reformat all to rpxdock style

.gitignore

@@ -82,6 +82,8 @@ _khash_ffi.c
 
 .worms_pytest_cache/splices
 .worms_pytest_cache/poses
+.worms_pytest_cache/bblock
+.worms_pytest_cache_disabled
 
 *.info
 *.pdb

docs/conf.py

@@ -192,20 +192,18 @@
 # -- Options for LaTeX output ------------------------------------------
 
 latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    #'papersize': 'letterpaper',
-    # The font size ('10pt', '11pt' or '12pt').
-    #'pointsize': '10pt',
-    # Additional stuff for the LaTeX preamble.
-    #'preamble': '',
+   # The paper size ('letterpaper' or 'a4paper').
+   #'papersize': 'letterpaper',
+   # The font size ('10pt', '11pt' or '12pt').
+   #'pointsize': '10pt',
+   # Additional stuff for the LaTeX preamble.
+   #'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass
 # [howto/manual]).
-latex_documents = [
-    ("index", "worms.tex", u"worms Documentation", u"Will Sheffler", "manual")
-]
+latex_documents = [("index", "worms.tex", u"worms Documentation", u"Will Sheffler", "manual")]
 
 # The name of an image file (relative to this directory) to place at
 # the top of the title page.
@@ -241,17 +239,15 @@
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
-texinfo_documents = [
-    (
-        "index",
-        "worms",
-        u"worms Documentation",
-        u"Will Sheffler",
-        "worms",
-        "One line description of project.",
-        "Miscellaneous",
-    )
-]
+texinfo_documents = [(
+   "index",
+   "worms",
+   u"worms Documentation",
+   u"Will Sheffler",
+   "worms",
+   "One line description of project.",
+   "Miscellaneous",
+)]
 
 # Documents to append as an appendix to all manuals.
 # texinfo_appendices = []

examples/build_worms_database.py

@@ -10,24 +10,24 @@
 
 if __name__ == "__main__":
 
-    info("sent to info")
-
-    args = get_cli_args(dbfiles=[""], cachedirs=[""], read_new_pdbs=False, parallel=0)
-    if args.parallel == 0:
-        args.parallel = 1
-
-    pyrosetta.init("-mute all -ignore_unrecognized_res")
-
-    try:
-        pp = CachingBBlockDB(
-            dbfiles=args.dbfiles,
-            nprocs=args.parallel,
-            cachedirs=args.cachedirs,
-            read_new_pdbs=args.read_new_pdbs,
-            lazy=False,
-        )
-        print("new entries", pp.n_new_entries)
-        print("missing entries", pp.n_missing_entries)
-        print("total entries", len(pp._bblock_cache))
-    except AssertionError as e:
-        print(e)
+   info("sent to info")
+
+   args = get_cli_args(dbfiles=[""], cachedirs=[""], read_new_pdbs=False, parallel=0)
+   if args.parallel == 0:
+      args.parallel = 1
+
+   pyrosetta.init("-mute all -ignore_unrecognized_res")
+
+   try:
+      pp = CachingBBlockDB(
+         dbfiles=args.dbfiles,
+         nprocs=args.parallel,
+         cachedirs=args.cachedirs,
+         read_new_pdbs=args.read_new_pdbs,
+         lazy=False,
+      )
+      print("new entries", pp.n_new_entries)
+      print("missing entries", pp.n_missing_entries)
+      print("total entries", len(pp._bblock_cache))
+   except AssertionError as e:
+      print(e)