Merge pull request #1 from galaxyproject/dev

Update from Galaxyproject repo

Author: Delphine-L

.ci/autopep8.sh

@@ -0,0 +1,2 @@
+exclude=$(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -s -d ',' - )
+autopep8 -i -r --exclude $exclude --select E11,E101,E127,E201,E202,E22,E301,E302,E303,E304,E306,E711,W291,W292,W293,W391 ./lib/ ./test/

.ci/check_py3_compatibility.sh

@@ -0,0 +1,35 @@
+#!/bin/sh
+
+if command -v ack-grep >/dev/null; then
+    ACK=ack-grep
+else
+    ACK=ack
+fi
+
+export ACK_OPTIONS=" --type python \
+--ignore-dir=.git \
+--ignore-dir=.tox \
+--ignore-dir=.venv \
+--ignore-dir=.venv3 \
+--ignore-dir=client/node_modules \
+--ignore-dir=database \
+--ignore-dir=doc/build \
+--ignore-dir=eggs \
+--ignore-dir=static/maps \
+--ignore-dir=static/scripts"
+
+PYTHON2_ONLY_MODULES="__builtin__ _winreg BaseHTTPServer CGIHTTPServer \
+ConfigParser Cookie cookielib copy_reg cPickle cStringIO Dialog dummy_thread \
+FileDialog gdbm htmlentitydefs HTMLParser httplib Queue robotparser \
+ScrolledText SimpleDialog SimpleHTTPServer SimpleXMLRPCServer SocketServer \
+StringIO thread Tix tkColorChooser tkCommonDialog Tkconstants Tkdnd tkFont \
+Tkinter tkFileDialog tkMessageBox tkSimpleDialog ttk urllib urllib2 urlparse \
+xmlrpclib"
+
+ret=0
+for mod in $PYTHON2_ONLY_MODULES; do
+    $ACK "^import $mod(\n|\.)|^from $mod import "
+    if [ $? -eq 0 ]; then ret=1; fi
+done
+
+exit $ret

.ci/first_startup.sh

@@ -10,7 +10,7 @@ bash run.sh --daemon && \
         sleep 1
         i=$((i + 1))
     done
-kill -9 "$(cat paster.pid)"
+kill -9 "$(cat galaxy.pid)"
 echo "exit code:$EXIT_CODE, showing startup log:"
-cat paster.log
+cat galaxy.log
 exit $EXIT_CODE

.ci/flake8_blacklist.txt

@@ -1,8 +1,12 @@
-.venv/
-.tox/
-client/node_modules/
-database/
+.git
+.tox
+.venv
+.venv3
+client/node_modules
+database
+doc/build
 doc/source/conf.py
-eggs/
+eggs
 lib/galaxy/util/jstree.py
-lib/galaxy/web/proxy/js/node_modules/
+static/maps
+static/scripts