Add test from nrntest using mcna.mod (#2308)

* Allow using coreneuron as a context manager.
* Reorganise tests a little to accommodate tests that
  are not compatible with CoreNEURON.
* nrntest: update 'submodule'.

CMakeLists.txt

@@ -494,7 +494,6 @@ if(NRN_ENABLE_CORENEURON)
   list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/coreneuron
        ${PROJECT_SOURCE_DIR}/cmake/coreneuron/packages)
 
-  set(nrn_using_ext_corenrn FALSE)
   # If NEURON tests are enabled then enable CoreNEURON tests too
   set(CORENRN_ENABLE_UNIT_TESTS
       ${NRN_ENABLE_TESTS}

share/lib/python/neuron/coreneuron.py

@@ -1,6 +1,32 @@
 import sys
 
 
+class CoreNEURONContextHelper(object):
+    def __init__(self, coreneuron, new_values):
+        self._coreneuron = coreneuron
+        self._new_values = new_values
+        self._old_values = None
+
+    def __enter__(self):
+        assert self._new_values is not None
+        assert self._old_values is None
+        self._old_values = {}
+        for k, v in self._new_values.items():
+            self._old_values[k] = getattr(self._coreneuron, k)
+            setattr(self._coreneuron, k, v)
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        assert self._new_values is not None
+        assert self._old_values is not None
+        assert self._new_values.keys() == self._old_values.keys()
+        # Make sure we restore values in reverse order to how we set them.
+        # This is important for pairs like gpu and cell_permute that interact.
+        for k in reversed(self._new_values.keys()):
+            assert getattr(self._coreneuron, k) == self._new_values[k]
+            setattr(self._coreneuron, k, self._old_values[k])
+        return False
+
+
 class coreneuron(object):
     """
     CoreNEURON configuration values.
@@ -9,6 +35,9 @@ class coreneuron(object):
     a class instead of a module allows getter/setter methods to be used, which
     lets us ensure its properties have consistent types and values.
 
+    This can also be used as a context manager to change CoreNEURON settings
+    only inside a particular scope.
+
     Attributes
     ----------
     cell_permute
@@ -25,6 +54,12 @@ class coreneuron(object):
     >>> coreneuron.enable = True
     >>> coreneuron.enable
     True
+
+    >>> coreneuron.enable = False
+    >>> with coreneuron(enable=True):
+    ...   assert coreneuron.enable
+    ... coreneuron.enable
+    False
     """
 
     def __init__(self):
@@ -38,6 +73,20 @@ def __init__(self):
         self._prcellstate = -1
         self._model_stats = False
 
+    def __call__(self, **kwargs):
+        """
+        Yields a context manager helper that can be used in a with statement.
+
+        This allows the syntax
+        with coreneuron(foo=bar):
+            assert coreneuron.foo == bar
+        assert coreneuron.foo == old_value
+
+        Discarding the return value, or using it in any way other than in a
+        with statement, will have no effect.
+        """
+        return CoreNEURONContextHelper(self, kwargs)
+
     def _default_cell_permute(self):
         return 1 if self._gpu else 0
 

share/lib/python/neuron/tests/utils/__init__.py

@@ -86,6 +86,19 @@ def cvode_use_long_double(cv, enabled):
             cv.use_long_double(old_setting)
 
 
+@contextmanager
+def fast_imem(enabled):
+    from neuron import h
+
+    cvode = h.CVode()
+    old_setting = cvode.use_fast_imem()
+    cvode.use_fast_imem(enabled)
+    try:
+        yield None
+    finally:
+        cvode.use_fast_imem(old_setting)
+
+
 @contextmanager
 def hh_table_disabled():
     """

test/CMakeLists.txt

@@ -205,21 +205,30 @@ if(NRN_ENABLE_PYTHON)
     list(APPEND pytest_args --cov-report=xml --cov=neuron)
   endif()
   set(pytest -m pytest ${pytest_args})
-  # TODO: consider allowing the group-related parts to be dropped here
+  # In brief:
+  #
+  # * tests and mod files under pytest/ are only compatible with NEURON
+  # * tests and mod files under pytest_coreneuron/ are compatible with both NEURON and CoreNEURON
+  #
+  # So, pytest/ should generally be viewed as a staging area en route to pytest_coreneuron. As the
+  # name implies, tests in these directories are executed using pytest.
+  nrn_add_test_group(NAME pytest MODFILE_PATTERNS test/pytest/*.mod)
   nrn_add_test_group(
     CORENEURON
-    NAME pynrn
-    MODFILE_PATTERNS test/pynrn/*.mod)
+    NAME pytest_coreneuron
+    MODFILE_PATTERNS test/pytest_coreneuron/*.mod)
   # In case of multiple Python versions, run these tests with all of them
   foreach(val RANGE ${NRN_PYTHON_ITERATION_LIMIT})
     list(GET NRN_PYTHON_EXECUTABLES ${val} exe)
     list(GET NRN_PYTHON_VERSIONS ${val} pyver)
-    nrn_add_test(
-      GROUP pynrn
-      NAME basic_tests_py${pyver}
-      PRELOAD_SANITIZER
-      COMMAND "${exe}" ${pytest} ./test/pynrn
-      SCRIPT_PATTERNS test/pynrn/*.json test/pynrn/*.py)
+    foreach(group pytest pytest_coreneuron)
+      nrn_add_test(
+        GROUP ${group}
+        NAME basic_tests_py${pyver}
+        PRELOAD_SANITIZER
+        COMMAND "${exe}" ${pytest} "./test/${group}"
+        SCRIPT_PATTERNS "test/${group}/*.json" "test/${group}/*.py")
+    endforeach()
   endforeach()
 
