diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
deleted file mode 100644
index d6384966..00000000
--- a/.github/workflows/ci.yml
+++ /dev/null
@@ -1,125 +0,0 @@
-name: CI
-
-on:
- pull_request:
- push:
- branches:
- - main
-
-jobs:
- # pre-commit:
- # name: Lint
- # runs-on: ubuntu-latest
- # steps:
- # - uses: actions/checkout@v4
- # - uses: actions/setup-python@v5
- # with:
- # python-version: '3.11'
- # - uses: pre-commit/action@v3.0.1
- unit:
- name: Unit tests
- runs-on: ubuntu-latest
-
- steps:
- - uses: actions/checkout@v4
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v5
- with:
- python-version: '3.11'
- - name: Install dependencies
- run: |
- python -m pip install --upgrade pip
- python -m pip install '.[dev,debug,inference]'
-
- - name: Run tests
- run: |
- python -m pytest --cov=sc2ts tests/
- # - name: Upload coverage to Coveralls
- # uses: coverallsapp/github-action@v2.3.0
- # with:
- # github-token: ${{ secrets.GITHUB_TOKEN }}
- # # The first coveralls upload will succeed and others seem to fail now.
- # # This is a quick workaround for doing a proper "parallel" setup:
- # # https://github.com/coverallsapp/github-action
- # fail-on-error: false
-
- end_to_end:
- name: End to end tests
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v4
- - uses: actions/setup-python@v5
- with:
- python-version: '3.11'
- - name: Install dependencies
- run: |
- python -m pip install --upgrade pip
- python -m pip install '.[inference]'
-
- - name: Create basedir
- run: |
- mkdir -p testrun
- gunzip -k tests/data/alignments.fasta.gz
-
- - name: Import alignments
- run: |
- sc2ts import-alignments -i testrun/dataset.zarr tests/data/alignments.fasta
-
- - name: Import metadata
- run: |
- sc2ts import-metadata testrun/dataset.zarr tests/data/metadata.tsv
-
- - name: Info dataset
- run: |
- sc2ts info-dataset testrun/dataset.zarr
-
- - name: Run inference
- run: |
- # doing ~10 days here as this is taking a while
- sc2ts infer tests/data/testrun-conf.toml --stop 2020-02-03
-
- - name: Validate
- run: |
- sc2ts validate -v --date-field=date testrun/dataset.zarr testrun/results/test/test_2020-02-02.ts
-
- - name: MatchDB
- run: |
- sc2ts info-matches testrun/test.matches.db
-
- bare_api:
- name: Bare API tests
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v4
- - uses: actions/setup-python@v5
- with:
- python-version: '3.11'
- - name: Install dependencies
- run: |
- python -m pip install --upgrade pip
- python -m pip install '.'
- python -m pip install pytest
- - name: Run tests
- run: |
- # We are careful to pull in the minimum dependencies here
- # and only operate on files stored in the repo
- python -m pytest -v -c /dev/null -p no:sc2ts_fixtures tests/test_api.py
-
- packaging:
- name: Packaging tests
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v4
- - uses: actions/setup-python@v5
- with:
- python-version: '3.11'
- - name: Install dependencies
- run: |
- python -m pip install --upgrade pip
- python -m pip install build twine validate-pyproject[all]
- - name: Check and install package
- run: |
- validate-pyproject pyproject.toml
- python -m build
- python -m twine check --strict dist/*
- python -m pip install dist/*.whl
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 928edb3a..940318ee 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -1,13 +1,11 @@
-name: Docs
+name: Build docs
on:
pull_request:
push:
branches: [main]
- tags:
- - '*'
merge_group:
jobs:
- Docs:
- uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@v1
+ docs:
+ uses: tskit-dev/.github/.github/workflows/docs.yml@v13
diff --git a/.github/workflows/integration.yml b/.github/workflows/integration.yml
new file mode 100644
index 00000000..8c0cdbe9
--- /dev/null
+++ b/.github/workflows/integration.yml
@@ -0,0 +1,61 @@
+name: Integration tests
+
+on:
+ pull_request:
+ push:
+ branches: [main, test]
+ merge_group:
+
+jobs:
+ end-to-end:
+ name: End to end tests
+ runs-on: ubuntu-24.04
+ steps:
+ - uses: actions/checkout@v4.2.2
+ - uses: astral-sh/setup-uv@v6
+ with:
+ python-version: "3.11"
+ version: "0.8.15"
+ - name: Install dependencies
+ run: uv sync --locked --group test
+
+ - name: Create basedir
+ run: |
+ mkdir -p testrun
+ gunzip -k tests/data/alignments.fasta.gz
+
+ - name: Import alignments
+ run: uv run sc2ts import-alignments -i testrun/dataset.zarr tests/data/alignments.fasta
+
+ - name: Import metadata
+ run: uv run sc2ts import-metadata testrun/dataset.zarr tests/data/metadata.tsv
+
+ - name: Info dataset
+ run: uv run sc2ts info-dataset testrun/dataset.zarr
+
+ - name: Run inference
+ run: |
+ # doing ~10 days here as this is taking a while
+ uv run sc2ts infer tests/data/testrun-conf.toml --stop 2020-02-03
+
+ - name: Validate
+ run: uv run sc2ts validate -v --date-field=date testrun/dataset.zarr testrun/results/test/test_2020-02-02.ts
+
+ - name: MatchDB
+ run: uv run sc2ts info-matches testrun/test.matches.db
+
+ bare-api:
+ name: Bare API tests
+ runs-on: ubuntu-24.04
+ steps:
+ - uses: actions/checkout@v4.2.2
+ - uses: astral-sh/setup-uv@v6
+ with:
+ python-version: "3.11"
+ version: "0.8.15"
+ - name: Install package only
+ run: uv pip install -e .
+ - name: Run tests
+ run: |
+ # Minimal deps only; avoid picking up conftest and fixtures
+ uv run pytest -v -c /dev/null -p no:sc2ts_fixtures tests/test_api.py
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 00000000..f44108f1
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,9 @@
+name: Lint
+
+on:
+ pull_request:
+ merge_group:
+
+jobs:
+ lint:
+ uses: tskit-dev/.github/.github/workflows/lint.yml@v13
diff --git a/.github/workflows/python-packaging.yml b/.github/workflows/python-packaging.yml
new file mode 100644
index 00000000..0372d647
--- /dev/null
+++ b/.github/workflows/python-packaging.yml
@@ -0,0 +1,12 @@
+name: Packaging
+
+on:
+ pull_request:
+ merge_group:
+
+jobs:
+ packaging:
+ uses: tskit-dev/.github/.github/workflows/python-packaging.yml@v13
+ with:
+ pyproject-directory: .
+ cli-test-cmd: sc2ts --help
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
new file mode 100644
index 00000000..2f0a1f69
--- /dev/null
+++ b/.github/workflows/tests.yml
@@ -0,0 +1,22 @@
+name: Tests
+
+on:
+ pull_request:
+ push:
+ branches: [main, test]
+ merge_group:
+
+jobs:
+ test:
+ name: Python
+ uses: tskit-dev/.github/.github/workflows/python-tests.yml@v13
+ with:
+ os: ${{ matrix.os }}
+ python-version: ${{ matrix.python }}
+ pyproject-directory: .
