updating to pkg_utils

.circleci/config.yml

@@ -13,13 +13,13 @@ jobs:
             - cache-v3-{{ .Branch }}-
             - cache-v3-
 
-      - run: pip2 install -e .
-      - run: pip2 install -U -e git+https://github.com/KarrLab/karr_lab_build_utils.git#egg=karr_lab_build_utils
+      - run: pip2 install -U git+https://github.com/KarrLab/karr_lab_build_utils.git#egg=karr_lab_build_utils
       - run: karr_lab_build_utils2 install-requirements
-
-      - run: pip3 install -e .
-      - run: pip3 install -U -e git+https://github.com/KarrLab/karr_lab_build_utils.git#egg=karr_lab_build_utils
+      - run: pip2 install -U -e .[all]
+
+      - run: pip3 install -U git+https://github.com/KarrLab/karr_lab_build_utils.git#egg=karr_lab_build_utils
       - run: karr_lab_build_utils3 install-requirements
+      - run: pip3 install -U -e .[all]
 
       - save_cache:
           key: cache-v3-{{ .Branch }}-{{ checksum "requirements.txt" }}

docs/requirements.txt

@@ -2,9 +2,9 @@ attrdict
 configparser
 networkx
 git+https://github.com/KarrLab/obj_model.git#egg=obj_model
-robpol86-sphinxcontrib-googleanalytics
+robpol86_sphinxcontrib_googleanalytics
 six
-Sphinx >= 1.6
+sphinx >= 1.6
 sphinx_rtd_theme
-sphinxcontrib-bibtex
-sphinxcontrib-spelling
+sphinxcontrib_bibtex
+sphinxcontrib_spelling

setup.py

@@ -1,52 +1,40 @@
-import pip
-pip.main(['install', 'git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils'])
-
-from setuptools import setup, find_packages
-from wc_utils.util.install import parse_requirements, install_dependencies
+import setuptools
+try:
+    import pkg_utils
+except ImportError:
+    import pip
+    pip.main(['install', 'git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils'])
+    import pkg_utils
 import os
 
-# get long description
-if os.path.isfile('README.rst'):
-    with open('README.rst', 'r') as file:
-        long_description = file.read()
-else:
-    long_description = ''
-
-# get version
-with open('wc_rules/VERSION', 'r') as file:
-    version = file.read().strip()
-
-# parse dependencies and links from requirements.txt files
-with open('requirements.txt', 'r') as file:
-    install_requires, dependency_links_install = parse_requirements(file.readlines())
-with open('tests/requirements.txt', 'r') as file:
-    tests_require, dependency_links_tests = parse_requirements(file.readlines())
-dependency_links = list(set(dependency_links_install + dependency_links_tests))
+name = 'wc_rules'
+dirname = os.path.dirname(__file__)
 
-# install non-PyPI dependencies
-install_dependencies(dependency_links)
+# get package metadata
+md = pkg_utils.get_package_metadata(dirname, name)
 
 # install package
-setup(
-    name="wc_rules",
-    version=version,
+setuptools.setup(
+    name=name,
+    version=md.version,
     description="Language for describing whole-cell models",
-    long_description=long_description,
-    url="https://github.com/KarrLab/wc_rules",
-    download_url='https://github.com/KarrLab/wc_rules',
+    long_description=md.long_description,
+    url="https://github.com/KarrLab/" + name,
+    download_url='https://github.com/KarrLab/' + name,
     author="John Sekar",
     author_email="johnarul.sekar@gmail.com",
     license="MIT",
     keywords='whole-cell systems biology',
-    packages=find_packages(exclude=['tests', 'tests.*']),
+    packages=setuptools.find_packages(exclude=['tests', 'tests.*']),
     package_data={
-        'wc_rules': [
+        name: [
             'VERSION',
         ],
     },
-    install_requires=install_requires,
-    tests_require=tests_require,
-    dependency_links=dependency_links,
+    install_requires=md.install_requires,
+    extras_require=md.extras_require,
+    tests_require=md.tests_require,
+    dependency_links=md.dependency_links,
     classifiers=[
         'Development Status :: 3 - Alpha',
         'Intended Audience :: Science/Research',