Tweaks to readme, doc, requirements and setup.py

README.md

@@ -3,14 +3,35 @@ fslpy
 
 The `fslpy` project is a [FSL](http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)
 programming library written in Python. It is used by
-[FSLeyes](https://git.fmrib.ox.ac.uk/paulmc/fsleyes/). 
+[FSLeyes](https://git.fmrib.ox.ac.uk/paulmc/fsleyes/).
+
+
+Dependencies
+------------
+
+
+All of the dependencies of `fslpy` are listed in the
+[requirements.txt](requirements.txt) file. Some `fslpy` modules require
+[wxPython](http://www.wxpython.org) 3.0.2.0.
 
 
 Documentation
 -------------
 
+`fslpy` is documented using [sphinx](http://http://sphinx-doc.org/). You can
+build the API documentation by installing `sphinx` and `sphinx-rtd-theme`, and
+running:
+
+    python setup.py doc
+
+The HTML documentation will be generated and saved in the `doc/html/` directory.
+
+
+Tests
+-----
+
+To run the tests, install `pytest` and `coverage`, and then run:
+
+       python setup.py test --addopts="-v --niters=50 --cov=fsl --cov-report=html"
 
-Take a look at the [Documentation for
-developers](http://users.fmrib.ox.ac.uk/~paulmc/fslpy/index.html), and the
-[requirements.txt file](requirements.txt) for details on
-``fslpy`` dependencies, if you want to program with `fslpy`.
+A code coverage report will be generated in `htmlcov/`.

doc/conf.py

@@ -55,7 +55,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'fslpy'
-copyright = u'{}, Paul McCarthy, FMRIB Centre, University of Oxford'.format(
+copyright = u'{}, Paul McCarthy, University of Oxford, Oxford, UK'.format(
     date.year)
 
 # Links to other things

requirements.txt

-cython>=0.24
-six>=1.10.0
-numpy>=1.11.1
-matplotlib>=1.5.1
-nibabel>=2.1
-sphinx>=1.4.1
-sphinx-rtd-theme>=0.1.9
-indexed_gzip>=0.3.1
+six>=1.10.0,<2.0
+numpy>=1.11.1,<2.0
+matplotlib>=1.5.1,<=2.0.0
+nibabel>=2.1,<3.0
+indexed_gzip>=0.3.1,<0.4
+wxPython==3.0.2.0

setup.py

@@ -5,15 +5,28 @@
 # Author: Paul McCarthy <pauldmccarthy@gmail.com>
 #
 
-import os.path as op
+
+from __future__ import print_function
+
+import               os
+import os.path    as op
+import subprocess as sp
+import               shutil
+import               pkgutil
 
 from setuptools import setup
 from setuptools import find_packages
+from setuptools import Command
 
 
 # The directory in which this setup.py file is contained.
 basedir = op.dirname(__file__)
 
+# Dependencies are listed in requirements.txt
+install_requires = open(op.join(basedir, 'requirements.txt'), 'rt').readlines()
+
+packages = find_packages(
+    exclude=('doc', 'tests', 'dist', 'build', 'fslpy.egg-info'))
 
 # Figure out the current fslpy version, as defined in fsl/version.py. We
 # don't want to import the fsl package,  as this may cause build problems.
@@ -26,10 +39,35 @@ with open(op.join(basedir, "fsl", "version.py")) as f:
             exec(line, version)
             break 
 
-install_requires = open(op.join(basedir, 'requirements.txt'), 'rt').readlines()
 
-dependency_links = [i for i in install_requires if     i.startswith('git')]
-install_requires = [i for i in install_requires if not i.startswith('git')]
+class doc(Command):
+    """Build the API documentation. """
+    
+    user_options = []
+    
+    def initialize_options(self):
+        pass
+
+    def finalize_options(self):
+        pass
+
+    def run(self):
+
+        docdir  = op.join(basedir, 'doc')
+        destdir = op.join(docdir, 'html')
+
+        if op.exists(destdir):
+            shutil.rmtree(destdir)
+
+        env   = dict(os.environ)
+        ppath = [op.join(pkgutil.get_loader('fsl').filename, '..')]
+        
+        env['PYTHONPATH'] = op.pathsep.join(ppath)
+
+        print('Building documentation [{}]'.format(destdir))
+
+        sp.call(['sphinx-build', docdir, destdir], env=env) 
+
 
 setup(
 
@@ -52,17 +90,19 @@ setup(
         'Intended Audience :: Developers',
         'License :: OSI Approved :: Apache Software License',
         'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.5',
         'Topic :: Software Development :: Libraries :: Python Modules'],
 
-    packages=find_packages(exclude=('doc', 'tests')),
+    packages=packages,
 
     install_requires=install_requires,
-    dependency_links=dependency_links,
 
     setup_requires=['pytest-runner'],
     tests_require=['pytest', 'pytest-runner'],
     test_suite='tests',
 
+    cmdclass={'doc' : doc},
+
     entry_points={
         'console_scripts' : [
             'fslpy_imcp = fsl.scripts.imcp:main',