#!/bin/sh
#!/bin/sh
Last login: Tue Nov 16 12:10:59 on ttys000
(base) thomastiotto@mac-mini ~ % conda activate brian
(brian) thomastiotto@mac-mini ~ % cd $CONDA_PREFIX
(brian) thomastiotto@mac-mini brian % mkdir -p ./etc/conda/activate.d
mkdir -p ./etc/conda/deactivate.d
(brian) thomastiotto@mac-mini brian % vim $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
(brian) thomastiotto@mac-mini brian % vim $CONDA_PREFIX/etc/conda/deactivate.d/env_vars.sh
(brian) thomastiotto@mac-mini brian % conda deactivate
(base) thomastiotto@mac-mini brian % conda activate brian
overriding CC,CLANG with gcc, and CLANGXX,CXX with g++
(brian) thomastiotto@mac-mini brian % python
Python 3.8.12 | packaged by conda-forge | (default, Oct 12 2021, 21:25:50)
[Clang 11.1.0 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import brian2
>>> brian2.test(additional_args=['-x'])
Running tests in /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2 for targets numpy, cython (excluding long tests)
Running Brian version 2.4.2 from '/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2'
Testing codegen-independent code
Resetting to default preferences

Running doctests

==================================== ERRORS ====================================
____________________ ERROR collecting sphinxext/briandoc.py ____________________
lib/python3.8/site-packages/brian2/sphinxext/briandoc.py:22: in <module>
    from docutils import statemachine
E   ModuleNotFoundError: No module named 'docutils'
=========================== short test summary info ============================
ERROR lib/python3.8/site-packages/brian2/sphinxext/briandoc.py - ModuleNotFou...
!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
1 error in 0.19s
Running tests that do not use code generation
........................................................................ [ 19%]
........................................................................ [ 39%]
.............................................ss......................... [ 59%]
........................................................................ [ 79%]
........................................................F
=================================== FAILURES ===================================
_________________________ test_numpy_functions_logical _________________________

    @pytest.mark.codegen_independent
    def test_numpy_functions_logical():
        '''
        Assure that logical numpy functions work on all quantities and return
        unitless boolean arrays.
        '''
        unit_values1 = [3 * mV, np.array([1, 2]) * mV, np.ones((3, 3)) * mV]
        unit_values2 = [3 * second, np.array([1, 2]) * second,
                        np.ones((3, 3)) * second]
        for ufunc in UFUNCS_LOGICAL:
            for value1, value2 in zip(unit_values1, unit_values2):
                try:
                    # one argument
>                   result_units = eval('np.%s(value1)' % ufunc)

lib/python3.8/site-packages/brian2/tests/test_units.py:976:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

>   ???
E   TypeError: logical_and() takes from 2 to 3 positional arguments but 1 were given

<string>:1: TypeError
=============================== warnings summary ===============================
tests/test_clocks.py: 3 warnings
tests/test_devices.py: 5 warnings
tests/test_network.py: 13 warnings
tests/test_spikegenerator.py: 7 warnings
tests/test_stateupdaters.py: 2 warnings
tests/test_synapses.py: 3 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/core/clocks.py:95: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    dtype=np.float, read_only=True, constant=True,

tests/test_codegen.py::test_apply_loop_invariant_optimisation_no_optimisation
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:253: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', 'rand() - rand()', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_no_optimisation
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:254: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', '3*rand() - 3*rand()', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_no_optimisation
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:255: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', '3*rand() - ((1+2)*rand())', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_no_optimisation
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:257: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', 's1*rand()*N', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_no_optimisation
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:258: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', 's2*rand()*N', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_no_optimisation
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:261: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', '0*rand()*N', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_no_optimisation
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:262: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', '0/rand()*N', '', np.float)

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:279: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', 'v1 - v1', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:280: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', 'N*v1 - N*v1', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:281: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', 'v1*N * 0', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:282: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', 'v1 * 0', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:283: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', 'v1 * 0.0', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:284: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', '0.0 / (v1*N)', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:286: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('i1', '=', 'i1*N * 0', '', np.int),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:287: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('i1', '=', '0 * i1', '', np.int),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:288: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('i1', '=', '0 * i1*N', '', np.int),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:289: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('i1', '=', 'i1 * 0', '', np.int),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:291: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v2', '=', '0 + v1*N', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:292: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v2', '=', 'v1*N + 0.0', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:293: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v2', '=', 'v1*N - 0', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:294: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v2', '=', 'v1*N - 0.0', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:295: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v2', '=', '1 * v1*N', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:296: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v2', '=', '1.0 * v1*N', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:297: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v2', '=', 'v1*N / 1.0', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_simplification
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:298: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v2', '=', 'v1*N / 1', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_constant_evaluation
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:355: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', 'v1 * (1 + 2 + 3)', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_constant_evaluation
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:356: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', 'exp(N)*v1', '', np.float),

tests/test_codegen.py::test_apply_loop_invariant_optimisation_constant_evaluation
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:357: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    Statement('v1', '=', 'exp(0)*v1', '', np.float),

tests/test_codegen.py::test_automatic_augmented_assignments
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_codegen.py:384: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    dtype=np.bool, device=device),

tests/test_monitor.py: 2 warnings
tests/test_network.py: 3 warnings
tests/test_neurongroup.py: 7 warnings
tests/test_spatialneuron.py: 3 warnings
tests/test_subgroup.py: 6 warnings
tests/test_synapses.py: 2 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/groups/group.py:257: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    if index_array.dtype == np.bool:

tests/test_network.py: 10 warnings
tests/test_neurongroup.py: 20 warnings
tests/test_poissongroup.py: 4 warnings
tests/test_refractory.py: 1 warning
tests/test_spatialneuron.py: 1 warning
tests/test_synapses.py: 16 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/groups/neurongroup.py:313: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    self.variables.add_auxiliary_variable('_cond', dtype=np.bool)

tests/test_network.py: 21 warnings
tests/test_neurongroup.py: 10 warnings
tests/test_subgroup.py: 1 warning
tests/test_timedarray.py: 4 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/core/variables.py:1027: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    variables.add_auxiliary_variable('_cond', dtype=np.bool)

tests/test_network.py: 8 warnings
tests/test_neurongroup.py: 1 warning
tests/test_subgroup.py: 1 warning
tests/test_synapses.py: 14 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses/synapses.py:1713: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    variables.add_auxiliary_variable('_cond', dtype=np.bool)

tests/test_neurongroup.py::test_variables
tests/test_neurongroup.py::test_get_dtype
tests/test_neurongroup.py::test_get_dtype
tests/test_neurongroup.py::test_no_code
tests/test_refractory.py::test_refractoriness_types
tests/test_refractory.py::test_refractoriness_types
tests/test_refractory.py::test_refractoriness_types
tests/test_refractory.py::test_refractoriness_types
tests/test_refractory.py::test_conditional_write_set
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/groups/group.py:148: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    return np.bool

tests/test_neurongroup.py: 15 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/groups/neurongroup.py:731: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    if not np.issubsctype(index_array.dtype, np.int):

tests/test_neurongroup.py::test_indices
tests/test_neurongroup.py::test_indices
tests/test_neurongroup.py::test_indices
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/groups/group.py:294: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    variables.add_auxiliary_variable('_cond', dtype=np.bool)

tests/test_neurongroup.py::test_get_dtype
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py:1438: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    assert get_dtype(eqs['b']) == np.bool

tests/test_neurongroup.py::test_get_dtype
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py:1445: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    assert get_dtype(eqs['b']) == np.bool

tests/test_parsing.py::test_is_boolean_expression
tests/test_parsing.py::test_is_boolean_expression
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/core/variables.py:324: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    dtype = np.bool

tests/test_spikequeue.py::test_spikequeue
tests/test_spikequeue.py::test_spikequeue
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses/spikequeue.py:92: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    delays = np.array(np.round(delays / dt)).astype(np.int)

tests/test_units.py::test_get_dimensions
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_units.py:126: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    assert get_dimensions(np.array(5, dtype=np.int)) is DIMENSIONLESS

tests/test_units.py::test_get_dimensions
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_units.py:132: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    assert is_scalar_type(np.array(5, dtype=np.int))

