Changes to release v0.4.1 on PyPI

Author: pafonta

MANIFEST.in

@@ -1,48 +1,67 @@
-[Getting started](#getting-started) |
+[Getting Started](#getting-started) |
 [Releases](#releases) |
 [Status](#status)
 
 # NeuroAnnotation Toolbox (NAT)
 
-Python package to use the annotations created with [NeuroCurator](https://github.com/BlueBrain/neurocurator), for example in a [Jupyter](https://jupyter.org/) notebook.
+Python module to use the annotations created with
+[NeuroCurator](https://github.com/BlueBrain/neurocurator), for example in a
+[Jupyter](https://jupyter.org/) notebook.
 
-This framework has been described in details in the following open-access paper: https://doi.org/10.3389/fninf.2017.00027.
+This framework has been described in details in the following open-access
+paper: https://doi.org/10.3389/fninf.2017.00027.
 
-NAT provides the necessary functions and utilities to reliably annotate the neuroscientific literature, curate published values for modeling parameters, and save them in reusable corpora.
+NAT provides the necessary functions and utilities to:
+- reliably annotate the neuroscientific literature,
+- curate published values for modeling parameters,
+- save them in reusable corpora.
 
 ---
 
-## Getting started
+## Getting Started
 
-Install the latest version with:
-```
-pip install git+https://github.com/BlueBrain/nat
-```
+**Requirements:**
 
-Install a specific version with:
-```
-pip install git+https://github.com/BlueBrain/nat.git@<tag>
-```
-(ex. '@v0.4.0')
+System side:
+
+- [Git 1.7.0+](https://git-scm.com/downloads)
+- [ImageMagick 6](http://docs.wand-py.org/en/latest/guide/install.html)
 
-NB: You don't need to install NAT to use a packaged executable of NeuroCurator.
+Python side:
+
+- [Beautiful Soup 4](https://www.crummy.com/software/BeautifulSoup/)
+- [GitPython](https://gitpython.readthedocs.io)
+- [lxml](http://lxml.de)
+- [NumPy](http://www.numpy.org)
+- [pandas](https://pandas.pydata.org)
+- [parse](https://pypi.python.org/pypi/parse)
+- [Pyzotero](https://pyzotero.readthedocs.io)
+- [quantities](https://python-quantities.readthedocs.io)
+- [SciPy](https://www.scipy.org/scipylib/index.html)
+- [Wand](http://docs.wand-py.org)
+
+**Installation:**
+
+```bash
+pip install nat
+```
 
 ## Releases
 
-In the [dedicated section](https://github.com/BlueBrain/nat/releases/), you can find:
-- the latest version,
-- the notable changes of each version.
+Versions and their notable changes are listed in the
+[releases section](https://github.com/BlueBrain/nat/releases/).
 
 Releases are synchronized with the ones of NeuroCurator.
 
 ## Status
 
 Created during 2016.
 
-Ongoing reengineering in the branch _refactor-architecture_.
+Ongoing stabilization and reengineering in the branch _refactor-architecture_.
 
 The branch _refactor-architecture_ is **not** intended to be used by end-users.
 
 New features, bug fixes and improvements are done on the reengineered code sections.
 
-When a reengineered code section is stable, it's merged into the branch _master_ and a release is published.
+When a reengineered code section is stable, it's merged into the branch
+_master_ and a release is published.

README.md

@@ -17,9 +17,9 @@ class ZoteroWrap:
     CACHE_REFERENCE_TYPES = "reference_types"
     CACHE_REFERENCE_TEMPLATES = "reference_templates"
 
-    def __init__(self, library_id, library_type, api_key, working_directory):
+    def __init__(self, library_id, library_type, api_key, directory):
         cache_filename = "{}-{}-{}.pkl".format(library_id, library_type, api_key)
-        self.cache_path = os.path.join(working_directory, cache_filename)
+        self.cache_path = os.path.join(directory, cache_filename)
         # reference_types and reference_templates must have the same ordering.
         self.reference_types = []
         self.reference_templates = {}

nat/zotero_wrap.py

@@ -1,60 +1,66 @@
-from distutils.core import setup
+__authors__ = ["Pierre-Alexandre Fonta", "Christian O'Reilly"]
+__maintainer__ = "Pierre-Alexandre Fonta"
+
 import os
 
