Refactor plot styling to add a base style; set PDF truetype

CHANGELOG.rst

@@ -7,6 +7,8 @@ Versioning <http://semver.org/>`__. The changelog format is inspired by
 
 `Unreleased <https://github.com/smtg-ucl/galore/compare/0.6.1...HEAD>`__
 -------------------------------------------------------------------------
+- Update citation information, add to README
+- Use a default base stylesheet to make more compatible PDF files
 
 `[0.6.1] <https://github.com/smtg-ucl/galore/compare/0.6.0...0.6.1>`__ - 2018-11-19
 -----------------------------------------------------------------------------------

MANIFEST.in

@@ -1,6 +1,6 @@
 include README.rst CHANGELOG.rst LICENSE CITATION.cff 
 include test/test*.py
-recursive-include galore/data cross_sections.json cross_sections_ups.json cross_sections_haxpes.json scofield_data.db
+recursive-include galore/data cross_sections.json cross_sections_ups.json cross_sections_haxpes.json scofield_data.db galore_base.mplstyle
 include test/DOSCAR.1 test/test_xy_data.csv test/json_test.json
 recursive-include test/CaF2 ir_lda_700.txt raman_lda_500.dat
 recursive-include test/CdTe CdTe.gpw

galore/__init__.py

@@ -21,18 +21,23 @@
 
 from __future__ import print_function
 
-import os.path
-from itertools import repeat
 from collections import OrderedDict
+from itertools import repeat
 import logging
-
 from math import sqrt, log
+import os.path
+from os.path import pardir
+from os.path import join as path_join
+from pkg_resources import resource_filename
+
 import numpy as np
 from scipy.interpolate import interp1d
 
 import galore.formats
 from galore.cross_sections import get_cross_sections, cross_sections_info
 
+base_style = resource_filename(__name__,
+                               path_join('data', 'galore_base.mplstyle'))
 
 def auto_limits(data_1d, padding=0.05):
     """Return limiting values outside data range

galore/cli/galore.py

@@ -19,7 +19,7 @@
 # If not, see <http://www.gnu.org/licenses/>.                                 #
 #                                                                             #
 ###############################################################################
-import os
+
 import argparse
 from collections import OrderedDict
 from json import load as json_load
@@ -39,7 +39,6 @@
 except ImportError:
     has_matplotlib = False
 
-
 def main():
     logging.basicConfig(filename='galore.log', level=logging.INFO)
     console = logging.StreamHandler()
@@ -86,9 +85,13 @@ def pdos_from_files(return_plt=False, **kwargs):
     # For plotting and writing, "None" means "write to screen"
     # while False means "do nothing"
     if kwargs['plot'] or kwargs['plot'] is None:
+        import matplotlib.pyplot
+        style_list = [galore.base_style]
+
         if 'style' in kwargs and kwargs['style'] is not None:
-            import matplotlib.pyplot
-            matplotlib.pyplot.style.use(kwargs['style'])
+            style_list += kwargs['style']
+        matplotlib.pyplot.style.use(style_list)
+
         plt = galore.plot.plot_pdos(pdos_plotting_data,
                                     **kwargs)  # flipx is included in kwargs
 
@@ -155,9 +158,12 @@ def simple_dos_from_files(return_plt=False, **kwargs):
         if not has_matplotlib:
             print("Can't plot, no Matplotlib")
         else:
+            import matplotlib.pyplot
+            style_list = [galore.base_style]
             if 'style' in kwargs and kwargs['style'] is not None:
-                import matplotlib.pyplot
-                matplotlib.pyplot.style.use(kwargs['style'])
+                style_list += kwargs['style']
+            matplotlib.pyplot.style.use(style_list)
+
             plt = galore.plot.plot_tdos(x_values, broadened_data, **kwargs)
             if kwargs['ylabel'] is not None:
                 plt.ylabel(kwargs['ylabel'])

galore/cli/galore_plot_cs.py

@@ -25,7 +25,6 @@
 import logging
 import numpy as np
 from matplotlib import pyplot as plt
-plt.style.use('seaborn-colorblind')
 
 from galore.cross_sections import get_cross_sections_scofield
 
@@ -67,8 +66,10 @@ def run(elements, emin=1, emax=10, megabarn=False, size=None, output=None,
     energies = np.linspace(emin, emax, 200)
     cross_sections = get_cross_sections_scofield(energies, elements)
 
+    style_list = [galore.base_style]
     if style is not None:
-        plt.style.use(style)
+        style_list += style
+    plt.style.use(style_list)
 
     if size is None:
         fig = plt.figure()

galore/data/galore_base.mplstyle

@@ -0,0 +1 @@
+pdf.fonttype = 42  # Use truetype; makes PDF files easier to modify