+ coverage-directory: sc2ts
+ secrets: inherit
+ strategy:
+ matrix:
+ python: ["3.10", "3.13"]
+ os: [macos-latest, ubuntu-24.04, windows-latest]
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
new file mode 100644
index 00000000..1ca87e43
--- /dev/null
+++ b/.github/workflows/wheels.yml
@@ -0,0 +1,47 @@
+name: Publish Python release
+
+on:
+ push:
+ branches: [test-publish]
+ release:
+ types: [published]
+
+jobs:
+ build:
+ runs-on: ubuntu-24.04
+ steps:
+ - uses: actions/checkout@v4.2.2
+ with:
+ fetch-depth: 0
+ - uses: astral-sh/setup-uv@v6
+ with:
+ python-version: "3.12"
+ version: "0.8.15"
+ - run: uv build
+ - uses: actions/upload-artifact@v4.6.1
+ with:
+ name: dist
+ path: dist/
+
+ publish:
+ runs-on: ubuntu-24.04
+ environment: release
+ needs: [build]
+ permissions:
+ id-token: write
+ steps:
+ - uses: actions/download-artifact@v4.2.0
+ with:
+ name: dist
+ path: dist
+
+ - name: Publish to Test PyPI
+ if: github.event_name == 'push' && github.ref_name == 'test-publish'
+ uses: pypa/gh-action-pypi-publish@v1.13.0
+ with:
+ repository-url: https://test.pypi.org/legacy/
+ verbose: true
+
+ - name: Publish to PyPI
+ if: github.event_name == 'release'
+ uses: pypa/gh-action-pypi-publish@v1.13.0
diff --git a/docs/Makefile b/docs/Makefile
index fe6c42d1..5fabd25d 100644
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -1,16 +1,6 @@
-# Need to set PYTHONPATH so that we pick up the local sc2ts
-PYPATH=${PWD}/..
-SC2TS_VERSION:=$(shell PYTHONPATH=${PYPATH} \
- python3 -c 'import sc2ts; print(sc2ts.__version__.split("+")[0])')
-dev:
- PYTHONPATH=${PYPATH} ./build.sh
-
-dist:
- @echo Building distribution for sc2ts version ${SC2TS_VERSION}
- sed -i s/__SC2TS_VERSION__/${SC2TS_VERSION}/g _config.yml
- PYTHONPATH=${PYPATH} ./build.sh
+all:
+ ./build.sh
clean:
rm -fR _build
-
diff --git a/docs/_config.yml b/docs/_config.yml
index 553428e6..8466510f 100644
--- a/docs/_config.yml
+++ b/docs/_config.yml
@@ -43,7 +43,7 @@ sphinx:
navigation_with_keys: false
pygments_dark_style: monokai
logo:
- text: "Version __SC2TS_VERSION__"
+ text: "Version __PKG_VERSION__"
myst_enable_extensions:
- colon_fence
diff --git a/docs/build.sh b/docs/build.sh
index 50be22cd..a3a3dbf1 100755
--- a/docs/build.sh
+++ b/docs/build.sh
@@ -6,7 +6,7 @@
REPORTDIR=_build/html/reports
-jupyter-book build -W .
+uv run --project=../python --group docs jupyter-book build . -vnW --keep-going
RETVAL=$?
if [ $RETVAL -ne 0 ]; then
if [ -e $REPORTDIR ]; then
@@ -18,4 +18,3 @@ else
rm -f $REPORTDIR/*
fi
exit $RETVAL
-
diff --git a/docs/make_sc2ts_arg_subset.py b/docs/make_sc2ts_arg_subset.py
index a2b01c88..8ebe3cc6 100644
--- a/docs/make_sc2ts_arg_subset.py
+++ b/docs/make_sc2ts_arg_subset.py
@@ -1,5 +1,5 @@
-import tszip
import numpy as np
+import tszip
ts = tszip.load("sc2ts_viridian_v1.2.trees.tsz")
diff --git a/docs/make_viridian_subset.py b/docs/make_viridian_subset.py
index 011cb521..953ad8ce 100644
--- a/docs/make_viridian_subset.py
+++ b/docs/make_viridian_subset.py
@@ -9,4 +9,3 @@
path = f"viridian_mafft_subset_{k}_v1.vcz"
ds.copy(path, sample_id=samples)
sc2ts.Dataset.create_zip(path, path + ".zip")
-
diff --git a/prek.toml b/prek.toml
new file mode 100644
index 00000000..3a258356
--- /dev/null
+++ b/prek.toml
@@ -0,0 +1,40 @@
+# The prek configuration defining linting requirements. This
+# setup is optimised for long-term stability and determinism,
+# and therefore only uses either "builtin" rules or "local"
+# rules implementing lint workflows. We do not use any remote
+# workflow repos.
+
+[[repos]]
+repo = "builtin"
+hooks = [
+ { id = "check-added-large-files" },
+ { id = "check-merge-conflict" },
+ { id = "mixed-line-ending" },
+ { id = "check-case-conflict" },
+ { id = "check-yaml" },
+ { id = "check-toml" },
+]
+
+[[repos]]
+repo = "local"
+hooks = [
+ {
+ id = "ruff-check",
+ name = "ruff check",
+ language = "system",
+ entry = "ruff check --fix --force-exclude",
+ types = ["python"],
+ },
+]
+
+[[repos]]
+repo = "local"
+hooks = [
+ {
+ id = "ruff-format",
+ name = "ruff format",
+ language = "system",
+ entry = "ruff format --force-exclude",
+ types = ["python"],
+ },
+]
diff --git a/pyproject.toml b/pyproject.toml
index 9c0f6740..b007047f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,18 +27,10 @@ Documentation = "https://tskit.dev/sc2ts/docs/"
"Bug Tracker" = "https://github.com/tskit-dev/sc2ts/issues"
GitHub = "https://github.com/tskit-dev/sc2ts/"
-
[project.scripts]
sc2ts = "sc2ts.cli:cli"
[project.optional-dependencies]
-dev = [
- "msprime",
- "sgkit",
- "pytest",
- "pytest-coverage",
- "tomli-w",
-]
inference = [
"scipy",
"biotite",
@@ -50,23 +42,54 @@ debug = [
"matplotlib",
"IPython",
]
+
+[dependency-groups]
+test = [
+ "msprime",
+ "pytest",
+ "pytest-cov",
+ "pytest-xdist",
+ "sgkit",
+ "tomli-w",
+ # inference and debug deps needed by the test suite
+ "scipy",
+ "biotite",
+ "tsinfer>=0.5",
+ "pyfaidx",
+ "numba",
+ "matplotlib",
+ "IPython",
+]
docs = [
- "jupyter-book==1.0.4.post1",
+ "jupyter-book",
"sphinx-book-theme",
"sphinx-copybutton",
"sphinx-click",
"setuptools_scm",
- "sphinx-argparse==0.5.2",
- "sphinx-issues==5.0.1",
+ "sphinx-argparse",
+ "sphinx-issues",
"IPython",
- # docs requires running the CLI, which means we need to full inference
- # requirements also
+ # docs require running the CLI, which means the full inference deps are needed
"scipy",
"biotite",
"tsinfer>=0.5",
"pyfaidx",
"numba",
]
+lint = [
+ "ruff==0.15.1",
+ "prek==0.3.3",
+]
+packaging = [
+ "twine",
+ "validate-pyproject[all]",
+]
+dev = [
+ {include-group = "docs"},
+ {include-group = "lint"},
+ {include-group = "test"},
+ {include-group = "packaging"},
+]
[build-system]
requires = [
@@ -84,4 +107,32 @@ write_to = "sc2ts/_version.py"
[tool.pytest.ini_options]
testpaths = "tests"
-addopts = "--cov=sc2ts --cov-report term-missing"
+
+[tool.ruff]
+target-version = "py310"
+line-length = 89
+
+[tool.ruff.lint]
+select = ["E", "F", "B", "W", "I", "N", "UP", "A", "PT"]
+fixable = ["ALL"]
+
+
+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
+ "F821", # Undefined name `List`
+ "B006", # Do not use mutable data structures for argument defaults
+ "E721", # Use `is` and `is not` for type comparisons, or `isinstance()`
+ "F841", # Local variable `shape` is assigned to but never
+ "PT018", # Assertion should be broken down into multiple parts
+ "B007", # Loop control variable `j` not used within
+ "PT006", # Wrong type passed to first argument of `pytest.mar
+ "PT007", # Wrong values type in `pytest.mark.parametrize`
+ "PT009", # Use a regular `assert` instead of unittest-style
+ # FIXME - line too long in debug.py
+ "E501",
+
+]
+
diff --git a/sc2ts/__init__.py b/sc2ts/__init__.py
index 69a09969..ca55d3a0 100644
