From 43d63a88c0c9fc5b33cd69d6c5ce0db77f6dea1e Mon Sep 17 00:00:00 2001
From: Werner Van Geit <werner.vangeit@epfl.ch>
Date: Mon, 25 Mar 2024 09:53:32 +0100
Subject: [PATCH] Fix pytest setup() deprecation in tests (#492)

* Fix pytest setup() deprecation in tests

* Replace setup() with setup_method() in func tests

* Fix issues in arbor tests, wrt to sorted dir content etc

* Make compatible with python 3.12

* Add python 3.12 to default tests
---
 .github/workflows/test.yml                    |   2 +-
 bluepyopt/ephys/create_acc.py                 | 571 +++++++++-------
 bluepyopt/ephys/simulators.py                 | 165 ++---
 bluepyopt/tests/test_ephys/test_create_acc.py | 611 ++++++++++--------
 bluepyopt/tests/test_ephys/test_locations.py  | 175 +++--
 bluepyopt/tests/test_ephys/test_simulators.py |  60 +-
 bluepyopt/tests/test_l5pc.py                  | 132 ++--
 bluepyopt/tests/test_lfpy.py                  |  12 +-
 bluepyopt/tests/test_simplecell.py            |  41 +-
 versioneer.py                                 | 288 ++++++---
 10 files changed, 1168 insertions(+), 889 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 7dc973ba..65e10fbe 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         include:
           - os: macos-latest
             python-version: "3.10"
diff --git a/bluepyopt/ephys/create_acc.py b/bluepyopt/ephys/create_acc.py
index 4d176014..b0974d1e 100644
--- a/bluepyopt/ephys/create_acc.py
+++ b/bluepyopt/ephys/create_acc.py
@@ -1,4 +1,4 @@
-'''create JSON/ACC files for Arbor from a set of BluePyOpt.ephys parameters'''
+"""create JSON/ACC files for Arbor from a set of BluePyOpt.ephys parameters"""
 
 # pylint: disable=R0914
 
@@ -14,14 +14,18 @@
 
 from bluepyopt.ephys.acc import arbor
 from bluepyopt.ephys.morphologies import ArbFileMorphology
-from bluepyopt.ephys.create_hoc import \
-    Location, RangeExpr, PointExpr, \
-    _get_template_params, format_float
+from bluepyopt.ephys.create_hoc import (
+    Location,
+    RangeExpr,
+    PointExpr,
+    _get_template_params,
+    format_float,
+)
 
 logger = logging.getLogger(__name__)
 
 # Inhomogeneous expression for scaled parameter in Arbor
-RangeIExpr = namedtuple('RangeIExpr', 'name, value, scale')
+RangeIExpr = namedtuple("RangeIExpr", "name, value, scale")
 
 
 class ArbVar:
@@ -39,25 +43,32 @@ def __init__(self, name, conv=None):
         self.conv = conv
 
     def __repr__(self):
-        return 'ArbVar(%s, %s)' % (self.name, self.conv)
+        return "ArbVar(%s, %s)" % (self.name, self.conv)
 
 
 class Nrn2ArbParamAdapter:
     """Converts a Neuron parameter to Arbor format (name and value)"""
 
     _mapping = dict(
-        v_init=ArbVar(name='membrane-potential'),
-        celsius=ArbVar(name='temperature-kelvin',
-                       conv=lambda celsius: celsius + 273.15),
-        Ra=ArbVar(name='axial-resistivity'),
-        cm=ArbVar(name='membrane-capacitance',
-                  conv=lambda cm: cm / 100.),  # NEURON: uF/cm^2, Arbor: F/m^2
-        **{species + loc[0]:
-            ArbVar(name='ion-%sternal-concentration \"%s\"' % (loc, species))
-            for species in ['na', 'k', 'ca'] for loc in ['in', 'ex']},
-        **{'e' + species:
-            ArbVar(name='ion-reversal-potential \"%s\"' % species)
-            for species in ['na', 'k', 'ca']}
+        v_init=ArbVar(name="membrane-potential"),
+        celsius=ArbVar(
+            name="temperature-kelvin", conv=lambda celsius: celsius + 273.15
+        ),
+        Ra=ArbVar(name="axial-resistivity"),
+        cm=ArbVar(
+            name="membrane-capacitance", conv=lambda cm: cm / 100.0
+        ),  # NEURON: uF/cm^2, Arbor: F/m^2
+        **{
+            species + loc[0]: ArbVar(
+                name='ion-%sternal-concentration "%s"' % (loc, species)
+            )
+            for species in ["na", "k", "ca"]
+            for loc in ["in", "ex"]
+        },
+        **{
+            "e" + species: ArbVar(name='ion-reversal-potential "%s"' % species)
+            for species in ["na", "k", "ca"]
+        },
     )
 
     @classmethod
@@ -77,13 +88,19 @@ def _param_value(cls, param):
             param (): A Neuron parameter with a value in Neuron units
         """
 
-        if param.name in cls._mapping and \
-                cls._mapping[param.name].conv is not None:
+        if (
+            param.name in cls._mapping
+            and cls._mapping[param.name].conv is not None
+        ):
             return format_float(
-                cls._mapping[param.name].conv(float(param.value)))
+                cls._mapping[param.name].conv(float(param.value))
+            )
         else:
-            return param.value if isinstance(param.value, str) else \
-                format_float(param.value)
+            return (
+                param.value
+                if isinstance(param.value, str)
+                else format_float(param.value)
+            )
 
     @classmethod
     def _conv_param(cls, param, name):
@@ -95,20 +112,26 @@ def _conv_param(cls, param, name):
         """
 
         if isinstance(param, Location):
-            return Location(name=cls._param_name(name),
-                            value=cls._param_value(param))
+            return Location(
+                name=cls._param_name(name), value=cls._param_value(param)
+            )
         elif isinstance(param, RangeExpr):
-            return RangeExpr(location=param.location,
-                             name=cls._param_name(name),
-                             value=cls._param_value(param),
-                             value_scaler=param.value_scaler)
+            return RangeExpr(
+                location=param.location,
+                name=cls._param_name(name),
+                value=cls._param_value(param),
+                value_scaler=param.value_scaler,
+            )
         elif isinstance(param, PointExpr):
-            return PointExpr(name=cls._param_name(name),
-                             point_loc=param.point_loc,
-                             value=cls._param_value(param))
+            return PointExpr(
+                name=cls._param_name(name),
+                point_loc=param.point_loc,
+                value=cls._param_value(param),
+            )
         else:
             raise CreateAccException(
-                'Unsupported parameter expression type %s.' % type(param))
+                "Unsupported parameter expression type %s." % type(param)
+            )
 
