Updated for pip and pypi release

.gitignore

@@ -5,3 +5,4 @@ build*
 oxasl_ve/_version.py
 dist
 oxasl_ve.egg-info/
+.pytest_cache

LICENSE

@@ -0,0 +1,123 @@
+Quantiphyse licence
+===================
+
+These licence terms apply to all licences granted by THE CHANCELLOR, MASTERS 
+AND SCHOLARS OF THE UNIVERSITY OF OXFORD whose administrative offices are at 
+office at University Offices, Wellington Square, Oxford OX1 2JD, United Kingdom
+(the "University") for use of or access to OXASL_VE ("the Software"), 
+a Python interface to the VEASLC tool for modelling vessel encoded ASL data.
+
+By using the Software provided directly to you by email, you (the "User") are 
+confirming that you agree that your use of the Software is subject to these 
+licence terms.
+
+PLEASE READ THESE LICENCE TERMS CAREFULLY BEFORE USING THE SOFTWARE.  IF YOU DO 
+NOT AGREE TO THESE LICENCE TERMS YOU SHOULD NOT USE THE SOFTWARE.
+
+THE SOFTWARE ARE INTENDED FOR ACADEMICS CARRYING OUT RESEARCH AND NOT FOR USE 
+BY CONSUMERS OR COMMERCIAL BUSINESSES.
+
+1.	Academic Use Licence
+
+1.1	The User is granted a limited non-exclusive and non-transferable royalty 
+      free licence to access and use the Software provided that the User will:
+
+  (a)	limit their use of the Software to their own internal academic 
+      non-commercial research which is undertaken for the purposes of education 
+      or other scholarly use; 
+
+  (b)	not use the Software for or on behalf of any third party or to provide a 
+      service or integrate all or part of the Software into a product for sale 
+      or license to third parties;
+
+  (c)	use the Software in accordance with the prevailing instructions and 
+      guidance for use given on the Website and comply with procedures on the 
+      Website for user identification, authentication and access;
+
+  (d)	comply with all applicable laws and regulations with respect to their use
+      of the Software; 
+
+  (e)	except to the extent expressly permitted under these terms, not attempt 
+      to: reverse compile, disassemble or copy, modify, duplicate, create 
+      derivative works from, frame, mirror, republish, download, display, 
+      transmit, or distribute all or any portion of the Software or Website in
+      any form or media or by any means; and 
+
+  (f)	ensure that the Copyright Notice "Copyright © 2018, University of Oxford"
+      appears prominently wherever results from the Software are used, and is 
+      referenced or cited with the Copyright Notice when the Software is 
+      described in any research publication or on any documents or other 
+      material created using the Software.
+
+1.2	the University reserves the right at any time and without liability or 
+      prior notice to the User to revise, modify and replace the functionality 
+      and performance of the access to and operation of the Software. 
+
+1.3	The User acknowledges and agrees that the University owns all 
+      intellectual property rights in the Software. The User shall not have any
+      right, title or interest in or to any results or other output from the 
+      Software.
+
+1.4	This Licence will terminate immediately and the User will no longer have
+      any right exercise any of the rights granted to the User upon any breach
+      of the conditions in Section 1.1 of this Licence.
+
+2.	Indemnity and Liability 
+
+2.1	The User shall defend, indemnify and hold harmless the University against
+      any claims, actions, proceedings, losses, damages, expenses and costs 
+      (including without limitation court costs and reasonable legal fees) 
+      arising out of or in connection with the User's possession or use of the
+      Software, or any breach of these terms by the User. 
+
+2.2	The Software are provided on an 'as is' basis and the User uses the 
+      Software at their own risk. No representations, conditions, warranties or
+      other terms of any kind are given in respect of the Software and all 
+      statutory warranties and conditions are excluded to the fullest extent 
+      permitted by law. Without affecting the generality of the previous 
+      sentences, the University gives no implied or express warranty and makes
+      no representation that the Software or any part of them: 
+
+  (a) will enable specific results to be obtained; or 
+
+  (b) meets a particular specification or is comprehensive within its field or
+      that it is error free or will operate without interruption; or 
+
+  (c) is suitable for any particular, or the User's specific purposes. 
+
+2.3	Except in relation to fraud, death or personal injury, the University's
+      liability to the User for any use of the Software, in negligence or 
+      arising in any other way out of the subject matter of these licence 
+      terms, will not extend to any incidental or consequential damages or 
+      losses, or any loss of profits, loss of revenue, loss of data, loss of
+      contracts or opportunity, whether direct or indirect.
+
+2.4	The User hereby irrevocably undertakes to the University not to make any
+      claim against any employee, student, researcher or other individual 
+      engaged by the University, being a claim which seeks to enforce against 
+      any of them any liability whatsoever in connection with this agreement 
+      or its subject-matter. 
+
+3.	General 
+
+3.1	Severability - If any provision (or part of a provision) of these licence
+      terms is found by any court or administrative body of competent 
+      jurisdiction to be invalid, unenforceable or illegal, the other 
+      provisions shall remain in force.
+
+3.2	Entire Agreement - These licence terms and any documents referred to in
+      them, constitute the whole agreement between the parties and supersede 
+      any previous arrangement, understanding or agreement between them 
+      relating to the Software. 
+
+3.3	Law and Jurisdiction - These licence terms and any disputes or claims 
+      arising out of or in connection with them shall be governed by, and 
+      construed in accordance with, the law of England. The User irrevocably 
+      submits to the exclusive jurisdiction of the English courts for any 
+      dispute or claim that arises out of or in connection with these licence 
+      terms.
+
+If you are interested in using the Software commercially, please contact 
+Oxford University Innovation Limited to negotiate a licence. Contact details 
+are chandra.ramanujan@innovation.ox.ac.uk quoting reference 14419.
+

