Merge pull request #775 from apdavison/spring-clean

Spring cleaning

Author: apdavison

.github/workflows/full-test.yml

@@ -32,8 +32,8 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install pytest pytest-cov coveralls flake8
-        python -m pip install mpi4py
         python -m pip install -r requirements.txt
+        python -m pip install mpi4py matplotlib
     - name: Install Brian 2
       run: |
         python -m pip install brian2

README.rst

@@ -30,7 +30,7 @@ your simulator, and are not restricted to the standard models.
 - Bug reports: https://github.com/NeuralEnsemble/PyNN/issues
 
 
-:copyright: Copyright 2006-2022 by the PyNN team, see AUTHORS.
+:copyright: Copyright 2006-2023 by the PyNN team, see AUTHORS.
 :license: CeCILL, see LICENSE for details.
 
 .. image:: https://travis-ci.org/NeuralEnsemble/PyNN.png?branch=master

ci/install.sh

@@ -5,6 +5,7 @@ set -e  # stop execution in case of errors
 pip install -r requirements.txt
 pip install coveralls
 pip install pytest pytest-cov
+pip install matplotlib
 source ci/install_brian.sh
 source ci/install_nest.sh
 source ci/install_neuron.sh

doc/conf.py

@@ -69,7 +69,7 @@ class MockNESTModule(mock.Mock):
 # General information about the project.
 project = u'PyNN'
 authors = u'the PyNN community'
-copyright = u'2006-2022, ' + authors
+copyright = u'2006-2023, ' + authors
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

pyNN/__init__.py

@@ -65,7 +65,7 @@
     random
     space
 
-:copyright: Copyright 2006-2022 by the PyNN team, see AUTHORS.
+:copyright: Copyright 2006-2023 by the PyNN team, see AUTHORS.
 :license: CeCILL, see LICENSE for details.
 """
 

pyNN/brian2/__init__.py

@@ -1,91 +1,49 @@
 """
 Brian2 implementation of the PyNN API.
 
-:copyright: Copyright 2006-2016 by the PyNN team, see AUTHORS.
+:copyright: Copyright 2006-2023 by the PyNN team, see AUTHORS.
 :license: CeCILL, see LICENSE for details.
 """
 
-import logging
-import brian2                                                             # noqa: F401
-from pyNN import common, space                                            # noqa: F401
-from pyNN.common.control import DEFAULT_MAX_DELAY, DEFAULT_TIMESTEP, DEFAULT_MIN_DELAY
-from pyNN.standardmodels import StandardCellType
-from pyNN.connectors import *                                             # noqa: F401, F403
-from pyNN.connectors import FixedProbabilityConnector
-from pyNN.brian2 import simulator
-from pyNN.brian2.standardmodels.cells import *                            # noqa: F401, F403
-from pyNN.brian2.standardmodels.synapses import *                         # noqa: F401, F403
-from pyNN.brian2.standardmodels.synapses import StaticSynapse
-from pyNN.brian2.standardmodels.electrodes import *                       # noqa: F401, F403
-from pyNN.brian2.standardmodels.electrodes import update_currents
-from pyNN.brian2.standardmodels.receptors import (                        # noqa: F401
-    CondAlphaPostSynapticResponse, AlphaPSR,
-    CondExpPostSynapticResponse, ExpPSR,
-    CurrExpPostSynapticResponse)
-from pyNN.brian2.populations import Population, PopulationView, Assembly  # noqa: F401
-from pyNN.brian2.projections import Projection
-from pyNN.recording import get_io
-
-logger = logging.getLogger("PyNN")
+from .. import errors, random, space                            # noqa: F401
+from ..network import Network                                   # noqa: F401
+from ..standardmodels import StandardCellType
+from ..random import NumpyRNG, GSLRNG, RandomDistribution       # noqa: F401
+from ..connectors import *                                      # noqa: F401, F403
+from .standardmodels.cells import *                             # noqa: F401, F403
+from .standardmodels.synapses import *                          # noqa: F401, F403
+from .standardmodels.electrodes import *                        # noqa: F401, F403
+from .standardmodels.receptors import (                         # noqa: F401
+    CondAlphaPostSynapticResponse,
+    AlphaPSR,
+    CondExpPostSynapticResponse,
+    ExpPSR,
+    CurrExpPostSynapticResponse,
+)
+from .populations import Population, PopulationView, Assembly   # noqa: F401
+from .projections import Projection                             # noqa: F401
+from .control import (                                          # noqa: F401
+    setup,
+    end,
+    run,
+    run_until,
+    run_for,
+    reset,
+    initialize,
+    get_current_time,
+    get_time_step,
+    get_min_delay,
+    get_max_delay,
+    num_processes,
+    rank,
+)
+from .procedural_api import create, connect, record, record_v, record_gsyn  # noqa: F401
 