     @classmethod
     def format(cls, param, mechs):
@@ -123,12 +146,16 @@ def format(cls, param, mechs):
             parameter in Arbor format
         """
         if not isinstance(param, PointExpr):
-            mech_matches = [i for i, mech in enumerate(mechs)
-                            if param.name.endswith("_" + mech)]
+            mech_matches = [
+                i
+                for i, mech in enumerate(mechs)
+                if param.name.endswith("_" + mech)
+            ]
         else:
             param_pprocesses = [loc.pprocess_mech for loc in param.point_loc]
-            mech_matches = [i for i, mech in enumerate(mechs)
-                            if mech in param_pprocesses]
+            mech_matches = [
+                i for i, mech in enumerate(mechs) if mech in param_pprocesses
+            ]
 
         if len(mech_matches) == 0:
             return None, cls._conv_param(param, name=param.name)
@@ -136,15 +163,17 @@ def format(cls, param, mechs):
         elif len(mech_matches) == 1:
             mech = mechs[mech_matches[0]]
             if not isinstance(param, PointExpr):
-                name = param.name[:-(len(mech) + 1)]
+                name = param.name[: -(len(mech) + 1)]
             else:
                 name = param.name
             return mech, cls._conv_param(param, name=name)
 
         else:
-            raise CreateAccException("Parameter name %s matches" % param.name +
-                                     " multiple mechanisms %s" %
-                                     [repr(mechs[i]) for i in mech_matches])
+            raise CreateAccException(
+                "Parameter name %s matches" % param.name
+                + " multiple mechanisms %s"
+                % [repr(mechs[i]) for i in mech_matches]
+            )
 
 
 class Nrn2ArbMechGrouper:
@@ -159,14 +188,21 @@ def _is_global_property(loc, param):
             param (): A parameter in Arbor format (name and units)
         """
 
-        return loc == ArbFileMorphology.region_labels['all'] and (
-            param.name in ['membrane-potential',
-                           'temperature-kelvin',
-                           'axial-resistivity',
-                           'membrane-capacitance'] or
-            param.name.split(' ')[0] in ['ion-internal-concentration',
-                                         'ion-external-concentration',
-                                         'ion-reversal-potential'])
+        return loc == ArbFileMorphology.region_labels["all"] and (
+            param.name
+            in [
+                "membrane-potential",
+                "temperature-kelvin",
+                "axial-resistivity",
+                "membrane-capacitance",
+            ]
+            or param.name.split(" ")[0]
+            in [
+                "ion-internal-concentration",
+                "ion-external-concentration",
+                "ion-reversal-potential",
+            ]
+        )
 
     @classmethod
     def _separate_global_properties(cls, loc, mechs):
@@ -187,7 +223,6 @@ def _separate_global_properties(cls, loc, mechs):
         global_properties = []
 
         for mech, params in mechs.items():
-
             if mech is None:
                 local_properties = []
                 for param in params:
@@ -213,8 +248,9 @@ def _format_params_and_group_by_mech(params, channels):
             Mapping of Arbor mechanism name to list of parameters in Arbor
             format
         """
-        mech_params = [Nrn2ArbParamAdapter.format(
-                       param, channels) for param in params]
+        mech_params = [
+            Nrn2ArbParamAdapter.format(param, channels) for param in params
+        ]
         mechs = {mech: [] for mech, _ in mech_params}
         for mech in channels:
             if mech not in mechs:
@@ -236,9 +272,11 @@ def process_global(cls, params):
             (mechanism name is None for non-mechanism parameters).
         """
         return cls._format_params_and_group_by_mech(
-            [Location(name=name, value=value)
-             for name, value in params.items()],
-            []  # no default mechanisms
+            [
+                Location(name=name, value=value)
+                for name, value in params.items()
+            ],
+            [],  # no default mechanisms
         )
 
     @classmethod
@@ -261,16 +299,19 @@ def process_local(cls, params, channels):
         global_properties = dict()
         for loc, loc_params in params:
             mechs = cls._format_params_and_group_by_mech(
-                loc_params, channels[loc])
+                loc_params, channels[loc]
+            )
 
             # move Arbor global properties to global_params
             mechs, global_props = cls._separate_global_properties(loc, mechs)
             if global_props.keys() != {None}:
                 raise CreateAccException(
-                    'Support for Arbor default mechanisms not implemented.')
+                    "Support for Arbor default mechanisms not implemented."
+                )
             # iterate over global_props items if above exception triggers
-            global_properties[None] = \
+            global_properties[None] = (
                 global_properties.get(None, []) + global_props[None]
+            )
             local_mechs[loc] = mechs
         return local_mechs, global_properties
 
@@ -289,8 +330,11 @@ def _arb_filter_point_proc_locs(pprocess_mechs):
         for mech, point_exprs in mechs.items():
             result[loc][mech.name] = dict(
                 mech=mech.suffix,
-                params=[Location(point_expr.name, point_expr.value)
-                        for point_expr in point_exprs])
+                params=[
+                    Location(point_expr.name, point_expr.value)
+                    for point_expr in point_exprs
+                ],
+            )
 
     return result
 
@@ -300,18 +344,21 @@ def _arb_append_scaled_mechs(mechs, scaled_mechs):
     for mech, scaled_params in scaled_mechs.items():
         if mech is None and len(scaled_params) > 0:
             raise CreateAccException(
-                'Non-mechanism parameters cannot have inhomogeneous'
-                ' expressions in Arbor %s' % scaled_params)
-        mechs[mech] = mechs.get(mech, []) + \
-            [RangeIExpr(
+                "Non-mechanism parameters cannot have inhomogeneous"
+                " expressions in Arbor %s" % scaled_params
+            )
+        mechs[mech] = mechs.get(mech, []) + [
+            RangeIExpr(
                 name=p.name,
                 value=p.value,
-                scale=p.value_scaler.acc_scale_iexpr(p.value))
-                for p in scaled_params]
+                scale=p.value_scaler.acc_scale_iexpr(p.value),
+            )
+            for p in scaled_params
+        ]
 
 
 # An mechanism's NMODL GLOBAL and RANGE variables in Arbor
-MechMetaData = namedtuple('MechMetaData', 'globals, ranges')
+MechMetaData = namedtuple("MechMetaData", "globals, ranges")
 
 
 class ArbNmodlMechFormatter:
@@ -338,37 +385,42 @@ def _load_catalogue_meta(cat_dir):
         """
         # used to generate arbor_mechanisms.json on NMODL from arbor/mechanisms
 
