modernized installation procedure

- set VERSION to 3.1.0 (introduce a patch level 0 so that it becomes
  easier to publish packages with small fixes, eg for installation)
- got rid of ancient ez_install: just use pip
- updated README and INSTALL
- updated classifiers in setup.py (license: LGPL v2.1 and other meta data);
  updated URL to point to http://propka.org because unlike http://propka.ki.ku.dk
  it is not completely dead and has a link to the pdb2pqr propka server as well
  as the GitHub page

INSTALL

@@ -1,19 +1,11 @@
 ## Installation
 
 Clone repository or unpack the tar ball and install with
-[setuptools](http://pythonhosted.org/setuptools/index.html) (note: if
+[pip](https://pip.pypa.io):
-you don't have setuptools installed you will need an internet
-connection so that the installation procedure can sownload the
-required files):
 
-    cd propka-3.1
+    pip install propka-3.1/
-    python setup.py install --user
 
-This will install the `propka31` script in your executable directory,
+This will install the `propka31` script in your executable
-as configured for setuptools, for instance `~/.local/bin`. You can
+directory. The `propka` Python module will also become available for
-change the bin directory with the `--install-scripts` option. For
+import.
-example, in order to install in my `bin` directory in my home
-directory:
-
-    python setup.py install --user --install-scripts ~/bin
 

MANIFEST.in

@@ -1,4 +1,4 @@
 include README.md INSTALL 
-include ez_setup.py setup.py 
+include setup.py 
 include propka.cfg
 

README.md

@@ -16,17 +16,6 @@ in publications:
 See [propka.ki.ku.dk](http://propka.ki.ku.dk/) for the PROPKA web server,
 using the [tutorial](http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutorial).
 
-## Modifications 
-
-This release of PROPKA 3.1 was modified by Oliver Beckstein
-<oliver.beckstein@asu.edu> from the released version.
-
-* Included patches from
-  https://github.com/schrodinger/propka-3.1/tree/python27-compat to
-  make it compatible with Python 2.7
-
-* Packaged for installation with setuptools.
-
 
