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Author: Steffen Moeller
Last-Update: 2020-03-26 04:21:08 +0100
Description: Use Python3 in test
Bug: https://github.com/PacificBiosciences/kineticsTools/pull/76
--- kineticstools.orig/test/test_gather_bigwig.py
+++ kineticstools/test/test_gather_bigwig.py
@@ -72,7 +72,7 @@
def test_gather_bigwig_cli(self):
tmp_dir = tempfile.mkdtemp()
ofn = op.join(tmp_dir, "gathered.bw")
- args = ["python", "-m", "kineticsTools.tasks.gather_bigwig",
+ args = ["python3", "-m", "kineticsTools.tasks.gather_bigwig",
ofn] + self._data_files
log.info("Output will be in %s", tmp_dir)
with open(op.join(tmp_dir, "stdout"), "w") as stdout:
--- kineticstools.orig/Makefile
+++ kineticstools/Makefile
@@ -6,17 +6,17 @@
all: build install
build:
- python setup.py build --executable="/usr/bin/env python"
+ python3 setup.py build --executable="/usr/bin/env python"
bdist:
- python setup.py build --executable="/usr/bin/env python"
- python setup.py bdist --formats=egg
+ python3 setup.py build --executable="/usr/bin/env python"
+ python3 setup.py bdist --formats=egg
install:
- python setup.py install
+ python3 setup.py install
develop:
- python setup.py develop
+ python3 setup.py develop
clean:
rm -rf build/;\
@@ -29,17 +29,17 @@
tests: cram-tests py-tests extra-tests
cram-tests:
- cram --verbose --xunit-file=cramtests.xml `ls test/cram/*.t | grep -v detection_bam`
+ cram3 --verbose --xunit-file=cramtests.xml `ls test/cram/*.t | grep -v detection_bam`
long-tests:
- cram test/cram/long_running/*.t
+ cram3 test/cram/long_running/*.t
py-tests:
# pytest --cov=kineticsTools # does not quite work since we run in test/ dir.
- cd test/; pytest -s -v -p no:warnings -n auto --dist=loadscope --durations=20 --junitxml=../nosetests.xml --cov-report=xml:../coverage.xml test_*.py
+ cd test/; pytest-3 -s -v -p no:warnings --durations=20 --junitxml=../nosetests.xml test_*.py
extra-tests:
- #cram --verbose --xunit-file=cramtests-extra.xml test/cram/extra/*.t
+ #cram3 --verbose --xunit-file=cramtests-extra.xml test/cram/extra/*.t
# TODO: Fix chemistry and re-enable this test.
pylint:
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