-        nmodl_pattern = '^\s*%s\s+((?:\w+\,\s*)*?\w+)\s*?$'  # NOQA
-        suffix_pattern = nmodl_pattern % 'SUFFIX'
-        globals_pattern = nmodl_pattern % 'GLOBAL'
-        ranges_pattern = nmodl_pattern % 'RANGE'
+        nmodl_pattern = r"^\s*%s\s+((?:\w+\,\s*)*?\w+)\s*?$"  # NOQA
+        suffix_pattern = nmodl_pattern % "SUFFIX"
+        globals_pattern = nmodl_pattern % "GLOBAL"
+        ranges_pattern = nmodl_pattern % "RANGE"
 
         def process_nmodl(nmodl_str):
             """Extract global and range params from Arbor-conforming NMODL"""
             try:
-                nrn = re.search(r'NEURON\s+{([^}]+)}', nmodl_str,
-                                flags=re.MULTILINE).group(1)
-                suffix_ = re.search(suffix_pattern, nrn,
-                                    flags=re.MULTILINE)
+                nrn = re.search(
+                    r"NEURON\s+{([^}]+)}", nmodl_str, flags=re.MULTILINE
+                ).group(1)
+                suffix_ = re.search(suffix_pattern, nrn, flags=re.MULTILINE)
                 suffix_ = suffix_ if suffix_ is None else suffix_.group(1)
-                globals_ = re.search(globals_pattern, nrn,
-                                     flags=re.MULTILINE)
-                globals_ = globals_ if globals_ is None \
-                    else re.findall(r'\w+', globals_.group(1))
-                ranges_ = re.search(ranges_pattern, nrn,
-                                    flags=re.MULTILINE)
-                ranges_ = ranges_ if ranges_ is None \
-                    else re.findall(r'\w+', ranges_.group(1))
+                globals_ = re.search(globals_pattern, nrn, flags=re.MULTILINE)
+                globals_ = (
+                    globals_
+                    if globals_ is None
+                    else re.findall(r"\w+", globals_.group(1))
+                )
+                ranges_ = re.search(ranges_pattern, nrn, flags=re.MULTILINE)
+                ranges_ = (
+                    ranges_
+                    if ranges_ is None
+                    else re.findall(r"\w+", ranges_.group(1))
+                )
             except Exception as e:
                 raise CreateAccException(
-                    'NMODL-inspection for %s failed.' % nmodl_file) from e
+                    "NMODL-inspection for %s failed." % nmodl_file
+                ) from e
 
             # skipping suffix_
             return MechMetaData(globals=globals_, ranges=ranges_)
 
         mechs = dict()
         cat_dir = pathlib.Path(cat_dir)
-        for nmodl_file in cat_dir.glob('*.mod'):
+        for nmodl_file in cat_dir.glob("*.mod"):
             with open(cat_dir.joinpath(nmodl_file)) as f:
                 mechs[nmodl_file.stem] = process_nmodl(f.read())
 
@@ -393,18 +445,23 @@ def _load_mech_catalogue_meta(cls, ext_catalogues):
         if ext_catalogues is not None:
             for cat, cat_nmodl in ext_catalogues.items():
                 arb_cats[cat] = cls._load_catalogue_meta(
-                    pathlib.Path(cat_nmodl).resolve())
+                    pathlib.Path(cat_nmodl).resolve()
+                )
 
-        builtin_catalogues = pathlib.Path(__file__).parent.joinpath(
-            'static/arbor_mechanisms.json').resolve()
+        builtin_catalogues = (
+            pathlib.Path(__file__)
+            .parent.joinpath("static/arbor_mechanisms.json")
+            .resolve()
+        )
         with open(builtin_catalogues) as f:
             builtin_arb_cats = json.load(f)
 
-        for cat in ['BBP', 'default', 'allen']:
+        for cat in ["BBP", "default", "allen"]:
             if cat not in arb_cats:
                 arb_cats[cat] = {
                     mech: MechMetaData(**meta)
-                    for mech, meta in builtin_arb_cats[cat].items()}
+                    for mech, meta in builtin_arb_cats[cat].items()
+                }
 
         return arb_cats
 
@@ -415,7 +472,7 @@ def _mech_name(name):
         Args:
             name (): A Neuron mechanism name
         """
-        if name in ['Exp2Syn', 'ExpSyn']:
+        if name in ["Exp2Syn", "ExpSyn"]:
             return name.lower()
         else:
             return name
@@ -441,51 +498,64 @@ def _translate_mech(cls, mech_name, mech_params, arb_cats):
         for cat in arb_cats:  # in order of precedence
             if arb_mech_name in arb_cats[cat]:
                 arb_mech = arb_cats[cat][arb_mech_name]
-                mech_name = cat + '::' + arb_mech_name
+                mech_name = cat + "::" + arb_mech_name
                 break
 
         if arb_mech is None:  # not Arbor built-in mech, no qualifier added
             if mech_name is not None:
                 logger.warn(
-                    'create_acc: Could not find Arbor mech for %s (%s).'
-                    % (mech_name, mech_params))
+                    "create_acc: Could not find Arbor mech for %s (%s)."
+                    % (mech_name, mech_params)
+                )
             return (mech_name, mech_params)
         else:
             if arb_mech.globals is None:  # only Arbor range params
                 for param in mech_params:
                     if param.name not in arb_mech.ranges:
                         raise CreateAccException(
-                            '%s not a GLOBAL or RANGE parameter of %s' %
-                            (param.name, mech_name))
+                            "%s not a GLOBAL or RANGE parameter of %s"
+                            % (param.name, mech_name)
+                        )
                 return (mech_name, mech_params)
             else:
                 for param in mech_params:
-                    if param.name not in arb_mech.globals and \
-                            param.name not in arb_mech.ranges:
+                    if (
+                        param.name not in arb_mech.globals
+                        and param.name not in arb_mech.ranges
+                    ):
                         raise CreateAccException(
-                            '%s not a GLOBAL or RANGE parameter of %s' %
-                            (param.name, mech_name))
+                            "%s not a GLOBAL or RANGE parameter of %s"
+                            % (param.name, mech_name)
+                        )
                 mech_name_suffix = []
                 remaining_mech_params = []
                 for mech_param in mech_params:
                     if mech_param.name in arb_mech.globals:
-                        mech_name_suffix.append(mech_param.name + '=' +
-                                                mech_param.value)
+                        mech_name_suffix.append(
+                            mech_param.name + "=" + mech_param.value
+                        )
                         if isinstance(mech_param, RangeIExpr):
                             remaining_mech_params.append(
-                                RangeIExpr(name=mech_param.name,
-                                           value=None,
-                                           scale=mech_param.scale))
+                                RangeIExpr(
+                                    name=mech_param.name,
+                                    value=None,
+                                    scale=mech_param.scale,
+                                )
+                            )
                     else:
                         remaining_mech_params.append(mech_param)
                 if len(mech_name_suffix) > 0:
-                    mech_name += '/' + ','.join(mech_name_suffix)
+                    mech_name += "/" + ",".join(mech_name_suffix)
                 return (mech_name, remaining_mech_params)
 
