update setup.py

requirements.txt

@@ -1,5 +1,5 @@
 matplotlib~=2.1.1
-numpy~=1.13.3
+numpy~=1.14.0
 pandas~=0.22.0
 pymatgen
 PyMonad

setup.py

@@ -4,43 +4,202 @@
 
 # -*- coding: utf-8 -*-
 
-import ast
+# uncomment this for compatibility with py27
+# from __future__ import print_function
 
+import os
+from datetime import date
 from setuptools import setup, find_packages
 
-package_name = 'XenonPy'
+# --- import your package ---
+import xenonpy as package
 
-def get_version(verFile):
-    with open(verFile) as f:
-        src = f.read()
-    module = ast.parse(src)
-    for e in module.body:
-        if isinstance(e, ast.Assign) and \
-                len(e.targets) == 1 and \
-                e.targets[0].id == '__version__' and \
-                isinstance(e.value, ast.Str):
-            return e.value.s
-    raise RuntimeError('__version__ not found')
+if __name__ == "__main__":
+    # --- Automatically generate setup parameters ---
+    # Your package name
+    PKG_NAME = package.__name__
 
+    # Your GitHub user name
+    try:
+        GITHUB_USERNAME = package.__github_username__
+    except:
+        GITHUB_USERNAME = "Unknown-Github-Username"
 
-def setup_package():
-    with open('README.md') as f:
-        readme = f.read()
+    # Short description will be the description on PyPI
+    try:
+        SHORT_DESCRIPTION = package.__short_description__  # GitHub Short Description
+    except:
+        print(
+            "'__short_description__' not found in '%s.__init__.py'!" % PKG_NAME)
+        SHORT_DESCRIPTION = "No short description!"
 
-    with open('LICENSE') as f:
-        this_license = f.read()
+    # Long description will be the body of content on PyPI page
+    try:
+        LONG_DESCRIPTION = open("README.rst", "rb").read().decode("utf-8")
+    except:
+        LONG_DESCRIPTION = "No long description!"
+
+    # Version number, VERY IMPORTANT!
+    VERSION = package.__version__
+
+    # Author and Maintainer
+    try:
+        AUTHOR = package.__author__
+    except:
+        AUTHOR = "Unknown"
+
+    try:
+        AUTHOR_EMAIL = package.__author_email__
+    except:
+        AUTHOR_EMAIL = None
+
+    try:
+        MAINTAINER = package.__maintainer__
+    except:
+        MAINTAINER = "Unknown"
+
+    try:
+        MAINTAINER_EMAIL = package.__maintainer_email__
+    except:
+        MAINTAINER_EMAIL = None
+
+    PACKAGES, INCLUDE_PACKAGE_DATA, PACKAGE_DATA, PY_MODULES = (
+        None, None, None, None,
+    )
+
+    # It's a directory style package
+    if os.path.exists(__file__[:-8] + PKG_NAME):
+        # Include all sub packages in package directory
+        PACKAGES = [PKG_NAME] + ["%s.%s" % (PKG_NAME, i)
+                                 for i in find_packages(PKG_NAME)]
+
+        # Include everything in package directory
+        INCLUDE_PACKAGE_DATA = True
+        PACKAGE_DATA = {
+            "": ["*.*"],
+        }
+
+    # It's a single script style package
+    elif os.path.exists(__file__[:-8] + PKG_NAME + ".py"):
+        PY_MODULES = [PKG_NAME, ]
+
+    # The project directory name is the GitHub repository name
+    repository_name = os.path.basename(os.path.dirname(__file__))
+
+    # Project Url
+    URL = "https://github.com/{0}/{1}".format(GITHUB_USERNAME, repository_name)
+    # Use todays date as GitHub release tag
+    github_release_tag = str(date.today())
+    # Source code download url
+    DOWNLOAD_URL = "https://github.com/{0}/{1}/tarball/{2}".format(
+        GITHUB_USERNAME, repository_name, github_release_tag)
+
+    try:
+        LICENSE = package.__license__
+    except:
+        print("'__license__' not found in '%s.__init__.py'!" % PKG_NAME)
+        LICENSE = ""
+
+    PLATFORMS = [
+        "Windows",
+        "MacOS",
+        "Unix",
+    ]
+
+    CLASSIFIERS = [
+        "Development Status :: 2 - Pre-Alpha",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: BSD License",
+        "Natural Language :: English",
+        "Operating System :: Microsoft :: Windows",
+        "Operating System :: MacOS",
+        "Operating System :: Unix",
+        "Programming Language :: Python",
+        # "Programming Language :: Python :: 2.7",
+        # "Programming Language :: Python :: 3.4",
+        "Programming Language :: Python :: 3.5",
+        "Programming Language :: Python :: 3.6",
+    ]
+
+    # Read requirements.txt, ignore comments
+    try:
+        REQUIRES = list()
+        f = open("requirements.txt", "rb")
+        for line in f.read().decode("utf-8").split("\n"):
+            line = line.strip()
+            if "#" in line:
+                line = line[:line.find("#")].strip()
+            if line:
+                REQUIRES.append(line)
+    except:
+        print("'requirements.txt' not found!")
+        REQUIRES = list()
 
