[Fix] Duplicate site_definition.yaml

- site_definition.yaml was collected twice.
- Update Makefile with format target and ignore
  pep8 rule that conflicts w/ YAPF formatting

Change-Id: I2bc6d40e9e9085558315224df7d9127a8945ee1c

Makefile

@@ -42,6 +42,10 @@ run_pegleg: build_pegleg
 .PHONY: lint
 lint: py_lint
 
+# Perform auto formatting
+.PHONY: format
+format: py_format
+
 .PHONY: build_pegleg
 build_pegleg:
 ifeq ($(USE_PROXY), true)
@@ -60,3 +64,7 @@ clean:
 .PHONY: py_lint
 py_lint:
 	cd src/bin/pegleg;tox -e lint
+
+.PHONY: py_format
+py_format:
+	cd src/bin/pegleg;tox -e fmt

src/bin/pegleg/pegleg/engine/util/definition.py

@@ -64,7 +64,6 @@ def site_files(site_name):
     params = load_as_params(site_name)
     for filename in files.search(files.directories_for(**params)):
         yield filename
-    yield path(site_name)
 
 
 def site_files_by_repo(site_name):
@@ -74,5 +73,3 @@ def site_files_by_repo(site_name):
     for repo, dl in dir_map.items():
         for filename in files.search(dl):
             yield (repo, filename)
-        if repo == config.get_primary_repo():
-            yield (repo, path(site_name))

src/bin/pegleg/tox.ini

@@ -12,7 +12,7 @@ commands=
 [testenv:fmt]
 deps = yapf==0.20.0
 commands =
-    yapf -ir {toxinidir}/pegleg
+    yapf --style=pep8 -ir {toxinidir}/pegleg
 
 [testenv:lint]
 deps =
@@ -23,4 +23,4 @@ commands =
     flake8 {toxinidir}/pegleg
 
 [flake8]
-ignore = E251
+ignore = E251,W503