MANIFEST.in

@@ -0,0 +1 @@
+include LICENSE requirements.txt

README.md

@@ -0,0 +1,10 @@
+# OXASL_VE
+
+Python interface to the C++ based VEASLC tool for Vessel-encoded ASL designed for use with the OXASL
+processing pipeline
+
+## Citation
+
+*A General Framework for the Analysis of Vessel Encoded Arterial Spin Labelling for Vascular Territory Mapping*
+M Chappell, T Okell, P Jezzard and M Woolrich
+Magnetic Resonance in Medicine 64:1529-1539 (2010)

requirements.txt

@@ -0,0 +1,4 @@
+oxasl
+numpy
+fslpy>=1.13
+

setup.py

@@ -1,73 +1,99 @@
 #!/usr/bin/env python
 """
-Build Python interface for veaslc
+Setup script for oxasl_ve
 """
 import os
-import sys
 import subprocess
 import re
+import io
 
-from setuptools import setup, find_packages
+from setuptools import setup
+from setuptools import find_packages
 
-def git_version():
-    # Full version includes the Git commit hash
-    full_version = subprocess.check_output('git describe --dirty', shell=True).decode("utf-8").strip(" \n")
+MODULE = 'oxasl_ve'
 
-    # Python standardized version in form major.minor.patch.dev<build>
-    version_regex = re.compile(r"v?(\d+\.\d+\.\d+(-\d+)?).*")
-    match = version_regex.match(full_version)
-    if match:
-        std_version = match.group(1).replace("-", ".dev")
-    else:
-        raise RuntimeError("Failed to parse version string %s" % full_version)
+def get_filetext(rootdir, filename):
+    """ Get the text of a local file """
+    with io.open(os.path.join(rootdir, filename), encoding='utf-8') as f:
+        return f.read()
+
+def git_version():
+    """ Get the full and python standardized version from Git tags (if possible) """
+    try:
+        # Full version includes the Git commit hash
+        full_version = subprocess.check_output('git describe --dirty', shell=True).decode("utf-8").strip(" \n")
 
-    return full_version, std_version
+        # Python standardized version in form major.minor.patch.post<build>
+        version_regex = re.compile(r"v?(\d+\.\d+\.\d+(-\d+)?).*")
+        match = version_regex.match(full_version)
+        if match:
+            std_version = match.group(1).replace("-", ".post")
+        else:
+            raise RuntimeError("Failed to parse version string %s" % full_version)
+        return full_version, std_version
+    except:
+        # Any failure, return None. We may not be in a Git repo at all
+        return None, None
 
 def git_timestamp():
-    return subprocess.check_output('git log -1 --format=%cd', shell=True).decode("utf-8").strip(" \n")
+    """ Get the last commit timestamp from Git (if possible)"""
+    try:
+        return subprocess.check_output('git log -1 --format=%cd', shell=True).decode("utf-8").strip(" \n")
+    except:
+        # Any failure, return None. We may not be in a Git repo at all
+        return None
+
+def update_metadata(rootdir, version_str, timestamp_str):
+    """ Update the version and timestamp metadata in the module _version.py file """
+    with io.open(os.path.join(rootdir, MODULE, "_version.py"), "w", encoding='utf-8') as f:
+        f.write("__version__ = '%s'\n" % version_str)
+        f.write("__timestamp__ = '%s'\n" % timestamp_str)
 
