From 86c9bf28661c760a228fcbde628703ca082c585f Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Thu, 12 Feb 2026 12:30:42 +0000 Subject: [PATCH 1/5] Drop python 3.10, move to uv lock file --- python/pyproject.toml | 53 +- python/uv.lock | 2913 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 2939 insertions(+), 27 deletions(-) create mode 100644 python/uv.lock diff --git a/python/pyproject.toml b/python/pyproject.toml index 71290bc056..2d486add9e 100644 --- a/python/pyproject.toml +++ b/python/pyproject.toml @@ -15,7 +15,6 @@ classifiers = [ "Programming Language :: C", "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", @@ -39,7 +38,7 @@ keywords = [ "phylogenetics", "tskit", ] -requires-python = ">=3.10" +requires-python = ">=3.11" dependencies = [ "jsonschema>=3.0.0", "numpy>=2", @@ 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f8b2a60c0a0293d990f1a42a3d803f22eb19f63a Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Thu, 12 Feb 2026 12:36:30 +0000 Subject: [PATCH 2/5] Drop 3.10 from workflows, use uv lockfile Switch to uv "dependency-groups" --- .github/workflows/docker/shared.env | 1 - .github/workflows/tests.yml | 15 ++-- .github/workflows/wheels.yml | 16 ++-- python/pyproject.toml | 2 +- python/uv.lock | 127 +++++++++++++++------------- 5 files changed, 82 insertions(+), 79 deletions(-) diff --git a/.github/workflows/docker/shared.env b/.github/workflows/docker/shared.env index 3579d5bdcc..a3542434b7 100644 --- a/.github/workflows/docker/shared.env +++ b/.github/workflows/docker/shared.env @@ -3,5 +3,4 @@ PYTHON_VERSIONS=( cp313-cp313 cp312-cp312 cp311-cp311 - cp310-cp310 ) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index dec222ecc0..0065c5055c 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -29,7 +29,7 @@ jobs: strategy: fail-fast: false matrix: - python: [ "3.10", 3.14 ] + python: [ 3.11, 3.14 ] os: [ macos-latest, ubuntu-24.04, windows-latest ] defaults: run: @@ -67,27 +67,26 @@ jobs: - name: Install dependencies working-directory: python run: | - uv venv - uv pip install -r pyproject.toml --extra test + uv sync --locked --group test # Remove tskit installed as a dep of msprime uv pip uninstall tskit - name: Build module working-directory: python run: | - uv run --no-sync python setup.py build_ext --inplace + uv run python setup.py build_ext --inplace - name: Minidom test working-directory: python # Importing either IPython or pytest causes import of xml.dom.minidom # So to actually test that tskit imports it, we need a minimal test run: | - uv run --no-sync python -c "import tskit;tskit.Tree.generate_star(5).tree_sequence.draw_svg(path='test.svg')" + uv run python -c "import tskit;tskit.Tree.generate_star(5).tree_sequence.draw_svg(path='test.svg')" - name: Run JIT code coverage working-directory: python run: | - NUMBA_DISABLE_JIT=1 uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_jit.py + NUMBA_DISABLE_JIT=1 uv run pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_jit.py - name: Upload coverage to Codecov uses: codecov/codecov-action@v5.5.2 @@ -102,9 +101,9 @@ jobs: working-directory: python run: | if [[ "${{ matrix.os }}" == "windows-latest" ]]; then - uv run --no-sync python -m pytest -x --skip-slow --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests + uv run pytest -x --skip-slow --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests else - uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests + uv run pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests fi - name: Upload coverage to Codecov diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml index 17efb3fb33..480d49e423 100644 --- a/.github/workflows/wheels.yml +++ b/.github/workflows/wheels.yml @@ -20,7 +20,7 @@ jobs: strategy: fail-fast: false matrix: - python: ["3.10", 3.11, 3.12, 3.13, 3.14] + python: [3.11, 3.12, 3.13, 3.14] steps: - name: Checkout uses: actions/checkout@v6.0.2 @@ -51,7 +51,7 @@ jobs: strategy: fail-fast: false matrix: - python: ["3.10", 3.11, 3.12, 3.13, 3.14] + python: [3.11, 3.12, 3.13, 3.14] wordsize: [64] steps: - name: Checkout @@ -91,10 +91,10 @@ jobs: - name: Checkout uses: actions/checkout@v6.0.2 - - name: Set up Python 3.10 + - name: Set up Python 3.11 uses: actions/setup-python@v6.1.0 with: - python-version: "3.10" + python-version: 3.11 - name: Build sdist shell: bash @@ -125,7 +125,7 @@ jobs: strategy: fail-fast: false matrix: - python: ["3.10", 3.11, 3.12, 3.13, 3.14] + python: [3.11, 3.12, 3.13, 3.14] runner: [macos-15, macos-15-intel] include: - runner: macos-15 @@ -163,7 +163,7 @@ jobs: strategy: fail-fast: false matrix: - python: ["3.10", 3.11, 3.12, 3.13, 3.14] + python: [3.11, 3.12, 3.13, 3.14] wordsize: [64] steps: - name: Download wheels @@ -188,10 +188,8 @@ jobs: strategy: fail-fast: false matrix: - python: ["3.10", 3.11, 3.12, 3.13, 3.14] + python: [3.11, 3.12, 3.13, 3.14] include: - - python: "3.10" - wheel: cp310 - python: 3.11 wheel: cp311 - python: 3.12 diff --git a/python/pyproject.toml b/python/pyproject.toml index 2d486add9e..71342f58ca 100644 --- a/python/pyproject.toml +++ b/python/pyproject.toml @@ -60,7 +60,7 @@ packages = ["tskit", "tskit.jit"] [tool.setuptools.dynamic] version = {attr = "tskit._version.tskit_version"} -[project.optional-dependencies] +[dependency-groups] test = [ "biopython", "coverage", diff --git a/python/uv.lock b/python/uv.lock index c043d814f0..faa09bb642 100644 --- a/python/uv.lock +++ b/python/uv.lock @@ -2597,7 +2597,7 @@ dependencies = [ { name = "numpy" }, ] -[package.optional-dependencies] +[package.dev-dependencies] dev = [ { name = "biopython" }, { name = "breathe" }, @@ -2664,67 +2664,74 @@ test = [ [package.metadata] requires-dist = [ - { name = "biopython", marker = "extra == 'dev'", specifier = ">=1.70" }, - { name = "biopython", marker = "extra == 'test'" }, - { name = "breathe", marker = "extra == 'dev'" }, - { name = "breathe", marker = "extra == 'docs'" }, - { name = "clang-format", marker = "extra == 'dev'", specifier = "==21.1.8" }, - { name = "coverage", marker = "extra == 'dev'" }, - { name = "coverage", marker = "extra == 'test'" }, - { name = "dendropy", marker = "extra == 'dev'" }, - { name = "dendropy", marker = "extra == 'test'" }, - { name = "flake8", marker = "extra == 'dev'" }, { name = "jsonschema", specifier = ">=3.0.0" }, - { name = "jupyter-book", marker = "extra == 'dev'", specifier = "<2" }, - { name = "jupyter-book", marker = "extra == 'docs'", specifier = "<2" }, - { name = "kastore", marker = "extra == 'dev'" }, - { name = "kastore", marker = "extra == 'test'" }, - { name = "lshmm", marker = "extra == 'dev'" }, - { name = "lshmm", marker = "extra == 'test'" }, - { name = "msgpack", marker = "extra == 'dev'" }, - { name = "msgpack", marker = "extra == 'test'" }, - { name = "msprime", marker = "extra == 'dev'" }, - { name = "msprime", marker = "extra == 'docs'" }, - { name = "msprime", marker = "extra == 'test'" }, - { name = "mypy", marker = "extra == 'dev'" }, - { name = "networkx", marker = "extra == 'dev'" }, - { name = "networkx", marker = "extra == 'test'" }, - { name = "newick", marker = "extra == 'dev'" }, - { name = "newick", marker = "extra == 'test'" }, - { name = "numba", marker = "extra == 'dev'" }, - { name = "numba", marker = "extra == 'docs'" }, - { name = "numba", marker = "extra == 'test'" }, { name = "numpy", specifier = ">=2" }, - { name = "pandas", marker = "extra == 'dev'" }, - { name = "pandas", marker = "extra == 'docs'" }, - { name = "portion", marker = "extra == 'dev'" }, - { name = "portion", marker = "extra == 'test'" }, - { name = "pre-commit", marker = "extra == 'dev'" }, - { name = "pytest", marker = "extra == 'dev'" }, - { name = "pytest", marker = "extra == 'test'" }, - { name = "pytest-cov", marker = "extra == 'dev'" }, - { name = "pytest-cov", marker = "extra == 'test'" }, - { name = "pytest-xdist", marker = "extra == 'dev'" }, - { name = "pytest-xdist", marker = "extra == 'test'" }, - { name = "setuptools-scm", marker = "extra == 'dev'" }, - { name = "sphinx-argparse", marker = "extra == 'dev'" }, - { name = "sphinx-argparse", marker = "extra == 'docs'" }, - { name = "sphinx-autodoc-typehints", marker = "extra == 'dev'" }, - { name = "sphinx-autodoc-typehints", marker = "extra == 'docs'" }, - { name = "sphinx-book-theme", marker = "extra == 'dev'" }, - { name = "sphinx-book-theme", marker = "extra == 'docs'" }, - { name = "sphinx-issues", marker = "extra == 'dev'" }, - { name = "sphinx-issues", marker = "extra == 'docs'" }, - { name = "svgwrite", marker = "extra == 'dev'" }, - { name = "svgwrite", marker = "extra == 'test'" }, - { name = "tszip", marker = "extra == 'dev'" }, - { name = "tszip", marker = "extra == 'test'" }, - { name = "xmlunittest", marker = "extra == 'dev'" }, - { name = "xmlunittest", marker = "extra == 'test'" }, - { name = "zarr", marker = "extra == 'dev'", specifier = "<3" }, - { name = "zarr", marker = "extra == 'test'", specifier = "<3" }, -] -provides-extras = ["test", "docs", "dev"] +] + +[package.metadata.requires-dev] +dev = [ + { name = "biopython", specifier = ">=1.70" }, + { name = "breathe" }, + { name = "clang-format", specifier = "==21.1.8" }, + { name = "coverage" }, + { name = "dendropy" }, + { name = "flake8" }, + { name = "jupyter-book", specifier = "<2" }, + { name = "kastore" }, + { name = "lshmm" }, + { name = "msgpack" }, + { name = "msprime" }, + { name = "mypy" }, + { name = "networkx" }, + { name = "newick" }, + { name = "numba" }, + { name = "pandas" }, + { name = "portion" }, + { name = "pre-commit" }, + { name = "pytest" }, + { name = "pytest-cov" }, + { name = "pytest-xdist" }, + { name = "setuptools-scm" }, + { name = "sphinx-argparse" }, + { name = "sphinx-autodoc-typehints" }, + { name = "sphinx-book-theme" }, + { name = "sphinx-issues" }, + { name = "svgwrite" }, + { name = "tszip" }, + { name = "xmlunittest" }, + { name = "zarr", specifier = "<3" }, +] +docs = [ + { name = "breathe" }, + { name = "jupyter-book", specifier = "<2" }, + { name = "msprime" }, + { name = "numba" }, + { name = "pandas" }, + { name = "sphinx-argparse" }, + { name = "sphinx-autodoc-typehints" }, + { name = "sphinx-book-theme" }, + { name = "sphinx-issues" }, +] +test = [ + { name = "biopython" }, + { name = "coverage" }, + { name = "dendropy" }, + { name = "kastore" }, + { name = "lshmm" }, + { name = "msgpack" }, + { name = "msprime" }, + { name = "networkx" }, + { name = "newick" }, + { name = "numba" }, + { name = "portion" }, + { name = "pytest" }, + { name = "pytest-cov" }, + { name = "pytest-xdist" }, + { name = "svgwrite" }, + { name = "tszip" }, + { name = "xmlunittest" }, + { name = "zarr", specifier = "<3" }, +] [[package]] name = "tszip" From 16a56f11abfbddabd0170ff0a66d9f712e1d5c0e Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Thu, 12 Feb 2026 12:53:24 +0000 Subject: [PATCH 3/5] Drop numpy 1.x CI tests --- .github/workflows/tests.yml | 54 ------------------------------------- 1 file changed, 54 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 0065c5055c..64c85deb2e 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -116,60 +116,6 @@ jobs: name: codecov-umbrella verbose: true - - test-numpy1: - name: Numpy 1.x - runs-on: ubuntu-24.04 - defaults: - run: - shell: bash - steps: - - name: Cancel Previous Runs - uses: styfle/cancel-workflow-action@0.13.0 - with: - access_token: ${{ github.token }} - - - name: Checkout - uses: actions/checkout@v6.0.2 - - - name: Setup Python - uses: actions/setup-python@v6.1.0 - with: - python-version: '3.12' - - - name: Install uv - uses: astral-sh/setup-uv@v7 - with: - version: "0.8.15" - - - name: Install dependencies - working-directory: python - run: | - uv venv - uv pip install -r pyproject.toml --extra test - uv pip uninstall tskit - uv pip install "numpy<2" - - - name: Build module - working-directory: python - run: | - uv run --no-sync python setup.py build_ext --inplace - - - name: Run tests with numpy 1.x - working-directory: python - run: | - uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_lowlevel.py tests/test_highlevel.py - - - name: Upload coverage to Codecov - uses: codecov/codecov-action@v5.5.2 - with: - token: ${{ secrets.CODECOV_TOKEN }} - working-directory: python - fail_ci_if_error: false - flags: python-tests-numpy1 - name: codecov-numpy1 - verbose: true - msys2: runs-on: windows-latest strategy: From 5671d6921a297a549cc3022294ccbd29603a17ac Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Thu, 12 Feb 2026 12:57:17 +0000 Subject: [PATCH 4/5] Drop pin on zarr<3 --- python/pyproject.toml | 4 ++-- python/uv.lock | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/python/pyproject.toml b/python/pyproject.toml index 71342f58ca..04520aef1e 100644 --- a/python/pyproject.toml +++ b/python/pyproject.toml @@ -79,7 +79,7 @@ test = [ "xmlunittest", "svgwrite", "newick", - "zarr<3", + "zarr", ] docs = [ @@ -116,7 +116,7 @@ dev = [ "tszip", "xmlunittest", "newick", - "zarr<3", + "zarr", "jupyter-book<2", "breathe", "sphinx-autodoc-typehints", diff --git a/python/uv.lock b/python/uv.lock index faa09bb642..34e6e50775 100644 --- a/python/uv.lock +++ b/python/uv.lock @@ -2699,7 +2699,7 @@ dev = [ { name = "svgwrite" }, { name = "tszip" }, { name = "xmlunittest" }, - { name = "zarr", specifier = "<3" }, + { name = "zarr" }, ] docs = [ { name = "breathe" }, @@ -2730,7 +2730,7 @@ test = [ { name = "svgwrite" }, { name = "tszip" }, { name = "xmlunittest" }, - { name = "zarr", specifier = "<3" }, + { name = "zarr" }, ] [[package]] From e08e86f392f0bbaf69006b963be5e40c0cad69aa Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Fri, 20 Feb 2026 16:11:22 +0000 Subject: [PATCH 5/5] Initial prek+ruff setup --- .codecov.yml | 83 +++-- .github/workflows/docs.yml | 6 +- .github/workflows/lint.yml | 10 + .github/workflows/tests.yml | 24 +- c/examples/error_handling.c | 3 +- c/examples/haploid_wright_fisher.c | 20 +- c/examples/multichrom_wright_fisher.c | 4 +- .../multichrom_wright_fisher_singlethreaded.c | 15 +- c/examples/tree_iteration.c | 6 +- docs/Makefile | 14 +- docs/_config.yml | 2 +- python/benchmark/run-for-all-releases.py | 2 +- python/benchmark/run.py | 3 +- python/lwt_interface/dict_encoding_testlib.py | 13 +- python/lwt_interface/setup.py | 6 +- python/prek.toml | 66 ++++ python/pyproject.toml | 83 +++-- python/setup.py | 3 +- python/tests/__init__.py | 1 + python/tests/conftest.py | 16 +- python/tests/ibd.py | 1 + python/tests/simplify.py | 8 +- python/tests/test_avl_tree.py | 5 +- python/tests/test_balance_metrics.py | 1 + python/tests/test_cli.py | 6 +- python/tests/test_coalrate.py | 17 +- python/tests/test_combinatorics.py | 4 +- python/tests/test_dict_encoding.py | 2 +- python/tests/test_distance_metrics.py | 1 + python/tests/test_divmat.py | 77 ++--- python/tests/test_drawing.py | 132 ++++---- python/tests/test_file_format.py | 13 +- python/tests/test_fileobj.py | 17 +- python/tests/test_genotype_matching.py | 7 +- python/tests/test_genotypes.py | 48 +-- python/tests/test_haplotype_matching.py | 5 +- python/tests/test_highlevel.py | 29 +- python/tests/test_ibd.py | 12 +- .../tests/test_immutable_table_collection.py | 29 +- python/tests/test_intervals.py | 1 + python/tests/test_ld_matrix.py | 16 +- python/tests/test_metadata.py | 1 + python/tests/test_ms.py | 1 + python/tests/test_parsimony.py | 6 +- python/tests/test_phylo_formats.py | 8 +- python/tests/test_provenance.py | 1 + .../{test_lowlevel.py => test_python_c.py} | 48 +-- python/tests/test_reference_sequence.py | 5 +- python/tests/test_relatedness_vector.py | 29 +- python/tests/test_stats.py | 1 + python/tests/test_table_transforms.py | 1 + python/tests/test_tables.py | 58 +--- python/tests/test_text_formats.py | 1 + python/tests/test_threads.py | 9 +- python/tests/test_topology.py | 65 +--- python/tests/test_tree_positioning.py | 1 + python/tests/test_tree_stats.py | 85 ++--- python/tests/test_util.py | 1 + python/tests/test_utilities.py | 10 +- python/tests/test_vcf.py | 22 +- python/tests/test_version.py | 1 + python/tests/test_wright_fisher.py | 1 + python/tests/tsutil.py | 1 + python/tskit/cli.py | 1 + python/tskit/combinatorics.py | 4 +- python/tskit/drawing.py | 53 +-- python/tskit/exceptions.py | 15 +- python/tskit/genotypes.py | 6 +- python/tskit/intervals.py | 1 + python/tskit/jit/numba.py | 4 +- python/tskit/metadata.py | 19 +- python/tskit/provenance.py | 2 + python/tskit/stats.py | 1 + python/tskit/tables.py | 26 +- python/tskit/text_formats.py | 30 +- python/tskit/trees.py | 100 +++--- python/tskit/util.py | 23 +- python/tskit/vcf.py | 1 + python/uv.lock | 310 ++++-------------- 79 files changed, 719 insertions(+), 1044 deletions(-) create mode 100644 .github/workflows/lint.yml create mode 100644 python/prek.toml rename python/tests/{test_lowlevel.py => test_python_c.py} (99%) diff --git a/.codecov.yml b/.codecov.yml index 0c774b11f0..9b33b3d056 100644 --- a/.codecov.yml +++ b/.codecov.yml @@ -1,34 +1,61 @@ -codecov: - require_ci_to_pass: false +# ignore: +# - "lib/tests/" +# - "lib/dev-tools/" +# - "lib/avl.c" +# - "lib/subprojects/**/*" + comment: - layout: "diff, flags, files" -fixes: - - "tskit/::python/tskit/" -flag_management: - individual_flags: - - name: python-tests + layout: "header, diff, flags, components" # show component info in the PR comment + +component_management: + individual_components: + - component_id: python_code + name: Python API paths: - python/tskit/*.py - statuses: - - type: project - target: 95% - - name: python-c-tests + + - component_id: python_c_code + name: Python C interface paths: - python/_tskitmodule.c - statuses: - - type: project - target: 85% - - name: c-tests + + - component_id: c_code + name: C library paths: - - c/tskit/*.c - - c/tskit/*.h - statuses: - - type: project - target: 85% - - name: lwt-tests - paths: - - python/lwt_interface/*.c - - python/lwt_interface/*.h - statuses: - - type: project - target: 80% + - c + +# +# codecov: +# require_ci_to_pass: false +# comment: +# layout: "diff, flags, files" +# fixes: +# - "tskit/::python/tskit/" +# flag_management: +# individual_flags: +# - name: python-tests +# paths: +# - python/tskit/*.py +# statuses: +# - type: project +# target: 95% +# - name: python-c-tests +# paths: +# - python/_tskitmodule.c +# statuses: +# - type: project +# target: 85% +# - name: c-tests +# paths: +# - c/tskit/*.c +# - c/tskit/*.h +# statuses: +# - type: project +# target: 85% +# - name: lwt-tests +# paths: +# - python/lwt_interface/*.c +# - python/lwt_interface/*.h +# statuses: +# - type: project +# target: 80% diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index a4e13ac143..daf6ad9e87 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -12,7 +12,7 @@ env: jobs: Docs: - uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@v1 + uses: tskit-dev/.github/.github/workflows/docs.yml@main with: - additional-setup: sudo apt-get install -y doxygen - make-command: make -C python \ No newline at end of file + pyproject-directory: python + doxygen-directory: docs/doxygen diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml new file mode 100644 index 0000000000..b4a753fd57 --- /dev/null +++ b/.github/workflows/lint.yml @@ -0,0 +1,10 @@ +name: Lint + +on: + pull_request: + +jobs: + Lint: + uses: tskit-dev/.github/.github/workflows/lint.yml@main + with: + pyproject-directory: python diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 64c85deb2e..ef93699be2 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -10,11 +10,6 @@ env: FORCE_COLOR: 1 jobs: - pre-commit: - name: Lint - uses: tskit-dev/.github/.github/workflows/lint.yml@v5 - with: - clang-format-version: 21.1.8 packaging: name: Python packaging @@ -23,13 +18,27 @@ jobs: working-directory: python cli-test-cmd: tskit --help + test-c: + name: C tests + uses: tskit-dev/.github/.github/workflows/c-tests.yml@main + with: + library-directory: c + secrets: inherit + + test-python-c: + name: Python-C tests + uses: tskit-dev/.github/.github/workflows/python-c-tests.yml@main + with: + pyproject-directory: python + secrets: inherit + test: name: Python runs-on: ${{ matrix.os }} strategy: fail-fast: false matrix: - python: [ 3.11, 3.14 ] + python: [ 3.11, 3.13 ] os: [ macos-latest, ubuntu-24.04, windows-latest ] defaults: run: @@ -97,6 +106,7 @@ jobs: flags: python-tests-no-jit name: codecov-umbrella verbose: true + - name: Run tests working-directory: python run: | @@ -113,7 +123,7 @@ jobs: working-directory: python fail_ci_if_error: false flags: python-tests - name: codecov-umbrella + gcov_args: --preserve-paths verbose: true msys2: diff --git a/c/examples/error_handling.c b/c/examples/error_handling.c index 88cab803fd..d6ec572395 100644 --- a/c/examples/error_handling.c +++ b/c/examples/error_handling.c @@ -21,8 +21,7 @@ main(int argc, char **argv) } printf("Loaded tree sequence with %lld nodes and %lld edges from %s\n", (long long) tsk_treeseq_get_num_nodes(&ts), - (long long) tsk_treeseq_get_num_edges(&ts), - argv[1]); + (long long) tsk_treeseq_get_num_edges(&ts), argv[1]); tsk_treeseq_free(&ts); return EXIT_SUCCESS; diff --git a/c/examples/haploid_wright_fisher.c b/c/examples/haploid_wright_fisher.c index 5689fefc7a..84ad896c9d 100644 --- a/c/examples/haploid_wright_fisher.c +++ b/c/examples/haploid_wright_fisher.c @@ -11,8 +11,7 @@ } void -simulate( - tsk_table_collection_t *tables, int N, int T, int simplify_interval) +simulate(tsk_table_collection_t *tables, int N, int T, int simplify_interval) { tsk_id_t *buffer, *parents, *children, child, left_parent, right_parent; double breakpoint; @@ -44,10 +43,10 @@ simulate( * research code and proper random number generator * libraries should be preferred. */ - left_parent = parents[(size_t)((rand()/(1.+RAND_MAX))*N)]; - right_parent = parents[(size_t)((rand()/(1.+RAND_MAX))*N)]; + left_parent = parents[(size_t) ((rand() / (1. + RAND_MAX)) * N)]; + right_parent = parents[(size_t) ((rand() / (1. + RAND_MAX)) * N)]; do { - breakpoint = rand()/(1.+RAND_MAX); + breakpoint = rand() / (1. + RAND_MAX); } while (breakpoint == 0); /* tiny proba of breakpoint being 0 */ ret = tsk_edge_table_add_row( &tables->edges, 0, breakpoint, left_parent, child, NULL, 0); @@ -58,18 +57,15 @@ simulate( children[j] = child; } if (t % simplify_interval == 0) { - printf("Simplify at generation %lld: (%lld nodes %lld edges)", - (long long) t, - (long long) tables->nodes.num_rows, - (long long) tables->edges.num_rows); + printf("Simplify at generation %lld: (%lld nodes %lld edges)", (long long) t, + (long long) tables->nodes.num_rows, (long long) tables->edges.num_rows); /* Note: Edges must be sorted for simplify to work, and we use a brute force * approach of sorting each time here for simplicity. This is inefficient. */ ret = tsk_table_collection_sort(tables, NULL, 0); check_tsk_error(ret); ret = tsk_table_collection_simplify(tables, children, N, 0, NULL); check_tsk_error(ret); - printf(" -> (%lld nodes %lld edges)\n", - (long long) tables->nodes.num_rows, + printf(" -> (%lld nodes %lld edges)\n", (long long) tables->nodes.num_rows, (long long) tables->edges.num_rows); for (j = 0; j < N; j++) { children[j] = j; @@ -90,7 +86,7 @@ main(int argc, char **argv) } ret = tsk_table_collection_init(&tables, 0); check_tsk_error(ret); - srand((unsigned)atoi(argv[5])); + srand((unsigned) atoi(argv[5])); simulate(&tables, atoi(argv[1]), atoi(argv[2]), atoi(argv[3])); /* Sort and index so that the result can be opened as a tree sequence */ diff --git a/c/examples/multichrom_wright_fisher.c b/c/examples/multichrom_wright_fisher.c index 9dafe5b524..f1c728635c 100644 --- a/c/examples/multichrom_wright_fisher.c +++ b/c/examples/multichrom_wright_fisher.c @@ -212,8 +212,8 @@ simulate( * research code and proper random number generator * libraries should be preferred. */ - left_parent = parents[(size_t)((rand() / (1. + RAND_MAX)) * N)]; - right_parent = parents[(size_t)((rand() / (1. + RAND_MAX)) * N)]; + left_parent = parents[(size_t) ((rand() / (1. + RAND_MAX)) * N)]; + right_parent = parents[(size_t) ((rand() / (1. + RAND_MAX)) * N)]; left_is_first = rand() < 0.5; chunk_left = 0.0; for (k = 0; k < num_chroms; k++) { diff --git a/c/examples/multichrom_wright_fisher_singlethreaded.c b/c/examples/multichrom_wright_fisher_singlethreaded.c index 649cd408d3..5aef562208 100644 --- a/c/examples/multichrom_wright_fisher_singlethreaded.c +++ b/c/examples/multichrom_wright_fisher_singlethreaded.c @@ -46,8 +46,8 @@ simulate( * research code and proper random number generator * libraries should be preferred. */ - left_parent = parents[(size_t)((rand() / (1. + RAND_MAX)) * N)]; - right_parent = parents[(size_t)((rand() / (1. + RAND_MAX)) * N)]; + left_parent = parents[(size_t) ((rand() / (1. + RAND_MAX)) * N)]; + right_parent = parents[(size_t) ((rand() / (1. + RAND_MAX)) * N)]; left_is_first = rand() < 0.5; chunk_left = 0.0; for (k = 0; k < num_chroms; k++) { @@ -68,18 +68,15 @@ simulate( children[j] = child; } if (t % simplify_interval == 0) { - printf("Simplify at generation %lld: (%lld nodes %lld edges)", - (long long) t, - (long long) tables->nodes.num_rows, - (long long) tables->edges.num_rows); + printf("Simplify at generation %lld: (%lld nodes %lld edges)", (long long) t, + (long long) tables->nodes.num_rows, (long long) tables->edges.num_rows); /* Note: Edges must be sorted for simplify to work, and we use a brute force * approach of sorting each time here for simplicity. This is inefficient. */ ret = tsk_table_collection_sort(tables, NULL, 0); check_tsk_error(ret); ret = tsk_table_collection_simplify(tables, children, N, 0, NULL); check_tsk_error(ret); - printf(" -> (%lld nodes %lld edges)\n", - (long long) tables->nodes.num_rows, + printf(" -> (%lld nodes %lld edges)\n", (long long) tables->nodes.num_rows, (long long) tables->edges.num_rows); for (j = 0; j < N; j++) { children[j] = j; @@ -104,7 +101,7 @@ main(int argc, char **argv) } ret = tsk_table_collection_init(&tables, 0); check_tsk_error(ret); - srand((unsigned)atoi(argv[5])); + srand((unsigned) atoi(argv[5])); simulate(&tables, atoi(argv[6]), atoi(argv[1]), atoi(argv[2]), atoi(argv[3])); /* Sort and index so that the result can be opened as a tree sequence */ diff --git a/c/examples/tree_iteration.c b/c/examples/tree_iteration.c index ceb9cab226..4dc5126e1a 100644 --- a/c/examples/tree_iteration.c +++ b/c/examples/tree_iteration.c @@ -26,16 +26,14 @@ main(int argc, char **argv) printf("Iterate forwards\n"); for (ret = tsk_tree_first(&tree); ret == TSK_TREE_OK; ret = tsk_tree_next(&tree)) { - printf("\ttree %lld has %lld roots\n", - (long long) tree.index, + printf("\ttree %lld has %lld roots\n", (long long) tree.index, (long long) tsk_tree_get_num_roots(&tree)); } check_tsk_error(ret); printf("Iterate backwards\n"); for (ret = tsk_tree_last(&tree); ret == TSK_TREE_OK; ret = tsk_tree_prev(&tree)) { - printf("\ttree %lld has %lld roots\n", - (long long) tree.index, + printf("\ttree %lld has %lld roots\n", (long long) tree.index, (long long) tsk_tree_get_num_roots(&tree)); } check_tsk_error(ret); diff --git a/docs/Makefile b/docs/Makefile index 7068c5f766..493f52efeb 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -1,9 +1,3 @@ - -# Need to set PYTHONPATH so that we pick up the local tskit -PYPATH=$(shell pwd)/../python/ -TSK_VERSION:=$(shell PYTHONPATH=${PYPATH} \ - python -c 'import tskit; print(tskit.__version__.split("+")[0])') - BUILDDIR = _build DOXYGEN_XML=doxygen/xml @@ -13,13 +7,7 @@ ${DOXYGEN_XML}: ../c/tskit/*.h cd doxygen && doxygen dev: - PYTHONPATH=${PYPATH} ./build.sh - -dist: - @echo Building distribution for tskit version ${TSK_VERSION} - cd doxygen && doxygen - sed -i -e s/__TSKIT_VERSION__/${TSK_VERSION}/g _config.yml - PYTHONPATH=${PYPATH} ./build.sh + uv --project=../python run jupyter-book build -Wn --keep-going . clean: rm -fR $(BUILDDIR) $(DOXYGEN_XML) diff --git a/docs/_config.yml b/docs/_config.yml index 56218516e1..28fba57b58 100644 --- a/docs/_config.yml +++ b/docs/_config.yml @@ -46,7 +46,7 @@ sphinx: pygments_dark_style: monokai navigation_with_keys: false logo: - text: "Version __TSKIT_VERSION__" + text: "Version __PKG_VERSION__" repository_url: https://github.com/tskit-dev/tskit repository_branch: main path_to_docs: docs diff --git a/python/benchmark/run-for-all-releases.py b/python/benchmark/run-for-all-releases.py index 3e64d443b1..2fa59614f8 100644 --- a/python/benchmark/run-for-all-releases.py +++ b/python/benchmark/run-for-all-releases.py @@ -1,9 +1,9 @@ import json import subprocess +from distutils.version import StrictVersion from urllib.request import urlopen import tqdm -from distutils.version import StrictVersion def versions(package_name): diff --git a/python/benchmark/run.py b/python/benchmark/run.py index bb6f7219c8..599d88b36f 100644 --- a/python/benchmark/run.py +++ b/python/benchmark/run.py @@ -14,9 +14,10 @@ tskit_dir = Path(__file__).parent.parent sys.path.append(str(tskit_dir)) -import tskit # noqa: E402 import msprime # noqa: E402 +import tskit # noqa: E402 + with open("config.yaml") as f: config = yaml.load(f, Loader=yaml.FullLoader) diff --git a/python/lwt_interface/dict_encoding_testlib.py b/python/lwt_interface/dict_encoding_testlib.py index 86c2418923..be58f1160a 100644 --- a/python/lwt_interface/dict_encoding_testlib.py +++ b/python/lwt_interface/dict_encoding_testlib.py @@ -26,6 +26,7 @@ compiled module exporting the LightweightTableCollection class. See the test_example_c_module file for an example. """ + import copy import kastore @@ -183,9 +184,7 @@ def test_example(self, tables): { "codec": "struct", "type": "object", - "properties": { - table: {"type": "string", "binaryFormat": "50p"} - }, + "properties": {table: {"type": "string", "binaryFormat": "50p"}}, } ) @@ -578,9 +577,7 @@ def test_migrations(self, tables): self.verify_required_columns( tables, "migrations", ["left", "right", "node", "source", "dest", "time"] ) - self.verify_offset_pair( - tables, len(tables.migrations), "migrations", "metadata" - ) + self.verify_offset_pair(tables, len(tables.migrations), "migrations", "metadata") self.verify_optional_column(tables, len(tables.nodes), "nodes", "individual") self.verify_metadata_schema(tables, "migrations") @@ -674,9 +671,7 @@ def get_refseq(d): assert get_refseq(d).is_null() # All empty strings is the same thing - d["reference_sequence"] = dict( - data="", url="", metadata_schema="", metadata=b"" - ) + d["reference_sequence"] = dict(data="", url="", metadata_schema="", metadata=b"") assert get_refseq(d).is_null() del refseq_dict["metadata_schema"] # handled above diff --git a/python/lwt_interface/setup.py b/python/lwt_interface/setup.py index 30ab1dc65a..ff2389ddae 100644 --- a/python/lwt_interface/setup.py +++ b/python/lwt_interface/setup.py @@ -1,17 +1,15 @@ import os.path import platform -from setuptools import Extension -from setuptools import setup +from setuptools import Extension, setup from setuptools.command.build_ext import build_ext - IS_WINDOWS = platform.system() == "Windows" # Obscure magic required to allow numpy be used as a 'setup_requires'. # Based on https://stackoverflow.com/questions/19919905 -class local_build_ext(build_ext): +class local_build_ext(build_ext): # noqa N801 def finalize_options(self): build_ext.finalize_options(self) import builtins diff --git a/python/prek.toml b/python/prek.toml new file mode 100644 index 0000000000..37395433b0 --- /dev/null +++ b/python/prek.toml @@ -0,0 +1,66 @@ +# 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. + +# files = { glob = [ +# "tskit/**", +# "benchmark/**", +# "tests/**", +# "_tskitmodule.c", +# "*.toml", +# "docs/**", +# ]} + +# exclude = { glob = ["lib/avl.*", "lib/subprojects/**"]} + +[[repos]] +repo = "builtin" +hooks = [ + # { id = "trailing-whitespace" }, + # { id = "end-of-file-fixer" }, + { 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"], + }, +] + +[[repos]] +repo = "local" +hooks = [ + { + id = "clang-format", + name = "clang-format", + language = "system", + entry = "clang-format -i", + types = ["c"], + verbose = true, + }, +] diff --git a/python/pyproject.toml b/python/pyproject.toml index 04520aef1e..dee63416f5 100644 --- a/python/pyproject.toml +++ b/python/pyproject.toml @@ -94,39 +94,62 @@ docs = [ "pandas", ] -dev = [ - "biopython>=1.70", - "coverage", - "dendropy", - "flake8", - "kastore", - "lshmm", - "msgpack", - "msprime", - "mypy", - "networkx", - "numba", - "portion", - "pre-commit", - "pytest", - "pytest-cov", - "pytest-xdist", - "setuptools_scm", - "svgwrite", - "tszip", - "xmlunittest", - "newick", - "zarr", - "jupyter-book<2", - "breathe", - "sphinx-autodoc-typehints", - "sphinx-issues", - "sphinx-argparse", - "sphinx-book-theme", - "pandas", +# Fully pin lint requirements for determinism. +lint = [ "clang-format==21.1.8", + "ruff==0.15.1", + "prek==0.3.3", +] + +dev = [ + {include-group = "docs"}, + {include-group = "lint"}, + {include-group = "test"}, ] [tool.pytest.ini_options] addopts = "-n 4" testpaths = ["tests"] + +[tool.ruff] +# Assume Python 3.11 +target-version = "py311" + +line-length = 89 +indent-width = 4 + +[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) + "E741", # using 'l' as a variable name + "N806", "N802", "N803", # Various nags about uppercase vars + "N818", # Exceptions not called "Error" + "UP032", # Don't upgrade to f strings + "UP031", # Allow old-skool format specifiers + "B904", # raise from-issues + "PT006", # Wrong type passed to first argument of `pytest.mark.parametrize` + "PT007", # Wrong values type in `pytest.mark.parametrize` expected `list` of `tuple` + "PT009", # Replace `assertAlmostEqual(...)` with `assert ...` + "PT018", # Assertion should be broken down into multiple parts + "PT030", # `pytest.warns(UserWarning)` is too broad, set the `match` + "PT009", # pytest.raises(ValueError) too broad + "PT011", # pytest.raises(ValueError) too broad + "PT012", # pytest.raises() block should contain a single simple statement + # "B028", # No stacklevel for warnings + "B018", # Found useless expression. Either assign it + "PT031", # `pytest.warns()` block should contain a single simple statement +] + +fixable = ["ALL"] +unfixable = [] + +[tool.ruff.lint.isort] +known-first-party = ["_tskit", "tskit", "lwt_interface"] +known-third-party = [ + "msprime", + "numpy", + "pytest", +] diff --git a/python/setup.py b/python/setup.py index 0f8e77abdb..b284e65b6b 100644 --- a/python/setup.py +++ b/python/setup.py @@ -2,8 +2,7 @@ import platform import numpy -from setuptools import Extension -from setuptools import setup +from setuptools import Extension, setup IS_WINDOWS = platform.system() == "Windows" diff --git a/python/tests/__init__.py b/python/tests/__init__.py index d4c39d400b..dcd915c1b1 100644 --- a/python/tests/__init__.py +++ b/python/tests/__init__.py @@ -22,6 +22,7 @@ import base64 import tskit + from . import tsutil from .simplify import * # NOQA diff --git a/python/tests/conftest.py b/python/tests/conftest.py index 311bcc6b98..e7d0d85b1f 100644 --- a/python/tests/conftest.py +++ b/python/tests/conftest.py @@ -38,9 +38,9 @@ def test_something(self, ts_fixture): Note that fixtures have a "scope" for example `ts_fixture` below is only created once per test session and re-used for subsequent tests. """ + import msprime import pytest -from pytest import fixture from . import tsutil @@ -93,29 +93,29 @@ def pytest_collection_modifyitems(config, items): item.add_marker(skip_network) -@fixture +@pytest.fixture def overwrite_viz(request): return request.config.getoption("--overwrite-expected-visualizations") -@fixture +@pytest.fixture def draw_plotbox(request): return request.config.getoption("--draw-svg-debug-box") -@fixture(scope="session") +@pytest.fixture(scope="session") def simple_degree1_ts_fixture(): return msprime.simulate(10, random_seed=42) -@fixture(scope="session") +@pytest.fixture(scope="session") def simple_degree2_ts_fixture(): ts = msprime.simulate(10, recombination_rate=0.2, random_seed=42) assert ts.num_trees == 2 return ts -@fixture(scope="session") +@pytest.fixture(scope="session") def ts_fixture(): """ A tree sequence with data in all fields @@ -123,7 +123,7 @@ def ts_fixture(): return tsutil.all_fields_ts() -@fixture(scope="session") +@pytest.fixture(scope="session") def ts_fixture_for_simplify(): """ A tree sequence with data in all fields execpt edge metadata and migrations @@ -131,7 +131,7 @@ def ts_fixture_for_simplify(): return tsutil.all_fields_ts(edge_metadata=False, migrations=False) -@fixture(scope="session") +@pytest.fixture(scope="session") def replicate_ts_fixture(): """ A list of tree sequences diff --git a/python/tests/ibd.py b/python/tests/ibd.py index 6db35201b7..d555f02458 100644 --- a/python/tests/ibd.py +++ b/python/tests/ibd.py @@ -22,6 +22,7 @@ """ Python implementation of the IBD-finding algorithms. """ + import argparse import collections diff --git a/python/tests/simplify.py b/python/tests/simplify.py index 9e416c3e78..010149a406 