diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 6d50952..bc30ea3 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -1,11 +1,11 @@ name: Docs + on: pull_request: push: branches: [main] - tags: - - '*' merge_group: + jobs: Docs: - uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@v1 \ No newline at end of file + uses: tskit-dev/.github/.github/workflows/docs.yml@main diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml new file mode 100644 index 0000000..ed6a18e --- /dev/null +++ b/.github/workflows/lint.yml @@ -0,0 +1,11 @@ +name: Lint + +on: + pull_request: + push: + branches: [main] + merge_group: + +jobs: + Lint: + uses: tskit-dev/.github/.github/workflows/lint.yml@main diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d631d7d..5de31e6 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -7,74 +7,19 @@ on: merge_group: jobs: - pre-commit: - name: Lint - uses: tskit-dev/.github/.github/workflows/lint.yml@v2 + packaging: + name: Python packaging + uses: tskit-dev/.github/.github/workflows/python-packaging.yml@main test: name: Python - runs-on: ${{ matrix.os }} + uses: tskit-dev/.github/.github/workflows/python-tests.yml@main + with: + os: ${{ matrix.os }} + python-version: ${{ matrix.python }} + coverage-directory: tstrait + secrets: inherit strategy: matrix: - python: [ "3.10", 3.13 ] - os: [ macos-latest, ubuntu-24.04, windows-latest ] - defaults: - run: - shell: bash - steps: - - name: Cancel Previous Runs - uses: styfle/cancel-workflow-action@0.12.1 - with: - access_token: ${{ github.token }} - - uses: actions/checkout@v4.2.2 - - name: Install uv and set the python version - uses: astral-sh/setup-uv@v6 - with: - python-version: ${{ matrix.python }} - version: "0.8.15" - - - name: Install dependencies - run: | - uv venv - uv pip install -r pyproject.toml --extra test - - name: Test with pytest - run: | - uv run --no-sync python -m pytest --cov=tstrait --cov-report=xml --cov-branch -n 0 tests - - name: Upload coverage reports to Codecov - uses: codecov/codecov-action@v5.1.1 - env: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} - - name: Delete coverage - run: | - rm .coverage - - dist-tests: - name: Distribution - runs-on: ubuntu-24.04 - steps: - - name: Cancel Previous Runs - uses: styfle/cancel-workflow-action@0.12.1 - with: - access_token: ${{ github.token }} - - uses: actions/checkout@v4.2.2 - - uses: actions/setup-python@v5.3.0 - with: - python-version: '3.12' - - name: Install dependencies - run: | - python3 -m pip install --upgrade pip - python3 -m pip install twine build - - name: Build sdist and wheel - run: | - python -m build - - name: Check distribution artefacts - run: | - python3 -m twine check dist/* - - name: Install wheel - run: | - python3 -m pip install dist/*.whl - - name: Import package - # Don't import from current dir - run: | - cd / - python3 -c "import tstrait" + python: ["3.11", "3.13"] + os: [macos-latest, ubuntu-24.04, windows-latest] diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml index 5333924..b8201fe 100644 --- a/.github/workflows/wheels.yml +++ b/.github/workflows/wheels.yml @@ -1,126 +1,52 @@ -name: Build and test wheels +name: Publish Python release on: push: - branches: - - main - - test - tags: - - '*' + branches: [test-publish] release: types: [published] jobs: - distbuild: - name: Build Distribution + build: runs-on: ubuntu-24.04 steps: - uses: actions/checkout@v4.2.2 - - uses: