Merge pull request #11 from jingpengw/master

release the package to pypi

.gitignore

@@ -6,4 +6,4 @@ build
 *checkpoints*
 *.nfs
 *.sw[pmno]
-waterz/evaluate.cpp
+jwu/

.travis.yml

@@ -0,0 +1,42 @@
+language: python
+
+python:
+- '3.7'
+- '3.8'
+- '3.9'
+
+services:
+- docker
+
+env:
+- DOCKER_IMAGE=quay.io/pypa/manylinux1_x86_64 PLAT=manylinux1_x86_64
+- DOCKER_IMAGE=quay.io/pypa/manylinux1_i686 PRE_CMD=linux32 PLAT=manylinux1_i686
+- DOCKER_IMAGE=quay.io/pypa/manylinux2010_x86_64 PLAT=manylinux2010_x86_64
+
+before_install:
+- docker pull $DOCKER_IMAGE
+
+install:
+- sudo find /usr -name '*.pyc' -delete
+- sudo apt update
+- sudo apt install libboost-dev
+- pip install -r requirements.txt
+- pip install .
+
+script:
+- pytest --cov-append --cov=./waterz ./tests --verbose
+
+after_success:
+- coveralls
+- chmod +x ./travis/build-wheels.sh
+- docker run --rm -e PLAT=$PLAT -v `pwd`:/io $DOCKER_IMAGE $PRE_CMD /io/travis/build-wheels.sh
+- ls wheelhouse/
+- |
+  if [[ $TRAVIS_TAG ]]; then
+    echo "upload wheel file."
+    python -m pip install twine
+    python -m twine upload wheelhouse/waterz*.whl
+  fi
+
+notifications:
+  email: false

MANIFEST.in

@@ -1,5 +1,10 @@
+include requirements.txt
 include README.md
+
 recursive-include waterz *.hpp
 recursive-include waterz *.pyx
 recursive-include waterz *.h
+recursive-include waterz *.h
+
 include waterz/frontend_agglomerate.cpp
+include waterz/evaluate.cpp

README.md

@@ -1,3 +1,11 @@
+[![Build Status](https://travis-ci.org/jingpengw/waterz.svg?branch=master)](https://travis-ci.org/jingpengw/waterz)
+[![PyPI version](https://badge.fury.io/py/waterz.svg)](https://badge.fury.io/py/waterz)
+
+<!--
+    the coerage is not working on c++ code, so the coverage is 0 now!
+    [![Coverage Status](https://coveralls.io/repos/github/jingpengw/waterz/badge.svg?branch=master)](https://coveralls.io/github/jingpengw/waterz?branch=master)
+-->
+
 # waterz
 
 Pronounced *water-zed*. A simple watershed and region agglomeration library for
@@ -7,9 +15,23 @@ Based on the watershed implementation of [Aleksandar Zlateski](https://bitbucket
 
 # Installation
 
-`python setup.py install`
+Install c++ dependencies:
+
+```
+sudo apt install libboost-dev
+```
+
+Install from PyPI
+
+```
+pip install waterz
+```
+
+install from local version
 
-Requires `numpy` and `cython`.
+```
+pip install .
+```
 
 # Usage
 
@@ -24,3 +46,14 @@ thresholds = [0, 100, 200]
 
