Merge pull request #761 from apdavison/pytest

Migrate test suite from nose to pytest

.github/workflows/full-test.yml

@@ -31,7 +31,7 @@ jobs:
     - name: Install basic Python dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install coverage coveralls nose-testconfig
+        python -m pip install pytest pytest-cov coveralls
         python -m pip install mpi4py
         python -m pip install -r requirements.txt
     - name: Install Brian 2
@@ -53,10 +53,32 @@ jobs:
         make install
     - name: Install PyNN itself
       run: |
-        python setup.py install
-    - name: Run unit tests
+        pip install -e .
+    - name: Compile NEURON mechanisms (Linux)
+      if: startsWith(matrix.os, 'ubuntu')
+      run: |
+        pushd pyNN/neuron/nmodl
+        nrnivmodl
+        popd
+    - name: Run unit and system tests
       run: |
-        nosetests --nologcapture --where=test/unittests --verbosity=2 test_assembly.py test_brian.py test_connectors_parallel.py test_connectors_serial.py test_core.py test_descriptions.py test_files.py test_idmixin.py test_lowlevelapi.py test_nest.py test_neuron.py test_parameters.py test_population.py test_populationview.py test_projection.py test_random.py test_recording.py test_simulation_control.py test_space.py test_standardmodels.py test_utility_functions.py
-    - name: Run system tests
+        pytest -v --cov=pyNN --cov-report=term test
+    - name: Upload coverage data
+      run: |
+        coveralls --service=github
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        COVERALLS_FLAG_NAME: ${{ matrix.test-name }}
+        COVERALLS_PARALLEL: true
+  coveralls:
+    name: Indicate completion to coveralls.io
+    needs: test
+    runs-on: ubuntu-latest
+    container: python:3-slim
+    steps:
+    - name: Finished
       run: |
-        nosetests --nologcapture --where=test/system --verbosity=2 test_nest.py test_brian2.py test_neuron.py
+        pip3 install --upgrade coveralls
+        coveralls --service=github --finish
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

ci/install.sh

@@ -3,9 +3,9 @@
 set -e  # stop execution in case of errors
 
 pip install -r requirements.txt
-pip install coverage coveralls
-pip install nose-testconfig
+pip install coveralls
+pip install pytest pytest-cov
 source ci/install_brian.sh
 source ci/install_nest.sh
 source ci/install_neuron.sh
-python setup.py install
+python setup.py develop

ci/test_script.sh

@@ -3,7 +3,9 @@
 set -e  # stop execution in case of errors
 
 if [ "$TRAVIS_PYTHON_VERSION" == "3.9" ]; then
-    python setup.py nosetests --verbose --nologcapture --with-coverage --cover-package=pyNN --tests=test;
+    pytest --verbose --cov=pyNN
 else
-    python setup.py nosetests --verbose --nologcapture -e backends --tests=test/unittests
+    pytest --verbose test/unittests
 fi
+
+exit $?

doc/conf.py

@@ -78,7 +78,7 @@ class MockNESTModule(mock.Mock):
 # The short X.Y version.
 version = '0.10'
 # The full version, including alpha/beta/rc tags.
-release = '0.10.1'
+release = '0.10.2.dev'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/developers/contributing.txt

@@ -19,7 +19,7 @@ Requirements
 In addition to the requirements listed in :doc:`../installation`, you will need to
 install:
 
-    * nose_
+    * pytest_
     * mock_
     * coverage_
 
@@ -86,15 +86,14 @@ We try to stay fairly close to PEP8_. Please note in particular:
 Testing
 =======
 
-Running the PyNN test suite requires the *nose_*, *mock_* and *nose-testconfig* packages,
-and optionally the *coverage_* package. To run the entire test suite, in the
-``test`` subdirectory of the source tree::
+Running the PyNN test suite requires the *pytest_* package,
+and optionally the *pytest-cov* package. To run the entire test suite::
 
-    $ nosetests
+    $ pytest
 
 To see how well the codebase is covered by the tests, run::
 
-    $ nosetests --with-coverage --cover-package=pyNN --cover-erase --cover-html
+    $ pytest --cov=pyNN --cov-report term --cov-report html
 
 There are currently two sorts of tests, unit tests, which aim to exercise
 small pieces of code such as individual functions and methods, and system tests,
@@ -110,31 +109,21 @@ Except when testing a specific simulator interface, unit tests should be able to
 run without a simulator installed.
 
