Merge pull request #25 from klarman-cell-observatory/yiming

reorg setup for linux wheel building

MANIFEST.in

@@ -7,3 +7,5 @@ exclude .*
 exclude tests/*
 exclude docs/**
 exclude notebooks/*
+exclude wheel_build/*
+exclude build_linux.sh

build_linux.sh

@@ -0,0 +1,4 @@
+docker pull quay.io/pypa/manylinux2014_x86_64
+docker run -it --rm -e PLAT=manylinux2014_x86_64 -v `pwd`:/src -v `pwd`/dist:/wheelhouse quay.io/pypa/manylinux2014_x86_64 /bin/sh -c "/src/wheel_build/build_wheel_for_linux.sh"
+docker pull quay.io/pypa/manylinux2014_i686
+docker run -it --rm -e PLAT=manylinux1_i686 -v `pwd`:/src -v `pwd`/dist:/wheelhouse quay.io/pypa/manylinux2014_i686 /bin/sh -c "/src/wheel_build/build_wheel_for_linux.sh"

pyproject.toml

@@ -1,3 +1,5 @@
 [build-system]
 requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4", "Cython"]
+
 [tool.setuptools_scm]
+write_to = "pegasusio/version.py"

requirements.txt

@@ -1,7 +1,11 @@
-anndata>=0.6.22rc1
-matplotlib>=2.0.0
-pandas>=0.21
-scipy<1.3
-scikit-learn>=0.21.3
-umap-learn>=0.3.9
-lightgbm==2.2.1
+Cython
+anndata
+loompy
+docopt
+natsort
+numpy
+pandas
+scipy
+setuptools
+importlib-metadata
+zarr

setup.py

@@ -2,27 +2,14 @@
 from setuptools.extension import Extension
 from Cython.Build import cythonize
 from codecs import open
+from pathlib import Path
 import os
 
 
 here = os.path.abspath(os.path.dirname(__file__))
 with open(os.path.join(here, "README.rst"), encoding="utf-8") as f:
     long_description = f.read()
 
-requires = [
-    "Cython",
-    "anndata",
-    "loompy",
-    "docopt",
-    "natsort",
-    "numpy",
-    "pandas",
-    "scipy",
-    "setuptools",
-    "importlib-metadata",
-    "zarr"
-]
-
 extensions = [
     Extension("pegasusio.cylib.funcs", ["ext_modules/fast_funcs.pyx"]),
     Extension("pegasusio.cylib.io", ["ext_modules/io_funcs.pyx"])
@@ -46,6 +33,7 @@
         "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
         "Framework :: Jupyter",
         "Natural Language :: English",
         "Operating System :: MacOS :: MacOS X",
@@ -56,7 +44,9 @@
     packages=find_packages(),
     ext_modules=cythonize(extensions),
     setup_requires=["Cython", "setuptools_scm"],
-    install_requires=requires,
+    install_requires=[
+        l.strip() for l in Path("requirements.txt").read_text("utf-8").splitlines()
+    ],
     python_requires="~=3.6",
     entry_points={"console_scripts": ["pegasusio=pegasusio.__main__:main"]},
 )

wheel_build/build_wheel_for_linux.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+set -e -u -x
+
+function repair_wheel {
+    wheel="$1"
+    if ! auditwheel show "$wheel"; then
+        echo "Skipping non-platform wheel $wheel"
+    else
+        auditwheel repair "$whl" --plat "$PLAT" -w /wheelhouse/
+        rm "$whl"
+    fi
+}
+
+if [[ $PLAT =~ .*_x86_64 ]]; then
+    declare -a PythonVersions=("cp36-cp36m" "cp37-cp37m" "cp38-cp38")
+else
+    declare -a PythonVersions=("cp36-cp36m" "cp37-cp37m")
+fi
+
+for val in ${PythonVersions[@]}; do
+    /opt/python/$val/bin/pip install -r /src/requirements.txt
+    /opt/python/$val/bin/pip wheel /src/ --no-deps -w /wheelhouse/
+done
+
+
+if [[ $PLAT =~ .*_x86_64 ]]; then
+    suffix=*_x86_64.whl
+else
+    suffix=*_i686.whl
+fi
+
+for whl in /wheelhouse/$suffix; do
+    repair_wheel "$whl"
+done