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setup.py
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setup.py
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# Always prefer setuptools over distutils
import os
import glob
import pathlib
from setuptools import setup, find_packages
from collections import defaultdict
from phyluce import __version__
# import pdb
# Copy the executable files to a single place. Used below.
scrpt = []
for d in [
"align",
"assembly",
"genetrees",
"ncbi",
"probes",
"utilities",
"workflow",
]:
scrpt.extend([i for i in glob.glob(os.path.join("bin", d, "*"))])
"""
# the following function and call are used to grab the data files
# that we need for workflows and tests
def package_files(directory):
paths = []
for (path, directories, filenames) in os.walk(directory):
# skip hidden files and dirs
filenames = [f for f in filenames if not f[0] == "."]
directories[:] = [d for d in directories if not d[0] == "."]
for filename in filenames:
paths.append(os.path.join("..", path, filename))
return paths
t_files = []
for dir in ["phyluce/tests/test-expected"]:
t_files.extend(package_files(dir))
"""
# the following function and call are used to grab the data files
# that we need for workflows and tests
def data_files(directory):
paths = defaultdict(list)
for (path, directories, filenames) in os.walk(directory):
# skip hidden files and dirs
filenames = [f for f in filenames if not f[0] == "."]
directories[:] = [d for d in directories if not d[0] == "."]
for filename in filenames:
# pdb.set_trace()
# paths.append([path,os.path.join(path, filename)])
paths[path].append(os.path.join(path, filename))
return paths
d_files = []
for dir in ["config", "workflows", "phyluce/tests/test-expected"]:
files = data_files(dir)
for k, v in files.items():
if k.startswith("config") or k.startswith("workflows"):
k = os.path.join("phyluce", k)
d_files.append((k, v))
setup(
name="phyluce", # Required
# Versions should comply with PEP 440:
# https://www.python.org/dev/peps/pep-0440/
#
# For a discussion on single-sourcing the version across setup.py and the
# project code, see
# https://packaging.python.org/en/latest/single_source_version.html
version=__version__, # Required
# This is a one-line description or tagline of what your project does. This
# corresponds to the "Summary" metadata field:
# https://packaging.python.org/specifications/core-metadata/#summary
description="Software for UCE (and general) phylogenomics", # Optional
# This is an optional longer description of your project that represents
# the body of text which users will see when they visit PyPI.
#
# Often, this is the same as your README, so you can just read it in from
# that file directly (as we have already done above)
#
# This field corresponds to the "Description" metadata field:
# https://packaging.python.org/specifications/core-metadata/#description-optional
# long_description=long_description, # Optional
# Denotes that our long_description is in Markdown; valid values are
# text/plain, text/x-rst, and text/markdown
#
# Optional if long_description is written in reStructuredText (rst) but
# required for plain-text or Markdown; if unspecified, "applications should
# attempt to render [the long_description] as text/x-rst; charset=UTF-8 and
# fall back to text/plain if it is not valid rst" (see link below)
#
# This field corresponds to the "Description-Content-Type" metadata field:
# https://packaging.python.org/specifications/core-metadata/#description-content-type-optional
long_description_content_type="text/x-rst", # Optional (see note above)
# This should be a valid link to your project's main homepage.
#
# This field corresponds to the "Home-Page" metadata field:
# https://packaging.python.org/specifications/core-metadata/#home-page-optional
url="https://github.com/faircloth-lab/phyluce", # Optional
# This should be your name or the name of the organization which owns the
# project.
author="Brant C. Faircloth", # Optional
# This should be a valid email address corresponding to the author listed
# above.
# Classifiers help users find your project by categorizing it.
#
# For a list of valid classifiers, see https://pypi.org/classifiers/
classifiers=[ # Optional
# How mature is this project? Common values are
# 3 - Alpha
# 4 - Beta
# 5 - Production/Stable
"Development Status :: 5 - Production/Stable",
# Indicate who your project is intended for
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
# Pick your license as you wish
"License :: OSI Approved :: BSD License",
# Specify the Python versions you support here. In particular, ensure
# that you indicate you support Python 3. These classifiers are *not*
# checked by 'pip install'. See instead 'python_requires' below.
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3 :: Only",
],
# This field adds keywords for your project which will appear on the
# project page. What does your project relate to?
#
# Note that this is a list of additional keywords, separated
# by commas, to be used to assist searching for the distribution in a
# larger catalog.
keywords="uce, phylogenomics, phylogenetics, genetics", # Optional
# When your source code is in a subdirectory under the project root, e.g.
# `src/`, it is necessary to specify the `package_dir` argument.
# package_dir={'': 'phyluce',}, # Optional
# You can just specify package directories manually here if your project is
# simple. Or you can use find_packages().
#
# Alternatively, if you just want to distribute a single Python file, use
# the `py_modules` argument instead as follows, which will expect a file
# called `my_module.py` to exist:
#
# py_modules=["my_module"],
#
packages=find_packages(), # Required
# Specify which Python versions you support. In contrast to the
# 'Programming Language' classifiers above, 'pip install' will check this
# and refuse to install the project if the version does not match. See
# https://packaging.python.org/guides/distributing-packages-using-setuptools/#python-requires
python_requires="~=3.6",
# This field lists other packages that your project depends on to run.
# Any package you put here will be installed by pip when your project is
# installed, so they must be valid existing projects.
#
# For an analysis of "install_requires" vs pip's requirements files see:
# https://packaging.python.org/en/latest/requirements.html
# install_requires=['peppercorn'], # Optional
# List additional groups of dependencies here (e.g. development
# dependencies). Users will be able to install these using the "extras"
# syntax, for example:
#
# $ pip install sampleproject[dev]
#
# Similar to `install_requires` above, these must be valid existing
# projects.
# extras_require={ # Optional
# 'dev': ['check-manifest'],
# 'test': ['coverage'],
# },
#
# If there are data files included in your packages that need to be
# installed, specify them here.
# package_data={"": t_files},
data_files=d_files,
# To provide executable scripts, use entry points in preference to the
# "scripts" keyword. Entry points provide cross-platform support and allow
# `pip` to create the appropriate form of executable for the target
# platform.
#
# For example, the following would provide a command called `sample` which
# executes the function `main` from this package when invoked:
# entry_points={ # Optional
# 'console_scripts': [
# 'sample=sample:main',
# ],
# },
scripts=scrpt,
# List additional URLs that are relevant to your project as a dict.
#
# This field corresponds to the "Project-URL" metadata fields:
# https://packaging.python.org/specifications/core-metadata/#project-url-multiple-use
#
# Examples listed include a pattern for specifying where the package tracks
# issues, where the source is hosted, where to say thanks to the package
# maintainers, and where to support the project financially. The key is
# what's used to render the link text on PyPI.
project_urls={ # Optional
"Bug Reports": "https://github.com/faircloth-lab/phyluce/issues/",
"Source": "https://github.com/faircloth-lab/phyluce/",
},
)