-- Docs: https://docs.pytest.org/en/stable/warnings.html
=========================== short test summary info ============================
FAILED lib/python3.8/site-packages/brian2/tests/test_units.py::test_numpy_functions_logical
!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
1 failed, 342 passed, 2 skipped, 304 deselected, 232 warnings in 53.08s
Running tests for target numpy:
.................................ssssss................................. [ 28%]
........................................................................ [ 56%]
........................................................................ [ 84%]
........................................                                 [100%]
=============================== warnings summary ===============================
tests/test_complex_examples.py: 1 warning
tests/test_functions.py: 1 warning
tests/test_monitor.py: 5 warnings
tests/test_neurongroup.py: 4 warnings
tests/test_poissoninput.py: 1 warning
tests/test_refractory.py: 26 warnings
tests/test_stateupdaters.py: 10 warnings
tests/test_synapses.py: 3 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/groups/group.py:148: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    return np.bool

tests/test_complex_examples.py: 1 warning
tests/test_functions.py: 1 warning
tests/test_monitor.py: 15 warnings
tests/test_network.py: 4 warnings
tests/test_neurongroup.py: 11 warnings
tests/test_poissongroup.py: 7 warnings
tests/test_poissoninput.py: 1 warning
tests/test_refractory.py: 21 warnings
tests/test_spikegenerator.py: 1 warning
tests/test_stateupdaters.py: 1 warning
tests/test_subgroup.py: 20 warnings
tests/test_synapses.py: 148 warnings
tests/test_thresholder.py: 2 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/groups/neurongroup.py:313: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    self.variables.add_auxiliary_variable('_cond', dtype=np.bool)

tests/test_complex_examples.py: 1 warning
tests/test_devices.py: 3 warnings
tests/test_functions.py: 9 warnings
tests/test_monitor.py: 3 warnings
tests/test_network.py: 1 warning
tests/test_neurongroup.py: 34 warnings
tests/test_stateupdaters.py: 20 warnings
tests/test_subgroup.py: 24 warnings
tests/test_synapses.py: 69 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/core/variables.py:1027: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    variables.add_auxiliary_variable('_cond', dtype=np.bool)

tests/test_complex_examples.py: 2 warnings
tests/test_functions.py: 1 warning
tests/test_monitor.py: 3 warnings
tests/test_neurongroup.py: 1 warning
tests/test_poissongroup.py: 3 warnings
tests/test_refractory.py: 3 warnings
tests/test_spikegenerator.py: 2 warnings
tests/test_subgroup.py: 39 warnings
tests/test_synapses.py: 198 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses/synapses.py:1713: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    variables.add_auxiliary_variable('_cond', dtype=np.bool)

tests/test_functions.py: 3 warnings
tests/test_monitor.py: 33 warnings
tests/test_network.py: 4 warnings
tests/test_neurongroup.py: 10 warnings
tests/test_refractory.py: 5 warnings
tests/test_spatialneuron.py: 18 warnings
tests/test_spikegenerator.py: 45 warnings
tests/test_subgroup.py: 79 warnings
tests/test_synapses.py: 68 warnings
tests/test_timedarray.py: 2 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/groups/group.py:257: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    if index_array.dtype == np.bool:

tests/test_monitor.py: 2 warnings
tests/test_neurongroup.py: 6 warnings
tests/test_subgroup.py: 13 warnings
tests/test_synapses.py: 7 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/core/variables.py:1073: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    variables.add_auxiliary_variable('_cond', dtype=np.bool)

tests/test_monitor.py: 1 warning
tests/test_neurongroup.py: 2 warnings
tests/test_spatialneuron.py: 2 warnings
tests/test_spikegenerator.py: 4 warnings
tests/test_stateupdaters.py: 3 warnings
tests/test_synapses.py: 4 warnings
tests/test_timedarray.py: 9 warnings
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/core/clocks.py:95: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    dtype=np.float, read_only=True, constant=True,

tests/test_monitor.py::test_synapses_state_monitor
tests/test_monitor.py::test_synapses_state_monitor
tests/test_synapses.py::test_indices
tests/test_synapses.py::test_indices
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/groups/group.py:294: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    variables.add_auxiliary_variable('_cond', dtype=np.bool)

tests/test_neurongroup.py::test_linked_subexpression
tests/test_neurongroup.py::test_linked_subexpression_3
tests/test_neurongroup.py::test_linked_subexpression_synapse
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/groups/neurongroup.py:731: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    if not np.issubsctype(index_array.dtype, np.int):

tests/test_neurongroup.py::test_semantics_floor_division
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py:1782: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    'x': np.float, 'y': np.double})

tests/test_neurongroup.py::test_semantics_floating_point_division
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py:1812: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    'x': np.float, 'y': np.double})

tests/test_neurongroup.py::test_semantics_mod
  /Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py:1846: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    'x': np.float, 'y': np.double})

-- Docs: https://docs.pytest.org/en/stable/warnings.html
250 passed, 6 skipped, 410 deselected, 1030 warnings in 128.11s (0:02:08)
Running tests for target cython:
F
=================================== FAILURES ===================================
_______________________________ test_active_flag _______________________________

self = <distutils.unixccompiler.UnixCCompiler object at 0x13c06bfd0>
obj = '/Users/thomastiotto/Library/Caches/cython/brian_extensions/Users/thomastiotto/Library/Caches/cython/brian_extensions/_cython_magic_3222b51974c5bfffb38fc4d2e4e2bfd2.o'
src = '/Users/thomastiotto/Library/Caches/cython/brian_extensions/_cython_magic_3222b51974c5bfffb38fc4d2e4e2bfd2.cpp'
ext = '.cpp'
cc_args = ['-I/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses', '-I/Users/thomastiotto/mam...an/lib/python3.8/site-packages/brian2/synapses', '-I/Users/thomastiotto/mambaforge/envs/brian/include/python3.8', '-c']
extra_postargs = ['-w', '-O3', '-ffast-math', '-fno-finite-math-only', '-march=native', '-std=c++11', ...]
pp_opts = ['-I/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses', '-I/Users/thomastiotto/mam...vs/brian/lib/python3.8/site-packages/brian2/synapses', '-I/Users/thomastiotto/mambaforge/envs/brian/include/python3.8']

    def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
        compiler_so = self.compiler_so
        if sys.platform == 'darwin':
            compiler_so = _osx_support.compiler_fixup(compiler_so,
                                                    cc_args + extra_postargs)
        try:
>           self.spawn(compiler_so + cc_args + [src, '-o', obj] +
                       extra_postargs)

lib/python3.8/distutils/unixccompiler.py:117:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <distutils.unixccompiler.UnixCCompiler object at 0x13c06bfd0>
cmd = ['gcc', '-Wno-unused-result', '-Wsign-compare', '-Wunreachable-code', '-DNDEBUG', '-g', ...]

    def spawn(self, cmd):
>       spawn(cmd, dry_run=self.dry_run)

lib/python3.8/distutils/ccompiler.py:910:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

cmd = ['gcc', '-Wno-unused-result', '-Wsign-compare', '-Wunreachable-code', '-DNDEBUG', '-g', ...]
search_path = 1, verbose = 0, dry_run = 0

    def spawn(cmd, search_path=1, verbose=0, dry_run=0):
        """Run another program, specified as a command list 'cmd', in a new process.