actions/setup-python@v5.3.0 with: - python-version: '3.12' - - name: Install dependencies - run: | - python3 -m pip install --upgrade pip - python3 -m pip install twine build - - name: Build sdist and wheel - run: | - python -m build - - name: Check distribution artefacts - run: | - python3 -m twine check dist/* - - name: Upload wheel and sdist - uses: actions/upload-artifact@v4.4.3 - with: - name: wheels - path: dist + fetch-depth: 0 - OSX-test: - needs: ['distbuild'] - runs-on: macos-latest - strategy: - matrix: - python: ["3.10", "3.11", "3.12", "3.13"] - steps: - - name: Download wheels - uses: actions/download-artifact@v4.1.8 - with: - name: wheels - - name: Set up Python ${{ matrix.python }} - uses: actions/setup-python@v5.3.0 + - name: Install uv + uses: astral-sh/setup-uv@v6 with: - python-version: ${{ matrix.python }} - - name: Install wheel and test - run: | - python -VV - # Install the local wheel - pip install tstrait --only-binary tstrait -f . - python -c "import tstrait" + python-version: "3.12" + version: "0.8.15" - windows-test: - needs: ['distbuild'] - runs-on: windows-latest - strategy: - matrix: - python: ["3.10", "3.11", "3.12", "3.13"] - wordsize: [64] - steps: - - name: Download wheels - uses: actions/download-artifact@v4.1.8 - with: - name: wheels - - name: Set up Python ${{ matrix.python }} - uses: actions/setup-python@v5.3.0 - with: - python-version: ${{ matrix.python }} - - name: Install wheel and test - run: | - python -VV - pip install wheel - # Install the local wheel - pip install tstrait --only-binary tstrait -f . - python -c "import tstrait" + - name: Build + run: uv build - linux-test: - runs-on: ubuntu-24.04 - needs: ['distbuild'] - strategy: - matrix: - python: ["3.10", "3.11", "3.12", "3.13"] - steps: - - name: Download wheels - uses: actions/download-artifact@v4.1.8 + - uses: actions/upload-artifact@v4 with: - name: wheels - - name: Set up Python - uses: actions/setup-python@v5.3.0 - with: - python-version: ${{ matrix.python }} - - name: Install wheel and test - run: | - python -VV - # Install the local wheel - pip install tstrait --only-binary tstrait -f . - python -c "import tstrait" + name: dist + path: dist/ - PyPI_Upload: + publish: runs-on: ubuntu-24.04 environment: release - needs: ['windows-test', 'OSX-test', 'linux-test'] + needs: [build] permissions: id-token: write steps: - - name: Download all - uses: actions/download-artifact@v4.1.8 - - name: Move to dist - run: | - mkdir dist - cp */*.{whl,gz} dist/. - - name: Publish distribution to Test PyPI - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') - uses: pypa/gh-action-pypi-publish@v1.12.3 + - uses: actions/download-artifact@v7.0.0 with: - repository_url: https://test.pypi.org/legacy/ - - name: Publish distribution to PRODUCTION PyPI + name: dist + path: dist + + - name: Publish to TestPyPI + if: github.event_name == 'push' && github.ref_name == 'test-publish' + uses: pypa/gh-action-pypi-publish@v1.13.0 + with: + repository-url: https://test.pypi.org/legacy/ + verbose: true + + - name: Publish to PyPI if: github.event_name == 'release' - uses: pypa/gh-action-pypi-publish@v1.12.3 + uses: pypa/gh-action-pypi-publish@v1.13.0 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml deleted file mode 100644 index 4933e12..0000000 --- a/.pre-commit-config.yaml +++ /dev/null @@ -1,39 +0,0 @@ -# pre-commit run --all-files -repos: - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v6.0.0 - hooks: - - id: check-merge-conflict - - id: debug-statements - - id: mixed-line-ending - - id: check-case-conflict - - id: check-yaml - - repo: https://github.com/asottile/reorder_python_imports - rev: v3.15.0 - hooks: - - id: reorder-python-imports - args: [--application-directories=python, - ] - - repo: https://github.com/asottile/pyupgrade - rev: v3.20.0 - hooks: - - id: pyupgrade - args: [--py3-plus, --py37-plus] - - repo: https://github.com/psf/black - rev: 25.1.0 - hooks: - - id: black - language_version: python3 - - repo: https://github.com/pycqa/flake8 - rev: 7.3.0 - hooks: - - id: flake8 - args: [--config=.flake8] - additional_dependencies: ["flake8-bugbear==22.10.27", "flake8-builtins==2.0.1"] - - repo: https://github.com/adamchainz/blacken-docs - rev: 1.20.0 - hooks: - - id: blacken-docs - args: [--skip-errors] - additional_dependencies: [black==23.7.0] - language_version: python3 \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md index 932fe8e..6b09bb9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.1.2] - 2026-XX-XX +Unreleased + +- Upgrade supported Python versions to 3.11 -> 3.14 + ## [0.1.1] - 2025-09-18 ### Update: @@ -56,7 +61,7 @@ ### Highlights: - Initial stable release of tstrait in PyPI https://pypi.org/project/tstrait/ -- Initial stable release of tstrait in conda-forge +- Initial stable release of tstrait in conda-forge ### Documentation: diff --git a/prek.toml b/prek.toml new file mode 100644 index 0000000..3a25835 --- /dev/null +++ b/prek.toml @@ -0,0 +1,40 @@ +# The prek configuration defining linting requirements. This +# setup is optimised for long-term stability and determinism, +# and therefore only uses either "builtin" rules or "local" +# rules implementing lint workflows. We do not use any remote +# workflow repos. + +[[repos]] +repo = "builtin" +hooks = [ + { id = "check-added-large-files" }, + { id = "check-merge-conflict" }, + { id = "mixed-line-ending" }, + { id = "check-case-conflict" }, + { id = "check-yaml" }, + { id = "check-toml" }, +] + +[[repos]] +repo = "local" +hooks = [ + { + id = "ruff-check", + name = "ruff check", + language = "system", + entry = "ruff check --fix --force-exclude", + types = ["python"], + }, +] + +[[repos]] +repo = "local" +hooks = [ + { + id = "ruff-format", + name = "ruff format", + language = "system", + entry = "ruff format --force-exclude", + types = ["python"], + }, +] diff --git a/pyproject.toml b/pyproject.toml index 41cb171..73480bf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,10 +34,10 @@ classifiers = [ "License :: OSI Approved :: MIT License", "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 :: Only", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics", @@ -45,12 +45,12 @@ classifiers = [ "Operating System :: POSIX", "Operating System :: MacOS", ] -requires-python = ">=3.10" +requires-python = ">=3.11" dependencies = [ - "numpy>=1.20.3", - "numba>=0.57.0", + "numpy>=2", + "numba", "pandas>=1.0", - "tskit>=0.5.5", + "tskit>=1", ] [project.license] @@ -62,44 +62,46 @@ Homepage = "https://tskit.dev/tstrait/" Documentation = "https://tskit.dev/tstrait/docs/" "Source Code" = "https://github.com/tskit-dev/tstrait" -[project.optional-dependencies] +[dependency-groups] test = [ - "msprime==1.3.4", - "numba==0.61.2", - "pandas==2.3.2", - "tskit==0.6.4", - "pytest==8.4.2", - "pytest-cov==6.3.0", - "pytest-xdist==3.8.0", - "scipy==1.15.3", + "msprime", + "numba", + "pandas", + "tskit", + "pytest", + "pytest-cov", + "pytest-xdist", + "scipy", ] + docs = [ - "jupyter-book==1.0.4.post1", - "matplotlib==3.10.6", - "msprime==1.3.4", - "numba==0.61.2", - "numpydoc==1.9.0", - "pandas==2.3.2", - "sphinx-issues==5.0.1", - "tskit==0.6.4", -] -dev = [ "jupyter-book<2", "matplotlib", "msprime", "numba", - "numpy", "numpydoc", "pandas", - "pre-commit", - "pytest", - "scipy", - "sphinx", "sphinx-issues", "tskit", - "pytest-cov", - "pytest-xdist", ] + +lint = [ + "ruff==0.15.1", + "prek==0.3.3", +] + +packaging = [ + "twine", + "validate-pyproject[all]", +] + +dev = [ + {include-group = "docs"}, + {include-group = "lint"}, + {include-group = "test"}, + {include-group = "packaging"}, +] + verification = [ "matplotlib", "numpy", @@ -119,8 +121,39 @@ packages = [ ] [tool.setuptools_scm] +local_scheme = "no-local-version" [tool.pytest.ini_options] testpaths = [ "tests", ] + +[tool.ruff] +target-version = "py311" +line-length = 89 + +[tool.ruff.lint] +select = ["E", "F", "B", "W", "I", "N", "UP", "A", "PT"] + +ignore = [ + "A001", "A002", "RUF", + "B905", #Don't add strict=False to zips (B905) + "N806", "N802", "N803", # Various nags about uppercase vars + "UP032", # Don't upgrade to f strings + "PT012", # pytest.raises() block should contain a single simple statement + # "B028", # No stacklevel for warnings + # "B018", # Found useless expression. Either assign it +] + +fixable = ["ALL"] +unfixable = [] + +[tool.ruff.lint.isort] +known-first-party = ["tstrait"] +known-third-party = [ + "msprime", + "tskit", + "numpy", + "pytest", +] + diff --git a/tests/test_base.py b/tests/test_base.py index 6eed76f..74f558f 100644 --- a/tests/test_base.py +++ b/tests/test_base.py @@ -5,12 +5,12 @@ import pytest from tstrait.base import ( - _check_int, - _check_val, - _check_instance, - _check_numeric_array, _check_dataframe, + _check_instance, + _check_int, _check_non_decreasing, + _check_numeric_array, + _check_val, ) # noreorder @@ -47,7 +47,7 @@ def test_val_inclusive(self): _check_val(0, "n", 0, inclusive=True) def test_val_below_min_inclusive(self): - with pytest.raises(ValueError, match="n must be a number not " "less than 0"): + with pytest.raises(ValueError, match="n must be a number not less than 0"): _check_val(-1, "n", 0, inclusive=True) @@ -63,7 +63,7 @@ def test_int_bad(self, n): _check_int(n, "n") def test_int_below_min(self): - with pytest.raises(ValueError, match="n must be an integer not " "less than 0"): + with pytest.raises(ValueError, match="n must be an integer not less than 0"): _check_int(-1, "n", 0) @@ -88,9 +88,7 @@ def test_type(self): def test_dataframe(self): df = pd.DataFrame({"first": [0, 1], "second": [3, 4]}) - with pytest.raises( - ValueError, match="columns must be included in df dataframe" - ): + with pytest.raises(ValueError, match="columns must be included in df dataframe"): _check_dataframe(df, ["column"], "df") pd.testing.assert_frame_equal( diff --git a/tests/test_genetic_value.py b/tests/test_genetic_value.py index b82b808..3d684cc 100644 --- a/tests/test_genetic_value.py +++ b/tests/test_genetic_value.py @@ -2,8 +2,11 @@ import numpy as np import pandas as pd import pytest + import tstrait from tstrait.base import _check_numeric_array +from tstrait.genetic_value import _GeneticValue + from .data import ( binary_tree, binary_tree_seq, @@ -11,7 +14,6 @@ non_binary_tree, triploid_tree, ) # noreorder -from tstrait.genetic_value