fixed PEP8 F633, and PEP8 problems in the documentation build

.github/workflows/pytest_flake8.yml

@@ -32,7 +32,7 @@ jobs:
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors
-        flake8 . --count --select=E9,F7 --show-source --statistics
+        flake8 . --count --select=E9,F7,F6 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         #flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: pytest

.gitignore

@@ -12,3 +12,5 @@ ush/python_utils/__pycache__/
 
 __pycache__
 *.swp
+.venv
+*~

doc/UsersGuide/source/conf.py

@@ -16,8 +16,6 @@
 import sys
 sys.path.insert(0, os.path.abspath('.'))
 
-
-
 # -- Project information -----------------------------------------------------
 
 project = 'RRFS-Workflow Users Guide'
@@ -56,7 +54,7 @@
 ]
 
 bibtex_bibfiles = ['references.bib']
-#bibtex_bibfiles = ['refs.bib']
+# bibtex_bibfiles = ['refs.bib']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -104,10 +102,11 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-#html_static_path = []
+# html_static_path = []
 html_static_path = ['_static']
 html_context = {}
 
+
 def setup(app):
     app.add_css_file('custom.css')  # may also be an URL
     app.add_css_file('theme_overrides.css')  # may also be a URL
@@ -134,19 +133,19 @@ def setup(app):
 latex_engine = 'pdflatex'
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
-      'papersize': 'letterpaper',
+    'papersize': 'letterpaper',
 
     # The font size ('10pt', '11pt' or '12pt').
-      'pointsize': '11pt',
+    'pointsize': '11pt',
 
     # Additional stuff for the LaTeX preamble.
-      'preamble': r'''
+    'preamble': r'''
         \usepackage{charter}
         \usepackage[defaultsans]{lato}
         \usepackage{inconsolata}
     ''',
     # Release name prefix
-      'releasename': ' ',
+    'releasename': ' ',
 
     # Latex figure (float) alignment
     #

ush/rocoto/rocoto_viewer.py

@@ -118,7 +118,7 @@ def sigwinch_handler(signum, frame):
 
 def usage(message=None):
     curses.endwin()
-    print>>sys.stderr, '''
+    print('''
 Usage: rocoto_status_viewer.py  -w workflow.xml -d database.db [--listtasks]\n                                                               [--html=filename.html]\n                                                               [--perfmetrics={True,False}]
 
 Mandatory arguments:
@@ -128,10 +128,10 @@ def usage(message=None):
   --listtasks             --- print out a list of all tasks
   --html=filename.html    --- creates an HTML document of status
   --perfmetrics=True      --- turn on/off extra columns for performance metrics 
-  --help                  --- print this usage message'''
+  --help                  --- print this usage message''', file=sys.stderr)
 
     if message is not None:
-        print>>sys.stderr,'\n'+str(message).rstrip()+'\n'
+        print('\n'+str(message).rstrip()+'\n', file=sys.stderr)
     sys.exit(-1)
 
 def augment_SQLite3(filename):