 ## Installation
 

ez_setup.py

@@ -1,258 +0,0 @@
-#!python
-"""Bootstrap setuptools installation
-
-If you want to use setuptools in your package's setup.py, just include this
-file in the same directory with it, and add this to the top of your setup.py::
-
-    from ez_setup import use_setuptools
-    use_setuptools()
-
-If you want to require a specific version of setuptools, set a download
-mirror, or use an alternate download directory, you can do so by supplying
-the appropriate options to ``use_setuptools()``.
-
-This file can also be run as a script to install or upgrade setuptools.
-"""
-import os
-import shutil
-import sys
-import tempfile
-import tarfile
-import optparse
-import subprocess
-
-from distutils import log
-
-try:
-    from site import USER_SITE
-except ImportError:
-    USER_SITE = None
-
-DEFAULT_VERSION = "0.9.6"
-DEFAULT_URL = "https://pypi.python.org/packages/source/s/setuptools/"
-
-def _python_cmd(*args):
-    args = (sys.executable,) + args
-    return subprocess.call(args) == 0
-
-def _install(tarball, install_args=()):
-    # extracting the tarball
-    tmpdir = tempfile.mkdtemp()
-    log.warn('Extracting in %s', tmpdir)
-    old_wd = os.getcwd()
-    try:
-        os.chdir(tmpdir)
-        tar = tarfile.open(tarball)
-        _extractall(tar)
-        tar.close()
-
-        # going in the directory
-        subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
-        os.chdir(subdir)
-        log.warn('Now working in %s', subdir)
-
-        # installing
-        log.warn('Installing Setuptools')
-        if not _python_cmd('setup.py', 'install', *install_args):
-            log.warn('Something went wrong during the installation.')
-            log.warn('See the error message above.')
-            # exitcode will be 2
-            return 2
-    finally:
-        os.chdir(old_wd)
-        shutil.rmtree(tmpdir)
-
-
-def _build_egg(egg, tarball, to_dir):
-    # extracting the tarball
-    tmpdir = tempfile.mkdtemp()
-    log.warn('Extracting in %s', tmpdir)
-    old_wd = os.getcwd()
-    try:
-        os.chdir(tmpdir)
-        tar = tarfile.open(tarball)
-        _extractall(tar)
-        tar.close()
-
-        # going in the directory
-        subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
-        os.chdir(subdir)
-        log.warn('Now working in %s', subdir)
-
-        # building an egg
-        log.warn('Building a Setuptools egg in %s', to_dir)
-        _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir)
-
-    finally:
-        os.chdir(old_wd)
-        shutil.rmtree(tmpdir)
-    # returning the result
-    log.warn(egg)
-    if not os.path.exists(egg):
-        raise IOError('Could not build the egg.')
-
-
-def _do_download(version, download_base, to_dir, download_delay):
-    egg = os.path.join(to_dir, 'setuptools-%s-py%d.%d.egg'
-                       % (version, sys.version_info[0], sys.version_info[1]))
-    if not os.path.exists(egg):
-        tarball = download_setuptools(version, download_base,
-                                      to_dir, download_delay)
-        _build_egg(egg, tarball, to_dir)
-    sys.path.insert(0, egg)
-    import setuptools
-    setuptools.bootstrap_install_from = egg
-
-
-def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
-                   to_dir=os.curdir, download_delay=15):
-    # making sure we use the absolute path
-    to_dir = os.path.abspath(to_dir)
-    was_imported = 'pkg_resources' in sys.modules or \
-        'setuptools' in sys.modules
-    try:
-        import pkg_resources
-    except ImportError:
-        return _do_download(version, download_base, to_dir, download_delay)
-    try:
-        pkg_resources.require("setuptools>=" + version)
-        return
-    except pkg_resources.VersionConflict:
-        e = sys.exc_info()[1]
-        if was_imported:
-            sys.stderr.write(
-            "The required version of setuptools (>=%s) is not available,\n"
-            "and can't be installed while this script is running. Please\n"
-            "install a more recent version first, using\n"
-            "'easy_install -U setuptools'."
-            "\n\n(Currently using %r)\n" % (version, e.args[0]))
-            sys.exit(2)
-        else:
-            del pkg_resources, sys.modules['pkg_resources']    # reload ok
-            return _do_download(version, download_base, to_dir,
-                                download_delay)
-    except pkg_resources.DistributionNotFound:
-        return _do_download(version, download_base, to_dir,
-                            download_delay)
-
-
-def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
-                        to_dir=os.curdir, delay=15):
-    """Download setuptools from a specified location and return its filename
-
-    `version` should be a valid setuptools version number that is available
-    as an egg for download under the `download_base` URL (which should end
-    with a '/'). `to_dir` is the directory where the egg will be downloaded.
-    `delay` is the number of seconds to pause before an actual download
-    attempt.
-    """
-    # making sure we use the absolute path
-    to_dir = os.path.abspath(to_dir)
-    try:
-        from urllib.request import urlopen
-    except ImportError:
-        from urllib2 import urlopen
-    tgz_name = "setuptools-%s.tar.gz" % version
-    url = download_base + tgz_name
-    saveto = os.path.join(to_dir, tgz_name)
-    src = dst = None
-    if not os.path.exists(saveto):  # Avoid repeated downloads
-        try:
-            log.warn("Downloading %s", url)
-            src = urlopen(url)
-            # Read/write all in one block, so we don't create a corrupt file
-            # if the download is interrupted.
-            data = src.read()
-            dst = open(saveto, "wb")
-            dst.write(data)
-        finally:
-            if src:
-                src.close()
-            if dst:
-                dst.close()
-    return os.path.realpath(saveto)
-
-
-def _extractall(self, path=".", members=None):
-    """Extract all members from the archive to the current working
-       directory and set owner, modification time and permissions on
-       directories afterwards. `path' specifies a different directory
-       to extract to. `members' is optional and must be a subset of the
-       list returned by getmembers().
-    """
-    import copy
-    import operator
-    from tarfile import ExtractError
-    directories = []
-
-    if members is None:
-        members = self
-
-    for tarinfo in members:
-        if tarinfo.isdir():
-            # Extract directories with a safe mode.
-            directories.append(tarinfo)
-            tarinfo = copy.copy(tarinfo)
-            tarinfo.mode = 448  # decimal for oct 0700
-        self.extract(tarinfo, path)
-
-    # Reverse sort directories.
-    if sys.version_info < (2, 4):
-        def sorter(dir1, dir2):
-            return cmp(dir1.name, dir2.name)
-        directories.sort(sorter)
-        directories.reverse()
-    else:
-        directories.sort(key=operator.attrgetter('name'), reverse=True)
-
-    # Set correct owner, mtime and filemode on directories.
-    for tarinfo in directories:
-        dirpath = os.path.join(path, tarinfo.name)
-        try:
-            self.chown(tarinfo, dirpath)
-            self.utime(tarinfo, dirpath)
-            self.chmod(tarinfo, dirpath)
-        except ExtractError:
-            e = sys.exc_info()[1]
-            if self.errorlevel > 1:
-                raise
-            else:
-                self._dbg(1, "tarfile: %s" % e)
-
-
-def _build_install_args(options):
-    """
-    Build the arguments to 'python setup.py install' on the setuptools package
-    """
-    install_args = []
-    if options.user_install:
-        if sys.version_info < (2, 6):
-            log.warn("--user requires Python 2.6 or later")
-            raise SystemExit(1)
-        install_args.append('--user')
-    return install_args
-
-def _parse_args():
-    """
-    Parse the command line for options
-    """
-    parser = optparse.OptionParser()
-    parser.add_option(
-        '--user', dest='user_install', action='store_true', default=False,
-        help='install in user site package (requires Python 2.6 or later)')
-    parser.add_option(
-        '--download-base', dest='download_base', metavar="URL",
-        default=DEFAULT_URL,
-        help='alternative URL from where to download the setuptools package')
-    options, args = parser.parse_args()
-    # positional arguments are ignored
-    return options
-
-def main(version=DEFAULT_VERSION):
-    """Install or upgrade setuptools and EasyInstall"""
-    options = _parse_args()
-    tarball = download_setuptools(download_base=options.download_base)
-    return _install(tarball, _build_install_args(options))
-
-if __name__ == '__main__':
-    sys.exit(main())

