add run.txt and test.txt into requirement, lint check for conf.py, extract.py, and prep.py (#17)

Author: stevenhua0320

Diff for: devutils/prep.py

@@ -88,7 +88,7 @@ def rm(directory, filerestr):
     rm("../doc/examples/output", r"known_dG.*\.pwa")
     rm("../doc/examples/output", r"unknown_dG.*\.pwa")
 
-    ### Testing examples
+    # Testing examples
     examples = Test()
     test_names = [
         "extract_single_peak",
@@ -110,7 +110,7 @@ def rm(directory, filerestr):
 
     examples.report()
 
-    ### Convert output of example files to Unix-style endlines for sdist.
+    # Convert output of example files to Unix-style endlines for sdist.
     if os.linesep != "\n":
         print("==== Scrubbing Endlines ====")
         # All *.srmise and *.pwa files in examples directory.

Diff for: diffpy.srmise/requirements/run.txt

@@ -0,0 +1,3 @@
+matplotlib-base
+numpy
+scipy

Diff for: diffpy.srmise/requirements/test.txt

@@ -0,0 +1,5 @@
+flake8
+pytest
+codecov
+coverage
+pytest-env

Diff for: diffpy/srmise/applications/extract.py

@@ -11,7 +11,8 @@
 #
 ##############################################################################
 
-from optparse import OptionGroup, OptionParser
+import textwrap
+from optparse import IndentedHelpFormatter, OptionGroup, OptionParser
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -539,7 +540,7 @@ def main():
         cov = None
         if options.performextraction:
             cov = ext.extract()
-        out = ext.extracted
+        ext.extracted
 
         if options.savefile is not None:
             try:
@@ -591,13 +592,10 @@ def parsepars(mp, parseq):
     return mp.actualize(pars, "internal", free=free)
 
 
-### Class to preserve newlines in optparse
+# Class to preserve newlines in optparse
 # Borrowed, with minor changes, from
 # http://groups.google.com/group/comp.lang.python/browse_frm/thread/6df6e6b541a15bc2/09f28e26af0699b1
 
-import textwrap
-from optparse import IndentedHelpFormatter
-
 
 class IndentedHelpFormatterWithNL(IndentedHelpFormatter):
     def _format_text(self, text):
@@ -652,7 +650,7 @@ def format_option(self, option):
         return "".join(result)
 
 
-### End class
+# End class
 
 if __name__ == "__main__":
     main()

Diff for: doc/manual/source/conf.py

@@ -16,6 +16,8 @@
 import sys
 import time
 
+from setup import versiondata
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -59,7 +61,6 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 sys.path.insert(0, os.path.abspath("../../.."))
-from setup import versiondata
 
 fullversion = versiondata.get("DEFAULT", "version")
 # The short X.Y version.
@@ -205,11 +206,11 @@
 
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
-    #'papersize': 'letterpaper',
+    # 'papersize': 'letterpaper',
     # The font size ('10pt', '11pt' or '12pt').
-    #'pointsize': '10pt',
+    # 'pointsize': '10pt',
     # Additional stuff for the LaTeX preamble.
-    #'preamble': '',
+    # 'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples