From 5e149d01baa73ad6bb9d1018b192c92dc245dd31 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sun, 12 Jul 2015 17:34:46 +0200
Subject: [PATCH] Switch over to a blacklist for linting.

---
 .ci/flake8_wrapper.sh |  6 +---
 .ci/pep8_sources.txt  | 73 +++++++++++++------------------------------
 2 files changed, 22 insertions(+), 57 deletions(-)

diff --git a/.ci/flake8_wrapper.sh b/.ci/flake8_wrapper.sh
index 63b56681881..80fe6c4c330 100755
--- a/.ci/flake8_wrapper.sh
+++ b/.ci/flake8_wrapper.sh
@@ -2,11 +2,7 @@
 
 set -e
 
-# Run broad range of checks over specific white-listed files, this uses
-# the default checks defined in setup.cfg.
-while read p; do
-    flake8 $(eval echo "$p")
-done <.ci/pep8_sources.txt
+flake8 --exclude database/,.venv/,`paste -sd, .ci/pep8_sources.txt` .
 
 # Look for obviously broken stuff lots more places.
 flake8 --select=E901,E902,F821,F822,F823,F831 --exclude lib/galaxy/util/pastescript/serve.py,lib/pkg_resources.py lib/ test/{api,unit}
diff --git a/.ci/pep8_sources.txt b/.ci/pep8_sources.txt
index 57405e3796b..e9f4925542e 100644
--- a/.ci/pep8_sources.txt
+++ b/.ci/pep8_sources.txt
@@ -1,52 +1,21 @@
-cron/parse_builds.py
-lib/galaxy/{__init__,app,config,main,queue_worker,queues,version}.py
-lib/galaxy/actions/
-lib/galaxy/auth/
-lib/galaxy/dataset_collections/
-lib/galaxy/datatypes/{assembly,binary,checkers,chrominfo,coverage,data,proteomics}.py
-lib/galaxy/datatypes/converters/{bedgraph_to_array_tree_converter,bgzip,wiggle_to_array_tree_converter}.py
-lib/galaxy/eggs/
-lib/galaxy/exceptions/
-lib/galaxy/external_services/
-lib/galaxy/forms/
-lib/galaxy/jobs/
-lib/galaxy/managers/
-lib/galaxy/model/orm/{__init__,scripts,engine_factory,now,scripts}.py
-lib/galaxy/model/{base,custom_types,search,util}.py
-lib/galaxy/model/migrate/check.py
-lib/galaxy/model/migrate/versions/{0001_initial_tables,0002_metadata_file_table,0003_security_and_libraries,0004_indexes_and_defaults,0005_cleanup_datasets_fix}.py
-lib/galaxy/model/tool_shed_install/{__init__,mapping}.py
-lib/galaxy/model/tool_shed_install/migrate/check.py
-lib/galaxy/objectstore/
-lib/galaxy/openid/
-lib/galaxy/quota/
-lib/galaxy/tags/
-lib/galaxy/tools/
-lib/galaxy/util/{__init__,json,permutations,plugin_config,properties,simplegraph,sockets,sleeper,streamball,submodules,xml_macros}.py
-lib/galaxy/visualization/
-lib/galaxy/web/
-lib/galaxy/webapps/__init__.py
-lib/galaxy/webapps/galaxy/__init__.py
-lib/galaxy/webapps/galaxy/api/{__init__,authenticate,dataset_collections,datatypes,folder_contents,folders,lda_datasets,job_files,libraries,library_contents,provenance,remote_files,search,users}.py
-lib/galaxy/webapps/galaxy/controllers/{__init__,admin,cloudlaunch,workflow}.py
-lib/galaxy/webapps/reports/app.py
-lib/galaxy/webapps/reports/controllers/{__init__,jobs,query,workflows}.py
-lib/galaxy/webapps/tool_shed/app.py
-lib/galaxy/webapps/tool_shed/controllers/__init__.py
-lib/galaxy/webapps/tool_shed/framework/__init__.py
-lib/galaxy/webapps/tool_shed/framework/middleware/__init__.py
-lib/galaxy/webapps/tool_shed/util/{__init__,shed_statistics}.py
-lib/galaxy/work/
-lib/galaxy/workflow/
-lib/pulsar
-lib/tool_shed/__init__.py
-lib/tool_shed/galaxy_install/{install_manager,repair_repository_manager}.py
-lib/tool_shed/galaxy_install/repository_dependencies
-lib/tool_shed/galaxy_install/tools/{__init__,tool_panel_manager}.py
-lib/tool_shed/repository_types/{__init__,registry,unrestricted}.py
-lib/tool_shed/util/{__init__,repository_content_util,tool_util,web_util,workflow_util}.py
-test/functional/tools
-test/unit/jobs/test_job_configuration.py
-test/unit/tools
-tools/data_source/upload.py
-tools/evolution/codingSnps_filter.py
+contrib/
+doc/patch.py
+doc/source/conf.py
+lib/galaxy/datatypes/converters/lped_to_fped_converter.py
+lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
+lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
+lib/galaxy/model/mapping.py
+lib/galaxy/model/migrate/versions/
+lib/galaxy/model/tool_shed_install/migrate/versions/
+lib/galaxy/util/pastescript/serve.py
+lib/galaxy/webapps/tool_shed/model/mapping.py
+lib/galaxy/webapps/tool_shed/model/migrate/versions/
+lib/galaxy_utils/
+lib/pkg_resources.py
+lib/tool_shed/
+scripts/
+test/base/
+test/casperjs/
+test/install_and_test_tool_shed_repositories/
+test/tool_shed/
+tools/