 
 def list_standard_models():
     """Return a list of all the StandardCellType classes available for this simulator."""
-    return [obj.__name__ for obj in globals().values()
-            if isinstance(obj, type) and issubclass(obj, StandardCellType)]
-
-
-def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY,
-          **extra_params):
-    """
-    Should be called at the very beginning of a script.
-    extra_params contains any keyword arguments that are required by a given
-    simulator but not by others.
-    """
-
-    max_delay = extra_params.get('max_delay', DEFAULT_MAX_DELAY)
-    common.setup(timestep, min_delay, **extra_params)
-    simulator.state.clear()
-    simulator.state.dt = timestep  # move to common.setup?
-    simulator.state.min_delay = min_delay
-    simulator.state.max_delay = max_delay
-    simulator.state.mpi_rank = 0
-    simulator.state.num_processes = 1
-
-    simulator.state.network.add(
-        brian2.NetworkOperation(update_currents, when="start", clock=simulator.state.network.clock)
-    )
-    return rank()
-
-
-def end(compatible_output=True):
-    """Do any necessary cleaning up before exiting."""
-    for (population, variables, filename) in simulator.state.write_on_end:
-        io = get_io(filename)
-        population.write_data(io, variables)
-    simulator.state.write_on_end = []
-    # should have common implementation of end()
-
-
-run, run_until = common.build_run(simulator)
-run_for = run
-
-reset = common.build_reset(simulator)
-
-initialize = common.initialize
-
-get_current_time, get_time_step, get_min_delay, get_max_delay, \
-    num_processes, rank = common.build_state_queries(simulator)
-
-create = common.build_create(Population)
-
-connect = common.build_connect(Projection, FixedProbabilityConnector, StaticSynapse)
-
-
-record = common.build_record(simulator)
-
-
-def record_v(source, filename): return record(['v'], source, filename)
-
-
-def record_gsyn(source, filename): return record(['gsyn_exc', 'gsyn_inh'], source, filename)
+    return [
+        obj.__name__
+        for obj in globals().values()
+        if isinstance(obj, type) and issubclass(obj, StandardCellType)
+    ]

pyNN/brian2/cells.py

@@ -1,19 +1,19 @@
 """
 Definition of cell classes for the brian2 module.
 
-:copyright: Copyright 2006-2016 by the PyNN team, see AUTHORS.
+:copyright: Copyright 2006-2023 by the PyNN team, see AUTHORS.
 :license: CeCILL, see LICENSE for details.
 
 """
 
-
+from functools import reduce
 import numpy as np
 import brian2
-from functools import reduce
-from pyNN.parameters import Sequence, simplify
-from pyNN.core import is_listlike
-from pyNN import errors
-from pyNN.brian2 import simulator
+
+from ..parameters import Sequence, simplify
+from ..core import is_listlike
+from .. import errors
+from . import simulator
 
 mV = brian2.mV
 ms = brian2.ms

pyNN/brian2/control.py

@@ -0,0 +1,56 @@
+"""
+Brian 2 implementation of simulation control functions
+
+:copyright: Copyright 2006-2023 by the PyNN team, see AUTHORS.
+:license: CeCILL, see LICENSE for details.
+"""
+
+import brian2
+from ..common.control import DEFAULT_MAX_DELAY, DEFAULT_TIMESTEP, DEFAULT_MIN_DELAY
+from .. import common
+from ..recording import get_io
+from . import simulator
+from .standardmodels.electrodes import update_currents
+
+
+def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY,
+          **extra_params):
+    """
+    Should be called at the very beginning of a script.
+    extra_params contains any keyword arguments that are required by a given
+    simulator but not by others.
+    """
+
+    max_delay = extra_params.get('max_delay', DEFAULT_MAX_DELAY)
+    common.setup(timestep, min_delay, **extra_params)
+    simulator.state.clear()
+    simulator.state.dt = timestep  # move to common.setup?
+    simulator.state.min_delay = min_delay
+    simulator.state.max_delay = max_delay
+    simulator.state.mpi_rank = 0
+    simulator.state.num_processes = 1
+
+    simulator.state.network.add(
+        brian2.NetworkOperation(update_currents, when="start", clock=simulator.state.network.clock)
+    )
+    return rank()
+
+
+def end(compatible_output=True):
+    """Do any necessary cleaning up before exiting."""
+    for (population, variables, filename) in simulator.state.write_on_end:
+        io = get_io(filename)
+        population.write_data(io, variables)
+    simulator.state.write_on_end = []
+    # should have common implementation of end()
+
+
+run, run_until = common.build_run(simulator)
+run_for = run
+
+reset = common.build_reset(simulator)
+
+initialize = common.initialize
+
+get_current_time, get_time_step, get_min_delay, get_max_delay, \
+    num_processes, rank = common.build_state_queries(simulator)

pyNN/brian2/populations.py

@@ -1,12 +1,15 @@
 """
+Brian 2 implementation of Population, PopulationView and Assembly.
 
+:copyright: Copyright 2006-2023 by the PyNN team, see AUTHORS.
+:license: CeCILL, see LICENSE for details.
 """
 
 from collections import defaultdict
 import numpy as np
-from pyNN import common
-from pyNN.standardmodels import StandardCellType
-from pyNN.parameters import ArrayParameter, ParameterSpace, simplify, LazyArray
+from .. import common
+from ..standardmodels import StandardCellType
+from ..parameters import ArrayParameter, ParameterSpace, simplify, LazyArray
 from . import simulator
 from .recording import Recorder
 import brian2

pyNN/brian2/procedural_api.py

@@ -0,0 +1,30 @@
+"""
+Brian 2 implementation of the "procedural" API
+
+:copyright: Copyright 2006-2023 by the PyNN team, see AUTHORS.
+:license: CeCILL, see LICENSE for details.
+"""
+
+from .. import common
+from ..connectors import FixedProbabilityConnector
+from .populations import Population
+from .projections import Projection
+from .standardmodels.synapses import StaticSynapse
+from . import simulator
+
+
+create = common.build_create(Population)
+
+
+connect = common.build_connect(Projection, FixedProbabilityConnector, StaticSynapse)
+
+
+record = common.build_record(simulator)
+
+
+def record_v(source, filename):
+    return record(['v'], source, filename)
+
+
+def record_gsyn(source, filename):
+    return record(['gsyn_exc', 'gsyn_inh'], source, filename)