(input_data): col_names, results = input_data.get_cohorts() diff --git a/tests/test_smoke.py b/tests/test_smoke.py index 122d522..509d911 100644 --- a/tests/test_smoke.py +++ b/tests/test_smoke.py @@ -4,7 +4,7 @@ # Created Date: 2026-01-08 # # Author: Matthew Carroll # # ----- # -# Last Modified: 2026-06-09 # +# Last Modified: 2026-06-25 # # Modified By: Matthew Carroll # # ----- # # Copyright (c) 2026 Syndemics Lab at Boston Medical Center # @@ -38,13 +38,30 @@ def test_data_import() -> None: @pytest.mark.smoke -def test_model() -> None: - 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