Small minor tweaks

1) Update README installation instructions
2) Put all set_up code into seperate named functions
3) Remove underhanded mpl backend setter

README.md

@@ -35,11 +35,48 @@ the stripped down [miniconda](http://conda.pydata.org/miniconda.html)
 installation, or the full-featured
 [anaconda](https://www.continuum.io/downloads) (these are essentially the
 same, but the `anaconda` version installs a variety of useful packages such as
-`numpy` and `scipy` by default.
+`numpy` and `scipy` by default). Instructions to install miniconda/anaconda
+are provided in the links.
+
+### Dependencies
+
+`pyfstat` makes use of a variety python modules listed as the
+`imports` in the top of `pyfstat.py`. The first set are core modules (such as
+`os`, `sys`) while the second set are external and need to be installed for
+`pyfstat` to work properly. Please install the following widely available
+modules:
+
+* [numpy](http://www.numpy.org/)
+* [matplotlib](http://matplotlib.org/)
+* [scipy](https://www.scipy.org/)
+* [emcee](http://dan.iel.fm/emcee/current/)
+* [corner](https://pypi.python.org/pypi/corner/)
+* [dill](https://pypi.python.org/pypi/dill)
+* [tqdm](https://pypi.python.org/pypi/tqdm)(optional), if installed, this
+  provides a useful progress bar and estimate of the remaining run-time.
+
+For an introduction to installing modules see
+[here](https://docs.python.org/3.5/installing/index.html). If you are using
+`pip`, to install all of these modules, run
+```
+$ pip install -r /PATH/TO/THIS/DIRECTORY/requirements.txt
+```
+If you have installed python from conda then `pip` itself can be installed via
+`conda install pip`.
+
+In addition to these modules, you also need a working **swig-enabled**
+[`lalapps`](http://software.ligo.org/docs/lalsuite/lalsuite/) with
+  at least `lalpulsar`. A minimal confuration line to use when installing
+`lalapps` is
+
+```
+$ ./configure --prefix=${HOME}/lalsuite-install --disable-all-lal --enable-lalpulsar --enable-lalapps --enable-swig
+```
+
 
 ### `pyfstat` installation
 
-The script can be installed system wide via
+The script can be installed system wide, assuming you are in this directory, via
 ```
 $ python setup.py install
 ```
@@ -55,8 +92,8 @@ the module will be installed to whichever python executable you call it from.
 
 The scripts require a path to ephemeris files in order to use the
 `lalpulsar.ComputeFstat` module. This can either be specified when initialising
-each search, or more simply by placing a file `~/.pyfstat.conf` into your home
-directory which looks like
+each search (as one of the arguments), or simply by placing a file
+`~/.pyfstat.conf` into your home directory which looks like
 
 ```
 earth_ephem = '/home/<USER>/lalsuite-install/share/lalpulsar/earth00-19-DE421.dat.gz'
@@ -64,34 +101,4 @@ sun_ephem = '/home/<USER>/lalsuite-install/share/lalpulsar/sun00-19-DE421.dat.gz
 ```
 here, we use the default ephemeris files provided with `lalsuite`.
 
-### Dependencies
-
-The installation above will complete succesfully without the following
-dependencies, but you will subsequently find various `ImportError` messages
-when running `pyfstat` scripts if you haven't installed the following modules.
-
-* swig-enabled [`lalapps`](http://software.ligo.org/docs/lalsuite/lalsuite/) with
-  at least `lalpulsar`. A minimal confuration line to use when installing
-`lalapps` is
-
-```
-$ ./configure --prefix=${HOME}/lalsuite-install --disable-all-lal --enable-lalpulsar --enable-lalapps --enable-swig
-```
-
-* If using the MCMC tools, you will need to install the following python
-  modules
-  * [numpy](http://www.numpy.org/)
-  * [scipy](https://www.scipy.org/)
-  * [emcee](http://dan.iel.fm/emcee/current/)
-  * [corner](https://pypi.python.org/pypi/corner/)
-  * [dill](https://pypi.python.org/pypi/dill)
-  * [tqdm](https://pypi.python.org/pypi/tqdm)(optional), if installed, this
-  provides a useful progress bar and estimate of the remaining run-time.
-
-  To install all of these modules, run
-```
-$ pip install -r /PATH/TO/THIS/DIRECTORY/requirements.txt
-```
-  where `pip` is the python package installer, if you have installed python
-  from conda then it can be installed via `conda install pip`.
 