100644 --- a/python/tests/simplify.py +++ b/python/tests/simplify.py @@ -23,6 +23,7 @@ """ Python implementation of the simplify algorithm. """ + import sys import numpy as np @@ -335,8 +336,7 @@ def merge_labeled_ancestors(self, S, input_id): # Fill in any gaps in the ancestry for the sample self.add_ancestry(input_id, prev_right, left, output_id) if self.keep_unary or ( - self.keep_unary_in_individuals - and self.ts.node(input_id).individual >= 0 + self.keep_unary_in_individuals and self.ts.node(input_id).individual >= 0 ): ancestry_node = output_id self.add_ancestry(input_id, left, right, ancestry_node) @@ -639,9 +639,7 @@ def process_parent_edges(self, edges): x = self.A_head[edge.child] while x is not None: if x.right > edge.left and edge.right > x.left: - y = Segment( - max(x.left, edge.left), min(x.right, edge.right), x.node - ) + y = Segment(max(x.left, edge.left), min(x.right, edge.right), x.node) S.append(y) x = x.next self.merge_labeled_ancestors(S, parent) diff --git a/python/tests/test_avl_tree.py b/python/tests/test_avl_tree.py index 2afaa0615e..ebb95f39ef 100644 --- a/python/tests/test_avl_tree.py +++ b/python/tests/test_avl_tree.py @@ -28,6 +28,7 @@ Note there is a bug in that Python translation which is missing P.B = 0 at the end of A9. """ + from __future__ import annotations import dataclasses @@ -36,7 +37,6 @@ import numpy as np import pytest - # The nodes of the tree are assumed to contain KEY, LLINK, and RLINK fields. # We also have a new field # @@ -60,8 +60,7 @@ def __str__(self): llink = None if self.llink is None else self.llink.key rlink = None if self.rlink is None else self.rlink.key return ( - f"Node(key={self.key}, balance={self.balance}, " - f"llink={llink}, rlink={rlink})" + f"Node(key={self.key}, balance={self.balance}, llink={llink}, rlink={rlink})" ) diff --git a/python/tests/test_balance_metrics.py b/python/tests/test_balance_metrics.py index 5571557a50..7b32575063 100644 --- a/python/tests/test_balance_metrics.py +++ b/python/tests/test_balance_metrics.py @@ -22,6 +22,7 @@ """ Tests for tree balance/imbalance metrics. """ + import math import numpy as np diff --git a/python/tests/test_cli.py b/python/tests/test_cli.py index 53d478b9b2..66be01e6d2 100644 --- a/python/tests/test_cli.py +++ b/python/tests/test_cli.py @@ -23,6 +23,7 @@ """ Test cases for the command line interfaces to tskit """ + import io import os import sys @@ -35,6 +36,7 @@ import tskit import tskit.cli as cli + from . import tsutil @@ -395,9 +397,7 @@ def setUpClass(cls): cls._tree_sequence = tsutil.insert_random_ploidy_individuals( ts, samples_only=True ) - fd, cls._tree_sequence_file = tempfile.mkstemp( - prefix="tsk_cli", suffix=".trees" - ) + fd, cls._tree_sequence_file = tempfile.mkstemp(prefix="tsk_cli", suffix=".trees") os.close(fd) cls._tree_sequence.dump(cls._tree_sequence_file) diff --git a/python/tests/test_coalrate.py b/python/tests/test_coalrate.py index c8cd0d9628..8281864fcd 100644 --- a/python/tests/test_coalrate.py +++ b/python/tests/test_coalrate.py @@ -22,6 +22,7 @@ """ Test cases for coalescence rate calculation in tskit. """ + import itertools import msprime @@ -45,9 +46,7 @@ def _single_tree_example(L, T): tables.edges.set_columns( left=np.repeat([0], 13), right=np.repeat([L], 13), - parent=np.array( - [8, 8, 9, 9, 10, 10, 11, 11, 11, 12, 12, 13, 13], dtype="int32" - ), + parent=np.array([8, 8, 9, 9, 10, 10, 11, 11, 11, 12, 12, 13, 13], dtype="int32"), child=np.array([1, 2, 3, 8, 0, 7, 4, 5, 10, 6, 11, 9, 12], dtype="int32"), ) tables.populations.add_row() @@ -1523,9 +1522,7 @@ def test_bad_windows(self): windows=np.array([0.0, 0.3, 0.2, 1.0]) * ts.sequence_length ) with pytest.raises(tskit.LibraryError, match="must be increasing list"): - ts.pair_coalescence_counts( - windows=np.array([0.0, 2.0]) * ts.sequence_length - ) + ts.pair_coalescence_counts(windows=np.array([0.0, 2.0]) * ts.sequence_length) def test_bad_sample_sets(self): ts = self.example_ts() @@ -1586,18 +1583,14 @@ def test_output_dim(self): implm = ts.pair_coalescence_counts(sample_sets=ss, windows=None, indexes=None) assert implm.shape == (ts.num_nodes,) windows = np.linspace(0.0, ts.sequence_length, 2) - implm = ts.pair_coalescence_counts( - sample_sets=ss, windows=windows, indexes=None - ) + implm = ts.pair_coalescence_counts(sample_sets=ss, windows=windows, indexes=None) assert implm.shape == (1, ts.num_nodes) indexes = [(0, 1), (1, 1)] implm = ts.pair_coalescence_counts( sample_sets=ss, windows=windows, indexes=indexes ) assert implm.shape == (1, 2, ts.num_nodes) - implm = ts.pair_coalescence_counts( - sample_sets=ss, windows=None, indexes=indexes - ) + implm = ts.pair_coalescence_counts(sample_sets=ss, windows=None, indexes=indexes) assert implm.shape == (2, ts.num_nodes) def test_extra_time_windows(self): diff --git a/python/tests/test_combinatorics.py b/python/tests/test_combinatorics.py index 8073b845df..0f476d5652 100644 --- a/python/tests/test_combinatorics.py +++ b/python/tests/test_combinatorics.py @@ -23,6 +23,7 @@ """ Test cases for combinatorial algorithms. """ + import collections import io import itertools @@ -38,8 +39,7 @@ import tskit import tskit.combinatorics as comb from tests import test_stats -from tskit.combinatorics import Rank -from tskit.combinatorics import RankTree +from tskit.combinatorics import Rank, RankTree class TestCombination: diff --git a/python/tests/test_dict_encoding.py b/python/tests/test_dict_encoding.py index 7ef4c70836..ac931120b1 100644 --- a/python/tests/test_dict_encoding.py +++ b/python/tests/test_dict_encoding.py @@ -23,6 +23,7 @@ Test cases for the low-level dictionary encoding used to move data around in C. """ + import pathlib import pickle @@ -30,7 +31,6 @@ import lwt_interface.dict_encoding_testlib import tskit - lwt_interface.dict_encoding_testlib.lwt_module = _tskit # Bring the tests defined in dict_encoding_testlib into the current namespace # so pytest will find and execute them. diff --git a/python/tests/test_distance_metrics.py b/python/tests/test_distance_metrics.py index c08351962f..e208bbdb49 100644 --- a/python/tests/test_distance_metrics.py +++ b/python/tests/test_distance_metrics.py @@ -22,6 +22,7 @@ """ Tests for tree distance metrics. """ + import io import itertools import math diff --git a/python/tests/test_divmat.py b/python/tests/test_divmat.py index 07de0b3acd..f927e5fdf1 100644 --- a/python/tests/test_divmat.py +++ b/python/tests/test_divmat.py @@ -22,6 +22,7 @@ """ Test cases for divergence matrix based pairwise stats """ + import array import collections import functools @@ -213,12 +214,10 @@ def branch_divergence_matrix(ts, sample_sets=None, windows=None, span_normalise= tv = ts.nodes_time[w] - ts.nodes_time[v] else: tu = ( - ts.nodes_time[local_root(tree, u)] - - ts.nodes_time[u] + ts.nodes_time[local_root(tree, u)] - ts.nodes_time[u] ) tv = ( - ts.nodes_time[local_root(tree, v)] - - ts.nodes_time[v] + ts.nodes_time[local_root(tree, v)] - ts.nodes_time[v] ) d = (tu + tv) * span D[i, j, k] += d @@ -680,9 +679,7 @@ def test_single_tree_multiroot(self, mode): ) np.testing.assert_array_equal(D1, D2) - @pytest.mark.parametrize( - ["left", "right"], [(0, 10), (1, 3), (3.25, 3.75), (5, 10)] - ) + @pytest.mark.parametrize(["left", "right"], [(0, 10), (1, 3), (3.25, 3.75), (5, 10)]) def test_single_tree_interval(self, left, right): # 2.00┊ 6 ┊ # ┊ ┏━┻━┓ ┊ @@ -691,9 +688,7 @@ def test_single_tree_interval(self, left, right): # 0.00┊ 0 1 2 3 ┊ # 0 1 ts = tskit.Tree.generate_balanced(4, span=10).tree_sequence - D1 = check_divmat( - ts, windows=[left, right], mode="branch", span_normalise=False - ) + D1 = check_divmat(ts, windows=[left, right], mode="branch", span_normalise=False) D2 = np.array( [ [0.0, 2.0, 4.0, 4.0], @@ -749,14 +744,14 @@ def test_all_trees_interval(self, interval, mode, span_normalise): check_divmat(ts, windows=interval, mode=mode, span_normalise=span_normalise) @pytest.mark.parametrize( - ["windows"], + "windows", [ - ([0, 26],), - ([0, 1, 2],), - (list(range(27)),), - ([5, 7, 9, 20],), - ([5.1, 5.2, 5.3, 5.5, 6],), - ([5.1, 5.2, 6.5],), + [0, 26], + [0, 1, 2], + list(range(27)), + [5, 7, 9, 20], + [5.1, 5.2, 5.3, 5.5, 6], + [5.1, 5.2, 6.5], ], ) @pytest.mark.parametrize("mode", DIVMAT_MODES) @@ -792,9 +787,7 @@ def test_small_sims(self, n, seed, mode): random_seed=seed, ) assert ts.num_trees >= 2 - ts = msprime.sim_mutations( - ts, rate=0.1, discrete_genome=False, random_seed=seed - ) + ts = msprime.sim_mutations(ts, rate=0.1, discrete_genome=False, random_seed=seed) assert ts.num_mutations > 1 check_divmat(ts, verbosity=0, mode=mode) @@ -1074,16 +1067,16 @@ def check(self, ts, num_threads, *, windows, samples=None, mode=None): @pytest.mark.parametrize("num_threads", [1, 2, 3, 5, 26, 27]) @pytest.mark.parametrize( - ["windows"], + "windows", [ - ([0, 26],), - ([0, 1, 2],), - (list(range(27)),), - ([5, 7, 9, 20],), - ([5.1, 5.2, 5.3, 5.5, 6],), - ([5.1, 5.2, 6.5],), - ("trees",), - ("sites",), + [0, 26], + [0, 1, 2], + list(range(27)), + [5, 7, 9, 20], + [5.1, 5.2, 5.3, 5.5, 6], + [5.1, 5.2, 6.5], + "trees", + "sites", ], ) @pytest.mark.parametrize("mode", DIVMAT_MODES) @@ -1094,12 +1087,12 @@ def test_all_trees(self, num_threads, windows, mode): @pytest.mark.parametrize("samples", [None, [0, 1]]) @pytest.mark.parametrize( - ["windows"], + "windows", [ - ([0, 26],), - (None,), - ("trees",), - ("sites",), + [0, 26], + None, + "trees", + "sites", ], ) @pytest.mark.parametrize("mode", DIVMAT_MODES) @@ -1109,15 +1102,15 @@ def test_all_trees_samples(self, samples, windows, mode): @pytest.mark.parametrize("num_threads", range(1, 5)) @pytest.mark.parametrize( - ["windows"], + "windows", [ - ([0, 100],), - ([0, 50, 75, 95, 100],), - ([50, 75, 95, 100],), - ([0, 50, 75, 95],), - (list(range(100)),), - ("trees",), - ("sites",), + [0, 100], + [0, 50, 75, 95, 100], + [50, 75, 95, 100], + [0, 50, 75, 95], + list(range(100)), + "trees", + "sites", ], ) @pytest.mark.parametrize("mode", DIVMAT_MODES) diff --git a/python/tests/test_drawing.py b/python/tests/test_drawing.py index e5885a52ac..9cd1384a52 100644 --- a/python/tests/test_drawing.py +++ b/python/tests/test_drawing.py @@ -23,6 +23,7 @@ """ Test cases for visualisation in tskit. """ + import collections import io import logging @@ -43,7 +44,6 @@ import tskit from tskit import drawing - IS_WINDOWS = platform.system() == "Windows" @@ -250,7 +250,7 @@ def fail(self, *args, **kwargs): """ Required for xmlunittest.XmlTestMixin to work with pytest not unittest """ - pytest.fail(*args, **kwargs) + pytest.fail(*args, **kwargs) # noqa: PT016 def closest_left_node(tree, u): @@ -685,13 +685,13 @@ def test_simple_tree(self): 0 1 2 1 """ ) + # fmt: off tree = ( - # fmt: off " 2 \n" "┏┻┓\n" "0 1" - # fmt: on ) + # fmt: on ts = tskit.load_text(nodes, edges, strict=False) t = next(ts.trees()) drawn = t.draw(format="unicode", order="tree") @@ -699,32 +699,32 @@ def test_simple_tree(self): drawn = t.draw_text() self.verify_text_rendering(drawn, tree) + # fmt: off tree = ( - # fmt: off " 2 \n" "+++\n" "0 1\n" - # fmt: on ) + # fmt: on drawn = t.draw_text(use_ascii=True, order="tree") self.verify_text_rendering(drawn, tree) + # fmt: off tree = ( - # fmt: off " ┏0\n" "2┫ \n" " ┗1\n" - # fmt: on ) + # fmt: on drawn = t.draw_text(orientation="left", order="tree") self.verify_text_rendering(drawn, tree) + # fmt: off tree = ( - # fmt: off " +0\n" "2+ \n" " +1\n" - # fmt: on ) + # fmt: on drawn = t.draw_text(orientation="left", use_ascii=True, order="tree") self.verify_text_rendering(drawn, tree) @@ -744,25 +744,25 @@ def test_simple_tree_long_label(self): 0 1 2 1 """ ) + # fmt: off tree = ( - # fmt: off "ABCDEF\n" "┏┻┓ \n" "0 1 \n" - # fmt: on ) + # fmt: on ts = tskit.load_text(nodes, edges, strict=False) t = next(ts.trees()) drawn = t.draw_text(node_labels={0: "0", 1: "1", 2: "ABCDEF"}, order="tree") self.verify_text_rendering(drawn, tree) + # fmt: off tree = ( - # fmt: off "0┓ \n" " ┣ABCDEF\n" "1┛ \n" - # fmt: on ) + # fmt: on drawn = t.draw_text( node_labels={0: "0", 1: "1", 2: "ABCDEF"}, orientation="right", order="tree" ) @@ -771,22 +771,22 @@ def test_simple_tree_long_label(self): drawn = t.draw_text( node_labels={0: "ABCDEF", 1: "1", 2: "2"}, orientation="right", order="tree" ) + # fmt: off tree = ( - # fmt: off "ABCDEF┓ \n" " ┣2\n" "1━━━━━┛ \n" - # fmt: on ) + # fmt: on self.verify_text_rendering(drawn, tree) + # fmt: off tree = ( - # fmt: off " ┏0\n" "ABCDEF┫ \n" " ┗1\n" - # fmt: on ) + # fmt: on drawn = t.draw_text( node_labels={0: "0", 1: "1", 2: "ABCDEF"}, orientation="left", order="tree" ) @@ -816,6 +816,7 @@ def test_four_leaves(self): 0.00000000 1.00000000 6 5 """ ) + # fmt: off tree = ( " 6 \n" "┏━┻━┓ \n" @@ -825,6 +826,7 @@ def test_four_leaves(self): "┃ ┃ ┏┻┓ \n" "1 2 0 3 \n" ) + # fmt: on ts = tskit.load_text(nodes, edges, strict=False) t = ts.first() drawn = t.draw(format="unicode", order="tree") @@ -832,6 +834,7 @@ def test_four_leaves(self): self.verify_text_rendering(t.draw_text(order="tree"), tree) drawn = t.draw_text(orientation="bottom", order="tree") + # fmt: off tree = ( "1 2 0 3\n" "┃ ┃ ┗┳┛\n" @@ -841,8 +844,10 @@ def test_four_leaves(self): "┗━┳━┛ \n" " 6 \n" ) + # fmt: on self.verify_text_rendering(drawn, tree) + # fmt: off tree = ( " ┏━━━━1\n" " ┃ \n" @@ -852,8 +857,10 @@ def test_four_leaves(self): " ┗4┫ \n" " ┗3\n" ) + # fmt: on self.verify_text_rendering(t.draw_text(orientation="left", order="tree"), tree) + # fmt: off tree = ( "2.92┊ 6 ┊\n" " ┊ ┏━┻━┓ ┊\n" @@ -864,8 +871,10 @@ def test_four_leaves(self): "0.00┊ 1 2 0 3 ┊\n" " 0 1\n" ) + # fmt: on self.verify_text_rendering(ts.draw_text(order="tree"), tree) + # fmt: off tree = ( " 6 \n" "+-+-+ \n" @@ -875,9 +884,11 @@ def test_four_leaves(self): "| | +++\n" "1 2 0 3\n" ) + # fmt: on drawn = t.draw(format="ascii", order="tree") self.verify_text_rendering(drawn, tree) + # fmt: off tree = ( " 6 \n" "┏━┻━┓ \n" @@ -887,11 +898,13 @@ def test_four_leaves(self): "┃ ┃ ┏┻┓ \n" "1 2 0 3 \n" ) + # fmt: on labels = {u: str(u) for u in t.nodes()} labels[5] = "xxxxxxxxxx" drawn = t.draw_text(node_labels=labels, order="tree") self.verify_text_rendering(drawn, tree) + # fmt: off tree = ( " ┏━━━━━━━━━━━━━1\n" " ┃ \n" @@ -901,9 +914,11 @@ def test_four_leaves(self): " ┗4┫ \n" " ┗3\n" ) + # fmt: on drawn = t.draw_text(node_labels=labels, orientation="left", order="tree") self.verify_text_rendering(drawn, tree) + # fmt: off tree = ( "2.92┊ 6 ┊\n" " ┊ ┏━┻━┓ ┊\n" @@ -914,6 +929,7 @@ def test_four_leaves(self): "0.00┊ 1 2 0 3 ┊\n" " 0 1\n" ) + # fmt: on drawn = ts.draw_text(node_labels=labels, order="tree") self.verify_text_rendering(drawn, tree) @@ -935,40 +951,40 @@ def test_trident_tree(self): 0 1 3 2 """ ) + # fmt: off tree = ( - # fmt: off " 3 \n" "┏━╋━┓\n" "0 1 2\n" - # fmt: on ) + # fmt: on ts = tskit.load_text(nodes, edges, strict=False) t = next(ts.trees()) drawn = t.draw(format="unicode", order="tree") self.verify_text_rendering(drawn, tree) self.verify_text_rendering(t.draw_text(), tree) + # fmt: off tree = ( - # fmt: off " ┏0\n" " ┃\n" "3╋1\n" " ┃\n" " ┗2\n" - # fmt: on ) + # fmt: on drawn = t.draw_text(orientation="left") self.verify_text_rendering(drawn, tree) + # fmt: off tree = ( - # fmt: off "0┓\n" " ┃\n" "1╋3\n" " ┃\n" "2┛\n" - # fmt: on ) + # fmt: on drawn = t.draw_text(orientation="right") self.verify_text_rendering(drawn, tree) @@ -994,43 +1010,43 @@ def test_pitchfork_tree(self): ) ts = tskit.load_text(nodes, edges, strict=False) t = next(ts.trees()) + # fmt: off tree = ( - # fmt: off " 4 \n" "┏━┳┻┳━┓\n" "0 1 2 3\n" - # fmt: on ) + # fmt: on drawn = t.draw(format="unicode", order="tree") self.verify_text_rendering(drawn, tree) self.verify_text_rendering(t.draw_text(), tree) # No labels + # fmt: off tree = ( - # fmt: off " ┃ \n" "┏━┳┻┳━┓\n" "┃ ┃ ┃ ┃\n" - # fmt: on ) + # fmt: on drawn = t.draw(format="unicode", node_labels={}, order="tree") self.verify_text_rendering(drawn, tree) self.verify_text_rendering(t.draw_text(node_labels={}), tree) # Some labels + # fmt: off tree = ( - # fmt: off " ┃ \n" "┏━┳┻┳━┓\n" "0 ┃ ┃ 3\n" - # fmt: on ) + # fmt: on labels = {0: "0", 3: "3"} drawn = t.draw(format="unicode", node_labels=labels, order="tree") self.verify_text_rendering(drawn, tree) self.verify_text_rendering(t.draw_text(node_labels=labels), tree) + # fmt: off tree = ( - # fmt: off " ┏0\n" " ┃\n" " ┣1\n" @@ -1038,13 +1054,13 @@ def test_pitchfork_tree(self): " ┣2\n" " ┃\n" " ┗3\n" - # fmt: on ) + # fmt: on drawn = t.draw_text(orientation="left") self.verify_text_rendering(drawn, tree) + # fmt: off tree = ( - # fmt: off "0┓\n" " ┃\n" "1┫\n" @@ -1052,8 +1068,8 @@ def test_pitchfork_tree(self): "2┫\n" " ┃\n" "3┛\n" - # fmt: on ) + # fmt: on drawn = t.draw_text(orientation="right") self.verify_text_rendering(drawn, tree) @@ -1073,30 +1089,30 @@ def test_stick_tree(self): 0 1 2 1 """ ) + # fmt: off tree = ( - # fmt: off "2\n" "┃\n" "1\n" "┃\n" "0\n" - # fmt: on ) + # fmt: on ts = tskit.load_text(nodes, edges, strict=False) t = next(ts.trees()) drawn = t.draw(format="unicode", order="tree") self.verify_text_rendering(drawn, tree) self.verify_text_rendering(t.draw_text(), tree) + # fmt: off tree = ( - # fmt: off "0\n" "┃\n" "1\n" "┃\n" "2\n" - # fmt: on ) + # fmt: on drawn = t.draw_text(orientation="bottom") self.verify_text_rendering(drawn, tree) @@ -1436,6 +1452,7 @@ def test_max_time(self): t = ts.first() self.verify_text_rendering(t.draw_text(max_time="ts"), tree) + # fmt: off tree = ( " 9 \n" " ┏━┻━┓ \n" @@ -1445,6 +1462,7 @@ def test_max_time(self): "┏┻┓ ┃ ┃\n" "0 1 2 3\n" ) + # fmt: on t = ts.first() self.verify_text_rendering(t.draw_text(max_time="tree"), tree) for bad_max_time in [1, "sdfr", ""]: @@ -1956,9 +1974,7 @@ def test_one_mutation_colour(self): def test_all_mutations_colour(self): t = self.get_binary_tree() - colours = { - mut.id: f"rgb({mut.id}, {mut.id}, {mut.id})" for mut in t.mutations() - } + colours = {mut.id: f"rgb({mut.id}, {mut.id}, {mut.id})" for mut in t.mutations()} svg = t.draw(format="svg", mutation_colours=colours) self.verify_basic_svg(svg) for colour in colours.values(): @@ -2258,7 +2274,7 @@ def test_y_axis_noticks(self): assert svg_no_css.count("y-axis") == 1 assert svg_no_css.count('"tick"') == 0 - def test_y_axis_tick_warning(sefl, caplog): + def test_y_axis_tick_warning(self, caplog): tree = msprime.simulate(4, random_seed=2).first() upper = int(tree.time(tree.root)) with caplog.at_level(logging.WARNING): @@ -2404,9 +2420,7 @@ def test_xlim_maintains_tree_ids(self): svg = ts.draw_svg(x_lim=[breaks[1], breaks[4]]) assert "t0" not in svg assert "t4" not in svg - svg = ts.draw_svg( - x_lim=[np.nextafter(breaks[1], 0), np.nextafter(breaks[4], 1)] - ) + svg = ts.draw_svg(x_lim=[np.nextafter(breaks[1], 0), np.nextafter(breaks[4], 1)]) assert "t0" in svg assert "t4" in svg @@ -2556,9 +2570,7 @@ def test_x_regions_ts(self): 3, sequence_length=100, recombination_rate=0.1, random_seed=1 ) regions = [(0, 10), (9, 20), (50, 90)] - svg = ts.draw_svg( - x_regions={r: f"reg{'ABC'[i]}" for i, r in enumerate(regions)} - ) + svg = ts.draw_svg(x_regions={r: f"reg{'ABC'[i]}" for i, r in enumerate(regions)}) self.verify_basic_svg(svg, width=200 * ts.num_trees) assert svg.count("x-regions") == 2 # one in stylesheet, one in svg assert svg.count("r0") == 1 @@ -2642,9 +2654,7 @@ def test_only_subset_nodes_in_rank(self, caplog): assert "Ticks {10: '10'} lie outside the plotted axis" in caplog.text def test_polytomy_collapsing(self): - tree = tskit.Tree.generate_balanced( - 20, arity=4, tracked_samples=np.arange(2, 8) - ) + tree = tskit.Tree.generate_balanced(20, arity=4, tracked_samples=np.arange(2, 8)) svg = tree.draw_svg(pack_untracked_polytomies=True) # Should have one collapsed node (untracked samples 8 and 9) # and two "polytomy lines" (from nodes 21 and 28 (the root)) @@ -2663,9 +2673,7 @@ def test_preamble(self, tree_or_ts): svg = tree_or_ts.draw_svg( size=(200, 200), canvas_size=(400, 200), - preamble=embed.draw_svg( - root_svg_attributes={"x": 200, "class": "embedded"} - ), + preamble=embed.draw_svg(root_svg_attributes={"x": 200, "class": "embedded"}), ) self.verify_basic_svg(svg, width=400, height=200) assert svg.count("NoDe{nd.id}!" in svg for m in ts.mutations(): - assert ( - svg.count(f"MuT{m.id}!") == 2 - ) # 1 on tree, 1 on x-axis + assert svg.count(f"MuT{m.id}!") == 2 # 1 on tree, 1 on x-axis self.verify_known_svg( svg, "ts_mut_times_titles.svg", overwrite_viz, width=200 * ts.num_trees ) @@ -3160,9 +3164,7 @@ def test_known_svg_tree_polytomy(self, overwrite_viz, draw_plotbox): size=(600, 200), style="".join(f".n{u} > .sym {{fill: cyan}}" for u in tracked_nodes + [39]), ) - self.verify_known_svg( - svg, "tree_poly.svg", overwrite_viz, width=600, height=200 - ) + self.verify_known_svg(svg, "tree_poly.svg", overwrite_viz, width=600, height=200) def test_known_svg_tree_polytomy_tracked(self, overwrite_viz, draw_plotbox): tracked_nodes = [20, 24, 25, 27, 28, 29] @@ -3179,9 +3181,7 @@ def test_known_svg_tree_polytomy_tracked(self, overwrite_viz, draw_plotbox): svg, "tree_poly_tracked.svg", overwrite_viz, width=600, height=200 ) - def test_known_svg_tree_polytomy_tracked_collapse( - self, overwrite_viz, draw_plotbox - ): + def test_known_svg_tree_polytomy_tracked_collapse(self, overwrite_viz, draw_plotbox): tracked_nodes = [20, 24, 25, 27, 28, 29] tree = tskit.Tree.generate_balanced(30, arity=4, tracked_samples=tracked_nodes) svg = tree.draw_svg( diff --git a/python/tests/test_file_format.py b/python/tests/test_file_format.py index ff35dc90bc..ec8a7af89d 100644 --- a/python/tests/test_file_format.py +++ b/python/tests/test_file_format.py @@ -23,6 +23,7 @@ """ Test cases for tskit's file format. """ + import os import tempfile import unittest @@ -397,9 +398,7 @@ def verify_dump_format(self, ts): assert np.array_equal(tables.metadata, b"".join(store["metadata"])) assert np.array_equal(tables.individuals.flags, store["individuals/flags"]) - assert np.array_equal( - tables.individuals.location, store["individuals/location"] - ) + assert np.array_equal(tables.individuals.location, store["individuals/location"]) assert np.array_equal( tables.individuals.location_offset, store["individuals/location_offset"] ) @@ -407,9 +406,7 @@ def verify_dump_format(self, ts): assert np.array_equal( tables.individuals.parents_offset, store["individuals/parents_offset"] ) - assert np.array_equal( - tables.individuals.metadata, store["individuals/metadata"] - ) + assert np.array_equal(tables.individuals.metadata, store["individuals/metadata"]) assert np.array_equal( tables.individuals.metadata_offset, store["individuals/metadata_offset"] ) @@ -513,9 +510,7 @@ def verify_dump_format(self, ts): store["mutations/metadata_schema"].astype("U") ) - assert np.array_equal( - tables.populations.metadata, store["populations/metadata"] - ) + assert np.array_equal(tables.populations.metadata, store["populations/metadata"]) assert np.array_equal( tables.populations.metadata_offset, store["populations/metadata_offset"] ) diff --git a/python/tests/test_fileobj.py b/python/tests/test_fileobj.py index 11cf66fac8..4980382a79 100644 --- a/python/tests/test_fileobj.py +++ b/python/tests/test_fileobj.py @@ -22,6 +22,7 @@ """ Test cases for loading and dumping different types of files and streams """ + import io import multiprocessing import os @@ -36,17 +37,15 @@ import pytest import tszip -from pytest import fixture import tskit - IS_WINDOWS = platform.system() == "Windows" IS_OSX = platform.system() == "Darwin" class TestPath: - @fixture + @pytest.fixture def tempfile_name(self): with tempfile.TemporaryDirectory() as tmp_dir: yield f"{tmp_dir}/plain_path" @@ -58,7 +57,7 @@ def test_pathlib(self, ts_fixture, tempfile_name): class TestPathLib: - @fixture + @pytest.fixture def pathlib_tempfile(self): fd, path = tempfile.mkstemp(prefix="tskit_test_pathlib") os.close(fd) @@ -73,7 +72,7 @@ def test_pathlib(self, ts_fixture, pathlib_tempfile): class TestFileObj: - @fixture + @pytest.fixture def fileobj(self): with tempfile.TemporaryDirectory() as tmp_dir: with open(f"{tmp_dir}/fileobj", "wb") as f: @@ -100,7 +99,7 @@ def test_fileobj_multi(self, replicate_ts_fixture, fileobj): class TestFileObjRW: - @fixture + @pytest.fixture def fileobj(self): with tempfile.TemporaryDirectory() as tmp_dir: pathlib.Path(f"{tmp_dir}/fileobj").touch() @@ -127,7 +126,7 @@ def test_fileobj_multi(self, replicate_ts_fixture, fileobj): class TestFD: - @fixture + @pytest.fixture def fd(self): with tempfile.TemporaryDirectory() as tmp_dir: pathlib.Path(f"{tmp_dir}/fd").touch() @@ -246,7 +245,7 @@ def stream(fifo, ts_list): @pytest.mark.skipif(IS_WINDOWS, reason="No FIFOs on Windows") @pytest.mark.skipif(IS_OSX, reason="FIFO flakey on OS X, issue #1170") class TestFIFO: - @fixture + @pytest.fixture def fifo(self): temp_dir = tempfile.mkdtemp(prefix="tsk_test_streaming") temp_fifo = os.path.join(temp_dir, "fifo") @@ -290,7 +289,7 @@ def server_process(q): @pytest.mark.network @pytest.mark.skipif(IS_WINDOWS or IS_OSX, reason="Errors on systems without proper fds") class TestSocket: - @fixture + @pytest.fixture def client_fd(self): # Use a queue to synchronise the startup of the server and the client. q = multiprocessing.Queue() diff --git a/python/tests/test_genotype_matching.py b/python/tests/test_genotype_matching.py index 01c8b40a59..091b0bde42 100644 --- a/python/tests/test_genotype_matching.py +++ b/python/tests/test_genotype_matching.py @@ -527,8 +527,7 @@ def process_site( if st1.tree_node != tskit.NULL: for st2 in st1.value_list: st2.value = ( - ((self.rho[site.id] / self.ts.num_samples) ** 2) - * b_last_sum + ((self.rho[site.id] / self.ts.num_samples) ** 2) * b_last_sum + (1 - self.rho[site.id]) * (self.rho[site.id] / self.ts.num_samples) * st2.inner_summation @@ -1169,9 +1168,7 @@ def ls_forward_tree(g, ts, rho, mu, precision=30): def ls_backward_tree(g, ts_mirror, rho, mu, normalisation_factor, precision=30): """Backward matrix computation based on a tree sequence.""" - ba = BackwardAlgorithm( - ts_mirror, rho, mu, normalisation_factor, precision=precision - ) + ba = BackwardAlgorithm(ts_mirror, rho, mu, normalisation_factor, precision=precision) return ba.run_backward(g) diff --git a/python/tests/test_genotypes.py b/python/tests/test_genotypes.py index b9b6916a2d..590350b413 100644 --- a/python/tests/test_genotypes.py +++ b/python/tests/test_genotypes.py @@ -22,6 +22,7 @@ """ Test cases for generating genotypes/haplotypes. """ + import itertools import logging import random @@ -699,9 +700,7 @@ def test_states_haplotypes_equiv(self, missing): tables.delete_intervals([[0, ts.site(4).position]]) tables.sites.replace_with(ts.tables.sites) ts = tables.tree_sequence() - states = np.array( - [v.states() for v in ts.variants(isolated_as_missing=missing)] - ) + states = np.array([v.states() for v in ts.variants(isolated_as_missing=missing)]) for h1, h2 in zip(ts.haplotypes(isolated_as_missing=missing), states.T): assert h1 == "".join(h2) @@ -974,9 +973,7 @@ def test_missing_data(self): h = list(ts.haplotypes(isolated_as_missing=False, impute_missing_data=True)) assert h == ["A", "A"] with pytest.warns(FutureWarning): - h = list( - ts.haplotypes(isolated_as_missing=False, impute_missing_data=False) - ) + h = list(ts.haplotypes(isolated_as_missing=False, impute_missing_data=False)) assert h == ["A", "A"] def test_restrict_samples(self): @@ -1028,9 +1025,7 @@ def test_simple_01_trailing_alleles(self): alleles = ("0", "1", "2", "xxxxx") G2 = ts.genotype_matrix(alleles=alleles) assert np.array_equal(G1, G2) - for v1, v2 in itertools.zip_longest( - ts.variants(), ts.variants(alleles=alleles) - ): + for v1, v2 in itertools.zip_longest(ts.variants(), ts.variants(alleles=alleles)): assert v2.alleles == alleles assert v1.site == v2.site assert np.array_equal(v1.genotypes, v2.genotypes) @@ -1042,9 +1037,7 @@ def test_simple_01_leading_alleles(self): alleles = ("A", "B", "C", "0", "1") G2 = ts.genotype_matrix(alleles=alleles) assert np.array_equal(G1 + 3, G2) - for v1, v2 in itertools.zip_longest( - ts.variants(), ts.variants(alleles=alleles) - ): + for v1, v2 in itertools.zip_longest(ts.variants(), ts.variants(alleles=alleles)): assert v2.alleles == alleles assert v1.site == v2.site assert np.array_equal(v1.genotypes + 3, v2.genotypes) @@ -1058,9 +1051,7 @@ def test_simple_01_duplicate_alleles(self): index = np.where(G1 == 1) G1[index] = 2 assert np.array_equal(G1, G2) - for v1, v2 in itertools.zip_longest( - ts.variants(), ts.variants(alleles=alleles) - ): + for v1, v2 in itertools.zip_longest(ts.variants(), ts.variants(alleles=alleles)): assert v2.alleles == alleles assert v1.site == v2.site g = np.array(v1.genotypes) @@ -1076,9 +1067,7 @@ def test_simple_acgt(self): assert ts.num_sites > 2 alleles = tskit.ALLELES_ACGT G = ts.genotype_matrix(alleles=alleles) - for v1, v2 in itertools.zip_longest( - ts.variants(), ts.variants(alleles=alleles) - ): + for v1, v2 in itertools.zip_longest(ts.variants(), ts.variants(alleles=alleles)): assert v2.alleles == alleles assert v1.site == v2.site h1 = "".join(v1.alleles[g] for g in v1.genotypes) @@ -1152,9 +1141,7 @@ class TestUserAllelesRoundTrip: """ def verify(self, ts, alleles): - for v1, v2 in itertools.zip_longest( - ts.variants(), ts.variants(alleles=alleles) - ): + for v1, v2 in itertools.zip_longest(ts.variants(), ts.variants(alleles=alleles)): h1 = [v1.alleles[g] for g in v1.genotypes] h2 = [v2.alleles[g] for g in v2.genotypes] assert h1 == h2 @@ -1653,9 +1640,7 @@ def test_alignments_default(self): def test_alignments_impute_missing(self): ref = "N" * 10 - A = list( - self.ts().alignments(reference_sequence=ref, isolated_as_missing=False) - ) + A = list(self.ts().alignments(reference_sequence=ref, isolated_as_missing=False)) assert A[0] == "NNGNNNNNNT" assert A[1] == "NNANNNNNNC" assert A[2] == "NNANNNNNNC" @@ -2146,8 +2131,7 @@ def test_internal_presence_switch(self): ] # Imputed ancestral at right site assert [ - vi.genotypes[0] - for vi in ts.variants(samples=[a], isolated_as_missing=False) + vi.genotypes[0] for vi in ts.variants(samples=[a], isolated_as_missing=False) ] == [1, 0] assert list(ts.haplotypes(samples=[a], isolated_as_missing=False)) == ["GC"] assert list(ts.haplotypes(samples=[a], isolated_as_missing=True)) == ["GN"] @@ -2596,14 +2580,14 @@ def test_not_decoded(self, ts_fixture): variant = tskit.Variant(ts_fixture) assert variant.index == tskit.NULL with pytest.raises(ValueError, match="not yet been decoded"): - variant.site + _ = variant.site assert variant.alleles == () with pytest.raises(ValueError, match="not yet been decoded"): assert variant.genotypes assert not variant.has_missing_data assert variant.num_alleles == 0 with pytest.raises(ValueError, match="not yet been decoded"): - variant.position + _ = variant.position assert np.array_equal(variant.samples, np.array(ts_fixture.samples())) def test_variant_decode(self, ts_fixture): @@ -2649,9 +2633,7 @@ def test_variant_simple_frequencies(self): tables.sites.add_row(position=0.6, ancestral_state="AS1") tables.mutations.add_row(site=0, derived_state="DS0_0", node=0) tables.mutations.add_row(site=0, derived_state="DS0_3", node=3) - tables.mutations.add_row( - site=1, derived_state="DS1", node=simple_tree.parent(0) - ) + tables.mutations.add_row(site=1, derived_state="DS1", node=simple_tree.parent(0)) ts = tables.tree_sequence() variant_0 = next(ts.variants()) freqs = variant_0.frequencies() @@ -2775,9 +2757,7 @@ def test_variant_str(self): ╟─+┼─+╢ ║Isolated as missing\s*│\s*True║ ╚═+╧═+╝ - """[ - 1: - ] + """[1:] ), str(v), ) diff --git a/python/tests/test_haplotype_matching.py b/python/tests/test_haplotype_matching.py index bd1448251a..92bdf63058 100644 --- a/python/tests/test_haplotype_matching.py +++ b/python/tests/test_haplotype_matching.py @@ -22,6 +22,7 @@ """ Python implementation of the Li and Stephens forwards and backwards algorithms. """ + import warnings import lshmm as ls @@ -162,9 +163,7 @@ def compute(u, parent_state): optimal_set[u, value_count == max_value_count] = 1 optimal_set = np.zeros((tree.tree_sequence.num_nodes, len(values)), dtype=int) - t_node_time = [ - -1 if st.tree_node == -1 else tree.time(st.tree_node) for st in T - ] + t_node_time = [-1 if st.tree_node == -1 else tree.time(st.tree_node) for st in T] order = np.argsort(t_node_time) for j in order: st = T[j] diff --git a/python/tests/test_highlevel.py b/python/tests/test_highlevel.py index 9ce5a928d2..e9531451d3 100644 --- a/python/tests/test_highlevel.py +++ b/python/tests/test_highlevel.py @@ -23,6 +23,7 @@ """ Test cases for the high level interface to tskit. """ + import collections import dataclasses import decimal @@ -930,7 +931,7 @@ def verify_trees(self, ts): assert st1.root == list(roots)[0] else: with pytest.raises(ValueError): - st1.root + _ = st1.root assert st2 == st1 assert not (st2 != st1) left, right = st1.get_interval() @@ -1529,7 +1530,7 @@ def test_first_last(self, ts): for kwargs in [{}, {"tracked_samples": ts.samples()}]: t1 = ts.first(**kwargs) t2 = next(ts.trees()) - assert not (t1 is t2) + assert t1 is not t2 assert t1.parent_dict == t2.parent_dict assert t1.index == 0 if "tracked_samples" in kwargs: @@ -1539,7 +1540,7 @@ def test_first_last(self, ts): t1 = ts.last(**kwargs) t2 = next(reversed(ts.trees())) - assert not (t1 is t2) + assert t1 is not t2 assert t1.parent_dict == t2.parent_dict assert t1.index == ts.num_trees - 1 if "tracked_samples" in kwargs: @@ -2690,9 +2691,7 @@ def verify_simplify_equality(self, ts, sample): sample, map_nodes=True, filter_sites=filter_sites ) t1 = s1.dump_tables() - s2, node_map2 = simplify_tree_sequence( - ts, sample, filter_sites=filter_sites - ) + s2, node_map2 = simplify_tree_sequence(ts, sample, filter_sites=filter_sites) t2 = s2.dump_tables() assert s1.num_samples == len(sample) assert s2.num_samples == len(sample) @@ -2772,9 +2771,12 @@ def test_simplify_bugs(self): edges_file = os.path.join(prefix, f"{j:02d}-edges.txt") sites_file = os.path.join(prefix, f"{j:02d}-sites.txt") mutations_file = os.path.join(prefix, f"{j:02d}-mutations.txt") - with open(nodes_file) as nodes, open(edges_file) as edges, open( - sites_file - ) as sites, open(mutations_file) as mutations: + with ( + open(nodes_file) as nodes, + open(edges_file) as edges, + open(sites_file) as sites, + open(mutations_file) as mutations, + ): ts = tskit.load_text( nodes=nodes, edges=edges, @@ -3096,9 +3098,7 @@ def test_table_metadata_schemas(self): assert repr(getattr(tables, f"{table}s").metadata_schema) == repr(schema) for other_table in self.metadata_tables: if other_table != table: - assert ( - repr(getattr(tables, f"{other_table}s").metadata_schema) == "" - ) + assert repr(getattr(tables, f"{other_table}s").metadata_schema) == "" # Check via tree-sequence API new_ts = tskit.TreeSequence.load_tables(tables) assert repr(getattr(new_ts.table_metadata_schemas, table)) == repr(schema) @@ -4027,7 +4027,7 @@ def test_deprecated_api_warnings(self): # Deprecated and will be removed t1 = self.get_tree() with pytest.warns(FutureWarning, match="Tree.tree_sequence.num_nodes"): - t1.num_nodes + _ = t1.num_nodes @pytest.mark.parametrize("skip", [False, True]) def test_seek_index(self, skip): @@ -5254,10 +5254,10 @@ def test_site_id_and_position_are_none(self): ts.site(None, position=None) def test_site_id_and_position_are_specified(self): + ts = self.get_example_ts_discrete_coordinates() with pytest.raises( TypeError, match="Only one of site id or position needs to be provided." ): - ts = self.get_example_ts_discrete_coordinates() ts.site(0, position=3) @@ -5366,7 +5366,6 @@ def test_multiroot_different_times(self, t, expected): (1, 2), (2, 2), (3, 2), - (3, 2), (4, 0), ], ) diff --git a/python/tests/test_ibd.py b/python/tests/test_ibd.py index 5e5c466a19..b5afe85cca 100644 --- a/python/tests/test_ibd.py +++ b/python/tests/test_ibd.py @@ -39,7 +39,7 @@ def ibd_segments( compare_lib=True, print_c=False, print_py=False, - squash=False + squash=False, ): """ Calculates IBD segments using Python and converts output to lists of segments. @@ -101,7 +101,7 @@ def naive_ibd_all_pairs(ts, samples=None): class TestIbdDefinition: @pytest.mark.skip("help") - @pytest.mark.xfail() + @pytest.mark.xfail @pytest.mark.parametrize("ts", get_example_tree_sequences(custom_max=15)) def test_all_pairs(self, ts): if ts.num_samples > 10: @@ -138,7 +138,7 @@ def test_wright_fisher_examples(self, N, T): class TestIbdImplementations: @pytest.mark.skip("help") - @pytest.mark.xfail() + @pytest.mark.xfail @pytest.mark.parametrize("ts", get_example_tree_sequences(custom_max=15)) def test_all_pairs(self, ts): # Automatically compares the two implementations @@ -629,9 +629,7 @@ def ts(self): return tskit.load_text(nodes=nodes, edges=edges, strict=False) def test_defaults(self): - ibd_segs = ibd_segments( - self.ts(), within=[1, 2], squash=True, compare_lib=False - ) + ibd_segs = ibd_segments(self.ts(), within=[1, 