--- a/sc2ts/__init__.py
+++ b/sc2ts/__init__.py
@@ -1,6 +1,11 @@
-from .core import __version__
-
# star imports are fine here as it's just a bunch of constants
-from .core import *
-from .dataset import mask_ambiguous, mask_flanking_deletions, decode_alleles, Dataset, Variant
-from .stats import node_data, mutation_data
+from .core import * # noqa
+from .core import __version__ # noqa
+from .dataset import (
+ Dataset, # noqa
+ Variant, # noqa
+ decode_alleles, # noqa
+ mask_ambiguous, # noqa
+ mask_flanking_deletions, # noqa
+)
+from .stats import mutation_data, node_data # noqa
diff --git a/sc2ts/__main__.py b/sc2ts/__main__.py
index 0b6a7bb7..91e12cb2 100644
--- a/sc2ts/__main__.py
+++ b/sc2ts/__main__.py
@@ -1,5 +1,4 @@
from . import cli
-
if __name__ == "__main__":
cli.cli()
diff --git a/sc2ts/cli.py b/sc2ts/cli.py
index 8df17e68..abbb45ed 100644
--- a/sc2ts/cli.py
+++ b/sc2ts/cli.py
@@ -1,31 +1,22 @@
-import json
import collections
import concurrent.futures as cf
+import datetime
+import json
import logging
-import itertools
import pathlib
import sys
-import contextlib
-import dataclasses
-import datetime
-import time
-from typing import List
-import tomli
-import numpy as np
-import tqdm
-import tskit
-import tszip
import click
import humanize
+import numpy as np
import pandas as pd
+import tomli
+import tqdm
+import tszip
import sc2ts
-from . import core
-from . import data_import
-from . import tree_ops
-from . import jit
-from . import validation
+
+from . import core, data_import, jit, tree_ops, validation
from . import inference as si # sc2ts inference
logger = logging.getLogger(__name__)
@@ -86,7 +77,11 @@ def summarise_usage(ts):
max_mem = d["max_memory"]
if max_mem > 0:
maxmem_str = "; max_memory=" + humanize.naturalsize(max_mem, binary=True)
- return f"elapsed={wall_time:.2f}m; user={user_time:.2f}m; sys={sys_time:.2f}m{maxmem_str}"
+ return (
+ f"elapsed={wall_time:.2f}m; "
+ f"user={user_time:.2f}m; "
+ f"sys={sys_time:.2f}m{maxmem_str}"
+ )
def setup_logging(verbosity, log_file=None, date=None):
@@ -129,8 +124,7 @@ def setup_logging(verbosity, log_file=None, date=None):
is_flag=True,
flag_value=True,
help=(
- "If true, initialise a new dataset. WARNING! This will erase an existing "
- "store"
+ "If true, initialise a new dataset. WARNING! This will erase an existing store"
),
)
@progress
@@ -280,9 +274,7 @@ def _run_extend(out_path, verbose, log_file, **params):
@click.command()
@click.argument("config_file", type=click.File(mode="rb"))
-@click.option(
- "--start", default=None, help="Start inference at this date (inclusive). "
-)
+@click.option("--start", default=None, help="Start inference at this date (inclusive). ")
@click.option(
"--stop",
default="3000",
@@ -373,9 +365,7 @@ def infer(config_file, start, stop, force):
base_ts = ts_file_pattern.format(date=date)
with cf.ProcessPoolExecutor(1) as executor:
- future = executor.submit(
- _run_extend, base_ts, log_level, log_file, **params
- )
+ future = executor.submit(_run_extend, base_ts, log_level, log_file, **params)
# Block and wait, raising exception if it occured
future.result()
@@ -428,9 +418,7 @@ def validate(
setup_logging(verbose)
ts = tszip.load(ts_file)
- ds = sc2ts.Dataset(
- dataset, date_field=date_field, chunk_cache_size=chunk_cache_size
- )
+ ds = sc2ts.Dataset(dataset, date_field=date_field, chunk_cache_size=chunk_cache_size)
if genotypes:
validation.validate_genotypes(ts, ds, deletions_as_missing, show_progress=True)
if metadata:
@@ -749,9 +737,7 @@ def find_previous_date_path(date, path_pattern):
if path.exists():
break
else:
- raise ValueError(
- f"No path exists for pattern {path_pattern} starting at {date}"
- )
+ raise ValueError(f"No path exists for pattern {path_pattern} starting at {date}")
return path
diff --git a/sc2ts/data_import.py b/sc2ts/data_import.py
index fbb1939b..dc14e961 100644
--- a/sc2ts/data_import.py
+++ b/sc2ts/data_import.py
@@ -1,6 +1,6 @@
import collections.abc
-import pathlib
import csv
+import pathlib
import numpy as np
import pyfaidx
@@ -140,4 +140,3 @@ def massage_viridian_metadata(df):
a[~missing] = np.array(data[~missing], dtype=int)
df[name] = a
return df
-
diff --git a/sc2ts/dataset.py b/sc2ts/dataset.py
index 61c89704..d6f1c02c 100644
--- a/sc2ts/dataset.py
+++ b/sc2ts/dataset.py
@@ -2,20 +2,19 @@
Methods for managing a sc2ts Zarr based dataset.
"""
-import dataclasses
-import os.path
-import zipfile
import collections
+import concurrent.futures as cf
+import dataclasses
import logging
+import os.path
import pathlib
-import concurrent.futures as cf
+import zipfile
-import tskit
-import tqdm
-import pandas as pd
-import zarr
import numcodecs
import numpy as np
+import pandas as pd
+import tqdm
+import zarr
from sc2ts import core
@@ -236,6 +235,7 @@ class Variant:
Represents a single variant, including the genomic position and the integer encoded
genotypes.
"""
+
position: int
genotypes: np.ndarray
alleles: list
@@ -252,6 +252,7 @@ class Dataset(collections.abc.Mapping):
:param int chunk_cache_size: Maximum number of chunks to cache for
alignments and metadata. Defaults to 1.
"""
+
def __init__(self, path, chunk_cache_size=1, date_field=None):
logger.info(f"Loading dataset @{path} using {date_field} as date field")
self.date_field = date_field
diff --git a/sc2ts/debug.py b/sc2ts/debug.py
index 80a76d4f..d489e848 100644
--- a/sc2ts/debug.py
+++ b/sc2ts/debug.py
@@ -4,28 +4,24 @@
included if the "debug"] option is included with the sc2ts
install.
"""
+
import collections
-import logging
-import json
-import warnings
import dataclasses
import datetime
+import json
+import logging
import re
-from typing import List
+import warnings
-import tskit
-import numpy as np
-from tqdm.auto import tqdm
-import pandas as pd
import humanize
import matplotlib.pyplot as plt
-from matplotlib import colors
-from IPython.display import Markdown, HTML
+import numpy as np
+import pandas as pd
+import tskit
+from IPython.display import HTML, Markdown
+from tqdm.auto import tqdm
-from . import jit
-from . import core
-from . import inference
-from . import data_import
+from . import core, data_import, inference, jit
logger = logging.getLogger(__name__)
@@ -89,7 +85,6 @@ def max_descendant_samples(ts, show_progress=True):
class CopyingTable:
-
default_colours = ( # Chosen to be light enough that black text on top is readable
"#FC0", # Gold for de-novo mutations
"#8D8", # Copy from first parent: light green
@@ -117,7 +112,7 @@ def line_cell(pos, prev_pos, next_pos):
dist_to_left = 0
if dist_to_right > 2:
dist_to_right = 0
- return f' | '
+ return f' | '
def node_mutations(self):
muts = {}
@@ -206,10 +201,11 @@ def html(
matches the first parent, ``colours[2]`` for the second parent, etc.
