First commit

.coveragerc

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+[run]
+branch = True
+source = klusta
+
+[report]
+exclude_lines =
+    pragma: no cover
+    raise AssertionError
+    raise NotImplementedError
+    pass
+    return

.travis.yml

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+language: python
+sudo: false
+python:
+  - "2.7"
+  - "3.4"
+  - "3.5"
+before_install:
+  - pip install codecov
+install:
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda info -a
+  # Create the environment.
+  - conda env create python=$TRAVIS_PYTHON_VERSION
+  - source activate klusta
+  - pip install klustakwik2
+  # Dev requirements
+  - pip install -r requirements-dev.txt
+  - pip install -e .
+script:
+  - make test
+after_success:
+  - codecov

MANIFEST.in

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+include LICENSE
+include README.md
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

Makefile

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+clean-build:
+	rm -fr build/
+	rm -fr dist/
+	rm -fr *.egg-info
+
+clean-pyc:
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean: clean-build clean-pyc
+
+lint:
+	flake8 klusta
+
+test: lint
+	py.test --cov-report term-missing --cov=klusta klusta
+
+coverage:
+	coverage --html
+
+apidoc:
+	python tools/api.py
+
+build:
+	python setup.py sdist --formats=zip
+
+upload:
+	python setup.py sdist --formats=zip upload

requirements-dev.txt

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+# Need development version of pytest for py35 compat
+# https://github.com/pytest-dev/pytest/issues/744
+git+https://github.com/pytest-dev/pytest.git
+
+flake8
+coverage==3.7.1
+coveralls
+responses
+pytest-cov
+nose

setup.cfg

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+[wheel]
+universal = 1
+
+[pytest]
+norecursedirs = experimental _*
+
+[flake8]
+ignore=E265,E731

setup.py

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+# -*- coding: utf-8 -*-
+# flake8: noqa
+
+"""Installation script."""
+
+
+#------------------------------------------------------------------------------
+# Imports
+#------------------------------------------------------------------------------
+
+import os
+import os.path as op
+import re
+
+from setuptools import setup
+
+
+#------------------------------------------------------------------------------
+# Setup
+#------------------------------------------------------------------------------
+
+def _package_tree(pkgroot):
+    path = op.dirname(__file__)
+    subdirs = [op.relpath(i[0], path).replace(op.sep, '.')
+               for i in os.walk(op.join(path, pkgroot))
+               if '__init__.py' in i[2]]
+    return subdirs
+
+
+curdir = op.dirname(op.realpath(__file__))
+readme = open(op.join(curdir, 'README.md')).read()
+
+
+# Find version number from `__init__.py` without executing it.
+filename = op.join(curdir, 'klusta/__init__.py')
+with open(filename, 'r') as f:
+    version = re.search(r"__version__ = '([^']+)'", f.read()).group(1)
+
+
+setup(
+    name='klusta',
+    version=version,
+    license="BSD",
+    description='Spike detection and automatic clustering for spike sorting',
+    long_description=readme,
+    author='Kwik Team',
+    author_email='cyrille.rossant at gmail.com',
+    url='https://klusta.cortexlab.net',
+    packages=_package_tree('klusta'),
+    package_dir={'klusta': 'klusta'},
+    package_data={
+        'klusta': ['*.txt', '*.prb'],
+    },
+    entry_points={
+        'console_scripts': [
+            'klusta = klusta.utils.cli:klusta'
+        ],
+    },
+    include_package_data=True,
+    keywords='klusta,neuroscience,spike sorting,klustakwik',
+    classifiers=[
+        'Development Status :: 3 - Alpha',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: BSD License',
+        'Natural Language :: English',
+        "Programming Language :: Python :: 2",
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+    ],
+)