     def translate_density(self, mechs):
         """Translate all density mechanisms in a specific region"""
-        return dict([self._translate_mech(mech, params, self.cats)
-                    for mech, params in mechs.items()])
+        return dict(
+            [
+                self._translate_mech(mech, params, self.cats)
+                for mech, params in mechs.items()
+            ]
+        )
 
     def translate_points(self, mechs):
         """Translate all point mechanisms for a specific locset"""
@@ -493,9 +563,9 @@ def translate_points(self, mechs):
 
         for synapse_name, mech_desc in mechs.items():
             mech, params = self._translate_mech(
-                mech_desc['mech'], mech_desc['params'], self.cats)
-            result[synapse_name] = dict(mech=mech,
-                                        params=params)
+                mech_desc["mech"], mech_desc["params"], self.cats
+            )
+            result[synapse_name] = dict(mech=mech, params=params)
 
         return result
 
@@ -527,13 +597,16 @@ def _arb_populate_label_dict(local_mechs, local_scaled_mechs, pprocess_mechs):
     acc_labels = ChainMap(local_mechs, local_scaled_mechs, pprocess_mechs)
 
     for acc_label in acc_labels:
-        if acc_label.name in label_dict and \
-                acc_label != label_dict[acc_label.name]:
+        if (
+            acc_label.name in label_dict
+            and acc_label != label_dict[acc_label.name]
+        ):
             raise CreateAccException(
-                'Label %s already exists in' % acc_label.name +
-                ' label_dict with different s-expression: '
-                ' %s != %s.' % (label_dict[acc_label.name].loc,
-                                acc_label.loc))
+                "Label %s already exists in"
+                % acc_label.name
+                + " label_dict with different s-expression: "
+                " %s != %s." % (label_dict[acc_label.name].loc, acc_label.loc)
+            )
         elif acc_label.name not in label_dict:
             label_dict[acc_label.name] = acc_label
 
@@ -542,10 +615,11 @@ def _arb_populate_label_dict(local_mechs, local_scaled_mechs, pprocess_mechs):
 
 def _read_templates(template_dir, template_filename):
     """Expand Jinja2 template filepath with glob and
-     return dict of target filename -> parsed template"""
+    return dict of target filename -> parsed template"""
     if template_dir is None:
-        template_dir = \
-            pathlib.Path(__file__).parent.joinpath('templates').resolve()
+        template_dir = (
+            pathlib.Path(__file__).parent.joinpath("templates").resolve()
+        )
 
     template_paths = pathlib.Path(template_dir).glob(template_filename)
 
@@ -554,17 +628,18 @@ def _read_templates(template_dir, template_filename):
         with open(template_path) as template_file:
             template = template_file.read()
             name = template_path.name
-            if name.endswith('.jinja2'):
+            if name.endswith(".jinja2"):
                 name = name[:-7]
-            if name.endswith('_template'):
+            if name.endswith("_template"):
                 name = name[:-9]
-            if '_' in name:
-                name = '.'.join(name.rsplit('_', 1))
+            if "_" in name:
+                name = ".".join(name.rsplit("_", 1))
             templates[name] = jinja2.Template(template)
 
     if templates == {}:
         raise FileNotFoundError(
-            f'No templates found for JSON/ACC-export in {template_dir}')
+            f"No templates found for JSON/ACC-export in {template_dir}"
+        )
 
     return templates
 
@@ -574,20 +649,22 @@ def _arb_loc_desc(location, param_or_mech):
     return location.acc_label()
 
 
-def create_acc(mechs,
-               parameters,
-               morphology=None,
-               morphology_dir=None,
-               ext_catalogues=None,
-               ignored_globals=(),
-               replace_axon=None,
-               create_mod_morph=False,
-               template_name='CCell',
-               template_filename='acc/*_template.jinja2',
-               disable_banner=None,
-               template_dir=None,
-               custom_jinja_params=None):
-    '''return a dict with strings containing the rendered JSON/ACC templates
+def create_acc(
+    mechs,
+    parameters,
+    morphology=None,
+    morphology_dir=None,
+    ext_catalogues=None,
+    ignored_globals=(),
+    replace_axon=None,
+    create_mod_morph=False,
+    template_name="CCell",
+    template_filename="acc/*_template.jinja2",
+    disable_banner=None,
+    template_dir=None,
+    custom_jinja_params=None,
+):
+    """return a dict with strings containing the rendered JSON/ACC templates
 
     Args:
         mechs (): All the mechs for the decor template
@@ -604,39 +681,45 @@ def create_acc(mechs,
         template_dir (str): dir name of the jinja2 templates
         custom_jinja_params (dict): dict of additional jinja2 params in case
         of a custom template
-    '''
+    """
 
     if custom_jinja_params is None:
         custom_jinja_params = {}
 
-    if pathlib.Path(morphology).suffix.lower() not in ['.swc', '.asc']:
-        raise CreateAccException("Morphology file %s not supported in Arbor "
-                                 " (only supported types are .swc and .asc)."
-                                 % morphology)
+    if pathlib.Path(morphology).suffix.lower() not in [".swc", ".asc"]:
+        raise CreateAccException(
+            "Morphology file %s not supported in Arbor "
+            " (only supported types are .swc and .asc)." % morphology
+        )
 
     if replace_axon is not None:
-        if not hasattr(arbor.segment_tree, 'tag_roots'):
-            raise NotImplementedError("Need a newer version of Arbor"
-                                      " for axon replacement.")
-        logger.debug("Obtain axon replacement by applying "
-                     "ArbFileMorphology.replace_axon after loading "
-                     "morphology in Arbor.")
-        replace_axon_path = \
-            pathlib.Path(morphology).stem + '_axon_replacement.acc'
+        if not hasattr(arbor.segment_tree, "tag_roots"):
+            raise NotImplementedError(
+                "Need a newer version of Arbor" " for axon replacement."
+            )
+        logger.debug(
+            "Obtain axon replacement by applying "
+            "ArbFileMorphology.replace_axon after loading "
+            "morphology in Arbor."
+        )
+        replace_axon_path = (
+            pathlib.Path(morphology).stem + "_axon_replacement.acc"
+        )
         replace_axon_acc = io.StringIO()
         arbor.write_component(replace_axon, replace_axon_acc)
         replace_axon_acc.seek(0)
 
         if create_mod_morph:
-            modified_morphology_path = \
-                pathlib.Path(morphology).stem + '_modified.acc'
+            modified_morphology_path = (
+                pathlib.Path(morphology).stem + "_modified.acc"
+            )
             modified_morpho = ArbFileMorphology.load(
                 pathlib.Path(morphology_dir).joinpath(morphology),
-                replace_axon_acc)
+                replace_axon_acc,
+            )
             replace_axon_acc.seek(0)
             modified_morphology_acc = io.StringIO()
-            arbor.write_component(
-                modified_morpho, modified_morphology_acc)
+            arbor.write_component(modified_morpho, modified_morphology_acc)
             modified_morphology_acc.seek(0)
             modified_morphology_acc = modified_morphology_acc.read()
         else:
@@ -652,47 +735,49 @@ def create_acc(mechs,
 
     default_location_order = list(ArbFileMorphology.region_labels.values())
 