        'cmd' is just the argument list for the new process, ie.
        cmd[0] is the program to run and cmd[1:] are the rest of its arguments.
        There is no way to run a program with a name different from that of its
        executable.

        If 'search_path' is true (the default), the system's executable
        search path will be used to find the program; otherwise, cmd[0]
        must be the exact path to the executable.  If 'dry_run' is true,
        the command will not actually be run.

        Raise DistutilsExecError if running the program fails in any way; just
        return on success.
        """
        # cmd is documented as a list, but just in case some code passes a tuple
        # in, protect our %-formatting code against horrible death
        cmd = list(cmd)
        if os.name == 'posix':
>           _spawn_posix(cmd, search_path, dry_run=dry_run)

lib/python3.8/distutils/spawn.py:36:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

cmd = 'gcc', search_path = 1, verbose = 0, dry_run = 0

    def _spawn_posix(cmd, search_path=1, verbose=0, dry_run=0):
        log.info(' '.join(cmd))
        if dry_run:
            return
        executable = cmd[0]
        exec_fn = search_path and os.execvp or os.execv
        env = None
        if sys.platform == 'darwin':
            global _cfg_target, _cfg_target_split
            if _cfg_target is None:
                from distutils import sysconfig
                _cfg_target = sysconfig.get_config_var(
                                      'MACOSX_DEPLOYMENT_TARGET') or ''
                if _cfg_target:
                    _cfg_target_split = [int(x) for x in _cfg_target.split('.')]
            if _cfg_target:
                # ensure that the deployment target of build process is not less
                # than that used when the interpreter was built. This ensures
                # extension modules are built with correct compatibility values
                cur_target = os.environ.get('MACOSX_DEPLOYMENT_TARGET', _cfg_target)
                if _cfg_target_split > [int(x) for x in cur_target.split('.')]:
                    my_msg = ('$MACOSX_DEPLOYMENT_TARGET mismatch: '
                              'now "%s" but "%s" during configure'
                                    % (cur_target, _cfg_target))
                    raise DistutilsPlatformError(my_msg)
                env = dict(os.environ,
                           MACOSX_DEPLOYMENT_TARGET=cur_target)
                exec_fn = search_path and os.execvpe or os.execve
        pid = os.fork()
        if pid == 0: # in the child
            try:
                if env is None:
                    exec_fn(executable, cmd)
                else:
                    exec_fn(executable, cmd, env)
            except OSError as e:
                if not DEBUG:
                    cmd = executable
                sys.stderr.write("unable to execute %r: %s\n"
                                 % (cmd, e.strerror))
                os._exit(1)

            if not DEBUG:
                cmd = executable
            sys.stderr.write("unable to execute %r for unknown reasons" % cmd)
            os._exit(1)
        else: # in the parent
            # Loop until the child either exits or is terminated by a signal
            # (ie. keep waiting if it's merely stopped)
            while True:
                try:
                    pid, status = os.waitpid(pid, 0)
                except OSError as exc:
                    if not DEBUG:
                        cmd = executable
                    raise DistutilsExecError(
                          "command %r failed: %s" % (cmd, exc.args[-1]))
                if os.WIFSIGNALED(status):
                    if not DEBUG:
                        cmd = executable
                    raise DistutilsExecError(
                          "command %r terminated by signal %d"
                          % (cmd, os.WTERMSIG(status)))
                elif os.WIFEXITED(status):
                    exit_status = os.WEXITSTATUS(status)
                    if exit_status == 0:
                        return   # hey, it succeeded!
                    else:
                        if not DEBUG:
                            cmd = executable
>                       raise DistutilsExecError(
                              "command %r failed with exit status %d"
E                             distutils.errors.DistutilsExecError: command 'gcc' failed with exit status 1

lib/python3.8/distutils/spawn.py:157: DistutilsExecError

During handling of the above exception, another exception occurred:

self = MagicNetwork()
run_namespace = {'@py_builtins': <module 'builtins' (built-in)>, '@pytest_ar': <module '_pytest.assertion.rewrite' from '/Users/thomas...e-packages/_pytest/assertion/rewrite.py'>, 'ALLOW_THREADS': 1, 'Annotation': <class 'matplotlib.text.Annotation'>, ...}

    @device_override('network_before_run')
    def before_run(self, run_namespace):
        '''
        before_run(namespace)

        Prepares the `Network` for a run.

        Objects in the `Network` are sorted into the correct running order, and
        their `BrianObject.before_run` methods are called.

        Parameters
        ----------
        run_namespace : dict-like, optional
            A namespace in which objects which do not define their own
            namespace will be run.
        '''
        all_objects = self.sorted_objects
        prefs.check_all_validated()

        # Check names in the network for uniqueness
        names = [obj.name for obj in all_objects]
        non_unique_names = [name for name, count in Counter(names).items()
                            if count > 1]
        if len(non_unique_names):
            formatted_names = ', '.join("'%s'" % name
                                        for name in non_unique_names)
            raise ValueError('All objects in a network need to have unique '
                             'names, the following name(s) were used more than '
                             'once: %s' % formatted_names)

        # Check that there are no SummedVariableUpdaters targeting the same
        # target variable
        _check_multiple_summed_updaters(all_objects)

        self._stopped = False
        Network._globally_stopped = False

        device = get_device()
        if device.network_schedule is not None:
            # The device defines a fixed network schedule
            if device.network_schedule != self.schedule:
                # TODO: The human-readable name of a device should be easier to get
                device_name = list(all_devices.keys())[list(all_devices.values()).index(device)]
                logger.warn(("The selected device '{device_name}' only "
                             "supports a fixed schedule, but this schedule is "
                             "not consistent with the network's schedule. The "
                             "simulation will use the device's schedule.\n"
                             "Device schedule: {device.network_schedule}\n"
                             "Network schedule: {net.schedule}\n"
                             "Set the network schedule explicitly or set the "
                             "core.network.default_schedule preference to "
                             "avoid this warning.").format(device_name=device_name,
                                                           device=device,
                                                           net=self),
                            name_suffix='schedule_conflict', once=True)

        logger.debug("Preparing network {self.name} with {numobj} "
                     "objects: {objnames}".format(self=self,
                        numobj=len(all_objects),
                        objnames=', '.join(obj.name for obj in all_objects)),
                     "before_run")

        self.check_dependencies()

        for obj in all_objects:
            if obj.active:
                try:
>                   obj.before_run(run_namespace)

lib/python3.8/site-packages/brian2/core/network.py:897:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = StateUpdater(clock=Clock(dt=100. * usecond, name='defaultclock'), when=groups, order=0, name='neurongroup_stateupdater')
run_namespace = {'@py_builtins': <module 'builtins' (built-in)>, '@pytest_ar': <module '_pytest.assertion.rewrite' from '/Users/thomas...e-packages/_pytest/assertion/rewrite.py'>, 'ALLOW_THREADS': 1, 'Annotation': <class 'matplotlib.text.Annotation'>, ...}

    def before_run(self, run_namespace):
>       self.create_code_objects(run_namespace)

lib/python3.8/site-packages/brian2/groups/group.py:1143:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = StateUpdater(clock=Clock(dt=100. * usecond, name='defaultclock'), when=groups, order=0, name='neurongroup_stateupdater')
run_namespace = {'@py_builtins': <module 'builtins' (built-in)>, '@pytest_ar': <module '_pytest.assertion.rewrite' from '/Users/thomas...e-packages/_pytest/assertion/rewrite.py'>, 'ALLOW_THREADS': 1, 'Annotation': <class 'matplotlib.text.Annotation'>, ...}