Default: None, treated as ``["#FC0", "#8D8", "#6AD", "#B9D", "#A88"]``.
:param exclude_stylesheet bool:
- If True, exclude the default stylesheet from the HTML output. This is useful
- simply to save space if you want to include the copying table in a larger HTML
- document (e.g. a Jupyter notebook) that already has one copying table shown with
- the standard stylesheet. If False or None (default), include the default stylesheet.
+ If True, exclude the default stylesheet from the HTML output. This
+ is useful simply to save space if you want to include the copying
+ table in a larger HTML document (e.g. a Jupyter notebook) that
+ already has one copying table shown with the standard stylesheet.
+ If False or None (default), include the default stylesheet.
:param font_family str:
The font family to use for the table. Default: None.
:param css_class str:
@@ -284,7 +280,7 @@ def label(allele, default=""):
except IndexError as e:
raise ValueError(
"Displaying the copying path only deals with a max of "
- f"{len(parent_colours)-1} parents"
+ f"{len(parent_colours) - 1} parents"
) from e
elif parent_allele == var.site.ancestral_state:
col = "#DDD"
@@ -350,7 +346,8 @@ def label(allele, default=""):
html += row_template.format(label=row_lab(child_label), data="".join(child))
for i, parent in enumerate(parents):
html += row_template.format(
- label=row_lab(parent_labels.get(i + 1, f"P{i+1}")), data="".join(parent)
+ label=row_lab(parent_labels.get(i + 1, f"P{i + 1}")),
+ data="".join(parent),
)
if not hide_runlengths:
p = np.concatenate(([-np.inf], positions, [np.inf]))
@@ -391,12 +388,8 @@ def __init__(
samples = ts.samples()
self.strain_map = dict(zip(top_level_md["samples_strain"], ts.samples()))
- self.sites_num_mutations = np.bincount(
- ts.mutations_site, minlength=ts.num_sites
- )
- self.nodes_num_mutations = np.bincount(
- ts.mutations_node, minlength=ts.num_nodes
- )
+ self.sites_num_mutations = np.bincount(ts.mutations_site, minlength=ts.num_sites)
+ self.nodes_num_mutations = np.bincount(ts.mutations_node, minlength=ts.num_nodes)
self.nodes_num_parents = np.bincount(ts.edges_child, minlength=ts.num_edges)
# The number of samples per day in time-ago (i.e., the nodes_time units).
@@ -456,9 +449,7 @@ def _preprocess_nodes(self, show_progress):
self.first_scorpio_sample = {}
# NOTE: keyed by *string* because of JSON
- exact_matches = ts.metadata["sc2ts"]["cumulative_stats"]["exact_matches"][
- "node"
- ]
+ exact_matches = ts.metadata["sc2ts"]["cumulative_stats"]["exact_matches"]["node"]
iterator = tqdm(
ts.nodes(),
@@ -567,7 +558,10 @@ def _preprocess_mutations(self, show_progress):
parent = ts.mutations_parent[mut_id]
if parent != -1:
mutations_num_inheritors[parent] -= descendants
- is_reversion[mut_id] = self.mutations_inherited_state[parent] == self.mutations_derived_state[mut_id]
+ is_reversion[mut_id] = (
+ self.mutations_inherited_state[parent]
+ == self.mutations_derived_state[mut_id]
+ )
if is_reversion[mut_id] and ts.mutations_node[parent] == tree.parent(
mutation_node
):
@@ -579,7 +573,10 @@ def _preprocess_mutations(self, show_progress):
parent = ts.mutations_parent[parent]
mutations_num_parents[mut_id] = num_parents
# Ts/Tvs
- key = (self.mutations_inherited_state[mut_id], self.mutations_derived_state[mut_id])
+ key = (
+ self.mutations_inherited_state[mut_id],
+ self.mutations_derived_state[mut_id],
+ )
mutations_is_transition[mut_id] = key in transitions
mutations_is_transversion[mut_id] = key in transversions
site = ts.mutations_site[mut_id]
@@ -612,7 +609,7 @@ def summary(self):
re_nodes = np.sum(self.ts.nodes_flags == core.NODE_IS_RECOMBINANT)
exact_matches = np.sum((self.ts.nodes_flags & core.NODE_IS_EXACT_MATCH) > 0)
imr_nodes = np.sum(
- (self.ts.nodes_flags == core.NODE_IS_IMMEDIATE_REVERSION_MARKER)
+ self.ts.nodes_flags == core.NODE_IS_IMMEDIATE_REVERSION_MARKER
)
samples = self.ts.samples()[1:] # skip reference
@@ -707,10 +704,7 @@ def _node_summary(self, u, child_mutations=True):
strain = md["strain"]
else:
md = md.get("sc2ts", {})
- if (
- flags & (core.NODE_IS_MUTATION_OVERLAP | core.NODE_IS_REVERSION_PUSH)
- > 0
- ):
+ if flags & (core.NODE_IS_MUTATION_OVERLAP | core.NODE_IS_REVERSION_PUSH) > 0:
try:
strain = f"{md['date_added']}:{', '.join(md['mutations'])}"
except KeyError:
@@ -1510,7 +1504,7 @@ def plot_samples_per_day(
first_date = self.nodes_date[self.first_scorpio_sample[col]]
first_scorpio_date.append((first_date, col))
except KeyError:
- warnings.warn(f"No samples for Scorpio {col} present")
+ warnings.warn(f"No samples for Scorpio {col} present", stacklevel=2)
df_scorpio = df_scorpio[keep_cols]
ax4.set_title("Scorpio composition of processed samples")
@@ -1629,7 +1623,7 @@ def draw_pango_lineage_subtree(
appropriate set of samples. See that function for more details.