     setup(
-        name=package_name,
-        version=get_version(package_name + '/__version__.py'),
-        description='A library to generate descriptors of elements',
-        long_description=readme,
-        author='TsumiNa(Chang Liu)',
-        author_email='liu.chang.1865@gmail.com',
-        url='https://github.com/yoshida-lab/XenonPy',
-        license=this_license,
-        packages=find_packages(exclude=('tests', 'docs'), install_requires=['numpy']))
-
-
-if __name__ == '__main__':
-    setup_package()
+        name=PKG_NAME,
+        description=SHORT_DESCRIPTION,
+        long_description=LONG_DESCRIPTION,
+        version=VERSION,
+        author=AUTHOR,
+        author_email=AUTHOR_EMAIL,
+        maintainer=MAINTAINER,
+        maintainer_email=MAINTAINER_EMAIL,
+        packages=PACKAGES,
+        include_package_data=INCLUDE_PACKAGE_DATA,
+        package_data=PACKAGE_DATA,
+        py_modules=PY_MODULES,
+        url=URL,
+        download_url=DOWNLOAD_URL,
+        classifiers=CLASSIFIERS,
+        platforms=PLATFORMS,
+        license=LICENSE,
+        install_requires=REQUIRES,
+    )
+
+"""
+Appendix
+--------
+::
+Frequent used classifiers List = [
+    "Development Status :: 1 - Planning",
+    "Development Status :: 2 - Pre-Alpha",
+    "Development Status :: 3 - Alpha",
+    "Development Status :: 4 - Beta",
+    "Development Status :: 5 - Production/Stable",
+    "Development Status :: 6 - Mature",
+    "Development Status :: 7 - Inactive",
+    "Intended Audience :: Customer Service",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: End Users/Desktop",
+    "Intended Audience :: Financial and Insurance Industry",
+    "Intended Audience :: Healthcare Industry",
+    "Intended Audience :: Information Technology",
+    "Intended Audience :: Legal Industry",
+    "Intended Audience :: Manufacturing",
+    "Intended Audience :: Other Audience",
+    "Intended Audience :: Religion",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: System Administrators",
+    "Intended Audience :: Telecommunications Industry",
+    "License :: OSI Approved :: BSD License",
+    "License :: OSI Approved :: MIT License",
+    "License :: OSI Approved :: Apache Software License",
+    "License :: OSI Approved :: GNU General Public License (GPL)",
+    "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
+    "Natural Language :: English",
+    "Natural Language :: Chinese (Simplified)",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: MacOS",
+    "Operating System :: Unix",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 2",
+    "Programming Language :: Python :: 2.7",
+    "Programming Language :: Python :: 2 :: Only",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.4",
+    "Programming Language :: Python :: 3.5",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3 :: Only",
+]
+"""

xenonpy/__init__.py

@@ -9,7 +9,6 @@
 except (ImportError, AttributeError):
     from pathlib2 import Path
 
-from .__version__ import __version__ as version
 from .decorator import *
 from .descriptor import *
 from .model import *
@@ -19,6 +18,15 @@
 PACKAGE_CONF_DIR = '.XenonPy'
 PACKAGE = 'XenonPy'
 
+__version__ = '0.1.0'
+__short_description__ = "material descriptor library"
+__license__ = "BSD3"
+__author__ = "TsumiNa"
+__author_email__ = "liu.chang.1865@gmail.com"
+__maintainer__ = "TsumiNa"
+__maintainer_email__ = "liu.chang.1865@gmail.com"
+__github_username__ = "TsumiNa"
+
 
 def get_version():
     """
@@ -29,7 +37,7 @@ def get_version():
     str
         package version.
     """
-    return version
+    return __version__
 
 
 def get_conf(key: str = None):

xenonpy/descriptor/element.py

@@ -29,7 +29,7 @@ def __init__(self,
                  *methods: str,
                  elements=None,
                  comps_col: str = 'composition',
-                 verbose: bool = True,
+                 verbose: bool = True
                  ):
         """
         :param str methods: calculation method(s) which to be used must in the :attr:`methods` list.

xenonpy/descriptor/pdf.py

@@ -29,7 +29,7 @@ def __init__(self,
                  cell_range: int = 1,
                  sigma: float = 0.1,
                  structure_col: str = 'structure',
-                 verbose: bool = True,
+                 verbose: bool = True
                  ):
         """
 

xenonpy/model/nn/base_model.py

@@ -21,7 +21,7 @@ def __init__(self, n_features: int, n_predict: int, *,
                  layer_func: [] = (nn.Linear,),
                  act_func: [] = (nn.ReLU(),),
                  batch_normalize: [bool] = (False,),
-                 momentum: [float] = (0.1,),
+                 momentum: [float] = (0.1,)
                  ):
         self.n_in, self.n_out = n_features, n_predict
 
@@ -84,7 +84,7 @@ def __init__(self, model: nn.Module, *,
                  ctx: str = 'cpu',
                  checkstep: int = 100,
                  check: tuple = ('epochs', 'loss'),
-                 save_to: str = '',
+                 save_to: str = ''
                  ):
         parent = Path(save_to)
         if not parent.exists():

xenonpy/model/nn/layer.py

@@ -13,7 +13,8 @@ def __init__(self, *,
                  layer_func=nn.Linear,
                  act_func=nn.ReLU(),
                  batch_normalize=False,
-                 momentum=0.1, ):
+                 momentum=0.1
+                 ):
         super().__init__()
         self.neuron = layer_func(n_in, n_out)
         self.batch_nor = None if not batch_normalize else nn.BatchNorm1d(n_out, momentum)