    def create_code_objects(self, run_namespace):
        # By default, we only have one code object for each CodeRunner.
        # Overwrite this function to use more than one.
>       code_object = self.create_default_code_object(run_namespace)

lib/python3.8/site-packages/brian2/groups/group.py:1136:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = StateUpdater(clock=Clock(dt=100. * usecond, name='defaultclock'), when=groups, order=0, name='neurongroup_stateupdater')
run_namespace = {'@py_builtins': <module 'builtins' (built-in)>, '@pytest_ar': <module '_pytest.assertion.rewrite' from '/Users/thomas...e-packages/_pytest/assertion/rewrite.py'>, 'ALLOW_THREADS': 1, 'Annotation': <class 'matplotlib.text.Annotation'>, ...}

    def create_default_code_object(self, run_namespace):
        self.update_abstract_code(run_namespace=run_namespace)
        # If the CodeRunner has variables, add them
        if hasattr(self, 'variables'):
            additional_variables = self.variables
        else:
            additional_variables = None

        if not self.generate_empty_code and len(self.abstract_code) == 0:
            self.codeobj = None
        else:
>           self.codeobj = create_runner_codeobj(group=self.group,
                                                 code=self.abstract_code,
                                                 user_code=self.user_code,
                                                 template_name=self.template,
                                                 name=self.name + '_codeobject*',
                                                 check_units=self.check_units,
                                                 additional_variables=additional_variables,
                                                 needed_variables=self.needed_variables,
                                                 run_namespace=run_namespace,
                                                 template_kwds=self.template_kwds,
                                                 override_conditional_write=self.override_conditional_write,
                                                 codeobj_class=self.codeobj_class
                                                 )

lib/python3.8/site-packages/brian2/groups/group.py:1118:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

group = <weakproxy at 0x13bb14130 to NeuronGroup at 0x13bea6100>
code = {None: '_v = dt/ms + v\nv = _v'}, template_name = 'stateupdate'
run_namespace = {'@py_builtins': <module 'builtins' (built-in)>, '@pytest_ar': <module '_pytest.assertion.rewrite' from '/Users/thomas...e-packages/_pytest/assertion/rewrite.py'>, 'ALLOW_THREADS': 1, 'Annotation': <class 'matplotlib.text.Annotation'>, ...}
user_code = {None: 'v = 1/ms'}, variable_indices = None
name = 'neurongroup_stateupdater_codeobject*', check_units = False
needed_variables = [], additional_variables = None, template_kwds = None
override_conditional_write = set()
codeobj_class = <class 'brian2.codegen.runtime.cython_rt.cython_rt.CythonCodeObject'>

    def create_runner_codeobj(group, code, template_name,
                              run_namespace,
                              user_code=None,
                              variable_indices=None,
                              name=None, check_units=True,
                              needed_variables=None,
                              additional_variables=None,
                              template_kwds=None,
                              override_conditional_write=None,
                              codeobj_class=None
                              ):
        ''' Create a `CodeObject` for the execution of code in the context of a
        `Group`.

        Parameters
        ----------
        group : `Group`
            The group where the code is to be run
        code : str or dict of str
            The code to be executed.
        template_name : str
            The name of the template to use for the code.
        run_namespace : dict-like
            An additional namespace that is used for variable lookup (either
            an explicitly defined namespace or one taken from the local
            context).
        user_code : str, optional
            The code that had been specified by the user before other code was
            added automatically. If not specified, will be assumed to be identical
            to ``code``.
        variable_indices : dict-like, optional
            A mapping from `Variable` objects to index names (strings).  If none is
            given, uses the corresponding attribute of `group`.
        name : str, optional
            A name for this code object, will use ``group + '_codeobject*'`` if
            none is given.
        check_units : bool, optional
            Whether to check units in the statement. Defaults to ``True``.
        needed_variables: list of str, optional
            A list of variables that are neither present in the abstract code, nor
            in the ``USES_VARIABLES`` statement in the template. This is only
            rarely necessary, an example being a `StateMonitor` where the
            names of the variables are neither known to the template nor included
            in the abstract code statements.
        additional_variables : dict-like, optional
            A mapping of names to `Variable` objects, used in addition to the
            variables saved in `group`.
        template_kwds : dict, optional
            A dictionary of additional information that is passed to the template.
        override_conditional_write: list of str, optional
            A list of variable names which are used as conditions (e.g. for
            refractoriness) which should be ignored.
        codeobj_class : class, optional
            The `CodeObject` class to run code with. If not specified, defaults to
            the `group`'s ``codeobj_class`` attribute.
        '''

        if name is None:
            if group is not None:
                name = '%s_%s_codeobject*' % (group.name, template_name)
            else:
                name = '%s_codeobject*' % template_name

        if user_code is None:
            user_code = code

        if isinstance(code, str):
            code = {None: code}
            user_code = {None: user_code}

        msg = 'Creating code object (group=%s, template name=%s) for abstract code:\n' % (group.name, template_name)
        msg += indent(code_representation(code))
        logger.diagnostic(msg)
        from brian2.devices import get_device
        device = get_device()

        if override_conditional_write is None:
            override_conditional_write = set([])
        else:
            override_conditional_write = set(override_conditional_write)

        if codeobj_class is None:
            codeobj_class = device.code_object_class(group.codeobj_class)
        else:
            codeobj_class = device.code_object_class(codeobj_class)

        template = getattr(codeobj_class.templater, template_name)
        template_variables = getattr(template, 'variables', None)

        all_variables = dict(group.variables)
        if additional_variables is not None:
            all_variables.update(additional_variables)

        # Determine the identifiers that were used
        identifiers = set()
        user_identifiers = set()
        for v, u_v in zip(code.values(), user_code.values()):
            _, uk, u = analyse_identifiers(v, all_variables, recursive=True)
            identifiers |= uk | u
            _, uk, u = analyse_identifiers(u_v, all_variables, recursive=True)
            user_identifiers |= uk | u

        # Add variables that are not in the abstract code, nor specified in the
        # template but nevertheless necessary
        if needed_variables is None:
            needed_variables = []
        # Resolve all variables (variables used in the code and variables needed by
        # the template)
        variables = group.resolve_all(identifiers | set(needed_variables) | set(template_variables),
                                      # template variables are not known to the user:
                                      user_identifiers=user_identifiers,
                                      additional_variables=additional_variables,
                                      run_namespace=run_namespace)
        # We raise this error only now, because there is some non-obvious code path
        # where Jinja tries to get a Synapse's "name" attribute via syn['name'],
        # which then triggers the use of the `group_get_indices` template which does
        # not exist for standalone. Putting the check for template == None here
        # means we will first raise an error about the unknown identifier which will
        # then make Jinja try syn.name
        if template is None:
            codeobj_class_name = codeobj_class.class_name or codeobj_class.__name__
            raise AttributeError(('"%s" does not provide a code generation '
                                  'template "%s"') % (codeobj_class_name,
                                                      template_name))


        conditional_write_variables = {}
        # Add all the "conditional write" variables
        for var in variables.values():
            cond_write_var = getattr(var, 'conditional_write', None)
            if cond_write_var in override_conditional_write:
                continue
            if cond_write_var is not None:
                if (cond_write_var.name in variables and
                        not variables[cond_write_var.name] is cond_write_var):
                    logger.diagnostic(('Variable "%s" is needed for the '
                                       'conditional write mechanism of variable '
                                       '"%s". Its name is already used for %r.') % (cond_write_var.name,
                                                                                    var.name,
                                                                                    variables[cond_write_var.name]))
                else:
                    conditional_write_variables[cond_write_var.name] = cond_write_var

        variables.update(conditional_write_variables)

        if check_units:
            for c in code.values():
                # This is the first time that the code is parsed, catch errors
                try:
                    check_units_statements(c, variables)
                except (SyntaxError, ValueError) as ex:
                    error_msg = _error_msg(c, name)
                    raise ValueError(error_msg) from ex

        all_variable_indices = copy.copy(group.variables.indices)
        if additional_variables is not None:
            all_variable_indices.update(additional_variables.indices)
        if variable_indices is not None:
            all_variable_indices.update(variable_indices)