"""
return self.draw_subtree(
- tracked_pango=[pango_lineage], position=position, *args, **kwargs
+ tracked_pango=[pango_lineage], position=position, *args, **kwargs # noqa B026
)
def draw_subtree(
@@ -1764,9 +1758,7 @@ def draw_subtree(
if extra_tracked_samples is not None:
tn_set = set(tracked_nodes)
- extra_tracked_samples = [
- e for e in extra_tracked_samples if e not in tn_set
- ]
+ extra_tracked_samples = [e for e in extra_tracked_samples if e not in tn_set]
tracked_nodes = np.concatenate((tracked_nodes, extra_tracked_samples))
tree = ts.at(position, tracked_samples=tracked_nodes)
order = np.array(
@@ -1868,7 +1860,7 @@ def draw_subtree(
re_nodes = np.where(ts.nodes_flags & core.NODE_IS_RECOMBINANT)[0]
styles.append(
",".join([f".node.n{u} > .sym" for u in re_nodes])
- + f"{{r:{symbol_size/2*1.5:.2f}px; stroke:black; fill:white}}"
+ + f"{{r:{symbol_size / 2 * 1.5:.2f}px; stroke:black; fill:white}}"
)
if date_format == "cal":
if y_ticks is not None:
@@ -1950,7 +1942,7 @@ class DeletionEvent:
start: int
node: int
length: int
- mutations: List
+ mutations: list
def country_abbr(country):
@@ -1971,7 +1963,7 @@ def country_abbr(country):
@dataclasses.dataclass
class SampleGroupInfo:
group_id: str
- nodes: List[int]
+ nodes: list[int]
ts: tskit.TreeSequence
attach_date: None
@@ -2081,7 +2073,7 @@ def draw_svg(
mutation_labels[label].append(mut.id)
# If more than one mutation has the same label, add a prefix with the counts
mutation_labels = {
- m_id: label + (f" ({i+1}/{len(ids)})" if len(ids) > 1 else "")
+ m_id: label + (f" ({i + 1}/{len(ids)})" if len(ids) > 1 else "")
for label, ids in mutation_labels.items()
for i, m_id in enumerate(ids)
}
@@ -2112,7 +2104,7 @@ def draw_svg(
re_nodes = np.where(ts.nodes_flags & core.NODE_IS_RECOMBINANT)[0]
styles.append(
",".join([f".node.n{u} > .sym" for u in re_nodes])
- + f"{{r: {symbol_size/2*1.5:.2f}px; stroke: black; fill: white}}"
+ + f"{{r: {symbol_size / 2 * 1.5:.2f}px; stroke: black; fill: white}}"
)
svg = self.ts.draw_svg(
size=size,
diff --git a/sc2ts/inference.py b/sc2ts/inference.py
index 575e63f7..9d89f17c 100644
--- a/sc2ts/inference.py
+++ b/sc2ts/inference.py
@@ -1,37 +1,31 @@
from __future__ import annotations
+
import bz2
-import logging
-import datetime
-import dataclasses
import collections
-import concurrent.futures as cf
+import dataclasses
+import datetime
+import hashlib
import inspect
-import time
import json
-import pickle
-import hashlib
-import sqlite3
+import logging
+import os
import pathlib
+import pickle
import random
-import os
+import sqlite3
import threading
+import time
-import tqdm
-import tskit
-import tszip
import _tsinfer
-import tsinfer
-import numpy as np
-import zarr
-import numba
import humanize
+import numpy as np
import pandas as pd
+import tqdm
+import tsinfer
+import tskit
+import tszip
-from . import core
-from . import data_import
-from . import jit
-from . import stats
-from . import tree_ops
+from . import core, data_import, jit, stats, tree_ops
from . import dataset as _dataset
logger = logging.getLogger(__name__)
@@ -227,7 +221,7 @@ def initialise(db_path):
with sqlite3.connect(db_path) as conn:
conn.execute(sql)
conn.execute(
- "CREATE INDEX [ix_samples_match_date] on 'samples' " "([match_date]);"
+ "CREATE INDEX [ix_samples_match_date] on 'samples' ([match_date]);"
)
logger.info(f"Created new MatchDb at {db_path}")
return MatchDb(db_path)
@@ -270,7 +264,9 @@ def mirror_ts_coordinates(ts):
return tables.tree_sequence()
-def initial_ts(problematic_sites=list()):
+def initial_ts(problematic_sites=None):
+ if problematic_sites is None:
+ problematic_sites = []
reference = data_import.get_reference_sequence()
L = core.REFERENCE_SEQUENCE_LENGTH
assert L == len(reference)
@@ -461,7 +457,7 @@ def match_samples(
deletions_as_missing=deletions_as_missing,
show_progress=show_progress,
progress_title=date,
- progress_phase=f"match(F)",
+ progress_phase="match(F)",
)
@@ -497,9 +493,7 @@ def preprocess(
# Do we need to do this here? Would be easier to do later, maybe
sample.haplotype = _dataset.mask_ambiguous(a)
counts = collections.Counter(a)
- sample.alignment_composition = {
- alleles[k]: count for k, count in counts.items()
- }
+ sample.alignment_composition = {alleles[k]: count for k, count in counts.items()}
samples.append(sample)
return samples
@@ -706,7 +700,7 @@ def _extend(
ts = add_exact_matches(ts=ts, match_db=match_db, date=date)
- logger.info(f"Update ARG with low-cost samples")
+ logger.info("Update ARG with low-cost samples")
ts, _ = add_matching_results(
f"match_date=='{date}' and hmm_cost>0 and hmm_cost<={hmm_cost_threshold}",
ts=ts,
@@ -735,8 +729,7 @@ def _extend(
)
for group in groups:
logger.warning(
- f"Add retro group {group.summary()}:"
- f"{group.tree_quality_metrics.summary()}"
+ f"Add retro group {group.summary()}:{group.tree_quality_metrics.summary()}"
)
return update_top_level_metadata(ts, date, groups, samples)
@@ -746,7 +739,6 @@ def update_top_level_metadata(ts, date, retro_groups, samples):
tables = ts.dump_tables()
md = tables.metadata
md["sc2ts"]["date"] = date
- num_samples = len(samples)
samples_strain = md["sc2ts"]["samples_strain"]
new_samples = ts.samples()[len(samples_strain) :]
inserted_samples = set()
@@ -823,7 +815,6 @@ def match_path_ts(group):
tables.nodes.metadata_schema = tskit.MetadataSchema.permissive_json()
tables.mutations.metadata_schema = tskit.MetadataSchema.permissive_json()
site_id_map = {}
- first_sample = len(tables.nodes)
root = len(group)
group_id = group.sample_hash
for sample in group:
@@ -1064,7 +1055,8 @@ def add_matching_results(
continue
if tqm.mean_mutations_per_sample > max_mutations_per_sample:
logger.debug(
- f"Skipping mean_mutations_per_sample={tqm.mean_mutations_per_sample} "
+ "Skipping "
+ f"mean_mutations_per_sample={tqm.mean_mutations_per_sample} "
f"exceeds threshold {group.summary()}"
)
continue
@@ -1544,9 +1536,6 @@ def summary(self):
f"={self.mutation_summary()}"
)
- def compute_cost(self, num_mismatches):
- self.cost = num_mismatches * (len(self.path) - 1) + len(self.mutations)
-
@property
def breakpoints(self):
breakpoints = [seg.left for seg in self.path]
@@ -1654,9 +1643,7 @@ def get_closest_mutation(node, site_id):
closest_mutation.inherited_state == mutation.derived_state
)
if mutation.is_reversion:
- mutation.is_immediate_reversion = (
- closest_mutation.node == seg.parent
- )
+ mutation.is_immediate_reversion = closest_mutation.node == seg.parent
logger.debug(f"Characterised {num_mutations} mutations")
@@ -1720,9 +1707,7 @@ def attach_tree(
tree = child_ts.first()
has_root_mutations = np.any(child_ts.mutations_node == tree.root)
condition = (
- has_root_mutations
- or len(attach_path) > 1
- or len(group.immediate_reversions) > 0
+ has_root_mutations or len(attach_path) > 1 or len(group.immediate_reversions) > 0
)
if condition:
child_ts = add_root_edge(child_ts)
@@ -2225,8 +2210,7 @@ def rewire_long_branch_splits(ts, rematch_results):
logger.info(f"Rewiring for {rematch.recombinant}")
for seg in rematch.original_match.path:
e = np.where(
- (ts.edges_child == rematch.recombinant)
- & (ts.edges_parent == seg.parent)
+ (ts.edges_child == rematch.recombinant) & (ts.edges_parent == seg.parent)
)[0]
assert ts.edges_left[e] == seg.left
assert ts.edges_right[e] == seg.right
@@ -2304,8 +2288,7 @@ def rewire_long_branch_splits(ts, rematch_results):
tables.nodes[rematch.recombinant] = row.replace(flags=0)
logger.info(
- f"Deleting {len(edges_to_delete)} edges and "
- f"{len(mutations_to_delete)} mutations"
+ f"Deleting {len(edges_to_delete)} edges and {len(mutations_to_delete)} mutations"
)
return tree_ops.update_tables(tables, edges_to_delete, mutations_to_delete)
@@ -2442,7 +2425,7 @@ def map_parsimony(ts, ds, sites=None, *, show_progress=False):
added_mutations = len(tables.mutations) - ts.num_mutations
logger.info(
- f"Added in {added_mutations} mutations at " f"{len(sites)} sites with parsimony"
+ f"Added in {added_mutations} mutations at {len(sites)} sites with parsimony"
)
keep_mutations = np.append(keep_mutations, np.ones(added_mutations, dtype=bool))
diff --git a/sc2ts/jit.py b/sc2ts/jit.py
index eaed6e47..dfaf75a7 100644
--- a/sc2ts/jit.py
+++ b/sc2ts/jit.py
@@ -1,10 +1,10 @@
import dataclasses
import logging
-import numpy as np
import numba
-import tskit.jit.numba as tskit_numba
+import numpy as np
import tskit
+import tskit.jit.numba as tskit_numba
NODE_IS_SAMPLE = tskit.NODE_IS_SAMPLE
diff --git a/sc2ts/stats.py b/sc2ts/stats.py
index eb857d3d..a20ba4be 100644
--- a/sc2ts/stats.py
+++ b/sc2ts/stats.py
@@ -1,9 +1,9 @@
-from . import core
-
import numpy as np
import pandas as pd
import tskit
+from . import core
+
def convert_date(ts, time_array):
time_zero_date = ts.metadata["time_zero_date"]
diff --git a/sc2ts/tree_ops.py b/sc2ts/tree_ops.py
index bb831d36..6e22fba8 100644
--- a/sc2ts/tree_ops.py
+++ b/sc2ts/tree_ops.py
@@ -4,21 +4,18 @@
objects.