 System tests should be written so that they can run with any of the simulators.
-The suggested way to do this is to write test functions, in a separate file,
-that take a simulator module as an argument, and then call these functions from
-``test_neuron.py``, ``test_nest.py``, etc.
+The suggested way to do this is to write test functions
+that take a simulator module as an argument, and then wrap these functions
+with the following decorator::
 
-System tests defined in the scenarios directory are treated as a single test
-(test_scenarios()) while running nosetests. To run only the tests within a file
+    @pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
+
+To run only the tests within a file
 named 'test_electrodes' located inside system/scenarios, use::
 
-    $ nosetests -s --tc=testFile:test_electrodes test_nest.py
+    $ pytest test/system/scenarios/test_electrodes.py
 
 To run a single specific test named 'test_changing_electrode' located within
 some file (and added to registry) inside system/scenarios, use::
 
-    $ nosetests -s --tc=testName:test_changing_electrode test_nest.py
-
-Note that this would also run the tests specified within the simulator specific
-files such as test_brian.py, test_nest.py and test_neuron.py. To avoid
-this, specify the 'test_scenarios function' on the command line::
-
-    $ nosetests -s --tc=testName:test_changing_electrode test_nest.py:test_scenarios
-
-The ``test/unsorted`` directory contains a number of old tests that are either
-no longer useful or have not yet been adapted to the nose framework. These are
-not part of the test suite, but we are gradually adapting those tests that are
-useful and deleting the others.
+    $ pytest test/system/scenarios/test_electrodes.py::test_changing_electrode
 
 
 Submitting code
@@ -190,11 +179,11 @@ in becoming release manager for PyNN, please contact us via the `mailing list`_.
 When you think a release is ready, run through the following checklist one
 last time:
 
-    * do all the tests pass? This means running :command:`nosetests` in
+    * do all the tests pass? This means running :command:`pytest` in
       :file:`test/unittests` and :file:`test/system` and running :command:`make doctest` in
       :file:`doc`. You should do this on at least two Linux systems -- one a very
       recent version and one at least a year old, and on at least one version of
-      Mac OS X. You should also do this with Python 2.7 and 3.4, 3.5 or 3.6.
+      Mac OS X. You should also do this with multiple Python versions (3.7+).
     * do all the example scripts generate the correct output? Run the
       :file:`run_all_examples.py` script in :file:`examples/tools` and then visually
       check the :file:`.png` files generated in :file:`examples/tools/Results`. Again,
@@ -254,7 +243,7 @@ If this is a final release, there are a few more steps:
 
 .. _Sphinx: http://sphinx-doc.org/
 .. _PEP8: http://www.python.org/dev/peps/pep-0008/
-.. _nose: https://nose.readthedocs.org/
+.. _pytest: https://docs.pytest.org
 .. _mock: http://www.voidspace.org.uk/python/mock/
 .. _coverage: http://nedbatchelder.com/code/coverage/
 .. _`Python Package Index`: http://pypi.python.org/

pyNN/__init__.py

@@ -69,7 +69,7 @@
 :license: CeCILL, see LICENSE for details.
 """
 