2], squash=True, compare_lib=False) true_segs = { (1, 2): [ tskit.IdentitySegment(0.0, 1.0, 4), @@ -776,7 +774,7 @@ def test_length(self): (1, 3): [tskit.IdentitySegment(0.3, 1, 4)], (2, 3): [tskit.IdentitySegment(0, 1, 5)], } - (ibd_segs, true_segs) + assert_ibd_equal(ibd_segs, true_segs) def test_input_within(self): ibd_segs = ibd_segments(self.ts(), within=[0, 1, 2]) diff --git a/python/tests/test_immutable_table_collection.py b/python/tests/test_immutable_table_collection.py index fc8f6d7e22..5c244fb1f5 100644 --- a/python/tests/test_immutable_table_collection.py +++ b/python/tests/test_immutable_table_collection.py @@ -8,7 +8,6 @@ import tests.tsutil as tsutil import tskit - pytestmark = pytest.mark.skipif( not getattr(_tskit, "HAS_NUMPY_2", False), reason="ImmutableTableCollection requires NumPy 2 runtime", @@ -154,9 +153,7 @@ def test_link_ancestors_parity(self, ts): class TestTablesParity: def test_table_name_map_and_lengths(self, ts): mutable, immutable = get_mutable_and_immutable(ts) - assert set(mutable.table_name_map.keys()) == set( - immutable.table_name_map.keys() - ) + assert set(mutable.table_name_map.keys()) == set(immutable.table_name_map.keys()) for name in mutable.table_name_map.keys(): mt = mutable.table_name_map[name] @@ -460,9 +457,7 @@ def test_table_attribute_assignment_raises(self, ts): for _, itab in immutable.table_name_map.items(): # Try setting a known column if any exist col_names = [ - c - for c in getattr(itab, "column_names", []) - if not c.endswith("_schema") + c for c in getattr(itab, "column_names", []) if not c.endswith("_schema") ] if col_names: col = col_names[0] @@ -520,9 +515,9 @@ def test_immutable_has_method_or_mutator(self, ts_fixture): continue missing.append(name) - assert ( - missing == [] - ), f"ImmutableTableCollection missing non-mutator methods: {missing}" + assert missing == [], ( + f"ImmutableTableCollection missing non-mutator methods: {missing}" + ) def test_immutable_tables_have_method_or_mutator(self, ts_fixture): tc = ts_fixture.dump_tables() @@ -553,9 +548,9 @@ def test_immutable_tables_have_method_or_mutator(self, ts_fixture): continue missing.append(name) - assert ( - missing == [] - ), f"Immutable {table_name} table missing non-mutator methods: {missing}" + assert missing == [], ( + f"Immutable {table_name} table missing non-mutator methods: {missing}" + ) class TestImmutableTimestampHandling: @@ -569,9 +564,7 @@ def test_assert_equals_ignore_timestamps_roundtrip(self): mutable_tables = ts.dump_tables() mutable_tables.provenances.clear() - mutable_tables.provenances.add_row( - record="{}", timestamp="2024-02-01T00:00:00Z" - ) + mutable_tables.provenances.add_row(record="{}", timestamp="2024-02-01T00:00:00Z") mutable_prov = mutable_tables.provenances with pytest.raises(AssertionError, match="timestamp"): @@ -594,9 +587,7 @@ def test_assert_equals_ignore_timestamps_other_difference(self): immutable = ts.tables mutable = ts.dump_tables() mutable.provenances.clear() - mutable.provenances.add_row( - record="different", timestamp="2024-02-01T00:00:00Z" - ) + mutable.provenances.add_row(record="different", timestamp="2024-02-01T00:00:00Z") immutable_msg = re.escape( "ImmutableProvenanceTable row 0 differs:\n" diff --git a/python/tests/test_intervals.py b/python/tests/test_intervals.py index e23f221e62..d09789fbf2 100644 --- a/python/tests/test_intervals.py +++ b/python/tests/test_intervals.py @@ -24,6 +24,7 @@ """ Test cases for the intervals module. """ + import decimal import fractions import gzip diff --git a/python/tests/test_ld_matrix.py b/python/tests/test_ld_matrix.py index f75b2b5ffd..4d6e47ddcc 100644 --- a/python/tests/test_ld_matrix.py +++ b/python/tests/test_ld_matrix.py @@ -22,14 +22,12 @@ """ Test cases for two-locus statistics """ + import contextlib import io -from collections.abc import Callable -from collections.abc import Generator +from collections.abc import Callable, Generator from dataclasses import dataclass -from itertools import combinations_with_replacement -from itertools import permutations -from itertools import product +from itertools import combinations_with_replacement, permutations, product from typing import Any import msprime @@ -900,9 +898,7 @@ def two_locus_count_stat( indexes = tskit.util.safe_np_int_cast(indexes, np.int32) idx_lens = {len(i) for i in indexes} if idx_lens != {2}: - raise ValueError( - f"Sample set indexes must be length 2, lengths: {idx_lens}" - ) + raise ValueError(f"Sample set indexes must be length 2, lengths: {idx_lens}") check_sample_stat_inputs(num_sample_sets, 2, result_dim, indexes) if mode == "site": if positions is not None: @@ -1840,9 +1836,7 @@ def __init__(self, ts, sample_sets, num_sample_sets, sample_index_map): for n in range(ts.num_nodes): for k in range(num_sample_sets): if sample_sets.contains(k, sample_index_map[n]): - self.node_samples.add( - (num_sample_sets * n) + k, sample_index_map[n] - ) + self.node_samples.add((num_sample_sets * n) + k, sample_index_map[n]) # these are empty for the uninitialized state (index = -1) self.edges_in = [] self.edges_out = [] diff --git a/python/tests/test_metadata.py b/python/tests/test_metadata.py index 316615cc12..09d3db4abd 100644 --- a/python/tests/test_metadata.py +++ b/python/tests/test_metadata.py @@ -23,6 +23,7 @@ """ Tests for metadata handling. """ + import collections import io import json diff --git a/python/tests/test_ms.py b/python/tests/test_ms.py index f98be6d876..7489b753da 100644 --- a/python/tests/test_ms.py +++ b/python/tests/test_ms.py @@ -26,6 +26,7 @@ is not used but an iterator over tree_sequences if the num_replicates argument is used. """ + import collections import itertools import os diff --git a/python/tests/test_parsimony.py b/python/tests/test_parsimony.py index 80cec45b96..99a524ea2f 100644 --- a/python/tests/test_parsimony.py +++ b/python/tests/test_parsimony.py @@ -22,6 +22,7 @@ """ Tests for the tree parsimony methods. """ + import dataclasses import io import itertools @@ -34,7 +35,6 @@ import tests.tsutil as tsutil import tskit - INF = np.inf @@ -384,9 +384,7 @@ def verify_infinite_sites(self, ts): assert ts.num_sites > 5 tree = ts.first() for variant in ts.variants(): - ancestral_state, transitions = sankoff_map_mutations( - tree, variant.genotypes - ) + ancestral_state, transitions = sankoff_map_mutations(tree, variant.genotypes) assert len(transitions) == 1 assert ancestral_state == 0 assert transitions[variant.site.mutations[0].node] == 1 diff --git a/python/tests/test_phylo_formats.py b/python/tests/test_phylo_formats.py index f5bb2ae993..7736712089 100644 --- a/python/tests/test_phylo_formats.py +++ b/python/tests/test_phylo_formats.py @@ -23,6 +23,7 @@ """ Tests for phylogenetics export functions, newick, nexus, FASTA etc. """ + import functools import io import textwrap @@ -938,7 +939,7 @@ def test_nexus_defaults(self): TREE t0^2 = [&R] (n0:3.25000000000000000,(n1:2.00000000000000000,n2:2.00000000000000000):1.25000000000000000); TREE t2^10 = [&R] (n1:2.00000000000000000,(n0:1.00000000000000000,n2:1.00000000000000000):1.00000000000000000); END; - """ # noqa: B950 + """ # noqa: E501 ) assert ts.as_nexus() == expected @@ -1009,7 +1010,7 @@ def test_nexus_defaults(self): TREE t0.00000000000000000^2.50000000000000000 = [&R] (n0:3,(n1:2,n2:2):1); TREE t2.50000000000000000^10.00000000000000000 = [&R] (n1:2,(n0:1,n2:1):1); END; - """ # noqa: B950 + """ # noqa: E501 ) assert ts.as_nexus() == expected @@ -1387,8 +1388,7 @@ def assert_missing_data_encoded(self, d): ) else: assert ( - a[j].state_denomination - == dendropy.StateAlphabet.AMBIGUOUS_STATE + a[j].state_denomination == dendropy.StateAlphabet.AMBIGUOUS_STATE ) def test_fasta(self): diff --git a/python/tests/test_provenance.py b/python/tests/test_provenance.py index 7b61308f8a..bb229e211d 100644 --- a/python/tests/test_provenance.py +++ b/python/tests/test_provenance.py @@ -23,6 +23,7 @@ """ Tests for the provenance information attached to tree sequences. """ + import json import os import platform diff --git a/python/tests/test_lowlevel.py b/python/tests/test_python_c.py similarity index 99% rename from python/tests/test_lowlevel.py rename to python/tests/test_python_c.py index 3021c25827..702010acf7 100644 --- a/python/tests/test_lowlevel.py +++ b/python/tests/test_python_c.py @@ -23,6 +23,7 @@ """ Test cases for the low level C interface to tskit. """ + import collections import gc import inspect @@ -38,7 +39,6 @@ import _tskit import tskit - NON_UTF8_STRING = "\ud861\udd37" @@ -1117,9 +1117,7 @@ def test_index(self): modify_indexes = tc.indexes modify_indexes["edge_insertion_order"] = np.arange(42, 42 + 18, dtype=np.int32) - modify_indexes["edge_removal_order"] = np.arange( - 4242, 4242 + 18, dtype=np.int32 - ) + modify_indexes["edge_removal_order"] = np.arange(4242, 4242 + 18, dtype=np.int32) tc.indexes = modify_indexes assert np.array_equal( tc.indexes["edge_insertion_order"], np.arange(42, 42 + 18, dtype=np.int32) @@ -1650,9 +1648,7 @@ def test_ld_matrix(self, stat_method_name): # happy path a = stat_method(ss_sizes, ss, row_sites, col_sites, None, None, "site") assert a.shape == (10, 10, 1) - a = stat_method( - ss_sizes, ss, row_sites_list, col_sites_list, None, None, "site" - ) + a = stat_method(ss_sizes, ss, row_sites_list, col_sites_list, None, None, "site") assert a.shape == (10, 10, 1) a = stat_method(ss_sizes, ss, None, None, None, None, "site") assert a.shape == (10, 10, 1) @@ -1740,14 +1736,10 @@ def test_ld_matrix(self, stat_method_name): with pytest.raises(tskit.LibraryError, match="TSK_ERR_STAT_UNSORTED_POSITIONS"): bad_pos = np.array([0.7, 0, 0.8], dtype=np.float64) stat_method(ss_sizes, ss, None, None, row_pos, bad_pos, "branch") - with pytest.raises( - tskit.LibraryError, match="TSK_ERR_STAT_DUPLICATE_POSITIONS" - ): + with pytest.raises(tskit.LibraryError, match="TSK_ERR_STAT_DUPLICATE_POSITIONS"): bad_pos = np.array([0.7, 0.7, 0.8], dtype=np.float64) stat_method(ss_sizes, ss, None, None, bad_pos, col_pos, "branch") - with pytest.raises( - tskit.LibraryError, match="TSK_ERR_STAT_DUPLICATE_POSITIONS" - ): + with pytest.raises(tskit.LibraryError, match="TSK_ERR_STAT_DUPLICATE_POSITIONS"): bad_pos = np.array([0.7, 0.7, 0.8], dtype=np.float64) stat_method(ss_sizes, ss, None, None, row_pos, bad_pos, "branch") with pytest.raises(tskit.LibraryError, match="TSK_ERR_POSITION_OUT_OF_BOUNDS"): @@ -1923,14 +1915,10 @@ def test_ld_matrix_multipop(self, stat_method_name): with pytest.raises(tskit.LibraryError, match="TSK_ERR_STAT_UNSORTED_POSITIONS"): bad_pos = np.array([0.7, 0, 0.8], dtype=np.float64) stat_method(ss_sizes, ss, indexes, None, None, row_pos, bad_pos, "branch") - with pytest.raises( - tskit.LibraryError, match="TSK_ERR_STAT_DUPLICATE_POSITIONS" - ): + with pytest.raises(tskit.LibraryError, match="TSK_ERR_STAT_DUPLICATE_POSITIONS"): bad_pos = np.array([0.7, 0.7, 0.8], dtype=np.float64) stat_method(ss_sizes, ss, indexes, None, None, bad_pos, col_pos, "branch") - with pytest.raises( - tskit.LibraryError, match="TSK_ERR_STAT_DUPLICATE_POSITIONS" - ): + with pytest.raises(tskit.LibraryError, match="TSK_ERR_STAT_DUPLICATE_POSITIONS"): bad_pos = np.array([0.7, 0.7, 0.8], dtype=np.float64) stat_method(ss_sizes, ss, indexes, None, None, row_pos, bad_pos, "branch") with pytest.raises(tskit.LibraryError, match="TSK_ERR_POSITION_OUT_OF_BOUNDS"): @@ -2101,9 +2089,7 @@ def test_load_tables_build_indexes(self): assert tables4.has_index() def test_clear_table(self, ts_fixture): - tables = _tskit.TableCollection( - sequence_length=ts_fixture.get_sequence_length() - ) + tables = _tskit.TableCollection(sequence_length=ts_fixture.get_sequence_length()) ts_fixture.ll_tree_sequence.dump_tables(tables) tables.clear() data_tables = [t for t in tskit.TABLE_NAMES if t != "provenances"] @@ -3318,9 +3304,7 @@ def test_window_errors(self): del params["windows"] for bad_array in ["asdf", None, [[[[]], [[]]]], np.zeros((10, 3, 4))]: with pytest.raises(ValueError): - ts.genetic_relatedness_vector( - windows=bad_array, mode="branch", **params - ) + ts.genetic_relatedness_vector(windows=bad_array, mode="branch", **params) for bad_windows in [[], [0]]: with pytest.raises(ValueError): @@ -3562,7 +3546,10 @@ def f(x): for bad_array in [[1, 1], range(10)]: with pytest.raises(ValueError): ts.general_stat( - W, lambda x: bad_array, 1, ts.get_breakpoints() # noqa:B023 + W, + lambda x: bad_array, # noqa:B023 + 1, + ts.get_breakpoints(), ) with pytest.raises(ValueError): ts.general_stat(W, lambda x: [1], 2, ts.get_breakpoints()) @@ -3571,7 +3558,10 @@ def f(x): for bad_array in [["sdf"], 0, "w4", None]: with pytest.raises(ValueError): ts.general_stat( - W, lambda x: bad_array, 1, ts.get_breakpoints() # noqa:B023 + W, + lambda x: bad_array, # noqa:B023 + 1, + ts.get_breakpoints(), ) @@ -3738,9 +3728,7 @@ def test_copy(self, isolated_as_missing, samples, alleles): alleles = variant.alleles site_id = variant.site_id variant.decode(1) - with pytest.raises( - tskit.LibraryError, match="Can't decode a copy of a variant" - ): + with pytest.raises(tskit.LibraryError, match="Can't decode a copy of a variant"): variant2.decode(1) assert site_id == variant2.site_id assert alleles == variant2.alleles diff --git a/python/tests/test_reference_sequence.py b/python/tests/test_reference_sequence.py index 99e849fd87..03297d398b 100644 --- a/python/tests/test_reference_sequence.py +++ b/python/tests/test_reference_sequence.py @@ -22,6 +22,7 @@ """ Tests for reference sequence support. """ + import pytest import tskit @@ -133,9 +134,7 @@ def test_fromdict_no_reference(self): def test_fromdict_all_values_empty(self): d = tskit.TableCollection(1).asdict() - d["reference_sequence"] = dict( - data="", url="", metadata_schema="", metadata=b"" - ) + d["reference_sequence"] = dict(data="", url="", metadata_schema="", metadata=b"") tables = tskit.TableCollection.fromdict(d) assert not tables.has_reference_sequence() diff --git a/python/tests/test_relatedness_vector.py b/python/tests/test_relatedness_vector.py index ebb74cf3a5..722e168759 100644 --- a/python/tests/test_relatedness_vector.py +++ b/python/tests/test_relatedness_vector.py @@ -22,6 +22,7 @@ """ Test cases for matrix-vector product stats """ + import msprime import numpy as np import pytest @@ -487,7 +488,6 @@ def check_relatedness_vector( class TestRelatednessVector: - def test_bad_weights(self): n = 5 ts = msprime.sim_ancestry( @@ -924,20 +924,19 @@ def assert_errors_bound(pca_res, D, U, w=None): Sigma = U @ np.diag(D) @ U.T Q = rs[:, :n] err = np.linalg.svd(Sigma - Q @ Q.T @ Sigma).S[0] - assert ( - err <= 5 * eps**2 - ), "Reconstruction error should be smaller than the bound squared." - assert ( - np.max(np.abs(ev - D[:n])) < 5 * eps - ), "Eigenvalue error should be smaller than error bound." + assert err <= 5 * eps**2, ( + "Reconstruction error should be smaller than the bound squared." + ) + assert np.max(np.abs(ev - D[:n])) < 5 * eps, ( + "Eigenvalue error should be smaller than error bound." + ) for k in range(n): - assert ( - np.sum((f[:, k] - U[:, k]) ** 2) < 5 * eps**2 / ev[-1] - ), "Factor error should be smaller than the bound squared." + assert np.sum((f[:, k] - U[:, k]) ** 2) < 5 * eps**2 / ev[-1], ( + "Factor error should be smaller than the bound squared." + ) class TestPCA: - def verify_error_est( self, ts, @@ -1257,12 +1256,8 @@ def test_num_iterations(self): range_sketch = np.linspace(0, 1, n * ploidy * (nc + no)).reshape( (n * ploidy, nc + no) ) - pca_res0 = ts.pca( - num_components=nc, range_sketch=range_sketch, num_iterations=5 - ) - pca_res1 = ts.pca( - num_components=nc, range_sketch=range_sketch, num_iterations=1 - ) + pca_res0 = ts.pca(num_components=nc, range_sketch=range_sketch, num_iterations=5) + pca_res1 = ts.pca(num_components=nc, range_sketch=range_sketch, num_iterations=1) for _ in range(4): pca_res1 = ts.pca( num_components=nc, range_sketch=pca_res1.range_sketch, num_iterations=1 diff --git a/python/tests/test_stats.py b/python/tests/test_stats.py index bfe2d270cf..98a59b7863 100644 --- a/python/tests/test_stats.py +++ b/python/tests/test_stats.py @@ -23,6 +23,7 @@ """ Test cases for stats calculations in tskit. """ + import contextlib import io diff --git a/python/tests/test_table_transforms.py b/python/tests/test_table_transforms.py index 5989d342f9..a3e4939fc3 100644 --- a/python/tests/test_table_transforms.py +++ b/python/tests/test_table_transforms.py @@ -22,6 +22,7 @@ """ Test cases for table transformation operations like trim(), decapitate, etc. """ + import decimal import fractions import io diff --git a/python/tests/test_tables.py b/python/tests/test_tables.py index 9fad08cbcd..b706381bfc 100644 --- a/python/tests/test_tables.py +++ b/python/tests/test_tables.py @@ -24,6 +24,7 @@ Test cases for the low-level tables used to transfer information between simulations and the tree sequence. """ + import dataclasses import io import json @@ -108,9 +109,7 @@ def make_transposed_input_data(self, num_rows): if len(data) == num_rows else ( bytes( - data[ - cols[f"{col}_offset"][j] : cols[f"{col}_offset"][j + 1] - ] + data[cols[f"{col}_offset"][j] : cols[f"{col}_offset"][j + 1]] ) if "metadata" in col else data[ @@ -576,9 +575,7 @@ def test_truncate(self): input_data[offset_col.name][: num_rows + 1], offset ) list_data = getattr(table, list_col.name) - assert np.array_equal( - list_data, input_data[list_col.name][: offset[-1]] - ) + assert np.array_equal(list_data, input_data[list_col.name][: offset[-1]]) used.add(offset_col.name) used.add(list_col.name) for name, data in input_data.items(): @@ -1102,8 +1099,7 @@ def test_round_trip_set_columns(self): del input_data["metadata_offset"] metadata_column = [self.metadata_example_data() for _ in range(num_rows)] encoded_metadata_column = [ - table.metadata_schema.validate_and_encode_row(r) - for r in metadata_column + table.metadata_schema.validate_and_encode_row(r) for r in metadata_column ] packed_metadata, metadata_offset = tskit.util.pack_bytes( encoded_metadata_column @@ -1236,9 +1232,7 @@ def verify_metadata_vector(self, table, key, dtype, default_value=9999): # does this more elegantly has_default = default_value != 9999 if has_default: - md_vec = table.metadata_vector( - key, default_value=default_value, dtype=dtype - ) + md_vec = table.metadata_vector(key, default_value=default_value, dtype=dtype) else: md_vec = table.metadata_vector(key, dtype=dtype) assert isinstance(md_vec, np.ndarray) @@ -1706,9 +1700,7 @@ class