pyfstat.py

@@ -13,7 +13,6 @@ from collections import OrderedDict
 
 import numpy as np
 import matplotlib
-matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 import scipy.special
 import scipy.optimize
@@ -23,60 +22,73 @@ import dill as pickle
 import lal
 import lalpulsar
 
-try:
+
+def set_up_optional_tqdm():
+    try:
         from tqdm import tqdm
-except ImportError:
+    except ImportError:
         def tqdm(x, *args, **kwargs):
             return x
 
-plt.rcParams['text.usetex'] = True
-plt.rcParams['axes.formatter.useoffset'] = False
 
-config_file = os.path.expanduser('~')+'/.pyfstat.conf'
-if os.path.isfile(config_file):
+def set_up_matplotlib_defaults():
+    plt.switch_backend('Agg')
+    plt.rcParams['text.usetex'] = True
+    plt.rcParams['axes.formatter.useoffset'] = False
+
+
+def set_up_ephemeris_configuration():
+    config_file = os.path.expanduser('~')+'/.pyfstat.conf'
+    if os.path.isfile(config_file):
         d = {}
         with open(config_file, 'r') as f:
             for line in f:
                 k, v = line.split('=')
                 k = k.replace(' ', '')
-            v = v.replace(' ', '').replace("'", "").replace('"', '').replace('\n', '')
+                for item in [' ', "'", '"', '\n']:
+                    v = v.replace(item, '')
                 d[k] = v
         earth_ephem = d['earth_ephem']
         sun_ephem = d['sun_ephem']
-else:
-    logging.warning('No ~/.pyfstat.conf file found please provide the paths '
-                    'when initialising searches')
+    else:
+        logging.warning('No ~/.pyfstat.conf file found please provide the '
+                        'paths when initialising searches')
         earth_ephem = None
         sun_ephem = None
 
-parser = argparse.ArgumentParser()
-parser.add_argument("-q", "--quite", help="Decrease output verbosity",
+
+def set_up_command_line_arguments():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-q", "--quite", help="Decrease output verbosity",
                         action="store_true")
-parser.add_argument("--no-interactive", help="Don't use interactive output",
+    parser.add_argument("--no-interactive", help="Don't use interactive",
                         action="store_true")
-parser.add_argument("-c", "--clean", help="Don't use cached data",
+    parser.add_argument("-c", "--clean", help="Don't use cached data",
                         action="store_true")
-parser.add_argument("-u", "--use-old-data", action="store_true")
-parser.add_argument('-s', "--setup-only", action="store_true")
-parser.add_argument('-n', "--no-template-counting", action="store_true")
-parser.add_argument('unittest_args', nargs='*')
-args, unknown = parser.parse_known_args()
-sys.argv[1:] = args.unittest_args
-
-if args.quite or args.no_interactive:
+    parser.add_argument("-u", "--use-old-data", action="store_true")
+    parser.add_argument('-s', "--setup-only", action="store_true")
+    parser.add_argument('-n', "--no-template-counting", action="store_true")
+    parser.add_argument('unittest_args', nargs='*')
+    args, unknown = parser.parse_known_args()
+    sys.argv[1:] = args.unittest_args
+    if args.quite or args.no_interactive:
         def tqdm(x, *args, **kwargs):
             return x
-
-logger = logging.getLogger()
-logger.setLevel(logging.DEBUG)
-stream_handler = logging.StreamHandler()
-if args.quite:
+    logger = logging.getLogger()
+    logger.setLevel(logging.DEBUG)
+    stream_handler = logging.StreamHandler()
+    if args.quite:
         stream_handler.setLevel(logging.WARNING)
-else:
+    else:
         stream_handler.setLevel(logging.DEBUG)
-stream_handler.setFormatter(logging.Formatter(
+    stream_handler.setFormatter(logging.Formatter(
         '%(asctime)s %(levelname)-8s: %(message)s', datefmt='%H:%M'))
-logger.addHandler(stream_handler)
+    logger.addHandler(stream_handler)
+
+set_up_optional_tqdm()
+set_up_matplotlib_defaults()
+set_up_ephemeris_configuration()
+set_up_command_line_arguments()
 
 
 def round_to_n(x, n):