import _GeneticValue # from tstrait.trait import sim_trait @@ -392,9 +394,7 @@ def test_output(self, sample_ts): genetic_array = normalised_df["genetic_value"].values np.testing.assert_almost_equal(np.mean(genetic_array), mean, decimal=2) np.testing.assert_almost_equal(np.var(genetic_array, ddof=1), var, decimal=2) - pd.testing.assert_series_equal( - normalised_df["trait_id"], genetic_df["trait_id"] - ) + pd.testing.assert_series_equal(normalised_df["trait_id"], genetic_df["trait_id"]) pd.testing.assert_series_equal( normalised_df["individual_id"], genetic_df["individual_id"] ) @@ -420,9 +420,7 @@ def test_default(self, sample_ts): genetic_array = normalised_df["genetic_value"].values np.testing.assert_almost_equal(np.mean(genetic_array), mean, decimal=2) np.testing.assert_almost_equal(np.var(genetic_array, ddof=1), var, decimal=2) - pd.testing.assert_series_equal( - normalised_df["trait_id"], genetic_df["trait_id"] - ) + pd.testing.assert_series_equal(normalised_df["trait_id"], genetic_df["trait_id"]) pd.testing.assert_series_equal( normalised_df["individual_id"], genetic_df["individual_id"] ) diff --git a/tests/test_sim_trait.py b/tests/test_sim_trait.py index dc69adb..8a21b74 100644 --- a/tests/test_sim_trait.py +++ b/tests/test_sim_trait.py @@ -2,6 +2,7 @@ import numpy as np import pandas as pd import pytest + import tstrait from tstrait.base import _check_numeric_array from tstrait.simulate_effect_size import _TraitSimulator @@ -117,10 +118,8 @@ def test_output(self, sample_ts, trait_model): ) self.check_dimensions(sim_result, num_causal) np.testing.assert_equal(sim_result["trait_id"], np.zeros(num_causal)) - assert ( - 0 <= np.min(sim_result["site_id"]) - and np.max(sim_result["site_id"]) < sample_ts.num_sites - ) + assert 0 <= np.min(sim_result["site_id"]) + assert np.max(sim_result["site_id"]) < sample_ts.num_sites def test_output_default_num_causal(self, sample_ts): model = tstrait.trait_model(distribution="normal", mean=0, var=1) @@ -165,10 +164,10 @@ def test_output_multivariate(self, sample_ts): df1 = df[df.trait_id == 1] self.check_dimensions(df0, num_causal) self.check_dimensions(df1, num_causal) - assert ( - 0 <= np.min(df["site_id"]) and np.max(df["site_id"]) < sample_ts.num_sites - ) - assert 0 <= np.min(df["trait_id"]) and np.max(df["trait_id"]) <= 1 + assert 0 <= np.min(df["site_id"]) + assert np.max(df["site_id"]) < sample_ts.num_sites + assert 0 <= np.min(df["trait_id"]) + assert np.max(df["trait_id"]) <= 1 def test_output_multivariate_alpha(self, sample_ts): mean = [0, 1] @@ -189,10 +188,10 @@ def test_output_multivariate_alpha(self, sample_ts): df1 = df[df.trait_id == 1] self.check_dimensions(df0, num_causal) self.check_dimensions(df1, num_causal) - assert ( - 0 <= np.min(df["site_id"]) and np.max(df["site_id"]) < sample_ts.num_sites - ) - assert 0 <= np.min(df["trait_id"]) and np.max(df["trait_id"]) <= 1 + assert 0 <= np.min(df["site_id"]) + assert np.max(df["site_id"]) < sample_ts.num_sites + assert 0 <= np.min(df["trait_id"]) + assert np.max(df["trait_id"]) <= 1 def test_multiple_causal_sites(self, sample_ts): mean = [0, 1] @@ -399,7 +398,7 @@ def test_tree_seq(self): assert trait_df.position.dtype == int -class Test_CausalSites: +class TestCausalSites: @pytest.mark.parametrize("causal_sites", [[0, 2], [3, 0, 1], [0]]) def test_causal_sites(self, sample_ts, sample_trait_model, causal_sites): trait_df = tstrait.sim_trait( diff --git