-def set_metadata(module_dir, version_str, timestamp_str):
-    vfile = open(os.path.join(module_dir, "oxasl_ve", "_version.py"), "w")
-    vfile.write("__version__ = '%s'\n" % version_str)
-    vfile.write("__timestamp__ = '%s'\n" % timestamp_str)
-    vfile.close()
+def get_requirements(rootdir):
+    """ Get a list of all entries in the requirements file """
+    with io.open(os.path.join(rootdir, 'requirements.txt'), encoding='utf-8') as f:
+        return [l.strip() for l in f.readlines()]
 
-# Read in requirements from the requirements.txt file.
-with open('requirements.txt', 'rt') as f:
-    requirements = [l.strip() for l in f.readlines()]
+def get_version(rootdir):
+    """ Get the current version number (and update it in the module _version.py file if necessary)"""
+    version, timestamp = git_version()[1], git_timestamp()
 
-# Generate a list of all of the packages that are in your project.
-packages = find_packages()
+    if version is not None and timestamp is not None:
+        # We got the metadata from Git - update the version file
+        update_metadata(rootdir, version, timestamp)
+    else:
+        # Could not get metadata from Git - use the version file if it exists
+        with io.open(os.path.join(rootdir, MODULE, '_version.py'), encoding='utf-8') as f:
+            md = f.read()
+            match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", md, re.M)
+            if match:
+                version = match.group(1)
+            else:
+                version = "unknown"
+    return version
 
-rootdir = os.path.join(os.path.abspath(os.path.dirname(__file__)))
-_, stdv = git_version()
-timestamp = git_timestamp()
-set_metadata(rootdir, stdv, timestamp)
+module_dir = os.path.abspath(os.path.dirname(__file__))
 
-desc = "Python interface for vessel-encoded ASL"
-longdesc = desc
+kwargs = {
+    'name' : 'oxasl-ve',
+    'version' : get_version(module_dir),
+    'description' : 'Python library for manipulating and modelling ASL data',
+    'long_description' : get_filetext(module_dir, 'README.md'),
+    'long_description_content_type' : 'text/markdown',
+    'url' : 'https://oxasl.readthedocs.io/',
+    'author' : 'Martin Craig',
+    'author_email' : 'martin.craig@eng.ox.ac.uk',
+    'license' : 'License granted by University of Oxford for use by academics carrying out research and not for use by consumers or commercial businesses. See LICENSE file for more details',
+    'install_requires' : get_requirements(module_dir),
+    'packages' : find_packages(),
+    'classifiers' : [
+        'Development Status :: 3 - Alpha',
+        'Intended Audience :: Science/Research',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'License :: Free for non-commercial use',
+    ],
+}
 
-# setup parameters
-setup(name='oxasl_ve',
-      version=stdv,
-      description=desc,
-      long_description=longdesc,
-      author='Michael Chappell, Martin Craig',
-      author_email='martin.craig@eng.ox.ac.uk',
-      packages=packages,
-      include_package_data=True,
-      data_files=[],
-      setup_requires=[],
-      install_requires=[],
-      entry_points={
-      },
-      classifiers=["Programming Language :: Python :: 2.7",
-                   "Development Status:: 3 - Alpha",
-                   'Programming Language :: Python',
-                   'Operating System :: MacOS :: MacOS X',
-                   'Operating System :: Microsoft :: Windows',
-                   'Operating System :: POSIX',
-                   "Intended Audience :: Education",
-                   "Intended Audience :: Science/Research",
-                   "Intended Audience :: End Users/Desktop",
-                   "Topic :: Scientific/Engineering :: Bio-Informatics",])
+setup(**kwargs)