        # Make "conditional write" variables use the same index as the variable
        # that depends on them
        for varname, var in variables.items():
            cond_write_var = getattr(var, 'conditional_write', None)
            if cond_write_var is not None:
                all_variable_indices[cond_write_var.name] = all_variable_indices[varname]

        # Check that all functions are available
        for varname, value in variables.items():
            if isinstance(value, Function):
                try:
                    value.implementations[codeobj_class]
                except KeyError as ex:
                    # if we are dealing with numpy, add the default implementation
                    from brian2.codegen.runtime.numpy_rt import NumpyCodeObject
                    if codeobj_class is NumpyCodeObject:
                        value.implementations.add_numpy_implementation(value.pyfunc)
                    else:
                        raise NotImplementedError(('Cannot use function '
                                                   '%s: %s') % (varname, ex)) from ex

        # Gather the additional compiler arguments declared by function
        # implementations
        all_keywords = [_gather_compiler_kwds(var, codeobj_class)
                        for var in variables.values()
                        if isinstance(var, Function)]
        compiler_kwds = _merge_compiler_kwds(all_keywords)

        # Add the indices needed by the variables
        for varname in list(variables):
            var_index = all_variable_indices[varname]
            if not var_index in ('_idx', '0'):
                variables[var_index] = all_variables[var_index]

>       return device.code_object(owner=group,
                                  name=name,
                                  abstract_code=code,
                                  variables=variables,
                                  template_name=template_name,
                                  variable_indices=all_variable_indices,
                                  template_kwds=template_kwds,
                                  codeobj_class=codeobj_class,
                                  override_conditional_write=override_conditional_write,
                                  compiler_kwds=compiler_kwds
                                  )

lib/python3.8/site-packages/brian2/codegen/codeobject.py:441:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <brian2.devices.device.RuntimeDevice object at 0x12de84a30>
owner = <weakproxy at 0x13bb14130 to NeuronGroup at 0x13bea6100>
name = 'neurongroup_stateupdater_codeobject'
abstract_code = {None: '_v = dt/ms + v\nv = _v'}
variables = {'N': <Constant(dimensions=Dimension(),  dtype=int64, scalar=True, constant=True, read_only=True)>, 'dt': <ArrayVariab...ly=True)>, 'v': <ArrayVariable(dimensions=Dimension(),  dtype=float64, scalar=False, constant=False, read_only=False)>}
template_name = 'stateupdate'
variable_indices = defaultdict(..., {'N': '0', 't': '0', 'dt': '0', 't_in_timesteps': '0', 'v': '_idx', 'ms': '_idx', '_v': '_idx'})
codeobj_class = <class 'brian2.codegen.runtime.cython_rt.cython_rt.CythonCodeObject'>
template_kwds = {'dt': '_array_defaultclock_dt[0]', 'load_namespace': '_var_N = _namespace["_var_N"]\ncdef int64_t N = _namespace["N"]...group_v\'])\ncdef double v\ncdef double _lio_1\ncdef double _v', 'support_code_lines': [], 'v': '_array_neurongroup_v'}
override_conditional_write = set()
compiler_kwds = defaultdict(<class 'list'>, {})

    def code_object(self, owner, name, abstract_code, variables, template_name,
                    variable_indices, codeobj_class=None,
                    template_kwds=None, override_conditional_write=None,
                    compiler_kwds=None):
        if compiler_kwds is None:
            compiler_kwds = {}
        name = find_name(name)
        codeobj_class = self.code_object_class(codeobj_class)
        template = getattr(codeobj_class.templater, template_name)
        iterate_all = template.iterate_all
        generator = codeobj_class.generator_class(variables=variables,
                                                  variable_indices=variable_indices,
                                                  owner=owner,
                                                  iterate_all=iterate_all,
                                                  codeobj_class=codeobj_class,
                                                  override_conditional_write=override_conditional_write,
                                                  allows_scalar_write=template.allows_scalar_write,
                                                  name=name,
                                                  template_name=template_name)
        if template_kwds is None:
            template_kwds = dict()
        else:
            template_kwds = template_kwds.copy()

        logger.diagnostic('%s abstract code:\n%s' % (name, indent(code_representation(abstract_code))))

        scalar_code, vector_code, kwds = generator.translate(abstract_code,
                                                             dtype=prefs['core.default_float_dtype'])
        # Add the array names as keywords as well
        for varname, var in variables.items():
            if isinstance(var, ArrayVariable):
                pointer_name = generator.get_array_name(var)
                if var.scalar:
                    pointer_name += '[0]'
                template_kwds[varname] = pointer_name
                if hasattr(var, 'resize'):
                    dyn_array_name = generator.get_array_name(var,
                                                              access_data=False)
                    template_kwds['_dynamic_'+varname] = dyn_array_name


        template_kwds.update(kwds)
        logger.diagnostic('%s snippet (scalar):\n%s' % (name, indent(code_representation(scalar_code))))
        logger.diagnostic('%s snippet (vector):\n%s' % (name, indent(code_representation(vector_code))))

        code = template(scalar_code, vector_code,
                        owner=owner, variables=variables, codeobj_name=name,
                        variable_indices=variable_indices,
                        get_array_name=generator.get_array_name,
                        **template_kwds)
        logger.diagnostic('%s code:\n%s' % (name, indent(code_representation(code))))

        codeobj = codeobj_class(owner, code, variables, variable_indices,
                                template_name=template_name,
                                template_source=template.template_source,
                                name=name, compiler_kwds=compiler_kwds)
>       codeobj.compile()

lib/python3.8/site-packages/brian2/devices/device.py:327:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <brian2.codegen.runtime.cython_rt.cython_rt.CythonCodeObject object at 0x13bbab7f0>

    def compile(self):
        for block in ['before_run', 'run', 'after_run']:
>           self.compiled_code[block] = self.compile_block(block)

lib/python3.8/site-packages/brian2/codegen/codeobject.py:101:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <brian2.codegen.runtime.cython_rt.cython_rt.CythonCodeObject object at 0x13bbab7f0>
block = 'run'

    def compile_block(self, block):
        code = getattr(self.code, block, '').strip()
        if not code or 'EMPTY_CODE_BLOCK' in code:
            return None
>       return cython_extension_manager.create_extension(
            code,
            define_macros=self.define_macros,
            libraries=self.libraries,
            extra_compile_args=self.extra_compile_args,
            extra_link_args=self.extra_link_args,
            include_dirs=self.include_dirs,
            library_dirs=self.library_dirs,
            compiler=self.compiler,
            owner_name=self.owner.name+'_'+self.template_name,
            sources=self.sources
            )