-    template_params = _get_template_params(mechs,
-                                           parameters,
-                                           ignored_globals,
-                                           disable_banner,
-                                           default_location_order,
-                                           _arb_loc_desc)
+    template_params = _get_template_params(
+        mechs,
+        parameters,
+        ignored_globals,
+        disable_banner,
+        default_location_order,
+        _arb_loc_desc,
+    )
 
     filenames = {
-        name: template_name + (name if name.startswith('.') else "_" + name)
-        for name in templates.keys()}
+        name: template_name + (name if name.startswith(".") else "_" + name)
+        for name in templates.keys()
+    }
 
     # postprocess template parameters for Arbor
-    channels = template_params['channels']
-    point_channels = template_params['point_channels']
-    banner = template_params['banner']
+    channels = template_params["channels"]
+    point_channels = template_params["point_channels"]
+    banner = template_params["banner"]
 
     # global_mechs refer to default density mechs/params in Arbor
     # [mech -> param] (params under mech == None)
-    global_mechs = \
-        Nrn2ArbMechGrouper.process_global(
-            template_params['global_params'])
+    global_mechs = Nrn2ArbMechGrouper.process_global(
+        template_params["global_params"]
+    )
 
     # local_mechs refer to locally painted density mechs/params in Arbor
     # [label -> mech -> param.name/.value] (params under mech == None)
-    local_mechs, additional_global_mechs = \
-        Nrn2ArbMechGrouper.process_local(
-            template_params['section_params'], channels)
+    local_mechs, additional_global_mechs = Nrn2ArbMechGrouper.process_local(
+        template_params["section_params"], channels
+    )
     for mech, params in additional_global_mechs.items():
-        global_mechs[mech] = \
-            global_mechs.get(mech, []) + params
+        global_mechs[mech] = global_mechs.get(mech, []) + params
 
     # scaled_mechs refer to iexpr params of scaled density mechs in Arbor
     # [label -> mech -> param.location/.name/.value/.value_scaler]
     range_params = {loc: [] for loc in default_location_order}
-    for param in template_params['range_params']:
+    for param in template_params["range_params"]:
         range_params[param.location].append(param)
     range_params = list(range_params.items())
 
-    local_scaled_mechs, global_scaled_mechs = \
-        Nrn2ArbMechGrouper.process_local(
-            range_params, channels)
+    local_scaled_mechs, global_scaled_mechs = Nrn2ArbMechGrouper.process_local(
+        range_params, channels
+    )
 
     # join each mech's constant params with inhomogeneous ones on mechanisms
     _arb_append_scaled_mechs(global_mechs, global_scaled_mechs)
@@ -701,12 +786,13 @@ def create_acc(mechs,
 
     # pprocess_mechs refer to locally placed mechs/params in Arbor
     # [label -> mech -> param.name/.value]
-    pprocess_mechs, global_pprocess_mechs = \
-        Nrn2ArbMechGrouper.process_local(
-            template_params['pprocess_params'], point_channels)
+    pprocess_mechs, global_pprocess_mechs = Nrn2ArbMechGrouper.process_local(
+        template_params["pprocess_params"], point_channels
+    )
     if any(len(params) > 0 for params in global_pprocess_mechs.values()):
-        raise CreateAccException('Point process mechanisms cannot be'
-                                 ' placed globally in Arbor.')
+        raise CreateAccException(
+            "Point process mechanisms cannot be" " placed globally in Arbor."
+        )
 
     # Evaluate synapse locations
     # (no new labels introduced, but locations explicitly defined)
@@ -720,36 +806,43 @@ def create_acc(mechs,
     global_mechs = nmodl_formatter.translate_density(global_mechs)
     local_mechs = {
         loc: nmodl_formatter.translate_density(mechs)
-        for loc, mechs in local_mechs.items()}
+        for loc, mechs in local_mechs.items()
+    }
     pprocess_mechs = {
         loc: nmodl_formatter.translate_points(mechs)
-        for loc, mechs in pprocess_mechs.items()}
+        for loc, mechs in pprocess_mechs.items()
+    }
 
     # get iexpr parameters of scaled density mechs
     global_scaled_mechs = _arb_project_scaled_mechs(global_mechs)
-    local_scaled_mechs = {loc: _arb_project_scaled_mechs(mechs)
-                          for loc, mechs in local_mechs.items()}
+    local_scaled_mechs = {
+        loc: _arb_project_scaled_mechs(mechs)
+        for loc, mechs in local_mechs.items()
+    }
 
     # populate label dict
-    label_dict = _arb_populate_label_dict(local_mechs,
-                                          local_scaled_mechs,
-                                          pprocess_mechs)
-
-    ret = {filenames[name]:
-           template.render(template_name=template_name,
-                           banner=banner,
-                           morphology=morphology,
-                           replace_axon=replace_axon_path,
-                           modified_morphology=modified_morphology_path,
-                           filenames=filenames,
-                           label_dict=label_dict,
-                           global_mechs=global_mechs,
-                           global_scaled_mechs=global_scaled_mechs,
-                           local_mechs=local_mechs,
-                           local_scaled_mechs=local_scaled_mechs,
-                           pprocess_mechs=pprocess_mechs,
-                           **custom_jinja_params)
-           for name, template in templates.items()}
+    label_dict = _arb_populate_label_dict(
+        local_mechs, local_scaled_mechs, pprocess_mechs
+    )
+
+    ret = {
+        filenames[name]: template.render(
+            template_name=template_name,
+            banner=banner,
+            morphology=morphology,
+            replace_axon=replace_axon_path,
+            modified_morphology=modified_morphology_path,
+            filenames=filenames,
+            label_dict=label_dict,
+            global_mechs=global_mechs,
+            global_scaled_mechs=global_scaled_mechs,
+            local_mechs=local_mechs,
+            local_scaled_mechs=local_scaled_mechs,
+            pprocess_mechs=pprocess_mechs,
+            **custom_jinja_params,
+        )
+        for name, template in templates.items()
+    }
 
     if replace_axon is not None:
         ret[replace_axon_path] = replace_axon_acc
@@ -759,12 +852,16 @@ def create_acc(mechs,
     return ret
 
 
-def write_acc(output_dir, cell, parameters,
-              template_filename='acc/*_template.jinja2',
-              ext_catalogues=None,
-              create_mod_morph=False,
-              sim=None):
-    '''Output mixed JSON/ACC format for Arbor cable cell to files
+def write_acc(
+    output_dir,
+    cell,
+    parameters,
+    template_filename="acc/*_template.jinja2",
+    ext_catalogues=None,
+    create_mod_morph=False,
+    sim=None,
+):
+    """Output mixed JSON/ACC format for Arbor cable cell to files
 