TestIndividualTable(*common_tests): def test_simple_example(self): t = tskit.IndividualTable() t.add_row(flags=0, location=[], parents=[], metadata=b"123") - t.add_row( - flags=1, location=(0, 1, 2, 3), parents=(4, 5, 6, 7), metadata=b"\xf0" - ) + t.add_row(flags=1, location=(0, 1, 2, 3), parents=(4, 5, 6, 7), metadata=b"\xf0") s = str(t) assert len(s) > 0 assert len(t) == 2 @@ -2219,16 +2211,14 @@ def test_assert_equals_ignore_timestamps_with_other_difference(self): with pytest.raises( AssertionError, match=re.escape( - "ProvenanceTable row 0 differs:\n" - "self.record={} other.record=different" + "ProvenanceTable row 0 differs:\nself.record={} other.record=different" ), ): t1.assert_equals(t2, ignore_timestamps=True) with pytest.raises( AssertionError, match=re.escape( - "ProvenanceTable row 0 differs:\n" - "self.record=different other.record={}" + "ProvenanceTable row 0 differs:\nself.record=different other.record={}" ), ): t2.assert_equals(t1, ignore_timestamps=True) @@ -4323,9 +4313,7 @@ def test_metadata(self, t1, t2): t2.metadata = {"foo": "bar"} with pytest.raises( AssertionError, - match=re.escape( - "Metadata differs: self=Test metadata other={'foo': 'bar'}" - ), + match=re.escape("Metadata differs: self=Test metadata other={'foo': 'bar'}"), ): t1.assert_equals(t2) t1.assert_equals(t2, ignore_metadata=True) @@ -5066,9 +5054,7 @@ def get_msprime_example(self, sample_size, T, seed): random_seed=seed, ) ts = tsutil.add_random_metadata(ts, seed) - ts = tsutil.insert_random_ploidy_individuals( - ts, max_ploidy=1, samples_only=True - ) + ts = tsutil.insert_random_ploidy_individuals(ts, max_ploidy=1, samples_only=True) return ts def get_wf_example(self, N, T, seed): @@ -5078,9 +5064,7 @@ def get_wf_example(self, N, T, seed): ts = ts.simplify() ts = tsutil.jukes_cantor(ts, 1, 10, seed=seed) ts = tsutil.add_random_metadata(ts, seed) - ts = tsutil.insert_random_ploidy_individuals( - ts, max_ploidy=2, samples_only=True - ) + ts = tsutil.insert_random_ploidy_individuals(ts, max_ploidy=2, samples_only=True) return ts def split_example(self, ts, T): @@ -5088,12 +5072,8 @@ def split_example(self, ts, T): shared_nodes = [n.id for n in ts.nodes() if n.time >= T] pop1 = list(ts.samples(population=0)) pop2 = list(ts.samples(population=1)) - tables1 = ts.simplify( - shared_nodes + pop1, record_provenance=False - ).dump_tables() - tables2 = ts.simplify( - shared_nodes + pop2, record_provenance=False - ).dump_tables() + tables1 = ts.simplify(shared_nodes + pop1, record_provenance=False).dump_tables() + tables2 = ts.simplify(shared_nodes + pop2, record_provenance=False).dump_tables() node_mapping = [ i if i < len(shared_nodes) else tskit.NULL for i in range(tables2.nodes.num_rows) @@ -5219,13 +5199,9 @@ def verify_union_consistency(self, tables, other, node_mapping): assert np.sum(i2.parents == tskit.NULL) == np.sum( iu.parents == tskit.NULL ) - md2 = [ - ts2.individual(p).metadata for p in i2.parents if p != tskit.NULL - ] + md2 = [ts2.individual(p).metadata for p in i2.parents if p != tskit.NULL] md2u = [indivs21[md] for md in md2] - mdu = [ - tsu.individual(p).metadata for p in iu.parents if p != tskit.NULL - ] + mdu = [tsu.individual(p).metadata for p in iu.parents if p != tskit.NULL] assert set(md2u) == set(mdu) else: # the individual *should* be there, but by a different name @@ -5324,9 +5300,7 @@ def test_provenance(self): ) tables_copy = tables.copy() tables.union(other, node_mapping) - uni_other_dict = json.loads(tables.provenances[-1].record)["parameters"][ - "other" - ] + uni_other_dict = json.loads(tables.provenances[-1].record)["parameters"]["other"] recovered_prov_table = tskit.ProvenanceTable() assert len(uni_other_dict["timestamp"]) == len(uni_other_dict["record"]) for timestamp, record in zip( diff --git a/python/tests/test_text_formats.py b/python/tests/test_text_formats.py index 92874af6fd..480217a381 100644 --- a/python/tests/test_text_formats.py +++ b/python/tests/test_text_formats.py @@ -22,6 +22,7 @@ """ Test cases for converting fam file to tskit """ + import dataclasses import tempfile from dataclasses import asdict diff --git a/python/tests/test_threads.py b/python/tests/test_threads.py index 6d835f5d01..62196b5404 100644 --- a/python/tests/test_threads.py +++ b/python/tests/test_threads.py @@ -23,6 +23,7 @@ """ Test cases for threading enabled aspects of the API. """ + import platform import threading @@ -58,9 +59,7 @@ class TestLdCalculatorReplicates: num_test_sites = 25 def get_tree_sequence(self): - ts = msprime.simulate( - 20, mutation_rate=10, recombination_rate=10, random_seed=8 - ) + ts = msprime.simulate(20, mutation_rate=10, recombination_rate=10, random_seed=8) return tsutil.subsample_sites(ts, self.num_test_sites) def test_get_r2_multiple_instances(self): @@ -142,9 +141,7 @@ def worker(thread_index, results): # Temporarily skipping these on Windows and OSX See # https://github.com/tskit-dev/tskit/issues/344 # https://github.com/tskit-dev/tskit/issues/1041 -@pytest.mark.skipif( - IS_WINDOWS or IS_OSX, reason="Can't test thread support on Windows." -) +@pytest.mark.skipif(IS_WINDOWS or IS_OSX, reason="Can't test thread support on Windows.") class TestTables: """ Tests to ensure that attempts to access tables in threads correctly diff --git a/python/tests/test_topology.py b/python/tests/test_topology.py index a69c62980a..f4801a7116 100644 --- a/python/tests/test_topology.py +++ b/python/tests/test_topology.py @@ -23,6 +23,7 @@ """ Test cases for the supported topological variations and operations. """ + import functools import io import itertools @@ -4481,9 +4482,7 @@ def verify_keep_input_roots(self, ts, samples): assert left <= position < right new_site = new_sites[position] # We assume the metadata contains a unique key for each mutation. - new_mutations = { - mut.metadata: mut for mut in new_site.mutations - } + new_mutations = {mut.metadata: mut for mut in new_site.mutations} # Just make sure the metadata is actually unique. assert len(new_mutations) == len(new_site.mutations) input_site = input_sites[position] @@ -4603,9 +4602,7 @@ def verify_nodes_unchanged(self, ts_in, resample_size=None, **kwargs): # Check that edges are identical to the normal simplify(), # with the normal "simplify" having altered IDs - simplified, node_map = ts.simplify( - samples=samples, map_nodes=True, **kwargs - ) + simplified, node_map = ts.simplify(samples=samples, map_nodes=True, **kwargs) simplified_edges = {e for e in simplified.tables.edges} filtered_edges = { e.replace(parent=node_map[e.parent], child=node_map[e.child]) @@ -4675,9 +4672,7 @@ def test_multiroot(self, resample_size): @pytest.mark.parametrize("resample_size", [None, 10]) def test_with_metadata(self, ts_fixture_for_simplify, resample_size): assert ts_fixture_for_simplify.num_nodes > 10 - self.verify_nodes_unchanged( - ts_fixture_for_simplify, resample_size=resample_size - ) + self.verify_nodes_unchanged(ts_fixture_for_simplify, resample_size=resample_size) @pytest.mark.parametrize("resample_size", [None, 7]) def test_complex_ts_with_unary(self, resample_size): @@ -5744,9 +5739,7 @@ def verify(self, ts): # except for the extra node and the details of the sib arrays. np.testing.assert_array_equal(tree_py.parent[:-1], tree_leg.parent) np.testing.assert_array_equal(tree_py.left_child[:-1], tree_leg.left_child) - np.testing.assert_array_equal( - tree_py.right_child[:-1], tree_leg.right_child - ) + np.testing.assert_array_equal(tree_py.right_child[:-1], tree_leg.right_child) # The sib arrays are identical except for root nodes. for u in range(ts.num_nodes): if u not in roots: @@ -6227,9 +6220,7 @@ def test_simple_recombination(self): self.verify(ts) def test_large_recombination(self): - ts = msprime.simulate( - 25, random_seed=12, recombination_rate=5, mutation_rate=15 - ) + ts = msprime.simulate(25, random_seed=12, recombination_rate=5, mutation_rate=15) self.verify(ts) def test_no_recombination(self): @@ -6664,9 +6655,7 @@ def test_hundred_intervals(self): self.do_keep_intervals(tables, intervals, simplify, rec_prov) def test_regular_intervals(self): - ts = msprime.simulate( - 3, random_seed=1234, recombination_rate=2, mutation_rate=2 - ) + ts = msprime.simulate(3, random_seed=1234, recombination_rate=2, mutation_rate=2) tables = ts.dump_tables() eps = 0.0125 for num_intervals in range(2, 10): @@ -6810,9 +6799,7 @@ def test_tables_single_tree_delete_middle(self): def test_ts_single_tree_keep_middle(self): ts = msprime.simulate(10, random_seed=2) ts_keep = ts.keep_intervals([[0.25, 0.5]], record_provenance=False) - ts_delete = ts.delete_intervals( - [[0, 0.25], [0.5, 1.0]], record_provenance=False - ) + ts_delete = ts.delete_intervals([[0, 0.25], [0.5, 1.0]], record_provenance=False) assert ts_keep == ts_delete def test_ts_single_tree_delete_middle(self): @@ -6990,23 +6977,17 @@ def test_ltrim_single_tree_tiny_left(self): self.verify_ltrim(ts, ts.ltrim()) def test_ltrim_many_trees(self): - ts = msprime.simulate( - 10, recombination_rate=10, mutation_rate=12, random_seed=2 - ) + ts = msprime.simulate(10, recombination_rate=10, mutation_rate=12, random_seed=2) ts = self.clear_left_mutate(ts, 0.5, 10) self.verify_ltrim(ts, ts.ltrim()) def test_ltrim_many_trees_left_min(self): - ts = msprime.simulate( - 10, recombination_rate=10, mutation_rate=12, random_seed=2 - ) + ts = msprime.simulate(10, recombination_rate=10, mutation_rate=12, random_seed=2) ts = self.clear_left_mutate(ts, sys.float_info.min, 10) self.verify_ltrim(ts, ts.ltrim()) def test_ltrim_many_trees_left_epsilon(self): - ts = msprime.simulate( - 10, recombination_rate=10, mutation_rate=12, random_seed=2 - ) + ts = msprime.simulate(10, recombination_rate=10, mutation_rate=12, random_seed=2) ts = self.clear_left_mutate(ts, sys.float_info.epsilon, 0) self.verify_ltrim(ts, ts.ltrim()) @@ -7052,23 +7033,17 @@ def test_rtrim_single_tree_tiny_left(self): self.verify_rtrim(ts, ts.rtrim()) def test_rtrim_many_trees(self): - ts = msprime.simulate( - 10, recombination_rate=10, mutation_rate=12, random_seed=2 - ) + ts = msprime.simulate(10, recombination_rate=10, mutation_rate=12, random_seed=2) ts = self.clear_right_mutate(ts, 0.5, 10) self.verify_rtrim(ts, ts.rtrim()) def test_rtrim_many_trees_left_min(self): - ts = msprime.simulate( - 10, recombination_rate=10, mutation_rate=12, random_seed=2 - ) + ts = msprime.simulate(10, recombination_rate=10, mutation_rate=12, random_seed=2) ts = self.clear_right_mutate(ts, sys.float_info.min, 10) self.verify_rtrim(ts, ts.rtrim()) def test_rtrim_many_trees_left_epsilon(self): - ts = msprime.simulate( - 10, recombination_rate=10, mutation_rate=12, random_seed=2 - ) + ts = msprime.simulate(10, recombination_rate=10, mutation_rate=12, random_seed=2) ts = self.clear_right_mutate(ts, sys.float_info.epsilon, 0) self.verify_rtrim(ts, ts.rtrim()) @@ -7084,9 +7059,7 @@ def test_rtrim_multiple_mutations(self): self.assertAlmostEqual(trimmed_ts.sequence_length, 0.5) assert trimmed_ts.num_sites == 2 assert trimmed_ts.num_mutations == 5 # We should have deleted 4 - assert ( - np.max(trimmed_ts.tables.edges.right) == trimmed_ts.tables.sequence_length - ) + assert np.max(trimmed_ts.tables.edges.right) == trimmed_ts.tables.sequence_length self.verify_rtrim(ts, trimmed_ts) def test_rtrim_migrations(self): @@ -7103,9 +7076,7 @@ def test_trim_multiple_mutations(self): assert trimmed_ts.num_mutations == 3 assert trimmed_ts.num_sites == 1 assert np.min(trimmed_ts.tables.edges.left) == 0 - assert ( - np.max(trimmed_ts.tables.edges.right) == trimmed_ts.tables.sequence_length - ) + assert np.max(trimmed_ts.tables.edges.right) == trimmed_ts.tables.sequence_length def test_trims_no_effect(self): # Deleting from middle should have no effect on any trim function @@ -7206,9 +7177,7 @@ def test_too_negative(self): def test_bad_seq_len(self): ts = tskit.Tree.generate_comb(2).tree_sequence - with pytest.raises( - tskit.LibraryError, match="TSK_ERR_RIGHT_GREATER_SEQ_LENGTH" - ): + with pytest.raises(tskit.LibraryError, match="TSK_ERR_RIGHT_GREATER_SEQ_LENGTH"): ts.shift(1, sequence_length=1) def test_reference_sequence(self): diff --git a/python/tests/test_tree_positioning.py b/python/tests/test_tree_positioning.py index e3e7e7a0be..d94426fac0 100644 --- a/python/tests/test_tree_positioning.py +++ b/python/tests/test_tree_positioning.py @@ -23,6 +23,7 @@ Tests for tree iterator schemes. Mostly used to develop the incremental iterator infrastructure. """ + import msprime import numpy as np import pytest diff --git a/python/tests/test_tree_stats.py b/python/tests/test_tree_stats.py index 39b6d70e34..da0fe83e7f 100644 --- a/python/tests/test_tree_stats.py +++ b/python/tests/test_tree_stats.py @@ -23,6 +23,7 @@ """ Test cases for generalized statistic computation. """ + import collections import contextlib import copy @@ -42,7 +43,6 @@ import tskit import tskit.exceptions as exceptions - np.random.seed(5) # Notes for refactoring: @@ -77,7 +77,7 @@ def cached_np(func): cache = {} def f(*args): - nonlocal cache # noqa: F824 + nonlocal cache key = tuple(x.tobytes() for x in args) if key not in cache: cache[key] = func(*args) @@ -191,8 +191,7 @@ def naive_branch_general_stat( s = sum(tree.branch_length(u) * f(x[u]) for u in tree.nodes()) else: s = sum( - tree.branch_length(u) * (f(x[u]) + f(total - x[u])) - for u in tree.nodes() + tree.branch_length(u) * (f(x[u]) + f(total - x[u])) for u in tree.nodes() ) sigma[tree.index] = s * tree.span if isinstance(windows, str) and windows == "trees": @@ -506,9 +505,7 @@ def node_summary(u): w_right = windows[window_index + 1] # Flush the contribution of all nodes to the current window. for u in range(ts.num_nodes): - result[window_index, u] += (w_right - last_update[u]) * current_values[ - u - ] + result[window_index, u] += (w_right - last_update[u]) * current_values[u] last_update[u] = w_right window_index += 1 @@ -1287,9 +1284,7 @@ def wrapped_summary_func(x): M = len(wrapped_summary_func(W[0])) sigma1 = ts.general_stat(W, wrapped_summary_func, M, windows, mode=self.mode) sigma2 = general_stat(ts, W, wrapped_summary_func, windows, mode=self.mode) - sigma3 = ts_method( - sample_sets, indexes=indexes, windows=windows, mode=self.mode - ) + sigma3 = ts_method(sample_sets, indexes=indexes, windows=windows, mode=self.mode) sigma4 = definition( ts, sample_sets, indexes=indexes, windows=windows, mode=self.mode ) @@ -1503,9 +1498,7 @@ def site_segregating_sites(ts, sample_sets, windows=None, span_normalise=True): site_positions = [x.position for x in ts.sites()] for i, X in enumerate(sample_sets): set_X = set(X) - X_index = np.where(np.fromiter((s in set_X for s in samples), dtype=bool))[ - 0 - ] + X_index = np.where(np.fromiter((s in set_X for s in samples), dtype=bool))[0] for k in range(ts.num_sites): if (site_positions[k] >= begin) and (site_positions[k] < end): num_alleles = len(set(haps[k, X_index])) @@ -1654,9 +1647,7 @@ def site_tajimas_d(ts, sample_sets, windows=None): S = 0 T = 0 set_X = set(X) - X_index = np.where(np.fromiter((s in set_X for s in samples), dtype=bool))[ - 0 - ] + X_index = np.where(np.fromiter((s in set_X for s in samples), dtype=bool))[0] for k in range(ts.num_sites): if (site_positions[k] >= begin) and (site_positions[k] < end): hX = haps[k, X_index] @@ -3647,8 +3638,7 @@ def node_f3(ts, sample_sets, indexes, windows=None, span_normalise=True): + (tA - nA) * (tA - nA - 1) * nB * nC ) SS[u] -= ( - nA * nC * (tA - nA) * (tB - nB) - + (tA - nA) * (tC - nC) * nA * nB + nA * nC * (tA - nA) * (tB - nB) + (tA - nA) * (tC - nC) * nA * nB ) S += SS * (min(end, t1.interval.right) - max(begin, t1.interval.left)) with suppress_division_by_zero_warning(): @@ -3834,12 +3824,10 @@ def node_f4(ts, sample_sets, indexes, windows=None, span_normalise=True): nD = t4.num_tracked_samples(u) # ac|bd - ad|bc SS[u] += ( - nA * nC * (tB - nB) * (tD - nD) - + (tA - nA) * (tC - nC) * nB * nD + nA * nC * (tB - nB) * (tD - nD) + (tA - nA) * (tC - nC) * nB * nD ) SS[u] -= ( - nA * nD * (tB - nB) * (tC - nC) - + (tA - nA) * (tD - nD) * nB * nC + nA * nD * (tB - nB) * (tC - nC) + (tA - nA) * (tD - nD) * nB * nC ) S += SS * (min(end, t1.interval.right) - max(begin, t1.interval.left)) with suppress_division_by_zero_warning(): @@ -3943,9 +3931,7 @@ class TestFold: def test_examples(self): A = np.arange(12) - Af = np.array( - [11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] - ) + Af = np.array([11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) assert np.all(foldit(A) == Af) @@ -4403,9 +4389,7 @@ def verify_single_sample_set(self, ts): self.assertArrayEqual(a1, a2) for windows in [None, (0, L), (0, L / 2, L)]: a1 = ts.allele_frequency_spectrum(mode=self.mode, windows=windows) - a2 = ts.allele_frequency_spectrum( - [samples], mode=self.mode, windows=windows - ) + a2 = ts.allele_frequency_spectrum([samples], mode=self.mode, windows=windows) self.assertArrayEqual(a1, a2) for polarised in [True, False]: a1 = ts.allele_frequency_spectrum(mode=self.mode, polarised=polarised) @@ -4427,9 +4411,7 @@ def verify_sample_sets(self, ts, sample_sets, windows, time_windows=None): # print(ts.draw_text()) # print("sample_sets = ", sample_sets) windows = ts.parse_windows(windows) - for span_normalise, polarised in itertools.product( - [True, False], [True, False] - ): + for span_normalise, polarised in itertools.product([True, False], [True, False]): try: _ = [len(x) for x in sample_sets] except TypeError: @@ -5271,9 +5253,7 @@ def branch_trait_covariance(ts, W, windows=None, span_normalise=True): SS = 0 for u in range(ts.num_nodes): tree_samples = set(tr.samples(u)) - below = np.fromiter( - (s in tree_samples for s in samples), dtype=bool - ) + below = np.fromiter((s in tree_samples for s in samples), dtype=bool) branch_length = tr.branch_length(u) SS += covsq(w, below) * branch_length S += SS * (min(end, tr.interval.right) - max(begin, tr.interval.left)) @@ -5309,9 +5289,7 @@ def node_trait_covariance(ts, W, windows=None, span_normalise=True): SS = np.zeros(ts.num_nodes) for u in range(ts.num_nodes): tree_samples = set(tr.samples(u)) - below = np.fromiter( - (s in tree_samples for s in samples), dtype=bool - ) + below = np.fromiter((s in tree_samples for s in samples), dtype=bool) SS[u] += covsq(w, below) S += SS * (min(end, tr.interval.right) - max(begin, tr.interval.left)) out[j, :, i] = S @@ -5488,9 +5466,7 @@ def branch_trait_correlation(ts, W, windows=None, span_normalise=True): SS = 0 for u in range(ts.num_nodes): tree_samples = set(tr.samples(u)) - below = np.fromiter( - (s in tree_samples for s in samples), dtype=bool - ) + below = np.fromiter((s in tree_samples for s in samples), dtype=bool) p = np.mean(below) if p > 0 and p < 1: branch_length = tr.branch_length(u) @@ -5532,9 +5508,7 @@ def node_trait_correlation(ts, W, windows=None, span_normalise=True): SS = np.zeros(ts.num_nodes) for u in range(ts.num_nodes): tree_samples = set(tr.samples(u)) - below = np.fromiter( - (s in tree_samples for s in samples), dtype=bool - ) + below = np.fromiter((s in tree_samples for s in samples), dtype=bool) p = np.mean(below) if p > 0 and p < 1: # SS[u] += sum(w[below])**2 / 2 @@ -5758,9 +5732,7 @@ def branch_trait_linear_model(ts, W, Z, windows=None, span_normalise=True): SS = 0 for u in range(ts.num_nodes): tree_samples = set(tr.samples(u)) - below = np.fromiter( - (s in tree_samples for s in samples), dtype=bool - ) + below = np.fromiter((s in tree_samples for s in samples), dtype=bool) branch_length = tr.branch_length(u) SS += linear_model(w, below, Z) * branch_length S += SS * (min(end, tr.interval.right) - max(begin, tr.interval.left)) @@ -5796,9 +5768,7 @@ def node_trait_linear_model(ts, W, Z, windows=None, span_normalise=True): SS = np.zeros(ts.num_nodes) for u in range(ts.num_nodes): tree_samples = set(tr.samples(u)) - below = np.fromiter( - (s in tree_samples for s in samples), dtype=bool - ) + below = np.fromiter((s in tree_samples for s in samples), dtype=bool) SS[u] += linear_model(w, below, Z) S += SS * (min(end, tr.interval.right) - max(begin, tr.interval.left)) out[j, :, i] = S @@ -6363,9 +6333,7 @@ def f(x): def f(x): return np.array( [ - float( - ((x[0] == 1) and (x[1] == 0)) or ((x[0] == 0) and (x[1] == 2)) - ) + float(((x[0] == 1) and (x[1] == 0)) or ((x[0] == 0) and (x[1] == 2))) / 2.0 ] ) @@ -6468,9 +6436,7 @@ def f(x): ) self.assertArrayAlmostEqual(py_r, ts_r) self.assertArrayAlmostEqual(true_cov, py_r * (geno_var[:, np.newaxis] ** 2)) - self.assertArrayAlmostEqual( - true_cor, ts_r * geno_var[:, np.newaxis] / trait_var - ) + self.assertArrayAlmostEqual(true_cor, ts_r * geno_var[:, np.newaxis] / trait_var) def test_case_odds_and_ends(self): # Tests having (a) the first site after the first window, and @@ -6800,9 +6766,7 @@ def f(x): def f(x): return np.array( [ - float( - ((x[0] == 1) and (x[1] == 0)) or ((x[0] == 0) and (x[1] == 2)) - ) + float(((x[0] == 1) and (x[1] == 0)) or ((x[0] == 0) and (x[1] == 2))) / 2.0 ] ) @@ -7128,9 +7092,7 @@ def verify_three_way_stat_windows(self, ts, method): self.assertArrayEqual(x, y) mode = "node" - x = method( - [A, B, C], indexes=[[0, 1, 2], [0, 2, 1]], windows=windows, mode=mode - ) + x = method([A, B, C], indexes=[[0, 1, 2], [0, 2, 1]], windows=windows, mode=mode) # Three windows, N nodes and 2 triples assert x.shape == (3, N, 2) @@ -7235,7 +7197,6 @@ def f_too_long(_): class TestTimeWindows: - def test_bad_time_windows(self, four_taxa_test_case): ts = four_taxa_test_case for bad_windows in ([0], [-1], [math.inf]): diff --git a/python/tests/test_util.py b/python/tests/test_util.py index 5d61df81b2..d58d834783 100644 --- a/python/tests/test_util.py +++ b/python/tests/test_util.py @@ -22,6 +22,7 @@ """ Tests for functions in util.py """ + import collections import itertools import math diff --git a/python/tests/test_utilities.py b/python/tests/test_utilities.py index ea107db22f..d4c1ee12c6 100644 --- a/python/tests/test_utilities.py +++ b/python/tests/test_utilities.py @@ -22,6 +22,7 @@ """ Tests for the various testing utilities. """ + import msprime import numpy as np import pytest @@ -59,10 +60,7 @@ def test_silent_mutations(self): ts = tsutil.jukes_cantor(ts, 5, 2, seed=2) num_silent = 0 for m in ts.mutations(): - if ( - m.parent != -1 - and ts.mutation(m.parent).derived_state == m.derived_state - ): + if m.parent != -1 and ts.mutation(m.parent).derived_state == m.derived_state: num_silent += 1 assert num_silent > 20 @@ -116,9 +114,7 @@ def test_n_5_mutations(self): def test_n_many_mutations(self): for n in range(10, 15): for num_mutations in range(0, n - 1): - ts = tsutil.caterpillar_tree( - n, num_sites=1, num_mutations=num_mutations - ) + ts = tsutil.caterpillar_tree(n, num_sites=1, num_mutations=num_mutations) self.verify(ts, n) assert ts.num_sites == 1 assert ts.num_mutations == num_mutations diff --git a/python/tests/test_vcf.py b/python/tests/test_vcf.py index 06ce4d771f..232d2b198e 100644 --- a/python/tests/test_vcf.py +++ b/python/tests/test_vcf.py @@ -23,6 +23,7 @@ """ Test cases for VCF output in tskit. """ + import contextlib import io import math @@ -190,9 +191,7 @@ class ExamplesMixin: def test_simple_infinite_sites_random_ploidy(self): ts = msprime.simulate(10, mutation_rate=1, random_seed=2) - ts = tsutil.insert_random_ploidy_individuals( - ts, min_ploidy=1, samples_only=True - ) + ts = tsutil.insert_random_ploidy_individuals(ts, min_ploidy=1, samples_only=True) assert ts.num_sites > 2 self.verify(ts) @@ -212,9 +211,7 @@ def test_simple_infinite_sites_ploidy_2_reversed_samples(self): def test_simple_jukes_cantor_random_ploidy(self): ts = msprime.simulate(10, random_seed=2) ts = tsutil.jukes_cantor(ts, num_sites=10, mu=1, seed=2) - ts = tsutil.insert_random_ploidy_individuals( - ts, min_ploidy=1, samples_only=True - ) + ts = tsutil.insert_random_ploidy_individuals(ts, min_ploidy=1, samples_only=True) self.verify(ts) def test_single_tree_multichar_mutations(self): @@ -570,13 +567,13 @@ def test_bad_length_ploidy(self): def test_bad_type(self): ts = msprime.simulate(2, mutation_rate=2, random_seed=1) with pytest.raises( - TypeError, match="sequence item 0: expected str instance," " NoneType found" + TypeError, match="sequence item 0: expected str instance, NoneType found" ): ts.write_vcf( io.StringIO(), individual_names=[None, "b"], allow_position_zero=True ) with pytest.raises( - TypeError, match="sequence item 0: expected str instance," " bytes found" + TypeError, match="sequence item 0: expected str instance, bytes found" ): ts.write_vcf( io.StringIO(), individual_names=[b"a", "b"], allow_position_zero=True @@ -630,8 +627,7 @@ def test_no_masks_triploid(self): 1\t6\t3\t0\t1\t.\tPASS\t.\tGT\t0|0|1""" expected = textwrap.dedent(s) assert ( - drop_header(self.ts().as_vcf(ploidy=3, allow_position_zero=True)) - == expected + drop_header(self.ts().as_vcf(ploidy=3, allow_position_zero=True)) == expected ) def test_site_0_masked(self): @@ -924,8 +920,7 @@ def test_individual_0(self): 1\t6\t3\t0\t1\t.\tPASS\t.\tGT\t0|1""" expected = textwrap.dedent(s) assert ( - drop_header(ts.as_vcf(individuals=[0], allow_position_zero=True)) - == expected + drop_header(ts.as_vcf(individuals=[0], allow_position_zero=True)) == expected ) def test_individual_1(self): @@ -938,8 +933,7 @@ def test_individual_1(self): 1\t6\t3\t0\t1\t.\tPASS\t.\tGT\t0""" expected = textwrap.dedent(s) assert ( - drop_header(ts.as_vcf(individuals=[1], allow_position_zero=True)) - == expected + drop_header(ts.as_vcf(individuals=[1], allow_position_zero=True)) == expected ) def test_reversed(self): diff --git a/python/tests/test_version.py b/python/tests/test_version.py index 65a8ab5b13..c04c59e207 100644 --- a/python/tests/test_version.py +++ b/python/tests/test_version.py @@ -22,6 +22,7 @@ """ Test python package versioning """ + from packaging.version import Version from tskit import _version diff --git a/python/tests/test_wright_fisher.py b/python/tests/test_wright_fisher.py index b2f58735ac..c062fa715a 100644 --- a/python/tests/test_wright_fisher.py +++ b/python/tests/test_wright_fisher.py @@ -23,6 +23,7 @@ """ Test various functions using messy tables output by a forwards-time simulator. """ + import itertools import random diff --git a/python/tests/tsutil.py b/python/tests/tsutil.py index a33b43f412..0037e06391 100644 --- a/python/tests/tsutil.py +++ b/python/tests/tsutil.py @@ -23,6 +23,7 @@ """ A collection of utilities to edit and construct tree sequences. """ + import collections import dataclasses import functools diff --git a/python/tskit/cli.py b/python/tskit/cli.py index 7b00e6888d..50e97d6784 100644 --- a/python/tskit/cli.py +++ b/python/tskit/cli.py @@ -24,6 +24,7 @@ """ Command line utilities for tskit. """ + import argparse import json import os diff --git a/python/tskit/combinatorics.py b/python/tskit/combinatorics.py index 058f6e633e..a1eba56e06 100644 --- a/python/tskit/combinatorics.py +++ b/python/tskit/combinatorics.py @@ -24,6 +24,7 @@ Module for ranking and unranking trees. Trees are considered only leaf-labelled and unordered, so order of children does not influence equality. """ + import collections import functools import heapq @@ -543,8 +544,7 @@ def __setitem__(self, sample_set_indexes, counter): def __iter__(self): raise TypeError( - "TopologyCounter object is not iterable, " - "iterate over '.topologies' instead" + "TopologyCounter object is not iterable, iterate over '.topologies' instead" ) @staticmethod diff --git a/python/tskit/drawing.py b/python/tskit/drawing.py index 357f1314c8..580d5e83c0 100644 --- a/python/tskit/drawing.py +++ b/python/tskit/drawing.py @@ -23,6 +23,7 @@ """ Module responsible for visualisations. """ + import collections import itertools import logging @@ -38,8 +39,7 @@ import tskit import tskit.util as util -from _tskit import NODE_IS_SAMPLE -from _tskit import NULL +from _tskit import NODE_IS_SAMPLE, NULL LEFT = "left" RIGHT = "right" @@ -322,9 +322,7 @@ def check_min_time(min_time, allow_numeric=True): if allow_numeric: is_numeric = isinstance(min_time, numbers.Real) if min_time not in ["tree", "ts"] and not is_numeric: - raise ValueError( - "min_time must be a numeric value or one of 'tree' or 'ts'" - ) + raise ValueError("min_time must be a numeric value or one of 'tree' or 'ts'") else: if min_time not in ["tree", "ts"]: raise ValueError("min_time must be 'tree' or 'ts'") @@ -385,7 +383,7 @@ def check_x_scale(x_scale): x_scales = ["physical", "treewise"] if x_scale not in x_scales: raise ValueError( - f"Unknown display x_scale '{x_scale}'. " f"Supported orders are {x_scales}" + f"Unknown display x_scale '{x_scale}'. Supported orders are {x_scales}" ) return x_scale @@ -529,9 +527,9 @@ def clip_ts(ts, x_min, x_max, max_num_trees=None): num_start_trees = max_num_trees // 2 + (1 if max_num_trees % 2 else 0) num_end_trees = max_num_trees // 2 assert num_start_trees + num_end_trees == max_num_trees - tree_status[ - (first_tree + num_start_trees) : (last_tree - num_end_trees + 1) - ] = (OMIT | OMIT_MIDDLE) + tree_status[(first_tree + num_start_trees) : (last_tree - num_end_trees + 1)] = ( + OMIT | OMIT_MIDDLE + ) return ts, tree_status, offsets @@ -586,9 +584,7 @@ def edge_and_sample_nodes(ts, omit_regions=None): for left, right in use_regions: used_edges = edges[np.logical_and(edges.left >= left, edges.right < right)] ids = np.concatenate((ids, used_edges.child, used_edges.parent)) - return np.unique( - np.concatenate((ids, np.where(ts.nodes_flags & NODE_IS_SAMPLE)[0])) - ) + return np.unique(np.concatenate((ids, np.where(ts.nodes_flags & NODE_IS_SAMPLE)[0]))) def _postorder_tracked_node_traversal(tree, root, collapse_tracked, key_dict=None): @@ -618,8 +614,7 @@ def _postorder_tracked_node_traversal(tree, root, collapse_tracked, key_dict=Non elif ( collapse_tracked is not None and tree.num_children(u) != 1 - and tree.num_tracked_samples(u) - >= collapse_tracked * tree.num_samples(u) + and tree.num_tracked_samples(u) >= collapse_tracked * tree.num_samples(u) ): yield u else: @@ -1068,9 +1063,7 @@ def set_spacing(self, top=0, left=0, bottom=0, right=0): right = self.y_axis_offset self.plotbox.set_padding(top, left, bottom, right) if self.debug_box: - self.root_groups["debug"] = self.dwg_base.add( - self.drawing.g(class_="debug") - ) + self.root_groups["debug"] = self.dwg_base.add(self.drawing.g(class_="debug")) self.plotbox.draw(self.drawing, self.root_groups["debug"]) def get_axes(self): @@ -1118,9 +1111,7 @@ def draw_x_axis( x2 = self.x_transform(right) y = self.plotbox.max_y - self.x_axis_offset region = regions_group.add(dwg.g(class_=f"r{i}")) - region.add( - dwg.rect((x1, y), (x2 - x1, self.line_height), class_="r{i}") - ) + region.add(dwg.rect((x1, y), (x2 - x1, self.line_height), class_="r{i}")) self.add_text_in_group( label, region, @@ -1611,8 +1602,8 @@ def draw_x_axis( # For a treewise plot, the only time the x_transform is used is to apply # to tick positions, so simply use positions 0..num_used_breaks for the # positions, and a simple transform - self.x_transform = ( - lambda x: self.plotbox.left + x / (len(breaks) - 1) * self.plotbox.width + self.x_transform = lambda x: ( + self.plotbox.left + x / (len(breaks) - 1) * self.plotbox.width ) tick_positions = np.arange(len(breaks)) @@ -1787,9 +1778,7 @@ def __init__( mutation_nodes = mut_t.node[focal_mutations] mutation_positions = ts.tables.sites.position[mut_t.site][focal_mutations] mutation_ids = np.arange(ts.num_mutations, dtype=int)[focal_mutations] - for m_id, node, pos in zip( - mutation_ids, mutation_nodes, mutation_positions - ): + for m_id, node, pos in zip(mutation_ids, mutation_nodes, mutation_positions): curr_edge = node_edges[node] if curr_edge >= 0: if ( @@ -1975,9 +1964,7 @@ def assign_y_coordinates( # In pathological cases, all the nodes are at the same time if max_time == min_time: max_time = min_time + 1 - self.node_height = { - u: depth[node_time[u]] for u in self.node_x_coord.keys() - } + self.node_height = {u: depth[node_time[u]] for u in self.node_x_coord.keys()} for u in self.node_mutations.keys(): if u in self.node_height: parent = self.tree.parent(u) @@ -2260,9 +2247,7 @@ def draw_tree(self): root_branch_l = self.min_root_branch_plot_length if root_branch_l > 0: if len(self.node_mutations[u]) > 0: - mtop = self.timescaling.transform( - self.node_mutations[u][0].time - ) + mtop = self.timescaling.transform(self.node_mutations[u][0].time) root_branch_l = max(root_branch_l, pu[1] - mtop) dx, dy = 0, -root_branch_l draw_edge_above_node = True @@ -2283,7 +2268,7 @@ def draw_tree(self): dy = self.timescaling.transform(mutation.time) - pu[1] mutation_id = mutation.id + self.offsets.mutation mutation_class = ( - f"mut m{mutation_id} " f"s{mutation.site + self.offsets.site}" + f"mut m{mutation_id} s{mutation.site + self.offsets.site}" ) # Use the real mutation ID here, since we are referencing into the ts if util.is_unknown_time(self.ts.mutation(mutation.id).time): @@ -2318,9 +2303,7 @@ def draw_tree(self): else: symbol = curr_svg_group.add(dwg.circle(**self.node_attrs[u])) multi_samples = None - if ( - is_tip and tree.num_samples(u) > 1 - ): # Multi-sample tip => trapezium shape + if is_tip and tree.num_samples(u) > 1: # Multi-sample tip => trapezium shape multi_samples = tree.num_samples(u) trapezium_attrs = self.node_attrs[u].copy() # Remove the shape-styling attributes diff --git a/python/tskit/exceptions.py b/python/tskit/exceptions.py index 087c7cbec9..cad7ea0153 100644 --- a/python/tskit/exceptions.py +++ b/python/tskit/exceptions.py @@ -23,13 +23,14 @@ """ Exceptions defined in tskit. """ -from _tskit import FileFormatError # noqa: F401 -from _tskit import IdentityPairsNotStoredError # noqa: F401 -from _tskit import IdentitySegmentsNotStoredError # noqa: F401 -from _tskit import LibraryError # noqa: F401 -from _tskit import TskitException # noqa: F401 -from _tskit import VersionTooNewError # noqa: F401 -from _tskit import VersionTooOldError # noqa: F401 + +from _tskit import FileFormatError # noqa F401 +from _tskit import IdentityPairsNotStoredError # noqa F401 +from _tskit import IdentitySegmentsNotStoredError # noqa F401 +from _tskit import LibraryError # noqa F401 +from _tskit import TskitException +from _tskit import VersionTooNewError # noqa F401 +from _tskit import VersionTooOldError # noqa F401 class DuplicatePositionsError(TskitException): diff --git a/python/tskit/genotypes.py b/python/tskit/genotypes.py index 1c553830d0..8e0a0c4f29 100644 --- a/python/tskit/genotypes.py +++ b/python/tskit/genotypes.py @@ -323,9 +323,7 @@ def frequencies(self, remove_missing=None) -> dict[str, float]: if remove_missing: total -= self.num_missing if total == 0: - logging.warning( - "No non-missing samples at this site, frequencies undefined" - ) + logging.warning("No non-missing samples at this site, frequencies undefined") return { allele: count / total if total > 0 else np.nan for allele, count in self.counts().items() @@ -353,7 +351,7 @@ def __str__(self) -> str: + [ [ f"Samples with allele " - f"""{'missing' if k is None else "'" + k + "'"}""", + f"""{"missing" if k is None else "'" + k + "'"}""", f"{util.format_number(counts[k], sep=',')} " f"({util.format_number(freqs[k] * 100, 2, sep=',')}%)", ] diff --git a/python/tskit/intervals.py b/python/tskit/intervals.py index 3f08e99016..fa610b6974 100644 --- a/python/tskit/intervals.py +++ b/python/tskit/intervals.py @@ -24,6 +24,7 @@ """ Utilities for working with intervals and interval maps. """ + from __future__ import annotations import collections.abc diff --git a/python/tskit/jit/numba.py b/python/tskit/jit/numba.py index 40534431d1..e33b488aaa 100644 --- a/python/tskit/jit/numba.py +++ b/python/tskit/jit/numba.py @@ -623,9 +623,7 @@ def jitwrap(ts): """ max_ancestral_length = max(1, max(map(len, ts.sites_ancestral_state), default=1)) max_derived_length = max(1, max(map(len, ts.mutations_derived_state), default=1)) - max_inherited_length = max( - 1, max(map(len, ts.mutations_inherited_state), default=1) - ) + max_inherited_length = max(1, max(map(len, ts.mutations_inherited_state), default=1)) JittedTreeSequence = _jitwrap( max_ancestral_length, max_derived_length, max_inherited_length diff --git a/python/tskit/metadata.py b/python/tskit/metadata.py index 4986e04cf9..b1e0768b9b 100644 --- a/python/tskit/metadata.py +++ b/python/tskit/metadata.py @@ -22,6 +22,7 @@ """ Classes for metadata decoding, encoding and validation """ + from __future__ import annotations import abc @@ -89,11 +90,11 @@ def __init__(self, schema: Mapping[str, Any]) -> None: raise NotImplementedError # pragma: no cover @classmethod - def modify_schema(self, schema: Mapping) -> Mapping: + def modify_schema(cls, schema: Mapping) -> Mapping: return schema @classmethod - def is_schema_trivial(self, schema: Mapping) -> bool: + def is_schema_trivial(cls, schema: Mapping) -> bool: return False @abc.abstractmethod @@ -126,6 +127,7 @@ def register_metadata_codec( class JSONCodec(AbstractMetadataCodec): + @staticmethod def