lib/python3.8/site-packages/brian2/codegen/runtime/cython_rt/cython_rt.py:143:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <brian2.codegen.runtime.cython_rt.extension_manager.CythonExtensionManager object at 0x12de930d0>
code = '#cython: language_level=3\n#cython: boundscheck=False\n#cython: wraparound=False\n#cython: cdivision=False\n#cython: ...       v = _array_neurongroup_v[_idx]\n        _v = _lio_1 + v\n        v = _v\n        _array_neurongroup_v[_idx] = v'
force = False, name = None, define_macros = []
include_dirs = ['/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses', '/Users/thomastiotto/mambafo...-packages/numpy/core/include', '/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses']
library_dirs = ['/Users/thomastiotto/mambaforge/envs/brian/lib']
runtime_library_dirs = None
extra_compile_args = ['-w', '-O3', '-ffast-math', '-fno-finite-math-only', '-march=native', '-std=c++11', ...]
extra_link_args = [], libraries = [], compiler = 'unix', sources = []
owner_name = 'neurongroup_stateupdate'

    def create_extension(self, code, force=False, name=None,
                         define_macros=None,
                         include_dirs=None,
                         library_dirs=None,
                         runtime_library_dirs=None,
                         extra_compile_args=None,
                         extra_link_args=None,
                         libraries=None,
                         compiler=None,
                         sources=None,
                         owner_name='',
                         ):
        if sources is None:
            sources = []
        self._simplify_paths()

        if Cython is None:
            raise ImportError('Cython is not available')

        code = deindent(code)

        lib_dir = get_cython_cache_dir()
        if '~' in lib_dir:
            lib_dir = os.path.expanduser(lib_dir)
        try:
            os.makedirs(lib_dir)
        except OSError:
            if not os.path.exists(lib_dir):
                raise IOError("Couldn't create Cython cache directory '%s', try setting the "
                              "cache directly with prefs.codegen.runtime.cython.cache_dir." % lib_dir)

        numpy_version = '.'.join(numpy.__version__.split('.')[:2])  # Only use major.minor version
        key = code, sys.version_info, sys.executable, Cython.__version__, numpy_version

        if force:
            # Force a new module name by adding the current time to the
            # key which is hashed to determine the module name.
            key += time.time(),

        if key in self._code_cache:
            return self._code_cache[key]

        if name is not None:
            module_name = name#py3compat.unicode_to_str(args.name)
        else:
            module_name = "_cython_magic_" + hashlib.md5(str(key).encode('utf-8')).hexdigest()
        if owner_name:
            logger.diagnostic('"{owner_name}" using Cython module "{module_name}"'.format(owner_name=owner_name,
                                                                                     module_name=module_name))


        module_path = os.path.join(lib_dir, module_name + self.so_ext)

        if prefs['codegen.runtime.cython.multiprocess_safe']:
            lock = FileLock(os.path.join(lib_dir, module_name + '.lock'))
            with lock:
>               module = self._load_module(module_path,
                                           define_macros=define_macros,
                                           include_dirs=include_dirs,
                                           library_dirs=library_dirs,
                                           extra_compile_args=extra_compile_args,
                                           extra_link_args=extra_link_args,
                                           libraries=libraries,
                                           code=code,
                                           lib_dir=lib_dir,
                                           module_name=module_name,
                                           runtime_library_dirs=runtime_library_dirs,
                                           compiler=compiler,
                                           key=key,
                                           sources=sources)

lib/python3.8/site-packages/brian2/codegen/runtime/cython_rt/extension_manager.py:112:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <brian2.codegen.runtime.cython_rt.extension_manager.CythonExtensionManager object at 0x12de930d0>
module_path = '/Users/thomastiotto/Library/Caches/cython/brian_extensions/_cython_magic_3222b51974c5bfffb38fc4d2e4e2bfd2.cpython-38-darwin.so'
define_macros = []
include_dirs = ['/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses', '/Users/thomastiotto/mambafo...-packages/numpy/core/include', '/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses']
library_dirs = ['/Users/thomastiotto/mambaforge/envs/brian/lib']
extra_compile_args = ['-w', '-O3', '-ffast-math', '-fno-finite-math-only', '-march=native', '-std=c++11', ...]
extra_link_args = [], libraries = []
code = '#cython: language_level=3\n#cython: boundscheck=False\n#cython: wraparound=False\n#cython: cdivision=False\n#cython: ...       v = _array_neurongroup_v[_idx]\n        _v = _lio_1 + v\n        v = _v\n        _array_neurongroup_v[_idx] = v'
lib_dir = '/Users/thomastiotto/Library/Caches/cython/brian_extensions'
module_name = '_cython_magic_3222b51974c5bfffb38fc4d2e4e2bfd2'
runtime_library_dirs = None, compiler = 'unix'
key = ('#cython: language_level=3\n#cython: boundscheck=False\n#cython: wraparound=False\n#cython: cdivision=False\n#cython:..., micro=12, releaselevel='final', serial=0), '/Users/thomastiotto/mambaforge/envs/brian/bin/python', '0.29.24', '1.21')
sources = []

    def _load_module(self, module_path, define_macros, include_dirs, library_dirs,
                     extra_compile_args, extra_link_args, libraries, code,
                     lib_dir, module_name, runtime_library_dirs, compiler,
                     key, sources):
        have_module = os.path.isfile(module_path)

        if not have_module:
            if define_macros is None:
                define_macros = []
            if include_dirs is None:
                include_dirs = []
            if library_dirs is None:
                library_dirs = []
            if extra_compile_args is None:
                extra_compile_args = []
            if extra_link_args is None:
                extra_link_args = []
            if libraries is None:
                libraries = []

            c_include_dirs = include_dirs
            if 'numpy' in code:
                import numpy
                c_include_dirs.append(numpy.get_include())

            # TODO: We should probably have a special folder just for header
            # files that are shared between different codegen targets
            import brian2.synapses as synapses
            synapses_dir = os.path.dirname(synapses.__file__)
            c_include_dirs.append(synapses_dir)

            pyx_file = os.path.join(lib_dir, module_name + '.pyx')
            # ignore Python 3 unicode stuff for the moment
            #pyx_file = py3compat.cast_bytes_py2(pyx_file, encoding=sys.getfilesystemencoding())
            #with io.open(pyx_file, 'w', encoding='utf-8') as f:
            #    f.write(code)
            with open(pyx_file, 'w') as f:
                f.write(code)

            for source in sources:
                if not source.lower().endswith('.pyx'):
                    raise ValueError('Additional Cython source files need to '
                                     'have an .pyx ending')
                # Copy source and header file (if present) to library directory
                shutil.copyfile(source, os.path.join(lib_dir,
                                                     os.path.basename(source)))
                name_without_ext = os.path.splitext(os.path.basename(source))[0]
                header_name = name_without_ext + '.pxd'
                if os.path.exists(os.path.join(os.path.dirname(source), header_name)):
                    shutil.copyfile(os.path.join(os.path.dirname(source), header_name),
                                    os.path.join(lib_dir, header_name))
            final_sources = [os.path.join(lib_dir, os.path.basename(source))
                             for source in sources]
            extension = Extension(
                name=module_name,
                sources=[pyx_file],
                define_macros=define_macros,
                include_dirs=c_include_dirs,
                library_dirs=library_dirs,
                runtime_library_dirs=runtime_library_dirs,
                extra_compile_args=extra_compile_args,
                extra_link_args=extra_link_args,
                libraries=libraries,
                language='c++')
            build_extension = self._get_build_extension(compiler=compiler)
            try:
                opts = dict(
                    quiet=True,
                    annotate=False,
                    force=True,
                    )
                # suppresses the output on stdout
                with std_silent():
                    build_extension.extensions = Cython_Build.cythonize([extension] + final_sources, **opts)

                    build_extension.build_temp = os.path.dirname(pyx_file)
                    build_extension.build_lib = lib_dir
>                   build_extension.run()

lib/python3.8/site-packages/brian2/codegen/runtime/cython_rt/extension_manager.py:258:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <distutils.command.build_ext.build_ext object at 0x13e756d60>

    def run(self):
        from distutils.ccompiler import new_compiler

        # 'self.extensions', as supplied by setup.py, is a list of
        # Extension instances.  See the documentation for Extension (in
        # distutils.extension) for details.
        #
        # For backwards compatibility with Distutils 0.8.2 and earlier, we
        # also allow the 'extensions' list to be a list of tuples:
        #    (ext_name, build_info)
        # where build_info is a dictionary containing everything that
        # Extension instances do except the name, with a few things being
        # differently named.  We convert these 2-tuples to Extension
        # instances as needed.

