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Merge pull request #108 from savitakartik/restructure_as_package
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code restructure to enable package install
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jeromekelleher authored Jan 16, 2024
2 parents ef65691 + cc69203 commit 45f52b2
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -5,8 +5,8 @@ This is targetted at ARGs that have been inferred using a variety of inference t

To launch the app use:

`python main.py /path/to/trees-file`
`python -m tsqc /path/to/trees-file`

On WSL, it may be necessary to disable Numba's CUDA support:

`NUMBA_DISABLE_CUDA=1 python main.py /path/to/trees-file`
`NUMBA_DISABLE_CUDA=1 python -m tsqc /path/to/trees-file`
12 changes: 0 additions & 12 deletions pages/__init__.py

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3 changes: 3 additions & 0 deletions pyproject.toml
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[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"
290 changes: 0 additions & 290 deletions qc_plots.py

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50 changes: 50 additions & 0 deletions setup.cfg
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[metadata]
name = tsqc
author = Tskit Developers
author_email = [email protected]
license = MIT
description = Visual QC of ARGs
project_urls =
Bug Tracker = https://github.com/tskit-dev/tsqc/issues
Source Code = https://github.com/tskit-dev/tsqc
classifiers:
Intended Audience :: Science/Research
License :: OSI Approved :: MIT License
Programming Language :: Python :: 3
Topic :: Scientific/Engineering
Topic :: Scientific/Engineering :: Bio-Informatics
long_description = file: README.md
long_description_content_type = text/markdown
url = https://tskit.dev/tsqc/
platforms =
POSIX
Windows
MacOS X
keywords =
tree sequence
ancestral recombination graph
tskit
quality control

[options]
packages = tsqc
python_requires = >=3.8
install_requires =
click
daiquiri
panel
diskcache
hvplot
xarray
datashader
tskit
seaborn
pytest
tszip
appdirs
setup_requires =
setuptools

[tool:pytest]
testpaths =
tests
5 changes: 5 additions & 0 deletions setup.py
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from setuptools import setup

setup(
use_scm_version={"write_to": "tsqc/_version.py"},
)
2 changes: 1 addition & 1 deletion tests/test_data_model.py
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Expand Up @@ -4,7 +4,7 @@
import numpy.testing as nt
import tskit

import model
from tsqc import model


def single_tree_example_ts():
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