setup.cfg

@@ -0,0 +1,2 @@
+[bdist_wheel]
+universal=1

setup.py

@@ -1,13 +1,12 @@
+#! /usr/bin/python
 # PROPKA 3.1
 #
 #
 # setuptools installation of  PROPKA 3.1
 
-import ez_setup
-ez_setup.use_setuptools()
 from setuptools import setup, find_packages
 
-VERSION = "3.1"
+VERSION = "3.1.0"
 
 setup(name="PROPKA",
       version=VERSION,
@@ -31,14 +30,23 @@ in publications:
   residues in empirical pKa predictions." Journal of Chemical Theory
   and Computation 7, no. 2 (2011): 525-537.
 
-See http://propka.ki.ku.dk/ for the PROPKA web server,
+See http://propka.org/ for the PROPKA web server.
-using the tutorial http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutorial .
 """,
       author="Jan H. Jensen",
       author_email="jhjensen@chem.ku.dk",
-      license="",
+      license="LGPL v2.1",
-      url="http://propka.ki.ku.dk/",
+      url="http://propka.org",
       keywords="science",
+      classifiers=[
+          'Development Status :: 6 - Mature',
+          'Environment :: Console',
+          'Intended Audience :: Science/Research',
+          'License :: OSI Approved :: GNU Lesser General Public License v2 (LGPLv2)',
+          'Operating System :: POSIX',
+          'Programming Language :: Python',
+          'Topic :: Scientific/Engineering :: Bio-Informatics',
+          'Topic :: Scientific/Engineering :: Chemistry',
+      ],
       packages=find_packages(exclude=['scripts']),
       package_data = {'propka': ['*.dat', '*.cfg']},
       #scripts = ["scripts/propka31.py"],  # use entry point below