-__version__ = '0.10.1'
+__version__ = '0.10.2.dev'
 __all__ = ["common", "random", "nest", "neuron", "brian2",
            "recording", "errors", "space", "descriptions",
            "standardmodels", "parameters", "core", "serialization"]

pyNN/common/populations.py

@@ -261,7 +261,7 @@ def sample(self, n, rng=None):
         assert isinstance(n, int)
         if not rng:
             rng = random.NumpyRNG()
-        indices = rng.permutation(np.arange(len(self), dtype=np.int))[0:n]
+        indices = rng.permutation(np.arange(len(self), dtype=int))[0:n]
         logger.debug("The %d cells selected have indices %s" % (n, indices))
         logger.debug("%s.sample(%s)", self.label, n)
         return self._get_view(indices)
@@ -658,7 +658,6 @@ def __init__(self, size, cellclass, cellparams=None, structure=None,
             else:
                 raise Exception(
                     "A maximum of 3 dimensions is allowed. What do you think this is, string theory?")
-            # NEST doesn't like np.int, so to be safe we cast to Python int
             size = int(reduce(operator.mul, size))
         self.size = size
         self.label = label or 'population%d' % Population._nPop
@@ -718,7 +717,7 @@ def id_to_index(self, id):
             if (self.first_id > id.min()) or (self.last_id < id.max()):
                 raise ValueError("ids should be in the range [%d,%d], actually [%d, %d]" % (
                     self.first_id, self.last_id, id.min(), id.max()))
-            return (id - self.first_id).astype(np.int)  # this assumes ids are consecutive
+            return (id - self.first_id).astype(int)  # this assumes ids are consecutive
 
     def id_to_local_index(self, id):
         """
@@ -906,7 +905,7 @@ def id_to_index(self, id):
             if self._is_sorted:
                 return np.searchsorted(self.all_cells, id)
             else:
-                result = np.array([], dtype=np.int)
+                result = np.array([], dtype=int)
                 for item in id:
                     data = np.where(self.all_cells == item)[0]
                     if len(data) == 0:
@@ -1159,7 +1158,7 @@ def id_to_index(self, id):
             if self._is_sorted:
                 return np.searchsorted(all_cells, id)
             else:
-                result = np.array([], dtype=np.int)
+                result = np.array([], dtype=int)
                 for item in id:
                     data = np.where(all_cells == item)[0]
                     if len(data) == 0:
@@ -1261,7 +1260,7 @@ def sample(self, n, rng=None):
         assert isinstance(n, int)
         if not rng:
             rng = random.NumpyRNG()
-        indices = rng.permutation(np.arange(len(self), dtype=np.int))[0:n]
+        indices = rng.permutation(np.arange(len(self), dtype=int))[0:n]
         logger.debug("The %d cells recorded have indices %s" % (n, indices))
         logger.debug("%s.sample(%s)", self.label, n)
         return self[indices]

pyNN/connectors.py

@@ -14,7 +14,6 @@
 from pyNN.recording import files
 from pyNN.parameters import LazyArray
 from pyNN.standardmodels import StandardSynapseType
-from pyNN.common import Population
 import numpy as np
 from itertools import repeat
 import logging
@@ -252,6 +251,7 @@ def _connect_with_map(self, projection, connection_map, distance_map=None):
         self._standard_connect(projection, connection_map.by_column, distance_map)
 
     def _get_connection_map_no_self_connections(self, projection):
+        from pyNN.common import Population
         if (isinstance(projection.pre, Population)
                 and isinstance(projection.post, Population)
                 and projection.pre == projection.post):
@@ -267,6 +267,7 @@ def _get_connection_map_no_self_connections(self, projection):
         return connection_map
 
     def _get_connection_map_no_mutual_connections(self, projection):
+        from pyNN.common import Population
         if (isinstance(projection.pre, Population)
             and isinstance(projection.post, Population)
                 and projection.pre == projection.post):

pyNN/nest/recording.py

@@ -63,7 +63,7 @@ def _get_data_arrays(self, variable, clear=False):
         if variable == "times":
             values = times
         else:
-            # I'm hoping numpy optimises for the case where scale_factor = 1, 
+            # I'm hoping numpy optimises for the case where scale_factor = 1,
             # otherwise should avoid this multiplication in that case
             values = events[nest_variable] * scale_factor
 

