Merge pull request #4 from UnseenBio/package

Package up coptr

.editorconfig

@@ -0,0 +1,20 @@
+# Editor Configuration (http://editorconfig.org)
+root = true
+
+[*]
+charset = utf-8
+indent_style = space
+indent_size = 4
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+max_line_length = 88
+
+[*.{json,yml}]
+indent_size = 2
+
+[*.{md,rst}]
+trim_trailing_whitespace = false
+
+[Makefile]
+indent_style = tab

.gitignore

@@ -0,0 +1,209 @@
+### Python template
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+### macOS template
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Linux template
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### Windows template
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+

docs/conf.py

@@ -16,6 +16,8 @@
 
 import os
 import sys
+
+
 sys.path.insert(0, os.path.abspath('..'))
 
 

pyproject.toml

@@ -0,0 +1,17 @@
+[build-system]
+build-backend = 'setuptools.build_meta'
+requires = [
+  'setuptools>=40.6.0',
+  'wheel'
+]
+
+[tool.black]
+line-length = 88
+python-version = ['py37']
+
+[tool.isort]
+profile = 'black'
+skip = ['__init__.py']
+lines_after_imports = 2
+known_first_party = 'coptr'
+known_third_party = ['numpy', 'pysam', 'scipy']

setup.cfg

@@ -0,0 +1,56 @@
+[metadata]
+name = coptr
+url = https://github.com/tyjo/coptr
+download_url = https://pypi.org/project/coptr/
+project_urls =
+    Source Code = https://github.com/tyjo/coptr
+    Documentation = https://coptr.readthedocs.io
+    Bug Tracker = https://github.com/tyjo/coptr/issues
+author = Tyler
+author_email = ?
+# Please consult https://pypi.org/classifiers/ for a full list.
+classifiers =
+    Development Status :: 3 - Alpha
+    Environment :: Console
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+    Natural Language :: English
+    Operating System :: OS Independent
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3 :: Only
+    Topic :: Scientific/Engineering :: Bio-Informatics
+license = GPL-3.0-or-later
+description = Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
+long_description = file: README.md
+long_description_content_type = text/markdown
+keywords =
+    growth rate
+    peak-to-trough ratio
+
+[options]
+zip_safe = True
+install_requires =
+    numpy
+    pysam
+    scipy
+python_requires = >=3.6
+tests_require =
+    tox
+packages = find:
+package_dir =
+     = src
+
+[options.entry_points]
+console_scripts =
+    coptr = coptr.cli:cli
+
+[options.packages.find]
+where = src
+
+[options.extras_require]
+development =
+    black
+    isort

setup.py

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+#!/usr/bin/env python
+
+
+# This file is part of CoPTR.
+#
+# CoPTR is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# CoPTR is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with CoPTR.  If not, see <https://www.gnu.org/licenses/>.
+
+
+"""Set up the CoPTR for Python package."""
+
+
+from setuptools import setup
+
+
+# All other arguments are defined in `setup.cfg`.
+setup()