-PACKAGE = "nat"
-NAME = "nat"
-DESCRIPTION = open(os.path.join(os.path.dirname(__file__), "README.md")).read()
-AUTHOR = "Christian O'Reilly, Pierre-Alexandre Fonta"
-AUTHOR_EMAIL = "christian.oreilly@epfl.ch"
-VERSION = "0.4.0"
-REQUIRED = ["numpy", "parse", "metapub", "pyzotero", "GitPython", "pandas",
-            "biopython", "beautifulsoup4", "quantities", "wand", "scipy"]
+from setuptools import setup
 
-def is_package(path):
-    return (
-        os.path.isdir(path) and
-        os.path.isfile(os.path.join(path, '__init__.py'))
-        )
+VERSION = "0.4.1"
 
-def find_packages(path, base="" ):
-    """ Find all packages in path """
-    packages = {}
-    for item in os.listdir(path):
-        dir = os.path.realpath(os.path.join(path, item))
-        if is_package( dir ):
-            if base:
-                module_name = "%(base)s.%(item)s" % vars()
-            else:
-                module_name = item
-            packages[module_name] = dir
-            packages.update(find_packages(dir, module_name))
-    return packages
+HERE = os.path.abspath(os.path.dirname(__file__))
 
-packages=find_packages(os.path.join(os.path.dirname(os.path.realpath(__file__)), "."))
+# Get the long description from the README file.
+# Convert to rst with: pandoc --from=markdown --to=rst README.md -o README.rst.
+with open(os.path.join(HERE, "README.rst"), encoding="utf-8") as f:
+    long_description = f.read()
 
 setup(
-    name=NAME,
-    packages=packages.keys(),
-    package_dir=packages,
-    package_data={PACKAGE: ["additionsToOntologies.csv", "modelingDictionary.csv"]},
+    name="nat",
     version=VERSION,
-    description=DESCRIPTION,
-    long_description=DESCRIPTION,
-    author=AUTHOR,
-    author_email=AUTHOR_EMAIL,
-    maintainer=AUTHOR,
-    maintainer_email=AUTHOR_EMAIL,  
-    license='LICENSE.txt',
-    requires=REQUIRED,
-	install_requires=REQUIRED,
-	url="https://github.com/christian-oreilly/nat",
-    classifiers=["Development Status :: 3 - Alpha",
-			"Environment :: MacOS X", #"Environment :: Win32 (MS Windows)",
-			"Environment :: X11 Applications",
-			"Intended Audience :: Developers",
-			"Intended Audience :: Science/Research",
-			"License :: Free for non-commercial use",
-			"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
-			"Natural Language :: English",
-			"Programming Language :: Python :: 3.4",
-			"Topic :: Scientific/Engineering"])
+    description="Module to use the annotations created with NeuroCurator.",
+    long_description=long_description,
+    keywords="neuroscience annotation curation literature modeling parameters",
+    url="https://github.com/BlueBrain/nat",
+    author="Christian O'Reilly, Pierre-Alexandre Fonta",
+    author_email="christian.oreilly@epfl.ch, pierre-alexandre.fonta@epfl.ch",
+    # NB: 'If maintainer is provided, distutils lists it as the author in PKG-INFO'.
+    # https://docs.python.org/3/distutils/setupscript.html#meta-data
+    # maintainer="Pierre-Alexandre Fonta",
+    # maintainer_email="pierre-alexandre@epfl.ch",
+    license="GPLv3",
+    packages=["nat"],
+    python_requires=">=3",  # unittest.mock needs Python 3.3+.
+    install_requires=[
+        "beautifulsoup4",
+        "gitpython",
+        "lxml",
+        "numpy",
+        "pandas",
+        "parse",
+        "pyzotero",
+        "quantities",
+        "scipy",
+        "wand"
+    ],
+    extras_require={
+        "test": ["pytest", "pytest-cov", "pytest-lazy-fixture", "pytest-mock"]
+    },
+    package_data={
+        "nat": ["data/*.csv"]
+    },
+    data_files=[("", ["LICENSE.txt"])],
+    classifiers=[
+        "Development Status :: 3 - Alpha",
+        "Intended Audience :: Science/Research",
+        "Intended Audience :: Developers",
+        "Topic :: Scientific/Engineering",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+        "License :: Free for non-commercial use",
+        "Programming Language :: Python :: 3 :: Only",
+        "Operating System :: MacOS",
+        "Operating System :: POSIX :: Linux",
+        "Operating System :: Microsoft :: Windows",
+        "Natural Language :: English"
+    ]
+)