     Args:
         output_dir (str): Output directory. If not exists, will be created
@@ -777,18 +874,24 @@ def write_acc(output_dir, cell, parameters,
         create_mod_morph (str): Output ACC with axon replacement
         sim (): Neuron simulator instance (only used used with axon
         replacement if morphology has not yet been instantiated)
-    '''
-    output = cell.create_acc(parameters, template=template_filename,
-                             ext_catalogues=ext_catalogues,
-                             create_mod_morph=create_mod_morph,
-                             sim=sim)
-
-    cell_json = [comp_rendered
-                 for comp, comp_rendered in output.items()
-                 if pathlib.Path(comp).suffix == '.json']
+    """
+    output = cell.create_acc(
+        parameters,
+        template=template_filename,
+        ext_catalogues=ext_catalogues,
+        create_mod_morph=create_mod_morph,
+        sim=sim,
+    )
+
+    cell_json = [
+        comp_rendered
+        for comp, comp_rendered in output.items()
+        if pathlib.Path(comp).suffix == ".json"
+    ]
     if len(cell_json) != 1:
         raise CreateAccException(
-            'JSON file from create_acc is non-unique: %s' % cell_json)
+            "JSON file from create_acc is non-unique: %s" % cell_json
+        )
 
     cell_json = json.loads(cell_json[0])
 
@@ -799,10 +902,10 @@ def write_acc(output_dir, cell, parameters,
         comp_filename = output_dir.joinpath(comp)
         if comp_filename.exists():
             raise CreateAccException("%s already exists!" % comp_filename)
-        with open(output_dir.joinpath(comp), 'w') as f:
+        with open(output_dir.joinpath(comp), "w") as f:
             f.write(comp_rendered)
 
-    morpho_filename = output_dir.joinpath(cell_json['morphology']['original'])
+    morpho_filename = output_dir.joinpath(cell_json["morphology"]["original"])
     if morpho_filename.exists():
         raise CreateAccException("%s already exists!" % morpho_filename)
     shutil.copy2(cell.morphology.morphology_path, morpho_filename)
@@ -810,12 +913,12 @@ def write_acc(output_dir, cell, parameters,
 
 # Read the mixed JSON/ACC-output, to be moved to Arbor in future release
 def read_acc(cell_json_filename):
-    '''Return constituents to build an Arbor cable cell from create_acc-export
+    """Return constituents to build an Arbor cable cell from create_acc-export
 
     Args:
         cell_json_filename (str): The path to the JSON file containing
         meta-information on morphology, label-dict and decor of exported cell
-    '''
+    """
 
     with open(cell_json_filename) as cell_json_file:
         cell_json = json.load(cell_json_file)
@@ -823,22 +926,24 @@ def read_acc(cell_json_filename):
     cell_json_dir = pathlib.Path(cell_json_filename).parent
 
     morpho_filename = cell_json_dir.joinpath(
-        cell_json['morphology']['original'])
-    replace_axon = cell_json['morphology'].get('replace_axon', None)
+        cell_json["morphology"]["original"]
+    )
+    replace_axon = cell_json["morphology"].get("replace_axon", None)
     if replace_axon is not None:
         replace_axon = cell_json_dir.joinpath(replace_axon)
     morpho = ArbFileMorphology.load(morpho_filename, replace_axon)
 
     decor = arbor.load_component(
-        cell_json_dir.joinpath(cell_json['decor'])).component
+        cell_json_dir.joinpath(cell_json["decor"])
+    ).component
     labels = arbor.load_component(
-        cell_json_dir.joinpath(cell_json['label_dict'])).component
+        cell_json_dir.joinpath(cell_json["label_dict"])
+    ).component
 
     return cell_json, morpho, decor, labels
 
 
 class CreateAccException(Exception):
-
     """Exceptions generated by create_acc module"""
 
     def __init__(self, message):
diff --git a/bluepyopt/ephys/simulators.py b/bluepyopt/ephys/simulators.py
index 71790bc8..de546633 100644
--- a/bluepyopt/ephys/simulators.py
+++ b/bluepyopt/ephys/simulators.py
@@ -2,26 +2,30 @@
 
 # pylint: disable=W0511
 
-import os
-import logging
-import imp
 import ctypes
+import importlib.util
+import logging
+import os
+import pathlib
 import platform
 import warnings
-import pathlib
 
 from bluepyopt.ephys.acc import arbor
 
-
 logger = logging.getLogger(__name__)
 
 
 class NrnSimulator(object):
-
     """Neuron simulator"""
 
-    def __init__(self, dt=None, cvode_active=True, cvode_minstep=None,
-                 random123_globalindex=None, mechanisms_directory=None):
+    def __init__(
+        self,
+        dt=None,
+        cvode_active=True,
+        cvode_minstep=None,
+        random123_globalindex=None,
+        mechanisms_directory=None,
+    ):
         """Constructor
 
         Args:
@@ -41,7 +45,7 @@ def __init__(self, dt=None, cvode_active=True, cvode_minstep=None,
         # hoc.so does not exist on NEURON Windows or MacOS
         # although \\hoc.pyd can work here, it gives an error for
         # nrn_nobanner_ line
-        self.disable_banner = platform.system() not in ['Windows', 'Darwin']
+        self.disable_banner = platform.system() not in ["Windows", "Darwin"]
         self.banner_disabled = False
         self.mechanisms_directory = mechanisms_directory
 
@@ -77,18 +81,21 @@ def cvode_minstep(self, value):
     def _nrn_disable_banner():
         """Disable Neuron banner"""
 
-        nrnpy_path = os.path.join(imp.find_module('neuron')[1])
-        import glob
-        hoc_so_list = \
-            glob.glob(os.path.join(nrnpy_path, 'hoc*.so'))
+        nrnpy_path = pathlib.Path(
+            importlib.util.find_spec("neuron").origin
+        ).parent
+
+        hoc_so_list = list(nrnpy_path.glob("hoc*.so"))
 
         if len(hoc_so_list) != 1:
-            warnings.warn('Unable to find Neuron hoc shared library in %s, '
-                          'not disabling banner' % nrnpy_path)
+            warnings.warn(
+                "Unable to find Neuron hoc shared library in %s, "
+                "not disabling banner" % nrnpy_path
+            )
         else:
             hoc_so = hoc_so_list[0]
-            nrndll = ctypes.cdll[hoc_so]
-            ctypes.c_int.in_dll(nrndll, 'nrn_nobanner_').value = 1
+            nrndll = ctypes.cdll[str(hoc_so)]
+            ctypes.c_int.in_dll(nrndll, "nrn_nobanner_").value = 1
 