        if not self.extensions:
            return

        # If we were asked to build any C/C++ libraries, make sure that the
        # directory where we put them is in the library search path for
        # linking extensions.
        if self.distribution.has_c_libraries():
            build_clib = self.get_finalized_command('build_clib')
            self.libraries.extend(build_clib.get_library_names() or [])
            self.library_dirs.append(build_clib.build_clib)

        # Setup the CCompiler object that we'll use to do all the
        # compiling and linking
        self.compiler = new_compiler(compiler=self.compiler,
                                     verbose=self.verbose,
                                     dry_run=self.dry_run,
                                     force=self.force)
        customize_compiler(self.compiler)
        # If we are cross-compiling, init the compiler now (if we are not
        # cross-compiling, init would not hurt, but people may rely on
        # late initialization of compiler even if they shouldn't...)
        if os.name == 'nt' and self.plat_name != get_platform():
            self.compiler.initialize(self.plat_name)

        # And make sure that any compile/link-related options (which might
        # come from the command-line or from the setup script) are set in
        # that CCompiler object -- that way, they automatically apply to
        # all compiling and linking done here.
        if self.include_dirs is not None:
            self.compiler.set_include_dirs(self.include_dirs)
        if self.define is not None:
            # 'define' option is a list of (name,value) tuples
            for (name, value) in self.define:
                self.compiler.define_macro(name, value)
        if self.undef is not None:
            for macro in self.undef:
                self.compiler.undefine_macro(macro)
        if self.libraries is not None:
            self.compiler.set_libraries(self.libraries)
        if self.library_dirs is not None:
            self.compiler.set_library_dirs(self.library_dirs)
        if self.rpath is not None:
            self.compiler.set_runtime_library_dirs(self.rpath)
        if self.link_objects is not None:
            self.compiler.set_link_objects(self.link_objects)

        # Now actually compile and link everything.
>       self.build_extensions()

lib/python3.8/distutils/command/build_ext.py:340:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <distutils.command.build_ext.build_ext object at 0x13e756d60>

    def build_extensions(self):
        # First, sanity-check the 'extensions' list
        self.check_extensions_list(self.extensions)
        if self.parallel:
            self._build_extensions_parallel()
        else:
>           self._build_extensions_serial()

lib/python3.8/distutils/command/build_ext.py:449:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <distutils.command.build_ext.build_ext object at 0x13e756d60>

    def _build_extensions_serial(self):
        for ext in self.extensions:
            with self._filter_build_errors(ext):
>               self.build_extension(ext)

lib/python3.8/distutils/command/build_ext.py:474:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <distutils.command.build_ext.build_ext object at 0x13e756d60>
ext = <setuptools.extension.Extension('_cython_magic_3222b51974c5bfffb38fc4d2e4e2bfd2') at 0x13c28b6a0>

    def build_extension(self, ext):
        sources = ext.sources
        if sources is None or not isinstance(sources, (list, tuple)):
            raise DistutilsSetupError(
                  "in 'ext_modules' option (extension '%s'), "
                  "'sources' must be present and must be "
                  "a list of source filenames" % ext.name)
        sources = list(sources)

        ext_path = self.get_ext_fullpath(ext.name)
        depends = sources + ext.depends
        if not (self.force or newer_group(depends, ext_path, 'newer')):
            log.debug("skipping '%s' extension (up-to-date)", ext.name)
            return
        else:
            log.info("building '%s' extension", ext.name)

        # First, scan the sources for SWIG definition files (.i), run
        # SWIG on 'em to create .c files, and modify the sources list
        # accordingly.
        sources = self.swig_sources(sources, ext)

        # Next, compile the source code to object files.

        # XXX not honouring 'define_macros' or 'undef_macros' -- the
        # CCompiler API needs to change to accommodate this, and I
        # want to do one thing at a time!

        # Two possible sources for extra compiler arguments:
        #   - 'extra_compile_args' in Extension object
        #   - CFLAGS environment variable (not particularly
        #     elegant, but people seem to expect it and I
        #     guess it's useful)
        # The environment variable should take precedence, and
        # any sensible compiler will give precedence to later
        # command line args.  Hence we combine them in order:
        extra_args = ext.extra_compile_args or []

        macros = ext.define_macros[:]
        for undef in ext.undef_macros:
            macros.append((undef,))

>       objects = self.compiler.compile(sources,
                                         output_dir=self.build_temp,
                                         macros=macros,
                                         include_dirs=ext.include_dirs,
                                         debug=self.debug,
                                         extra_postargs=extra_args,
                                         depends=ext.depends)

lib/python3.8/distutils/command/build_ext.py:528:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <distutils.unixccompiler.UnixCCompiler object at 0x13c06bfd0>
sources = ['/Users/thomastiotto/Library/Caches/cython/brian_extensions/_cython_magic_3222b51974c5bfffb38fc4d2e4e2bfd2.cpp']
output_dir = '/Users/thomastiotto/Library/Caches/cython/brian_extensions'
macros = []
include_dirs = ['/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses', '/Users/thomastiotto/mambafo...-packages/numpy/core/include', '/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses']
debug = None, extra_preargs = None
extra_postargs = ['-w', '-O3', '-ffast-math', '-fno-finite-math-only', '-march=native', '-std=c++11', ...]
depends = ['/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses/stdint_compat.h', '/Users/thom...s.h', '/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/numpy/core/include/numpy/npy_math.h', ...]

    def compile(self, sources, output_dir=None, macros=None,
                include_dirs=None, debug=0, extra_preargs=None,
                extra_postargs=None, depends=None):
        """Compile one or more source files.

        'sources' must be a list of filenames, most likely C/C++
        files, but in reality anything that can be handled by a
        particular compiler and compiler class (eg. MSVCCompiler can
        handle resource files in 'sources').  Return a list of object
        filenames, one per source filename in 'sources'.  Depending on
        the implementation, not all source files will necessarily be
        compiled, but all corresponding object filenames will be
        returned.

        If 'output_dir' is given, object files will be put under it, while
        retaining their original path component.  That is, "foo/bar.c"
        normally compiles to "foo/bar.o" (for a Unix implementation); if
        'output_dir' is "build", then it would compile to
        "build/foo/bar.o".

        'macros', if given, must be a list of macro definitions.  A macro
        definition is either a (name, value) 2-tuple or a (name,) 1-tuple.
        The former defines a macro; if the value is None, the macro is
        defined without an explicit value.  The 1-tuple case undefines a
        macro.  Later definitions/redefinitions/ undefinitions take
        precedence.

        'include_dirs', if given, must be a list of strings, the
        directories to add to the default include file search path for this
        compilation only.

        'debug' is a boolean; if true, the compiler will be instructed to
        output debug symbols in (or alongside) the object file(s).