a/tests/test_simulate_environment.py b/tests/test_simulate_environment.py index 9a69d72..df829cc 100644 --- a/tests/test_simulate_environment.py +++ b/tests/test_simulate_environment.py @@ -2,6 +2,7 @@ import numpy as np import pandas as pd import pytest + import tstrait from tstrait.base import _check_numeric_array @@ -47,8 +48,7 @@ class TestInput: def test_input_type(self): with pytest.raises( TypeError, - match="genetic_df must be a " - " instance", + match="genetic_df must be a instance", ): tstrait.sim_env(genetic_df=1, h2=0.3) diff --git a/tests/test_simulate_phenotype.py b/tests/test_simulate_phenotype.py index 5ea0988..fac9ba8 100644 --- a/tests/test_simulate_phenotype.py +++ b/tests/test_simulate_phenotype.py @@ -2,6 +2,7 @@ import numpy as np import pandas as pd import pytest + import tstrait @@ -329,9 +330,7 @@ def test_ddof(self, sample_ts, ddof): phenotype_array, ddof=ddof ) - np.testing.assert_array_almost_equal( - normalised_phenotype_array, phenotype_array - ) + np.testing.assert_array_almost_equal(normalised_phenotype_array, phenotype_array) def test_pleiotropy(self, sample_ts): mean = 0 diff --git a/tests/test_trait_model.py b/tests/test_trait_model.py index f52289b..0a0ba52 100644 --- a/tests/test_trait_model.py +++ b/tests/test_trait_model.py @@ -1,5 +1,6 @@ import numpy as np import pytest + import tstrait diff --git a/tstrait/base.py b/tstrait/base.py index 77d77d6..061ab27 100644 --- a/tstrait/base.py +++ b/tstrait/base.py @@ -31,9 +31,7 @@ def _check_int(value, name, minimum=None): except TypeError: raise TypeError(f"{name} must be an integer") from None if minimum is not None and value < minimum: - raise ValueError( - f"{name} must be an integer not less " f"than {minimum}" - ) from None + raise ValueError(f"{name} must be an integer not less than {minimum}") from None return value diff --git a/tstrait/genetic_value.py b/tstrait/genetic_value.py index 30b8954..d641523 100644 --- a/tstrait/genetic_value.py +++ b/tstrait/genetic_value.py @@ -3,7 +3,7 @@ import pandas as pd import tskit -from .base import _check_instance, _check_dataframe, _check_non_decreasing # noreorder +from .base import _check_dataframe, _check_instance, _check_non_decreasing # noreorder @numba.njit @@ -57,9 +57,7 @@ class _GeneticValue: """ def __init__(self, ts, trait_df): - self.trait_df = trait_df[ - ["site_id", "effect_size", "trait_id", "causal_allele"] - ] + self.trait_df = trait_df[["site_id", "effect_size", "trait_id", "causal_allele"]] self.ts = ts def _individual_genetic_values(self, tree, site, causal_allele, effect_size): diff --git a/tstrait/simulate_effect_size.py b/tstrait/simulate_effect_size.py index d9354d6..5342c63 100644 --- a/tstrait/simulate_effect_size.py +++ b/tstrait/simulate_effect_size.py @@ -3,11 +3,10 @@ import numpy as np import pandas as pd import tskit + import tstrait -from .base import _check_instance -from .base import _check_int -from .base import _check_val +from .base import _check_instance, _check_int, _check_val @dataclass diff --git a/tstrait/simulate_phenotype.py b/tstrait/simulate_phenotype.py index 428bb8a..92d47c8 100644 --- a/tstrait/simulate_phenotype.py +++ b/tstrait/simulate_phenotype.py @@ -2,6 +2,7 @@ import numpy as np import pandas as pd + import tstrait from .base import _check_dataframe @@ -123,9 +124,7 @@ def sim_phenotype( random_seed=random_seed, ) genetic_df = tstrait.genetic_value(ts=ts, trait_df=trait_df) - phenotype_df = tstrait.sim_env( - genetic_df=genetic_df, h2=h2, random_seed=random_seed - ) + phenotype_df = tstrait.sim_env(genetic_df=genetic_df, h2=h2, random_seed=random_seed) result = tstrait.PhenotypeResult(trait=trait_df, phenotype=phenotype_df) diff --git a/tstrait/trait_model.py b/tstrait/trait_model.py index 3db405f..c597c5a 100644 --- a/tstrait/trait_model.py +++ b/tstrait/trait_model.py @@ -1,12 +1,11 @@ -from abc import ABCMeta -from abc import abstractmethod +from abc import ABCMeta, abstractmethod import numpy as np from .base import ( + _check_instance, _check_int, _check_val, - _check_instance, ) # noreorder diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..5ed700e --- /dev/null +++ b/uv.lock @@ -0,0 +1,3141 @@ +version = 1 +revision = 3 +requires-python = ">=3.11" +resolution-markers = [ + "python_full_version >= '3.12'", + "python_full_version < '3.12'", +] + +[[package]] +name = "accessible-pygments" +version = "0.0.5" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = 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b/verification.py index be465f0..c8f9e18 100644 --- a/verification.py +++ b/verification.py @@ -64,9 +64,10 @@ import seaborn as sns import stdpopsim import tqdm -import tstrait from matplotlib import pyplot +import tstrait + matplotlib.use("Agg") import statsmodels.api as sm # noqa: E402 @@ -106,9 +107,7 @@ def _plot_qq_dist( pyplot.close("all") def _plot_qq_compare(self, data1, data1_name, data2, data2_name): - sm.qqplot_2samples( - data1, data2, xlabel=data1_name, ylabel=data2_name, line="45" - ) + sm.qqplot_2samples(data1, data2, xlabel=data1_name, ylabel=data2_name, line="45") f = self._build_filename("compare", data1_name, data2_name) pyplot.title(f"compare_{data1_name}_{data2_name}") pyplot.savefig(f, dpi=72) @@ -354,9 +353,7 @@ def _simulate_arg_needle(ts, alpha, h2, random_seed, num_rep=1): } ) - phenotype_result = pd.concat( - [phenotype_result, phenotype_df], ignore_index=True - ) + phenotype_result = pd.concat([phenotype_result, phenotype_df], ignore_index=True) trait_result = pd.concat([trait_result, trait_df], ignore_index=True) trait_result = trait_result.astype({"site_id": int}) @@ -443,7 +440,7 @@ def _compare_simplePHENOTYPES( ts=ts, trait_df=simulation_output.trait, numericalization=numericalization ) grouped = phenotype_df.groupby("trait_id")[["phenotype"]] - phenotype_df = grouped.transform(lambda x: (x - x.mean())) + phenotype_df = grouped.transform(lambda x: x - x.mean()) np.testing.assert_array_almost_equal( phenotype_df["phenotype"].values, @@ -768,9 +765,7 @@ def _simulate_out_of_africa(self, random_seed): class ComparisonTestSimplePHENOTYPES(ComparisonTest): - def _qqplot_simplePHENOTYPES( - self, num_rep, h2, random_seed, mean=0, var=1, alpha=0 - ): + def _qqplot_simplePHENOTYPES(self, num_rep, h2, random_seed, mean=0, var=1, alpha=0): ts, ind_id = self._simulate_out_of_africa(random_seed=random_seed) tstrait_phenotype = self._simulate_tstrait( ts=ts, @@ -1307,9 +1302,7 @@ def __run_sequential(self, tests, basedir, progress): progress.update() def __run_parallel(self, tests, basedir, num_threads, progress): - with concurrent.futures.ProcessPoolExecutor( - max_workers=num_threads - ) as executor: + with concurrent.futures.ProcessPoolExecutor(max_workers=num_threads) as executor: futures = [executor.submit(test.run, basedir) for test in tests] exception = None for future in concurrent.futures.as_completed(futures):