pyNN/neuron/__init__.py

@@ -78,7 +78,7 @@ def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY, **extra_params
     simulator.state.min_delay = min_delay
     simulator.state.max_delay = extra_params.get('max_delay', DEFAULT_MAX_DELAY)
     if 'use_cvode' in extra_params:
-        simulator.state.record_sample_times = extra_params['use_cvode'] 
+        simulator.state.record_sample_times = extra_params['use_cvode']
         simulator.state.cvode.active(int(extra_params['use_cvode']))
         if 'rtol' in extra_params:
             simulator.state.cvode.rtol(float(extra_params['rtol']))

pyNN/parameters.py

@@ -6,10 +6,7 @@
 """
 
 import numpy as np
-try:
-    from collections import Sized
-except ImportError:
-    from collections.abc import Sized
+from collections.abc import Sized
 from pyNN.core import is_listlike
 from pyNN import errors
 from pyNN.random import RandomDistribution, NativeRNG

pyNN/recording/__init__.py

@@ -303,9 +303,9 @@ def _get_current_segment(self, filter_ids=None, variables='all', clear=False):
                         times = times[mask]
                         id_array = id_array[mask]
                     segment.spiketrains = neo.spiketrainlist.SpikeTrainList.from_spike_time_array(
-                        times, id_array, 
+                        times, id_array,
                         np.array(sids, dtype=int),
-                        t_stop=t_stop, 
+                        t_stop=t_stop,
                         units="ms",
                         t_start=self._recording_start_time,
                         source_population=self.population.label

requirements.txt

@@ -7,5 +7,4 @@ lazyarray>=0.5.2
 neo>=0.11.0
 #git+https://github.com/NeuralEnsemble/python-neo.git@master#egg=neo
 setuptools>=20.5
-nose
 h5py

setup.py

@@ -83,7 +83,7 @@ def find(self, command):
 
 setup(
     name="PyNN",
-    version="0.10.1",
+    version="0.10.2.dev",
     packages=['pyNN', 'pyNN.nest', 'pyNN.neuron',
               'pyNN.brian2', 'pyNN.common', 'pyNN.mock', 'pyNN.neuroml',
               'pyNN.recording', 'pyNN.standardmodels', 'pyNN.descriptions',

test/system/scenarios/__init__.py

@@ -1,24 +0,0 @@
-# encoding: utf-8
-from testconfig import config
-
-
-if 'testFile' in config:
-    file_name = config['testFile']
-    exec("from . import ( %s )" % file_name)
-else:
-    from . import (scenario1,
-                   scenario2,
-                   scenario3,
-                   ticket166,
-                   test_simulation_control,
-                   test_recording,
-                   test_cell_types,
-                   test_electrodes,
-                   scenario4,
-                   test_parameter_handling,
-                   test_procedural_api,
-                   issue274,
-                   test_connectors,
-                   issue231,
-                   test_connection_handling,
-                   test_synapse_types)

test/system/scenarios/fixtures.py

@@ -0,0 +1,44 @@
+import functools
+import pytest
+
+available_modules = {}
+
+try:
+    import pyNN.neuron
+    available_modules["neuron"] = pyNN.neuron
+except ImportError:
+    pass
+
+try:
+    import pyNN.nest
+    available_modules["nest"] = pyNN.nest
+except ImportError:
+    pass
+
+try:
+    import pyNN.brian2
+    available_modules["brian2"] = pyNN.brian2
+except ImportError:
+    pass
+
+
+class SimulatorNotAvailable:
+
+    def __init__(self, sim_name):
+        self.sim_name = sim_name
+
+    def setup(self, *args, **kwargs):
+        pytest.skip(f"{self.sim_name} not available")
+
+
+def get_simulator(sim_name):
+    if sim_name in available_modules:
+        return pytest.param(available_modules[sim_name], id=sim_name)
+    else:
+        return pytest.param(SimulatorNotAvailable(sim_name), id=sim_name)
+
+
+def run_with_simulators(*sim_names):
+    sim_modules = (get_simulator(sim_name) for sim_name in sim_names)
+
+    return pytest.mark.parametrize("sim", sim_modules)