"""
-import time
import collections
-import logging
import dataclasses
-from typing import List
+import logging
-import tskit
-import tqdm
+import biotite.sequence.phylo as bsp
import numpy as np
-import scipy.spatial.distance
import scipy.cluster.hierarchy
-import biotite.sequence.phylo as bsp
+import scipy.spatial.distance
+import tqdm
+import tskit
-from . import core
-from . import stats
+from . import core, stats
logger = logging.getLogger(__name__)
@@ -647,8 +644,6 @@ def split_branch(ts, node, mutations):
return tables.tree_sequence()
-
-
def drop_vestigial_root_edge(ts):
"""
Drop the edge joining 1 (the reference) to the vestigial root, needed
diff --git a/sc2ts/validation.py b/sc2ts/validation.py
index 3c7c83c1..356e7809 100644
--- a/sc2ts/validation.py
+++ b/sc2ts/validation.py
@@ -1,13 +1,13 @@
import logging
import unittest
-import numpy as np
import numpy.testing as nt
import tqdm
+import sc2ts
+
logger = logging.getLogger(__name__)
-import sc2ts
MISSING = -1
DELETION = sc2ts.IUPAC_ALLELES.index("-")
diff --git a/tests/data/make_ba2_recomb.py b/tests/data/make_ba2_recomb.py
index 0987237e..f091f078 100644
--- a/tests/data/make_ba2_recomb.py
+++ b/tests/data/make_ba2_recomb.py
@@ -1,16 +1,14 @@
-import tskit
+import pathlib
+
import numpy as np
import pandas as pd
-
-import pathlib
+import tskit
prefix = pathlib.Path("/home/jk/work/github/sc2ts-paper")
orig_ts = tskit.load(prefix / "inference/results/v1-beta1/v1-beta1_2023-02-21.ts")
recomb_df = pd.read_csv(prefix / "data/recombinants.csv").set_index("sample_id")
-strain2nodeid = dict(
- zip(orig_ts.metadata["sc2ts"]["samples_strain"], orig_ts.samples())
-)
+strain2nodeid = dict(zip(orig_ts.metadata["sc2ts"]["samples_strain"], orig_ts.samples()))
ba_2_sample = "SRR17461792"
re_node = recomb_df.loc[ba_2_sample, "recombinant"]
re_node_children = orig_ts.edges_child[orig_ts.edges_parent == re_node]
diff --git a/tests/sc2ts_fixtures.py b/tests/sc2ts_fixtures.py
index e68a3b48..30b579bc 100644
--- a/tests/sc2ts_fixtures.py
+++ b/tests/sc2ts_fixtures.py
@@ -1,17 +1,15 @@
import dataclasses
+import gzip
import pathlib
import shutil
-import gzip
-import tskit
import numpy as np
import pandas as pd
import pytest
+import tskit
import sc2ts
-from sc2ts import cli
-from sc2ts import data_import
-from sc2ts import jit
+from sc2ts import data_import, jit
from sc2ts import inference as si
@@ -103,9 +101,7 @@ def fx_dataset(tmp_path, fx_data_cache, fx_alignments_fasta, fx_metadata_df):
# Use an awkward chunk size here to make sure we're hitting across
# chunk stuff by default
sc2ts.Dataset.new(fs_path, samples_chunk_size=7)
- sc2ts.Dataset.append_alignments(
- fs_path, encoded_alignments(fx_alignments_fasta)
- )
+ sc2ts.Dataset.append_alignments(fs_path, encoded_alignments(fx_alignments_fasta))
sc2ts.Dataset.add_metadata(fs_path, fx_metadata_df)
sc2ts.Dataset.create_zip(fs_path, cache_path)
return sc2ts.Dataset(cache_path, date_field="date")
diff --git a/tests/test_api.py b/tests/test_api.py
index 3789ef10..414f4482 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -15,7 +15,6 @@ def fx_ds_v1():
class TestStatFuncs:
-
def test_top_level_md(self, fx_ts_v1):
ts = fx_ts_v1
assert ts.metadata == {"time_zero_date": "2020-02-15"}
@@ -32,7 +31,6 @@ def test_mutation_data(self, fx_ts_v1):
class TestDataset:
-
def test_basics(self, fx_ds_v1):
ds = fx_ds_v1
G = ds["call_genotype"][:].squeeze()
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 584f699e..a2a6d7eb 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,23 +1,20 @@
import io
import json
-import collections
+import click.testing as ct
import numpy as np
import numpy.testing as nt
-import click.testing as ct
+import pandas as pd
import pytest
-import tskit
import tomli_w
-import pandas as pd
+import tskit
import sc2ts
-from sc2ts import __main__ as main
from sc2ts import cli
from sc2ts import inference as si
class TestImportAlignments:
-
def test_init(self, tmp_path, fx_alignments_fasta):
ds_path = tmp_path / "ds.zarr"
runner = ct.CliRunner()
@@ -61,7 +58,10 @@ def test_suite_data(self, tmp_path, fx_metadata_tsv, fx_alignments_fasta):
result = runner.invoke(
cli.cli,
- f"import-metadata {ds_path} {fx_metadata_tsv} --field-descriptions={fields_path}",
+ (
+ f"import-metadata {ds_path} {fx_metadata_tsv} "
+ f"--field-descriptions={fields_path}"
+ ),
catch_exceptions=False,
)
ds = sc2ts.Dataset(ds_path)
@@ -87,7 +87,6 @@ def test_viridian_metadata(
class TestRunHmm:
-
def test_single_defaults(self, tmp_path, fx_ts_map, fx_dataset):
strain = "ERR4206593"
ts = fx_ts_map["2020-02-04"]
@@ -159,7 +158,6 @@ def test_single_options(self, tmp_path, fx_ts_map, fx_dataset):
class TestInfer:
-
def make_config(
self,
tmp_path,
@@ -379,7 +377,6 @@ def test_multiple_override(self, tmp_path, fx_ts_map, fx_dataset):
class TestPostprocess:
-
def test_example(self, tmp_path, fx_ts_map, fx_match_db):
ts = fx_ts_map["2020-02-13"]
out_ts_path = tmp_path / "ts.ts"
@@ -399,7 +396,6 @@ def test_example(self, tmp_path, fx_ts_map, fx_match_db):
class TestMinimiseMetadata:
-
def test_example(self, tmp_path, fx_ts_map):
ts = fx_ts_map["2020-02-13"]
out_ts_path = tmp_path / "ts.ts"
@@ -411,9 +407,7 @@ def test_example(self, tmp_path, fx_ts_map):
)
assert result.exit_code == 0
out = tskit.load(out_ts_path)
- ts.tables.assert_equals(
- out.tables, ignore_metadata=True, ignore_provenance=True
- )
+ ts.tables.assert_equals(out.tables, ignore_metadata=True, ignore_provenance=True)
dfn = sc2ts.node_data(out, inheritance_stats=False)
assert "sample_id" in dfn
# Check we've kept the vestigial root edge
@@ -447,16 +441,13 @@ def test_example_args(self, tmp_path, fx_ts_map):
)
assert result.exit_code == 0
out = tskit.load(out_ts_path)
- ts.tables.assert_equals(
- out.tables, ignore_metadata=True, ignore_provenance=True
- )
+ ts.tables.assert_equals(out.tables, ignore_metadata=True, ignore_provenance=True)