        'extra_preargs' and 'extra_postargs' are implementation- dependent.
        On platforms that have the notion of a command-line (e.g. Unix,
        DOS/Windows), they are most likely lists of strings: extra
        command-line arguments to prepend/append to the compiler command
        line.  On other platforms, consult the implementation class
        documentation.  In any event, they are intended as an escape hatch
        for those occasions when the abstract compiler framework doesn't
        cut the mustard.

        'depends', if given, is a list of filenames that all targets
        depend on.  If a source file is older than any file in
        depends, then the source file will be recompiled.  This
        supports dependency tracking, but only at a coarse
        granularity.

        Raises CompileError on failure.
        """
        # A concrete compiler class can either override this method
        # entirely or implement _compile().
        macros, objects, extra_postargs, pp_opts, build = \
                self._setup_compile(output_dir, macros, include_dirs, sources,
                                    depends, extra_postargs)
        cc_args = self._get_cc_args(pp_opts, debug, extra_preargs)

        for obj in objects:
            try:
                src, ext = build[obj]
            except KeyError:
                continue
>           self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)

lib/python3.8/distutils/ccompiler.py:574:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <distutils.unixccompiler.UnixCCompiler object at 0x13c06bfd0>
obj = '/Users/thomastiotto/Library/Caches/cython/brian_extensions/Users/thomastiotto/Library/Caches/cython/brian_extensions/_cython_magic_3222b51974c5bfffb38fc4d2e4e2bfd2.o'
src = '/Users/thomastiotto/Library/Caches/cython/brian_extensions/_cython_magic_3222b51974c5bfffb38fc4d2e4e2bfd2.cpp'
ext = '.cpp'
cc_args = ['-I/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses', '-I/Users/thomastiotto/mam...an/lib/python3.8/site-packages/brian2/synapses', '-I/Users/thomastiotto/mambaforge/envs/brian/include/python3.8', '-c']
extra_postargs = ['-w', '-O3', '-ffast-math', '-fno-finite-math-only', '-march=native', '-std=c++11', ...]
pp_opts = ['-I/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/brian2/synapses', '-I/Users/thomastiotto/mam...vs/brian/lib/python3.8/site-packages/brian2/synapses', '-I/Users/thomastiotto/mambaforge/envs/brian/include/python3.8']

    def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
        compiler_so = self.compiler_so
        if sys.platform == 'darwin':
            compiler_so = _osx_support.compiler_fixup(compiler_so,
                                                    cc_args + extra_postargs)
        try:
            self.spawn(compiler_so + cc_args + [src, '-o', obj] +
                       extra_postargs)
        except DistutilsExecError as msg:
>           raise CompileError(msg)
E           distutils.errors.CompileError: command 'gcc' failed with exit status 1

lib/python3.8/distutils/unixccompiler.py:120: CompileError

The above exception was the direct cause of the following exception:

    @pytest.mark.standalone_compatible
    @pytest.mark.multiple_runs
    def test_active_flag():
        G = NeuronGroup(1, 'dv/dt = 1/ms : 1')
        mon = StateMonitor(G, 'v', record=0)
        mon.active = False
>       run(1*ms)

lib/python3.8/site-packages/brian2/tests/test_base.py:73:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/python3.8/site-packages/brian2/units/fundamentalunits.py:2434: in new_f
    result = f(*args, **kwds)
lib/python3.8/site-packages/brian2/core/magic.py:373: in run
    return magic_network.run(duration, report=report, report_period=report_period,
lib/python3.8/site-packages/brian2/core/magic.py:231: in run
    Network.run(self, duration, report=report, report_period=report_period,
lib/python3.8/site-packages/brian2/core/base.py:278: in device_override_decorated_function
    return func(*args, **kwds)
lib/python3.8/site-packages/brian2/units/fundamentalunits.py:2434: in new_f
    result = f(*args, **kwds)
lib/python3.8/site-packages/brian2/core/network.py:1008: in run
    self.before_run(namespace)
lib/python3.8/site-packages/brian2/core/base.py:278: in device_override_decorated_function
    return func(*args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = MagicNetwork()
run_namespace = {'@py_builtins': <module 'builtins' (built-in)>, '@pytest_ar': <module '_pytest.assertion.rewrite' from '/Users/thomas...e-packages/_pytest/assertion/rewrite.py'>, 'ALLOW_THREADS': 1, 'Annotation': <class 'matplotlib.text.Annotation'>, ...}

    @device_override('network_before_run')
    def before_run(self, run_namespace):
        '''
        before_run(namespace)

        Prepares the `Network` for a run.

        Objects in the `Network` are sorted into the correct running order, and
        their `BrianObject.before_run` methods are called.

        Parameters
        ----------
        run_namespace : dict-like, optional
            A namespace in which objects which do not define their own
            namespace will be run.
        '''
        all_objects = self.sorted_objects
        prefs.check_all_validated()

        # Check names in the network for uniqueness
        names = [obj.name for obj in all_objects]
        non_unique_names = [name for name, count in Counter(names).items()
                            if count > 1]
        if len(non_unique_names):
            formatted_names = ', '.join("'%s'" % name
                                        for name in non_unique_names)
            raise ValueError('All objects in a network need to have unique '
                             'names, the following name(s) were used more than '
                             'once: %s' % formatted_names)

        # Check that there are no SummedVariableUpdaters targeting the same
        # target variable
        _check_multiple_summed_updaters(all_objects)

        self._stopped = False
        Network._globally_stopped = False

        device = get_device()
        if device.network_schedule is not None:
            # The device defines a fixed network schedule
            if device.network_schedule != self.schedule:
                # TODO: The human-readable name of a device should be easier to get
                device_name = list(all_devices.keys())[list(all_devices.values()).index(device)]
                logger.warn(("The selected device '{device_name}' only "
                             "supports a fixed schedule, but this schedule is "
                             "not consistent with the network's schedule. The "
                             "simulation will use the device's schedule.\n"
                             "Device schedule: {device.network_schedule}\n"
                             "Network schedule: {net.schedule}\n"
                             "Set the network schedule explicitly or set the "
                             "core.network.default_schedule preference to "
                             "avoid this warning.").format(device_name=device_name,
                                                           device=device,
                                                           net=self),
                            name_suffix='schedule_conflict', once=True)

        logger.debug("Preparing network {self.name} with {numobj} "
                     "objects: {objnames}".format(self=self,
                        numobj=len(all_objects),
                        objnames=', '.join(obj.name for obj in all_objects)),
                     "before_run")

        self.check_dependencies()

        for obj in all_objects:
            if obj.active:
                try:
                    obj.before_run(run_namespace)
                except Exception as ex:
>                   raise BrianObjectException("An error occurred when preparing an object.", obj) from ex
E                   brian2.core.base.BrianObjectException: Error encountered with object named "neurongroup_stateupdater".
E                   Object was created here (most recent call only, full details in debug log):
E                     File "/Users/thomastiotto/mambaforge/envs/brian/lib/python3.8/site-packages/_pytest/python.py", line 183, in pytest_pyfunc_call
E                       result = testfunction(**testargs)
E
E                   An error occurred when preparing an object. (See above for original error message and traceback.)

lib/python3.8/site-packages/brian2/core/network.py:899: BrianObjectException
----------------------------- Captured stderr call -----------------------------
clang: error: the clang compiler does not support '-march=native'
clang: error: the clang compiler does not support '-march=native'
=========================== short test summary info ============================
FAILED lib/python3.8/site-packages/brian2/tests/test_base.py::test_active_flag
!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
1 failed, 410 deselected in 0.85s
ERROR: 3/4 test suite(s) did not complete successfully (see above).
False