 segmentations = waterz.agglomerate(affinities, thresholds)
 ```
+
+# Development
+## Release to pypi
+We use travis to create release
+
+upgrade the version number in the `setup.py` file, then
+```
+git tag v0.9.5
+git push origin v0.9.5
+```
+the travis build system will get a `TRAVIS_TAG` variable, and triger the `twine upload` command.

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "numpy", "wheel"]
+build-backend = "setuptools.build_meta"

requirements.txt

@@ -0,0 +1,8 @@
+numpy
+cython
+
+# dev
+
+pytest
+coveralls
+pytest-cov

setup.py

@@ -1,47 +1,75 @@
-from setuptools import setup
+from setuptools import setup, find_packages
 from setuptools.extension import Extension
-from Cython.Build import cythonize
-import numpy
+from setuptools.command.build_ext import build_ext as _build_ext
+# from Cython.Build import cythonize
 import os
+import builtins
+
+VERSION = '0.9.5'
+
+PACKAGE_DIR = os.path.dirname(os.path.abspath(__file__))
+
+
+with open(os.path.join(PACKAGE_DIR, "README.md"), "r") as fh:
+    long_description = fh.read()
+
+
+class build_ext(_build_ext):
+    """We assume no numpy at the begining
+    https://stackoverflow.com/questions/19919905/how-to-bootstrap-numpy-installation-in-setup-py
+    """
+    def finalize_options(self):
+        _build_ext.finalize_options(self)
+        # Prevent numpy from thinking it is still in its setup process:
+        builtins.__NUMPY_SETUP__ = False
+        import numpy
+        self.include_dirs.append(numpy.get_include())
+
 
 source_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'waterz')
 include_dirs = [
     source_dir,
     os.path.join(source_dir, 'backend'),
     # os.path.dirname(get_python_inc()),
-    numpy.get_include(),
+    # numpy.get_include(),
 ]
 extensions = [
     Extension(
         'waterz.evaluate',
-        sources=['waterz/evaluate.pyx', 'waterz/frontend_evaluate.cpp'],
+        sources=['waterz/evaluate.cpp', 'waterz/frontend_evaluate.cpp'],
         include_dirs=include_dirs,
         language='c++',
         extra_link_args=['-std=c++11'],
         extra_compile_args=['-std=c++11', '-w'])
 ]
 
+
 setup(
-        name='waterz',
-        version='0.8',
-        description='Simple watershed and agglomeration for affinity graphs.',
-        url='https://github.com/funkey/waterz',
-        author='Jan Funke',
-        author_email='[email protected]',
-        license='MIT',
-        requires=['cython','numpy'],
-        packages=['waterz'],
-        package_data={
-            '': [
-                'waterz/*.h',
-                'waterz/*.hpp',
-                'waterz/*.cpp',
-                'waterz/*.cpp',
-                'waterz/*.pyx',
-                'waterz/backend/*.hpp',
-            ]
-        },
-        include_package_data=True,
-        zip_safe=False,
-        ext_modules=cythonize(extensions)
+    name='waterz',
+    version=VERSION,
+    description='Simple watershed and agglomeration for affinity graphs.',
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url='https://github.com/funkey/waterz',
+    author='Jan Funke, Jingpeng Wu',
+    author_email='[email protected]',
+    license='MIT',
+    cmdclass={'build_ext': build_ext},
+    setup_requires=['numpy'],
+    install_requires=['numpy', 'cython'],
+    tests_require=['pytest'],
+    packages=find_packages(),
+    package_data={
+        '': ['*.pyx', '*.hpp', '*.cpp', '*.h', '*.py', 'backend/*.hpp'],
+        'backend': ['*.hpp']
+    },
+    zip_safe=False,
+    ext_modules=extensions,
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Intended Audience :: Developers",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    requires_python=">=3.6, <4",
 )

tests/conftest.py

@@ -0,0 +1,9 @@
+import sys
+from pathlib import Path
+
+# waterz is not locally importable;
+# this snippet forces the tests to use the installed version.
+# See here for more details:
+# https://stackoverflow.com/questions/67176036/how-to-prevent-pytest-using-local-module
+project_dir = str(Path(__file__).resolve().parent.parent)
+sys.path = [p for p in sys.path if not p.startswith(project_dir)]

tests/test_evaluate.py

@@ -0,0 +1,27 @@
+import numpy as np
+import waterz as wz
+from math import isclose
+
+
+def test_evaluate():
+    # make the random value consistent with different runs
+    np.random.seed(0)
+
+    seg = np.random.randint(500, size=(3, 3, 3), dtype=np.uint64)
+    scores = wz.evaluate(seg, seg)
+    assert scores['voi_split'] == 0.0
+    assert scores['voi_merge'] == 0.0
+    assert scores['rand_split'] == 1.0
+    assert scores['rand_merge'] == 1.0
+
+    seg2 = np.random.randint(500, size=(3,3,3), dtype=np.uint64)
+    scores = wz.evaluate(seg, seg2)
+    #print('scores: ', scores)
+    # Note that these values are from the first run 
+    # I have not double checked that this is correct or not.
+    # This assertion only make sure that future changes of 
+    # code will not change the result of the evaluation
+    assert isclose(scores['rand_split'], 0.8181818181818182)
+    assert isclose(scores['rand_merge'], 0.8709677419354839)
+    assert isclose(scores['voi_split'], 0.22222222222222232)
+    assert isclose(scores['voi_merge'], 0.14814814814814792)

travis/build-wheels.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+set -e -x
+
+# Install a system package required by our library
+#yum check-update
+yum install -y boost-devel
+
+# Compile wheels
+for PYBIN in /opt/python/*/bin; do
+    "${PYBIN}/pip" install -r /io/requirements.txt
+    "${PYBIN}/pip" wheel /io/ -w wheelhouse/
+done
+
+# Bundle external shared libraries into the wheels
+for whl in wheelhouse/*.whl; do
+    auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/
+done
+
+# Install packages and test
+for PYBIN in /opt/python/*/bin/; do
+    "${PYBIN}/pip" install waterz --no-index -f /io/wheelhouse
+done