     # pylint: disable=R0201
     @property
@@ -110,24 +117,26 @@ def neuron(self):
 
     def initialize(self):
         """Initialize simulator: Set Neuron variables"""
-        self.neuron.h.load_file('stdrun.hoc')
+        self.neuron.h.load_file("stdrun.hoc")
         self.neuron.h.dt = self.dt
         self.neuron.h.cvode_active(1 if self.cvode_active else 0)
 
     def run(
-            self,
-            tstop=None,
-            dt=None,
-            cvode_active=None,
-            random123_globalindex=None):
+        self,
+        tstop=None,
+        dt=None,
+        cvode_active=None,
+        random123_globalindex=None,
+    ):
         """Run protocol"""
 
         self.neuron.h.tstop = tstop
 
         if cvode_active and dt is not None:
             raise ValueError(
-                'NrnSimulator: Impossible to combine the dt argument when '
-                'cvode_active is True in the NrnSimulator run method')
+                "NrnSimulator: Impossible to combine the dt argument when "
+                "cvode_active is True in the NrnSimulator run method"
+            )
 
         if cvode_active is None:
             cvode_active = self.cvode_active
@@ -135,11 +144,12 @@ def run(
         if not cvode_active and dt is None:  # use dt of simulator
             if self.neuron.h.dt != self.dt:
                 raise Exception(
-                    'NrnSimulator: Some process has changed the '
-                    'time step dt of Neuron since the creation of this '
-                    'NrnSimulator object. Not sure this is intended:\n'
-                    'current dt: %.6g\n'
-                    'init dt: %.6g' % (self.neuron.h.dt, self.dt))
+                    "NrnSimulator: Some process has changed the "
+                    "time step dt of Neuron since the creation of this "
+                    "NrnSimulator object. Not sure this is intended:\n"
+                    "current dt: %.6g\n"
+                    "init dt: %.6g" % (self.neuron.h.dt, self.dt)
+                )
             dt = self.dt
 
         self.neuron.h.cvode_active(1 if cvode_active else 0)
@@ -148,14 +158,13 @@ def run(
             self.cvode_minstep = self.cvode_minstep_value
 
         if cvode_active:
-            logger.debug('Running Neuron simulator %.6g ms, with cvode', tstop)
+            logger.debug("Running Neuron simulator %.6g ms, with cvode", tstop)
         else:
             self.neuron.h.dt = dt
             self.neuron.h.steps_per_ms = 1.0 / dt
             logger.debug(
-                'Running Neuron simulator %.6g ms, with dt=%r',
-                tstop,
-                dt)
+                "Running Neuron simulator %.6g ms, with dt=%r", tstop, dt
+            )
 
         if random123_globalindex is None:
             random123_globalindex = self.random123_globalindex
@@ -167,16 +176,15 @@ def run(
         try:
             self.neuron.h.run()
         except Exception as e:
-            raise NrnSimulatorException('Neuron simulator error', e)
+            raise NrnSimulatorException("Neuron simulator error", e)
 
         if self.cvode_minstep_value is not None:
             self.cvode_minstep = save_minstep
 
-        logger.debug('Neuron simulation finished')
+        logger.debug("Neuron simulation finished")
 
 
 class NrnSimulatorException(Exception):
-
     """All exception generated by Neuron simulator"""
 
     def __init__(self, message, original):
@@ -187,11 +195,16 @@ def __init__(self, message, original):
 
 
 class LFPySimulator(NrnSimulator):
-
     """LFPy simulator"""
 
-    def __init__(self, dt=None, cvode_active=True, cvode_minstep=None,
-                 random123_globalindex=None, mechanisms_directory=None):
+    def __init__(
+        self,
+        dt=None,
+        cvode_active=True,
+        cvode_minstep=None,
+        random123_globalindex=None,
+        mechanisms_directory=None,
+    ):
         """Constructor
 
         Args:
@@ -213,17 +226,18 @@ def __init__(self, dt=None, cvode_active=True, cvode_minstep=None,
             cvode_active=cvode_active,
             cvode_minstep=cvode_minstep,
             random123_globalindex=random123_globalindex,
-            mechanisms_directory=mechanisms_directory
+            mechanisms_directory=mechanisms_directory,
         )
 
     def run(
-            self,
-            lfpy_cell,
-            lfpy_electrode,
-            tstop=None,
-            dt=None,
-            cvode_active=None,
-            random123_globalindex=None):
+        self,
+        lfpy_cell,
+        lfpy_electrode,
+        tstop=None,
+        dt=None,
+        cvode_active=None,
+        random123_globalindex=None,
+    ):
         """Run protocol"""
         _ = self.neuron
 
@@ -235,8 +249,9 @@ def run(
 
         if cvode_active and dt is not None:
             raise ValueError(
-                'NrnSimulator: Impossible to combine the dt argument when '
-                'cvode_active is True in the NrnSimulator run method')
+                "NrnSimulator: Impossible to combine the dt argument when "
+                "cvode_active is True in the NrnSimulator run method"
+            )
 
         if cvode_active is None:
             cvode_active = self.cvode_active
@@ -276,7 +291,6 @@ def run(
 
 
 class LFPySimulatorException(Exception):
-
     """All exception generated by LFPy simulator"""
 
     def __init__(self, message, original):
@@ -287,7 +301,6 @@ def __init__(self, message, original):
 
 
 class ArbSimulator(object):
-
     """Arbor simulator"""
 
     def __init__(self, dt=None, ext_catalogues=None):
@@ -303,14 +316,15 @@ def __init__(self, dt=None, ext_catalogues=None):
         self.ext_catalogues = ext_catalogues
         if ext_catalogues is not None:
             for cat, cat_path in ext_catalogues.items():
-                cat_lib = '%s-catalogue.so' % cat
+                cat_lib = "%s-catalogue.so" % cat
                 cat_path = pathlib.Path(cat_path).resolve()
                 if not os.path.exists(cat_path / cat_lib):
                     raise ArbSimulatorException(
-                        'Cannot find %s at %s - first build' % (cat_lib,
-                                                                cat_path) +
-                        ' mechanism catalogue with modcc:' +
-                        ' arbor-build-catalogue %s %s' % (cat, cat_path))
+                        "Cannot find %s at %s - first build"
+                        % (cat_lib, cat_path)
+                        + " mechanism catalogue with modcc:"
+                        + " arbor-build-catalogue %s %s" % (cat, cat_path)
+                    )
         # TODO: add parameters for discretization
 
     def initialize(self):
@@ -318,9 +332,9 @@ def initialize(self):
         pass
 
     def instantiate(self, morph, decor, labels):
-        cable_cell = arbor.cable_cell(morphology=morph,
-                                      decor=decor,
-                                      labels=labels)
+        cable_cell = arbor.cable_cell(
+            morphology=morph, decor=decor, labels=labels
+        )
 
         arb_cell_model = arbor.single_cell_model(cable_cell)
 