   # Add some tests that are specifically aimed at NEURON - Python integration, covering different
@@ -321,7 +330,7 @@ if(NRN_ENABLE_PYTHON)
       endif()
     endif()
   endif()
-  nrn_add_test_group(NAME parallel MODFILE_PATTERNS test/pynrn/*.mod)
+  nrn_add_test_group(NAME parallel MODFILE_PATTERNS test/pytest_coreneuron/*.mod)
   nrn_add_test(
     GROUP parallel
     NAME subworld
@@ -335,17 +344,17 @@ if(NRN_ENABLE_PYTHON)
     NAME partrans
     PROCESSORS 2
     REQUIRES mpi
-    SCRIPT_PATTERNS test/pynrn/test_partrans.py
+    SCRIPT_PATTERNS test/pytest_coreneuron/test_partrans.py
     COMMAND ${MPIEXEC_NAME} ${MPIEXEC_NUMPROC_FLAG} 2 ${MPIEXEC_OVERSUBSCRIBE} ${MPIEXEC_PREFLAGS}
-            nrniv ${MPIEXEC_POSTFLAGS} -mpi -python test/pynrn/test_partrans.py)
+            nrniv ${MPIEXEC_POSTFLAGS} -mpi -python test/pytest_coreneuron/test_partrans.py)
   nrn_add_test(
     GROUP parallel
     NAME netpar
     PROCESSORS 2
     REQUIRES mpi
-    SCRIPT_PATTERNS test/pynrn/test_hoc_po.py test/pynrn/test_netpar.py
+    SCRIPT_PATTERNS test/pytest_coreneuron/test_hoc_po.py test/pytest_coreneuron/test_netpar.py
     COMMAND ${MPIEXEC_NAME} ${MPIEXEC_NUMPROC_FLAG} 2 ${MPIEXEC_OVERSUBSCRIBE} ${MPIEXEC_PREFLAGS}
-            nrniv ${MPIEXEC_POSTFLAGS} -mpi -python test/pynrn/test_netpar.py)
+            nrniv ${MPIEXEC_POSTFLAGS} -mpi -python test/pytest_coreneuron/test_netpar.py)
   nrn_add_test(
     GROUP parallel
     NAME bas
@@ -363,10 +372,11 @@ if(NRN_ENABLE_PYTHON)
     PROCESSORS 2
     REQUIRES mpi
     ENVIRONMENT "NRN_PYTEST_ARGS=${pytest_arg_string}"
-    SCRIPT_PATTERNS test/pynrn/run_pytest.py test/pynrn/test_nrntest_fast.json
-                    test/pynrn/test_nrntest_fast.py
+    SCRIPT_PATTERNS
+      test/pytest_coreneuron/run_pytest.py test/pytest_coreneuron/test_nrntest_fast.json
+      test/pytest_coreneuron/test_nrntest_fast.py
     COMMAND ${MPIEXEC_NAME} ${MPIEXEC_NUMPROC_FLAG} 2 ${MPIEXEC_OVERSUBSCRIBE} ${MPIEXEC_PREFLAGS}
-            special ${MPIEXEC_POSTFLAGS} -mpi -python test/pynrn/run_pytest.py)
+            special ${MPIEXEC_POSTFLAGS} -mpi -python test/pytest_coreneuron/run_pytest.py)
   # CoreNEURON's reports require MPI and segfault if it is not initialised. This is a crude
   # workaround.
   if(CORENRN_ENABLE_REPORTING)
@@ -429,11 +439,8 @@ if(NRN_ENABLE_PYTHON)
         ${MPIEXEC_POSTFLAGS})
   endif()
 