dfn = sc2ts.node_data(out, inheritance_stats=False)
assert "sample_id" in dfn
assert "pango" in dfn
class TestMapParsimony:
-
def test_example(self, tmp_path, fx_ts_map, fx_dataset):
ts = fx_ts_map["2020-02-13"]
out_ts_path = tmp_path / "ts.ts"
@@ -494,9 +485,7 @@ def test_example_no_report(self, tmp_path, fx_ts_map, fx_dataset):
)
assert result.exit_code == 0
out = tskit.load(out_ts_path)
- ts.tables.assert_equals(
- out.tables, ignore_metadata=True, ignore_provenance=True
- )
+ ts.tables.assert_equals(out.tables, ignore_metadata=True, ignore_provenance=True)
def test_example_no_sites(self, tmp_path, fx_ts_map, fx_dataset):
ts = fx_ts_map["2020-02-13"]
@@ -516,7 +505,6 @@ def test_example_no_sites(self, tmp_path, fx_ts_map, fx_dataset):
class TestApplyParsimonyHeuristics:
-
def test_example(self, tmp_path, fx_ts_map):
ts = fx_ts_map["2020-02-13"]
out_ts_path = tmp_path / "out.ts"
@@ -537,7 +525,6 @@ def test_example(self, tmp_path, fx_ts_map):
class TestRematchRecombinant:
-
def test_recombinant_example_1(self, fx_recombinant_example_1_info):
info = fx_recombinant_example_1_info
@@ -555,7 +542,6 @@ def test_recombinant_example_1(self, fx_recombinant_example_1_info):
class TestRematchRecombinantLbs:
-
def test_recombinant_example_1(self, fx_recombinant_example_1_info):
info = fx_recombinant_example_1_info
@@ -595,7 +581,6 @@ def test_ba2_example(self, tmp_path):
class TestValidate:
-
@pytest.mark.parametrize("date", ["2020-01-01", "2020-02-11"])
def test_date(self, tmp_path, fx_ts_map, fx_dataset, date):
ts = fx_ts_map[date]
diff --git a/tests/test_dataset.py b/tests/test_dataset.py
index 253ff690..315aca4e 100644
--- a/tests/test_dataset.py
+++ b/tests/test_dataset.py
@@ -1,14 +1,13 @@
import itertools
import numpy as np
-import pytest
import numpy.testing as nt
-import xarray.testing as xt
+import pytest
import sgkit
+import xarray.testing as xt
import sc2ts
-from sc2ts import jit
-from sc2ts import data_import
+from sc2ts import data_import, jit
def assert_datasets_equal(ds1, ds2):
@@ -36,7 +35,6 @@ def test_massaged_viridian_metadata(fx_raw_viridian_metadata_df):
class TestCreateDataset:
-
def test_new(self, tmp_path):
path = tmp_path / "dataset.vcz"
sc2ts.Dataset.new(path)
@@ -227,7 +225,6 @@ def test_copy_subset(self, tmp_path, fx_dataset, sample_id):
class TestDatasetFasta:
-
def test_write_fasta_all(self, tmp_path, fx_dataset, fx_alignments_fasta):
path = tmp_path / "export.fa"
with open(path, "w") as f:
@@ -288,7 +285,6 @@ def test_write_fasta_subset(
class TestDatasetVariants:
-
def test_all(self, fx_dataset):
G = fx_dataset["call_genotype"][:].squeeze()
pos = fx_dataset["variant_position"][:]
@@ -351,7 +347,6 @@ def test_sample_slice(self, fx_dataset, start, stop):
class TestDatasetMethods:
-
def test_zarr_mapping(self, fx_dataset):
assert len(fx_dataset) == len(fx_dataset.root)
assert list(fx_dataset) == list(fx_dataset.root)
@@ -382,7 +377,6 @@ def test_repr_markdown(self, fx_dataset):
class TestMafftAlignments:
-
def test_import(self, tmp_path, fx_encoded_alignments_mafft):
path = tmp_path / "dataset.vcz"
sc2ts.Dataset.new(path)
@@ -398,7 +392,6 @@ def test_import(self, tmp_path, fx_encoded_alignments_mafft):
class TestDatasetAlignments:
-
def test_fetch_known(self, fx_dataset):
a = fx_dataset.alignment["SRR11772659"]
assert a.shape == (sc2ts.REFERENCE_SEQUENCE_LENGTH - 1,)
@@ -449,7 +442,6 @@ def test_chunk_size_cache_size(
class TestDatasetMetadata:
-
def test_len(self, fx_dataset):
assert len(fx_dataset.metadata) == 55
@@ -602,7 +594,6 @@ def test_too_large(self, a):
class TestMaskFlankingDeletions:
-
@pytest.mark.parametrize(
["nucs", "expected"],
[
diff --git a/tests/test_debug.py b/tests/test_debug.py
index ce47e466..4f79e264 100644
--- a/tests/test_debug.py
+++ b/tests/test_debug.py
@@ -1,18 +1,13 @@
-import datetime
import inspect
+import matplotlib
import numpy as np
import numpy.testing as nt
import pandas as pd
-import matplotlib
import pytest
-import msprime
-import tskit
-
import sc2ts
from sc2ts import debug
-from sc2ts import inference as si
@pytest.fixture
@@ -161,12 +156,6 @@ def test_summary(self, fx_ti_2020_02_15):
assert df.loc["sample_groups"].value == 27
assert df.loc["retro_sample_groups"].value == 1
- def test_summary(self, fx_ti_2020_02_15):
- df = fx_ti_2020_02_15.summary()
- assert df.loc["samples"].value == 43
- assert df.loc["sample_groups"].value == 27
- assert df.loc["retro_sample_groups"].value == 1
-
def test_recombinants_summary_example_1(self, fx_ti_recombinant_example_1):
df = fx_ti_recombinant_example_1.recombinants_summary()
assert df.shape[0] == 1
@@ -263,7 +252,6 @@ def test_draw_svg(self, fx_ti_2020_02_13):
class TestDataFuncsEquivalant:
-
def test_example_node(self, fx_ts_min_2020_02_15, fx_ti_2020_02_15):
ts = fx_ts_min_2020_02_15
ti = fx_ti_2020_02_15
diff --git a/tests/test_inference.py b/tests/test_inference.py
index 685787ff..0f429372 100644
--- a/tests/test_inference.py
+++ b/tests/test_inference.py
@@ -1,22 +1,16 @@
import dataclasses
-import collections
import hashlib
-import logging
import json
+import msprime
import numpy as np
import numpy.testing as nt
+import pandas as pd
import pytest
-import tsinfer
import tskit
-import msprime
-import pandas as pd
import sc2ts
-from sc2ts import debug
-from sc2ts import jit
-from sc2ts import tree_ops
-from sc2ts import validation
+from sc2ts import debug, jit, tree_ops, validation
from sc2ts import inference as si
@@ -85,7 +79,6 @@ def test_get_group_strains(fx_ts_map):
class TestRecombinantHandling:
-
def test_get_recombinant_strains_ex1(self, fx_recombinant_example_1):
d = si.get_recombinant_strains(fx_recombinant_example_1)
assert d == {55: ["recombinant_example_1_0", "recombinant_example_1_1"]}
@@ -529,9 +522,7 @@ def test_2020_02_02_max_missing_sites(
assert np.sum(ts.nodes_time[ts.samples()] == 0) == new_samples