default_validator(validator, types, instance, schema): # For json codec defaults must be at the top level if validator.is_type(instance, "object"): @@ -142,7 +144,7 @@ def default_validator(validator, types, instance, schema): ) @classmethod - def is_schema_trivial(self, schema: Mapping) -> bool: + def is_schema_trivial(cls, schema: Mapping) -> bool: return len(schema.get("properties", {})) == 0 def __init__(self, schema: Mapping[str, Any]) -> None: @@ -266,9 +268,7 @@ def array_length_validator(validator, types, instance, schema): def required_validator(validator, required, instance, schema): # Do the normal validation try: - yield from jsonschema._validators.required( - validator, required, instance, schema - ) + yield from jsonschema._validators.required(validator, required, instance, schema) except AttributeError: # Needed since jsonschema==4.19.1 yield from jsonschema._keywords.required(validator, required, instance, schema) @@ -277,7 +277,7 @@ def required_validator(validator, required, instance, schema): for prop, sub_schema in instance["properties"].items(): if prop not in instance["required"] and "default" not in sub_schema: yield jsonschema.ValidationError( - f"Optional property '{prop}' must have" f" a default value" + f"Optional property '{prop}' must have a default value" ) @@ -460,8 +460,7 @@ def decode_object_or_null(buffer): else: buffer = iter(buffer) return { - key: sub_decoder(buffer) - for key, sub_decoder in sub_decoders.items() + key: sub_decoder(buffer) for key, sub_decoder in sub_decoders.items() } return decode_object_or_null @@ -1040,7 +1039,7 @@ def assert_equals(self, other: MetadataProvider): ) if self.metadata != other.metadata: raise AssertionError( - f"Metadata differs: self={self.metadata} " f"other={other.metadata}" + f"Metadata differs: self={self.metadata} other={other.metadata}" ) diff --git a/python/tskit/provenance.py b/python/tskit/provenance.py index 2c24165ae9..0e5dd5d0e2 100644 --- a/python/tskit/provenance.py +++ b/python/tskit/provenance.py @@ -24,6 +24,7 @@ Common provenance methods used to determine the state and versions of various dependencies and the OS. """ + import json import os.path import platform @@ -39,6 +40,7 @@ import _tskit import tskit.exceptions as exceptions + from . import _version __version__ = _version.tskit_version diff --git a/python/tskit/stats.py b/python/tskit/stats.py index f7212e819a..16123db012 100644 --- a/python/tskit/stats.py +++ b/python/tskit/stats.py @@ -22,6 +22,7 @@ """ Module responsible for computing various statistics on tree sequences. """ + import sys import threading diff --git a/python/tskit/tables.py b/python/tskit/tables.py index f3db1c8a5a..40523248f8 100644 --- a/python/tskit/tables.py +++ b/python/tskit/tables.py @@ -24,6 +24,7 @@ """ Tree sequence IO via the tables API. """ + import collections import dataclasses import datetime @@ -261,9 +262,7 @@ def __eq__(self, other): and self.metadata == other.metadata and ( self.time == other.time - or ( - util.is_unknown_time(self.time) and util.is_unknown_time(other.time) - ) + or (util.is_unknown_time(self.time) and util.is_unknown_time(other.time)) ) ) @@ -376,9 +375,7 @@ def nbytes(self) -> int: nbytes += sum(col.nbytes for col in d.values()) return nbytes - def _equals_internal( - self, other, ignore_metadata=False, *, ignore_timestamps=False - ): + def _equals_internal(self, other, ignore_metadata=False, *, ignore_timestamps=False): if self is other: return True @@ -576,9 +573,7 @@ def _text_header_and_rows(self, limit=None): elif col in ["location", "parents"]: # Array columns - join with commas if col == "parents": - formatted_values.append( - ", ".join([f"{p:,}" for p in value]) - ) + formatted_values.append(", ".join([f"{p:,}" for p in value])) else: formatted_values.append(", ".join(map(str, value))) elif col in float_columns: @@ -3018,12 +3013,11 @@ def assert_equals(self, other, ignore_metadata=False): if self.data != other.data: raise AssertionError( - f"Reference sequence data differs: self={self.data} " - f"other={other.data}" + f"Reference sequence data differs: self={self.data} other={other.data}" ) if self.url != other.url: raise AssertionError( - f"Reference sequence url differs: self={self.url} " f"other={other.url}" + f"Reference sequence url differs: self={self.url} other={other.url}" ) @property @@ -3494,8 +3488,8 @@ def __setstate__(self, state): self.__init__() self._ll_tables.fromdict(state) - @classmethod - def fromdict(self, tables_dict): + @staticmethod + def fromdict(tables_dict): ll_tc = _tskit.TableCollection() ll_tc.fromdict(tables_dict) return TableCollection(ll_tables=ll_tc) @@ -4018,9 +4012,7 @@ def keep_intervals(self, intervals, simplify=True, record_provenance=True): self.sites.position >= s, self.sites.position < e ) keep_sites = np.logical_or(keep_sites, curr_keep_sites) - keep_edges = np.logical_not( - np.logical_or(edges.right <= s, edges.left >= e) - ) + keep_edges = np.logical_not(np.logical_or(edges.right <= s, edges.left >= e)) metadata, metadata_offset = keep_with_offset( keep_edges, edges.metadata, edges.metadata_offset ) diff --git a/python/tskit/text_formats.py b/python/tskit/text_formats.py index e44668d6ad..d8a89d0be6 100644 --- a/python/tskit/text_formats.py +++ b/python/tskit/text_formats.py @@ -22,6 +22,7 @@ """ Module responsible for working with text format data. """ + import base64 import numpy as np @@ -73,7 +74,7 @@ def parse_fam(fam_file): ) for plink_fid, plink_iid, pat, mat, sex in individuals: sex = int(sex) - if not (sex in range(3)): + if sex not in range(3): raise ValueError( "Sex must be one of the following: 0 (unknown), 1 (male), 2 (female)" ) @@ -326,9 +327,7 @@ def dump_text( print("position", "ancestral_state", "metadata", sep="\t", file=sites) for site in ts.sites(): metadata = text_metadata(base64_metadata, encoding, site) - row = ( - "{position:.{precision}f}\t" "{ancestral_state}\t" "{metadata}" - ).format( + row = ("{position:.{precision}f}\t{ancestral_state}\t{metadata}").format( precision=precision, position=site.position, ancestral_state=site.ancestral_state, @@ -351,12 +350,7 @@ def dump_text( for mutation in site.mutations: metadata = text_metadata(base64_metadata, encoding, mutation) row = ( - "{site}\t" - "{node}\t" - "{time}\t" - "{derived_state}\t" - "{parent}\t" - "{metadata}" + "{site}\t{node}\t{time}\t{derived_state}\t{parent}\t{metadata}" ).format( site=mutation.site, node=mutation.node, @@ -385,9 +379,7 @@ def dump_text( metadata = text_metadata(base64_metadata, encoding, individual) location = ",".join(map(str, individual.location)) parents = ",".join(map(str, individual.parents)) - row = ( - "{id}\t" "{flags}\t" "{location}\t" "{parents}\t" "{metadata}" - ).format( + row = ("{id}\t{flags}\t{location}\t{parents}\t{metadata}").format( id=individual.id, flags=individual.flags, location=location, @@ -400,7 +392,7 @@ def dump_text( print("id", "metadata", sep="\t", file=populations) for population in ts.populations(): metadata = text_metadata(base64_metadata, encoding, population) - row = ("{id}\t" "{metadata}").format(id=population.id, metadata=metadata) + row = ("{id}\t{metadata}").format(id=population.id, metadata=metadata) print(row, file=populations) if migrations is not None: @@ -418,13 +410,7 @@ def dump_text( for migration in ts.migrations(): metadata = text_metadata(base64_metadata, encoding, migration) row = ( - "{left}\t" - "{right}\t" - "{node}\t" - "{source}\t" - "{dest}\t" - "{time}\t" - "{metadata}\t" + "{left}\t{right}\t{node}\t{source}\t{dest}\t{time}\t{metadata}\t" ).format( left=migration.left, right=migration.right, @@ -439,7 +425,7 @@ def dump_text( if provenances is not None: print("id", "timestamp", "record", sep="\t", file=provenances) for provenance in ts.provenances(): - row = ("{id}\t" "{timestamp}\t" "{record}\t").format( + row = ("{id}\t{timestamp}\t{record}\t").format( id=provenance.id, timestamp=provenance.timestamp, record=provenance.record, diff --git a/python/tskit/trees.py b/python/tskit/trees.py index 38433ac6e7..45d2da59e0 100644 --- a/python/tskit/trees.py +++ b/python/tskit/trees.py @@ -23,6 +23,7 @@ """ Module responsible for managing trees and tree sequences. """ + from __future__ import annotations import base64 @@ -37,8 +38,7 @@ import numbers import warnings from dataclasses import dataclass -from typing import Any -from typing import NamedTuple +from typing import Any, NamedTuple import numpy as np @@ -52,9 +52,7 @@ import tskit.text_formats as text_formats import tskit.util as util import tskit.vcf as vcf -from tskit import NODE_IS_SAMPLE -from tskit import NULL -from tskit import UNKNOWN_TIME +from tskit import NODE_IS_SAMPLE, NULL, UNKNOWN_TIME LEGACY_MS_LABELS = "legacy_ms" @@ -522,9 +520,7 @@ def __eq__(self, other): and self.metadata == other.metadata and ( self.time == other.time - or ( - util.is_unknown_time(self.time) and util.is_unknown_time(other.time) - ) + or (util.is_unknown_time(self.time) and util.is_unknown_time(other.time)) ) ) @@ -700,8 +696,7 @@ def __init__( options = 0 if sample_counts is not None: warnings.warn( - "The sample_counts option is not supported since 0.2.4 " - "and is ignored", + "The sample_counts option is not supported since 0.2.4 and is ignored", RuntimeWarning, stacklevel=4, ) @@ -4867,10 +4862,7 @@ def edgesets(self): children[edge.parent].add(edge.child) # Update the active edgesets for edge in itertools.chain(edges_out, edges_in): - if ( - len(children[edge.parent]) > 0 - and edge.parent not in active_edgesets - ): + if len(children[edge.parent]) > 0 and edge.parent not in active_edgesets: active_edgesets[edge.parent] = Edgeset(left, right, edge.parent, []) for parent in active_edgesets.keys(): @@ -6953,7 +6945,7 @@ def to_macs(self): bytes_genotypes[:] = lookup[variant.genotypes] genotypes = bytes_genotypes.tobytes().decode() output.append( - f"SITE:\t{variant.index}\t{variant.position / m}\t0.0\t" f"{genotypes}" + f"SITE:\t{variant.index}\t{variant.position / m}\t0.0\t{genotypes}" ) return "\n".join(output) + "\n" @@ -7304,9 +7296,7 @@ def concatenate( if add_populations is None: add_populations = True if len(node_mappings) != len(args): - raise ValueError( - "You must provide the same number of node_mappings as args" - ) + raise ValueError("You must provide the same number of node_mappings as args") samples = self.samples() tables = self.dump_tables() @@ -8053,7 +8043,8 @@ def f(x): .. code-block:: python - ts.sample_count_stat([A, B], f, 1, windows="sites", polarised=False, mode="site") + ts.sample_count_stat( + [A, B], f, 1, windows="sites", polarised=False, mode="site") would compute, for each site, the product of the derived allele frequencies in the two sample sets, in a (num sites, 1) array. If @@ -8083,7 +8074,7 @@ def f(x): window (defaults to True). :param bool strict: Whether to check that f(0) and f(total weight) are zero. :return: A ndarray with shape equal to (num windows, num statistics). - """ # noqa: B950 + """ # helper function for common case where weights are indicators of sample sets for U in sample_sets: if len(U) != len(set(U)): @@ -8337,8 +8328,9 @@ def __k_way_two_locus_sample_set_stat( drop_dimension = True if len(indexes.shape) != 2 or indexes.shape[1] != k: raise ValueError( - "Indexes must be convertable to a 2D numpy array with {} " - "columns".format(k) + "Indexes must be convertable to a 2D numpy array with {} columns".format( + k + ) ) result = ll_method( sample_set_sizes, @@ -8392,8 +8384,9 @@ def __k_way_sample_set_stat( drop_dimension = True if len(indexes.shape) != 2 or indexes.shape[1] != k: raise ValueError( - "Indexes must be convertable to a 2D numpy array with {} " - "columns".format(k) + "Indexes must be convertable to a 2D numpy array with {} columns".format( + k + ) ) stat = self.__run_windowed_stat( windows, @@ -8439,8 +8432,9 @@ def __k_way_weighted_stat( drop_dimension = True if len(indexes.shape) != 2 or indexes.shape[1] != k: raise ValueError( - "Indexes must be convertable to a 2D numpy array with {} " - "columns".format(k) + "Indexes must be convertable to a 2D numpy array with {} columns".format( + k + ) ) stat = self.__run_windowed_stat( windows, @@ -9141,9 +9135,7 @@ def genetic_relatedness_weighted( :return: A ndarray with shape equal to (num windows, num statistics). """ if len(W) != self.num_samples: - raise ValueError( - "First trait dimension must be equal to number of samples." - ) + raise ValueError("First trait dimension must be equal to number of samples.") return self.__k_way_weighted_stat( self._ll_tree_sequence.genetic_relatedness_weighted, 2, @@ -9395,9 +9387,9 @@ def pca( if time_windows is None: tree_sequence_low, tree_sequence_high = None, self else: - assert ( - time_windows[0] < time_windows[1] - ), "The second argument should be larger." + assert time_windows[0] < time_windows[1], ( + "The second argument should be larger." + ) tree_sequence_low, tree_sequence_high = ( self.decapitate(time_windows[0]), self.decapitate(time_windows[1]), @@ -9465,9 +9457,7 @@ def _rand_pow_range_finder( """ Algorithm 9 in https://arxiv.org/pdf/2002.01387 """ - assert ( - num_vectors >= rank > 0 - ), "num_vectors should not be smaller than rank" + assert num_vectors >= rank > 0, "num_vectors should not be smaller than rank" for _ in range(depth): Q = np.linalg.qr(Q)[0] Q = operator(Q) @@ -9613,9 +9603,7 @@ def trait_covariance(self, W, windows=None, mode="site", span_normalise=True): If windows=None and W is a single column, a numpy scalar is returned. """ if W.shape[0] != self.num_samples: - raise ValueError( - "First trait dimension must be equal to number of samples." - ) + raise ValueError("First trait dimension must be equal to number of samples.") return self.__run_windowed_stat( windows, self._ll_tree_sequence.trait_covariance, @@ -9679,9 +9667,7 @@ def trait_correlation(self, W, windows=None, mode="site", span_normalise=True): If windows=None and W is a single column, a numpy scalar is returned. """ if W.shape[0] != self.num_samples: - raise ValueError( - "First trait dimension must be equal to number of samples." - ) + raise ValueError("First trait dimension must be equal to number of samples.") sds = np.std(W, axis=0) if np.any(sds == 0): raise ValueError( @@ -9772,9 +9758,7 @@ def trait_linear_model( If windows=None and W is a single column, a numpy scalar is returned. """ if W.shape[0] != self.num_samples: - raise ValueError( - "First trait dimension must be equal to number of samples." - ) + raise ValueError("First trait dimension must be equal to number of samples.") if Z is None: Z = np.ones((self.num_samples, 1)) else: @@ -10023,11 +10007,7 @@ def tjd_func(sample_set_sizes, flattened, **kwargs): g = np.array([np.sum(1 / np.arange(1, nn) ** 2) for nn in n]) with np.errstate(invalid="ignore", divide="ignore"): a = (n + 1) / (3 * (n - 1) * h) - 1 / h**2 - b = ( - 2 * (n**2 + n + 3) / (9 * n * (n - 1)) - - (n + 2) / (h * n) - + g / h**2 - ) + b = 2 * (n**2 + n + 3) / (9 * n * (n - 1)) - (n + 2) / (h * n) + g / h**2 D = (T - S / h) / np.sqrt(a * S + (b / (h**2 + g)) * S * (S - 1)) return D @@ -10556,9 +10536,7 @@ def count_topologies(self, sample_sets=None): internal samples. """ if sample_sets is None: - sample_sets = [ - self.samples(population=pop.id) for pop in self.populations() - ] + sample_sets = [self.samples(population=pop.id) for pop in self.populations()] yield from combinatorics.treeseq_count_topologies(self, sample_sets) @@ -10718,16 +10696,14 @@ def pair_coalescence_counts( sample_sets = util.safe_np_int_cast(np.hstack(sample_sets), np.int32) coalescing_pairs = np.zeros((num_windows, num_indexes, num_time_windows)) - coalescing_pairs[..., :num_bins] = ( - self.ll_tree_sequence.pair_coalescence_counts( - sample_sets=sample_sets, - sample_set_sizes=sample_set_sizes, - windows=windows, - indexes=indexes, - node_bin_map=node_bin_map, - span_normalise=span_normalise, - pair_normalise=pair_normalise, - ) + coalescing_pairs[..., :num_bins] = self.ll_tree_sequence.pair_coalescence_counts( + sample_sets=sample_sets, + sample_set_sizes=sample_set_sizes, + windows=windows, + indexes=indexes, + node_bin_map=node_bin_map, + span_normalise=span_normalise, + pair_normalise=pair_normalise, ) if drop_middle_dimension: diff --git a/python/tskit/util.py b/python/tskit/util.py index 1acbc152f5..730d2db8fb 100644 --- a/python/tskit/util.py +++ b/python/tskit/util.py @@ -22,6 +22,7 @@ """ Module responsible for various utility functions used in other modules. """ + import dataclasses import datetime import html @@ -394,7 +395,7 @@ def truncate_string_end(string, length): """ if len(string) <= length: return string - return f"{string[:length - 3]}..." + return f"{string[: length - 3]}..." def render_metadata(md, length=40): @@ -438,7 +439,7 @@ def unicode_table( inner_width = sum(widths) + len(header or rows[0]) - 1 if title is not None: out += [ - f"╔{'═' * inner_width}╗\n" f"║{title.ljust(inner_width)}║\n", + f"╔{'═' * inner_width}╗\n║{title.ljust(inner_width)}║\n", f"╠{'╤'.join('═' * w for w in widths)}╣\n", ] if header is not None: @@ -541,8 +542,9 @@ def tree_sequence_html(ts): {format_number(table.num_rows)} {naturalsize(table.nbytes)} - {'✅' if hasattr(table, "metadata") and len(table.metadata) > 0 - else ''} + { + "✅" if hasattr(table, "metadata") and len(table.metadata) > 0 else "" + } """ @@ -665,7 +667,7 @@ def tree_sequence_html(ts): To cite this software, please consult the citation manual: https://tskit.dev/citation/ - """ # noqa: B950 + """ # noqa: E501 def tree_html(tree): @@ -705,7 +707,7 @@ def tree_html(tree): - """ # noqa: B950 + """ # noqa: E501 def variant_html(variant): @@ -742,7 +744,7 @@ def variant_html(variant): - """ # noqa: B950 + """ # noqa: E501 html_body_tail = """ @@ -753,8 +755,6 @@ def variant_html(variant): """ try: - variant.site - site_id = variant.site.id site_position = variant.site.position num_samples = len(variant.samples) @@ -775,8 +775,9 @@ def variant_html(variant): """ + "\n".join( [ - f"""Nodes with Allele {'missing' if k is None - else "'" + k + "'"}""" + f"""Nodes with Allele { + "missing" if k is None else "'" + k + "'" + }""" + f"{format_number(counts[k])}" + " " + f"({format_number(freqs[k] * 100, 2)}%)" diff --git a/python/tskit/vcf.py b/python/tskit/vcf.py index c8a4655020..987ec27e00 100644 --- a/python/tskit/vcf.py +++ b/python/tskit/vcf.py @@ -23,6 +23,7 @@ """ Convert tree sequences to VCF. 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