Commit 5fb1748a authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

Merge branch '46-switch-to-galaxy-23-1' into 'dev' 

update to Galaxy 23.1

Closes #46

See merge request !50
parents ef4bbaba 8e78804b

.ci/autopep8.sh

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exclude=$(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_ignorelist.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

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#!/bin/sh



if command -v ack-grep >/dev/null; then

    ACK=ack-grep

else

    ACK=ack

fi





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 --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 \

    "^import $mod(\n|\.)|^from $mod import "

    if [ $? -eq 0 ]; then ret=1; fi

done



exit $ret

.ci/check_test_class_names.sh

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#!/bin/sh

TEST=$(mktemp)

TEST_EXTRA_CLASSES=$(mktemp)



pytest --collect-only --ignore=test/functional lib/galaxy_test/ test/ > "$TEST"

pytest -o python_classes='Test* *Test *TestCase' --collect-only --ignore=test/functional lib/galaxy_test/ test/ > "$TEST_EXTRA_CLASSES"



n_tests=$(grep 'tests collected' "$TEST" | sed -e 's/[^0-9]*\([0-9]*\) tests collected.*/\1/')

n_tests_extra_classes=$(grep 'tests collected' "$TEST_EXTRA_CLASSES" | sed -e 's/[^0-9]*\([0-9]*\) tests collected.*/\1/')



if [ "$n_tests_extra_classes" -gt "$n_tests" ]; then

    echo "New test class with name not starting with Test introduced, change it to have tests collected by pytest"

    diff "$TEST" "$TEST_EXTRA_CLASSES"

    exit 1

fi

.ci/eslint_wrapper.sh

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@@ -5,4 +5,4 @@ set -e 
# Setting NODE_PATH and config appropriately, using dependencies from

# client/node_modules, run eslint against args passed to this script.

# Primary use case here is for a pre-commit check.

NODE_PATH=src/ node client/node_modules/eslint/bin/eslint.js -c client/.eslintrc.json "$@"
 
NODE_PATH=src/ node client/node_modules/eslint/bin/eslint.js -c client/.eslintrc.js "$@"

.ci/flake8_ignorelist.txt

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@@ -9,9 +9,7 @@ packages/venv 
node_modules

database

doc/build

doc/source/conf.py

eggs

lib/galaxy/util/jstree.py

lib/galaxy/web/proxy/js/node_modules

static/maps

static/scripts