hopefully, final fix to the circle deployment

* fixed nipypecmd tests
* removed -n from py.test, which was making py.test think all tests passed (when some were failing)
* fixed the coverage collection when running the examples

Author: oesteban

.coveragerc

@@ -1,29 +1,2 @@
 [run]
 branch = True
-data_file = .coverage
-source = .
-omit =
-    nipype/external/*
-    nipype/fixes/*
-    tools/*
-    doc/*
-    */tests/*
-include =
-    tools/run_examples.py
-
-[report]
-exclude_lines =
-    # Have to re-enable the standard pragma
-    pragma: no cover
-
-    # Don't complain about missing debug-only code:
-    def __repr__
-    if self\.debug
-
-    # Don't complain if tests don't hit defensive assertion code:
-    raise AssertionError
-    raise NotImplementedError
-
-    # Don't complain if non-runnable code isn't run:
-    if 0:
-    if __name__ == .__main__.:

docker/files/run_examples.sh

@@ -17,17 +17,16 @@ echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg
 echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg
 
 # Set up coverage
-export COVERAGE_PROCESS_START=/src/nipype/.coveragerc
-sed -i -E "s/(source = ).*'/\1\/src\/nipype\/nipype/" /src/nipype/.coveragerc
-sed -i -E "s/(data_file = ).*'/\1\/\/work\/.coverage/" /src/nipype/.coveragerc
+export COVERAGE_FILE=${WORKDIR}/.coverage_${example_id}
+#sed -i -E "s/(source = ).*'/\1\/src\/nipype\/nipype/" /src/nipype/.coveragerc
 
 if [ "$2" == "MultiProc" ]; then
 	echo "concurrency = multiprocessing" >> /src/nipype/.coveragerc
 fi
 
-coverage run --rcfile=/src/nipype/.coveragerc /src/nipype/tools/run_examples.py $@
+coverage run /src/nipype/tools/run_examples.py $@
 exit_code=$?
 
-coverage xml --rcfile=/src/nipype/.coveragerc -o ${WORKDIR}/smoketest_${example_id}.xml || true
+coverage xml -o ${WORKDIR}/smoketest_${example_id}.xml || true
 
 exit $exit_code

docker/files/run_pytests.sh

@@ -3,6 +3,8 @@ set -e
 set -x
 set -u
 
+
+TESTPATH=${1:-/src/nipype/}
 WORKDIR=${WORK:-/work}
 PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )
 
@@ -22,15 +24,16 @@ if [[ "${PYTHON_VERSION}" -lt "30" ]]; then
 fi
 
 # Run tests using pytest
-py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}.xml --cov-config /src/nipype/.coveragerc --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}.xml /src/nipype/
+export COVERAGE_FILE=${WORKDIR}/.coverage_py${PYTHON_VERSION}
+py.test -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}.xml --cov nipype --cov-config /src/nipype/.coveragerc --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}.xml ${TESTPATH}
 exit_code=$?
 
 # Workaround: run here the profiler tests in python 3
 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
     echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg
-    py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_profiler.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_profiler.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py && \
-    py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_multiproc.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_multiproc.xml /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
+    export COVERAGE_FILE=${WORKDIR}/.coverage_py${PYTHON_VERSION}_extra
+    py.test -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
     exit_code=$(( $exit_code + $? ))
 fi
 

nipype/info.py

@@ -144,7 +144,6 @@ def get_nipype_gitversion():
 TESTS_REQUIRES = [
     'pytest>=%s' % PYTEST_MIN_VERSION,
     'pytest-cov',
-    'pytest-xdist',
     'mock',
     'codecov',
     'dipy',

nipype/utils/tests/test_cmd.py

@@ -11,7 +11,7 @@
 from io import StringIO
 from ...utils import nipype_cmd
 
-PY3 = sys.version_info[0] >= 3
+PY2 = sys.version_info[0] < 3
 
 @contextmanager
 def capture_sys_output():
@@ -34,10 +34,17 @@ def test_main_returns_2_on_empty(self):
 
         exit_exception = cm.value
         assert exit_exception.code == 2
-        assert stderr.getvalue() == \
-            """usage: nipype_cmd [-h] module interface
+
+        msg = """usage: nipype_cmd [-h] module interface
+nipype_cmd: error: the following arguments are required: module, interface
+"""
+
+        if PY2:
+            msg = """usage: nipype_cmd [-h] module interface
 nipype_cmd: error: too few arguments
 """
+        assert stderr.getvalue() == msg
+        assert stdout.getvalue() == ''
 
     def test_main_returns_0_on_help(self):
         with pytest.raises(SystemExit) as cm:
@@ -105,7 +112,12 @@ def test_run_4d_realign_without_arguments(self):
                                                        in_file [in_file ...]
                                                        tr"""
 
-        error_message += """
+        if not PY2:
+            error_message += """
+nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: the following arguments are required: in_file, tr
+"""
+        else:
+            error_message += """
 nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: too few arguments
 """