Fix pip installation to work without pre-installed numpy/cython

.circleci/config.yml

@@ -50,10 +50,10 @@ jobs:
             name: Get Python running
             command: |
               python -m pip install --user --upgrade --progress-bar off pip
+              python -m pip install --user -e .
               python -m pip install --user --upgrade --progress-bar off -r requirements.txt
               python -m pip install --user --upgrade --progress-bar off -r docs/requirements.txt
               python -m pip install --user --upgrade --progress-bar off ipython "https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master" memory_profiler
-              python -m pip install --user -e .
 
         - save_cache:
             key: pip-cache
@@ -183,4 +183,4 @@ workflows:
             branches:
               ignore: /.*/
             tags:
-              only: /[0-9]+(\.[0-9]+)*$/
+              only: /[0-9]+(\.[0-9]+)*$/

README.md

@@ -82,13 +82,6 @@ The library has been tested on Linux, MacOSX and Windows. It requires a C++ comp
 
 #### Pip installation
 
-Note that due to a limitation of pip, `cython` and `numpy` need to be installed
-prior to installing POT. This can be done easily with
-
-```console
-pip install numpy cython
-```
-
 You can install the toolbox through PyPI with:
 
 ```console

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "wheel", "numpy>=1.16", "cython>=0.23"]
+build-backend = "setuptools.build_meta"

setup.py

@@ -5,12 +5,9 @@
 import subprocess
 import sys
 
-from setuptools import find_packages, setup
-from setuptools.extension import Extension
+from setuptools import find_packages, setup, Extension
 
 import numpy
-from Cython.Build import cythonize
-
 
 # dirty but working
 __version__ = re.search(
@@ -34,7 +31,8 @@
 if sys.platform.startswith('darwin'):
     compile_args.append("-stdlib=libc++")
     sdk_path = subprocess.check_output(['xcrun', '--show-sdk-path'])
-    os.environ['CFLAGS'] = '-isysroot "{}"'.format(sdk_path.rstrip().decode("utf-8"))
+    os.environ['CFLAGS'] = '-isysroot "{}"'.format(
+        sdk_path.rstrip().decode("utf-8"))
 
 setup(
     name='POT',
@@ -46,19 +44,22 @@
     author_email='remi.flamary@gmail.com, ncourty@gmail.com',
     url='https://github.com/PythonOT/POT',
     packages=find_packages(),
-    ext_modules=cythonize(Extension(
-        name="ot.lp.emd_wrap",
-        sources=["ot/lp/emd_wrap.pyx", "ot/lp/EMD_wrapper.cpp"],  # cython/c++ src files
-        language="c++",
-        include_dirs=[numpy.get_include(), os.path.join(ROOT, 'ot/lp')],
-        extra_compile_args=compile_args,
-    )),
+    ext_modules=[
+        Extension(
+            name="ot.lp.emd_wrap",
+            sources=["ot/lp/emd_wrap.pyx",
+                     "ot/lp/EMD_wrapper.cpp"],  # cython/c++ src files
+            language="c++",
+            include_dirs=[numpy.get_include()],
+            extra_compile_args=compile_args,
+        )
+    ],
     platforms=['linux', 'macosx', 'windows'],
-    download_url='https://github.com/PythonOT/POT/archive/{}.tar.gz'.format(__version__),
+    download_url='https://github.com/PythonOT/POT/archive/{}.tar.gz'.format(
+        __version__),
     license='MIT',
     scripts=[],
     data_files=[],
-    setup_requires=["numpy>=1.16", "cython>=0.23"],
     install_requires=["numpy>=1.16", "scipy>=1.0"],
     classifiers=[
         'Development Status :: 5 - Production/Stable',
@@ -85,5 +86,4 @@
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
-    ]
-)
+    ])