-  # External coreneuron can be used for testing but for simplicity we are testing only submodule
-  # builds (in near future we want to support only internal builds anyway). This test uses the
-  # standard NEURON installation that does not have a `special` statically linked against
-  # CoreNEURON, so we cannot run this in static builds.
-  if(NOT nrn_using_ext_corenrn AND CORENRN_ENABLE_SHARED)
+  # This test uses the standard NEURON installation (without nrnivmodl having been run)
+  if(CORENRN_ENABLE_SHARED)
     nrn_add_test_group(
       CORENEURON
       NAME coreneuron_standalone
@@ -488,15 +495,16 @@ if(NRN_ENABLE_PYTHON)
     SCRIPT_PATTERNS test/coreneuron/test_spikes.py
     MODFILE_PATTERNS
       "test/coreneuron/mod files/*.mod" "test/coreneuron/mod files/axial.inc"
-      test/pynrn/unitstest.mod test/pynrn/version_macros.mod test/gjtests/natrans.mod)
+      test/pytest_coreneuron/unitstest.mod test/pytest_coreneuron/version_macros.mod
+      test/gjtests/natrans.mod)
   nrn_add_test(
     GROUP coreneuron_modtests
     NAME version_macros
     REQUIRES coreneuron ${modtests_preload_sanitizer}
-    SCRIPT_PATTERNS test/pynrn/test_version_macros.py
+    SCRIPT_PATTERNS test/pytest_coreneuron/test_version_macros.py
     ENVIRONMENT COVERAGE_FILE=.coverage.coreneuron_version_macros NRN_CORENEURON_ENABLE=true
                 ${sonata_zero_gid_env} ${nrnpython_mpi_env}
-    COMMAND ${modtests_launch_py} test/pynrn/test_version_macros.py)
+    COMMAND ${modtests_launch_py} test/pytest_coreneuron/test_version_macros.py)
   # In GPU builds run all of the tests on both CPU and GPU
   set(coreneuron_modtests_gpu_env CORENRN_ENABLE_GPU=true)
   foreach(processor cpu gpu)
@@ -544,10 +552,10 @@ if(NRN_ENABLE_PYTHON)
       GROUP coreneuron_modtests
       NAME fast_imem_py_${processor}
       REQUIRES coreneuron ${processor} ${modtests_preload_sanitizer}
-      SCRIPT_PATTERNS test/pynrn/test_fast_imem.py
+      SCRIPT_PATTERNS test/pytest_coreneuron/test_fast_imem.py
       ENVIRONMENT ${modtests_processor_env} ${nrnpython_mpi_env}
                   COVERAGE_FILE=.coverage.coreneuron_fast_imem_py
-      COMMAND ${modtests_launch_py} test/pynrn/test_fast_imem.py)
+      COMMAND ${modtests_launch_py} test/pytest_coreneuron/test_fast_imem.py)
     nrn_add_test(
       GROUP coreneuron_modtests
       NAME datareturn_py_${processor}
@@ -735,7 +743,7 @@ function(add_modlunit_test mod_file)
       "${TESTS}"
       PARENT_SCOPE)
 endfunction()
-add_modlunit_test("${PROJECT_SOURCE_DIR}/test/pynrn/unitstest.mod")
+add_modlunit_test("${PROJECT_SOURCE_DIR}/test/pytest_coreneuron/unitstest.mod")
 add_modlunit_test("${PROJECT_SOURCE_DIR}/src/nrnoc/hh.mod")
 add_modlunit_test("${PROJECT_SOURCE_DIR}/src/nrnoc/stim.mod")
 add_modlunit_test("${PROJECT_SOURCE_DIR}/src/nrnoc/pattern.mod")

test/coreneuron/test_spikes.py

@@ -75,13 +75,6 @@ def test_spikes(
     nrn_spike_t = nrn_spike_t.to_python()
     nrn_spike_gids = nrn_spike_gids.to_python()
 
-    # CORENEURON run
-    from neuron import coreneuron
-
-    coreneuron.enable = True
-    coreneuron.gpu = enable_gpu
-    coreneuron.file_mode = file_mode
-    coreneuron.verbose = 0
     corenrn_all_spike_t = h.Vector()
     corenrn_all_spike_gids = h.Vector()
 
@@ -122,11 +115,13 @@ def run(mode):
         assert nrn_spike_t == corenrn_all_spike_t_py
         assert nrn_spike_gids == corenrn_all_spike_gids_py
 
-    if file_mode is False:
-        for mode in [0, 1, 2]:
+    # CORENEURON run
+    from neuron import coreneuron
+
+    with coreneuron(enable=True, gpu=enable_gpu, file_mode=file_mode, verbose=0):
+        run_modes = [0] if file_mode else [0, 1, 2]
+        for mode in run_modes:
             run(mode)
-    else:
-        run(0)
 
     return h
 

test/external/CMakeLists.txt

@@ -19,7 +19,7 @@ FetchContent_Declare(
 FetchContent_Declare(
   nrntest
   GIT_REPOSITORY https://github.com/neuronsimulator/nrntest
-  GIT_TAG 0cc9c95425b6a9e4d222be1b4cc912d50a274a2f
+  GIT_TAG fe7029e38f518787fd61fb61b0d861f680cbcf39
   SOURCE_DIR ${PROJECT_SOURCE_DIR}/external/tests/nrntest)
 
 FetchContent_Declare(