for u in ts.samples()[-new_samples:]:
- assert (
- ts.node(u).metadata["sc2ts"]["num_missing_sites"] <= max_missing_sites
- )
+ assert ts.node(u).metadata["sc2ts"]["num_missing_sites"] <= max_missing_sites
@pytest.mark.parametrize(
["strain", "start", "length"],
@@ -754,8 +745,7 @@ def test_2020_02_14_skip_max_mutations(
retro_groups = ts.metadata["sc2ts"]["retro_groups"]
assert len(retro_groups) == 0
assert (
- "Skipping mean_mutations_per_sample=1.0 exceeds threshold"
- in caplog.text
+ "Skipping mean_mutations_per_sample=1.0 exceeds threshold" in caplog.text
)
def test_2020_02_14_skip_root_mutations(
@@ -980,7 +970,6 @@ def test_exact_matches(self, fx_ts_map, strain, parent):
class TestSyntheticAlignments:
-
def test_exact_match(self, tmp_path, fx_ts_map, fx_dataset):
# Pick two unique strains and we should match exactly with them
strains = ["SRR11597218", "ERR4204459"]
@@ -1252,7 +1241,6 @@ def test_match_recombinant(self, fx_ts_map):
class TestRunHmm:
-
@pytest.mark.parametrize("direction", ["F", "R", "forwards", "backwards", "", None])
def test_bad_direction(self, fx_dataset, fx_ts_map, direction):
strain = "SRR11597164"
@@ -1272,7 +1260,6 @@ def test_no_strains(self, fx_dataset, fx_ts_map):
class TestCharacteriseRecombinants:
-
def test_example_1(self, fx_ts_map):
ts, s = recombinant_example_1(fx_ts_map)
@@ -1389,7 +1376,6 @@ def test_example_3_way_same_parent(self, fx_recombinant_example_3):
class TestExtractHaplotypes:
-
@pytest.mark.parametrize(
["samples", "result"],
[
@@ -1536,9 +1522,7 @@ def test_validate(self, fx_ts_map, fx_dataset):
ts = fx_ts_map["2020-02-13"]
sites = [1547, 3951, 3952, 3953]
result = si.map_parsimony(ts, fx_dataset, sites)
- validation.validate(
- result.tree_sequence, fx_dataset, deletions_as_missing=False
- )
+ validation.validate(result.tree_sequence, fx_dataset, deletions_as_missing=False)
def test_provenance(self, fx_ts_map, fx_dataset):
ts = fx_ts_map["2020-02-13"]
@@ -1614,13 +1598,10 @@ def test_provenance(self, fx_ts_map, fx_match_db):
class TestMinimiseMetadata:
-
def test_equivalent(self, fx_ts_map):
ts = fx_ts_map["2020-02-13"]
tsp = si.minimise_metadata(ts)
- ts.tables.assert_equals(
- tsp.tables, ignore_metadata=True, ignore_provenance=True
- )
+ ts.tables.assert_equals(tsp.tables, ignore_metadata=True, ignore_provenance=True)
def test_properties(self, fx_ts_map):
ts = fx_ts_map["2020-02-13"]
@@ -1672,7 +1653,6 @@ def test_provenance(self, fx_ts_map):
class TestPushUpRecombinantMutations:
-
def test_no_recombinants(self, fx_ts_map):
ts = fx_ts_map["2020-02-13"]
tsp = si.push_up_unary_recombinant_mutations(ts)
@@ -1811,7 +1791,6 @@ def test_ba2_recombinant(self):
class TestRematchRecombinantsLbs:
-
def test_bad_node(self, fx_recombinant_example_1_info):
info = fx_recombinant_example_1_info
base_ts = tskit.load(info.base_ts)
diff --git a/tests/test_jit.py b/tests/test_jit.py
index cb088a33..b633469f 100644
--- a/tests/test_jit.py
+++ b/tests/test_jit.py
@@ -1,7 +1,7 @@
-import numpy as np
import msprime
-import tskit
+import numpy as np
import numpy.testing as nt
+import tskit
from sc2ts import jit
@@ -63,7 +63,6 @@ def multiple_trees_example_ts():
class TestArgCounts:
-
def test_single_tree_example(self):
ts = single_tree_example_ts()
c = jit.count(ts)
diff --git a/tests/test_tree_ops.py b/tests/test_tree_ops.py
index f6982f52..c8bb5bdf 100644
--- a/tests/test_tree_ops.py
+++ b/tests/test_tree_ops.py
@@ -1,13 +1,11 @@
+import biotite.sequence.phylo as bsp
+import msprime
import numpy as np
+import numpy.testing as nt
import pytest
import tskit
-import msprime
-import biotite.sequence.phylo as bsp
-import numpy.testing as nt
-import sc2ts
-from sc2ts import tree_ops
-from sc2ts import inference
+from sc2ts import inference, tree_ops
def all_trees_ts(n):
@@ -73,7 +71,6 @@ def prepare(tables):
class TestSplitBranch:
-
def test_root(self):
# 2.00┊ 6 ┊
# ┊ ┏━┻━┓ ┊
@@ -658,7 +655,6 @@ def test_simulation(self, n, mutation_rate):
class TestFullSpanSibs:
-
@pytest.mark.parametrize(
["nodes", "sibs"],
[
@@ -707,7 +703,6 @@ def test_all_trees_ts(self, nodes):
class TestInferBinary:
-
def check_properties(self, ts):
assert ts.num_trees == 1
tree = ts.first()
@@ -777,7 +772,6 @@ def test_simulation_root_mutations(self, n, num_mutations):
class TestFromBiotite:
-
def check_round_trip(self, tsk_tree):
node_labels = {u: f"{u}" for u in tsk_tree.tree_sequence.samples()}
nwk = tsk_tree.as_newick(node_labels=node_labels)
@@ -798,7 +792,6 @@ def test_comb(self, n):
class TestRerooting:
-
def check_properties(self, before, after, root):
assert after.num_trees == 1
assert before.sequence_length == after.sequence_length
@@ -924,7 +917,6 @@ def test_example_same_root(self):
class TestDropVestigialRootEdge:
-
def test_example(self, fx_ts_map):
ts = fx_ts_map["2020-02-13"]
e = ts.edge(-1)
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 00000000..b91c3e76
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,4973 @@
+version = 1
+revision = 3
+requires-python = ">=3.10"
+resolution-markers = [
+ "python_full_version >= '3.14' and sys_platform == 'win32'",
+ "python_full_version >= '3.14' and sys_platform == 'emscripten'",
+ "python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'",
+ "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'win32'",
+ "python_full_version == '3.11.*' and sys_platform == 'win32'",
+ "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'emscripten'",
+ "python_full_version == '3.11.*' and sys_platform == 'emscripten'",
+ "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'",
+ "python_full_version == '3.11.*' and sys_platform != 'emscripten' and sys_platform != 'win32'",
+ "python_full_version < '3.11'",
+]
+
+[[package]]
+name = "accessible-pygments"
+version = "0.0.5"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+ { name = "pygments" },
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