@@ -330,35 +344,31 @@ def instantiate(self, morph, decor, labels):
         # User-supplied catalogues take precedence
         if self.ext_catalogues is not None:
             for cat, cat_path in self.ext_catalogues.items():
-                cat_lib = '%s-catalogue.so' % cat
+                cat_lib = "%s-catalogue.so" % cat
                 cat_path = pathlib.Path(cat_path).resolve()
                 arb_cell_model.properties.catalogue.extend(
-                    arbor.load_catalogue(cat_path / cat_lib),
-                    cat + "::")
+                    arbor.load_catalogue(cat_path / cat_lib), cat + "::"
+                )
 
         # Built-in catalogues are always added (could be made optional)
-        if self.ext_catalogues is None or \
-                'default' not in self.ext_catalogues:
+        if self.ext_catalogues is None or "default" not in self.ext_catalogues:
             arb_cell_model.properties.catalogue.extend(
-                arbor.default_catalogue(), "default::")
+                arbor.default_catalogue(), "default::"
+            )
 
-        if self.ext_catalogues is None or \
-                'BBP' not in self.ext_catalogues:
+        if self.ext_catalogues is None or "BBP" not in self.ext_catalogues:
             arb_cell_model.properties.catalogue.extend(
-                arbor.bbp_catalogue(), "BBP::")
+                arbor.bbp_catalogue(), "BBP::"
+            )
 
-        if self.ext_catalogues is None or \
-                'allen' not in self.ext_catalogues:
+        if self.ext_catalogues is None or "allen" not in self.ext_catalogues:
             arb_cell_model.properties.catalogue.extend(
-                arbor.allen_catalogue(), "allen::")
+                arbor.allen_catalogue(), "allen::"
+            )
 
         return arb_cell_model
 
-    def run(self,
-            arb_cell_model,
-            tstop=None,
-            dt=None):
-
+    def run(self, arb_cell_model, tstop=None, dt=None):
         dt = dt if dt is not None else self.dt
 
         if dt is not None:
@@ -368,7 +378,6 @@ def run(self,
 
 
 class ArbSimulatorException(Exception):
-
     """All exception generated by Arbor simulator"""
 
     def __init__(self, message):
diff --git a/bluepyopt/tests/test_ephys/test_create_acc.py b/bluepyopt/tests/test_ephys/test_create_acc.py
index 649b0af5..baae6def 100644
--- a/bluepyopt/tests/test_ephys/test_create_acc.py
+++ b/bluepyopt/tests/test_ephys/test_create_acc.py
@@ -2,46 +2,47 @@
 
 # pylint: disable=W0212
 
+import json
 import os
-import sys
 import pathlib
 import re
-import json
+import sys
 import tempfile
 
-from bluepyopt.ephys.acc import arbor, ArbLabel
-from bluepyopt.ephys.morphologies import ArbFileMorphology
-from bluepyopt.ephys.parameterscalers import NrnSegmentSomaDistanceScaler
-
-from . import utils
+import pytest
 
 from bluepyopt import ephys
 from bluepyopt.ephys import create_acc
-from bluepyopt.ephys.create_acc import (Nrn2ArbParamAdapter,
-                                        Nrn2ArbMechGrouper,
-                                        ArbNmodlMechFormatter)
+from bluepyopt.ephys.acc import ArbLabel, arbor
+from bluepyopt.ephys.create_acc import (
+    ArbNmodlMechFormatter,
+    Nrn2ArbMechGrouper,
+    Nrn2ArbParamAdapter,
+)
+from bluepyopt.ephys.morphologies import ArbFileMorphology
+from bluepyopt.ephys.parameterscalers import NrnSegmentSomaDistanceScaler
 
-import pytest
+from . import utils
 
 DEFAULT_ARBOR_REGION_ORDER = [
-    ('soma', 1),
-    ('axon', 2),
-    ('dend', 3),
-    ('apic', 4),
-    ('myelin', 5)]
+    ("soma", 1),
+    ("axon", 2),
+    ("dend", 3),
+    ("apic", 4),
+    ("myelin", 5),
+]
 
 
-testdata_dir = pathlib.Path(__file__).parent.joinpath(
-    'testdata')
+testdata_dir = pathlib.Path(__file__).parent.joinpath("testdata")
 
 
 @pytest.mark.unit
 def test_read_templates():
     """Unit test for _read_templates function."""
-    template_dir = testdata_dir / 'acc/templates'
+    template_dir = testdata_dir / "acc/templates"
     template_filename = "*_template.jinja2"
     templates = create_acc._read_templates(template_dir, template_filename)
-    assert templates.keys() == {'label_dict.acc', 'cell.json', 'decor.acc'}
+    assert templates.keys() == {"label_dict.acc", "cell.json", "decor.acc"}
 
     with pytest.raises(FileNotFoundError):
         create_acc._read_templates("DOES_NOT_EXIST", template_filename)
@@ -52,13 +53,14 @@ def test_Nrn2ArbParamAdapter_param_name():
     """Test Neuron to Arbor parameter mapping."""
     # Identity
     mech_param_name = "gSKv3_1bar_SKv3_1"
-    assert Nrn2ArbParamAdapter._param_name(mech_param_name) \
-        == mech_param_name
+    assert Nrn2ArbParamAdapter._param_name(mech_param_name) == mech_param_name
 
     # Non-trivial transformation
     global_property_name = "v_init"
-    assert Nrn2ArbParamAdapter._param_name(global_property_name) \
+    assert (
+        Nrn2ArbParamAdapter._param_name(global_property_name)
         == "membrane-potential"
+    )
 
 
 @pytest.mark.unit
@@ -75,7 +77,8 @@ def test_Nrn2ArbParamAdapter_param_value():
     # Non-trivial name and value/units transformation
     global_property = create_acc.Location(name="celsius", value=34)
     assert Nrn2ArbParamAdapter._param_value(global_property) == (
-        "307.14999999999998")
+        "307.14999999999998"
+    )
 
 
 @pytest.mark.unit
@@ -85,38 +88,39 @@ def test_Nrn2ArbParamAdapter_format():
     mech_param = create_acc.Location(name="gSKv3_1bar_SKv3_1", value="1.025")
     mech = "SKv3_1"
     arb_mech_param = create_acc.Location(name="gSKv3_1bar", value="1.025")
-    assert (
-        Nrn2ArbParamAdapter.format(
-            mech_param, mechs=[mech])
-        == (mech, arb_mech_param)
+    assert Nrn2ArbParamAdapter.format(mech_param, mechs=[mech]) == (
+        mech,
+        arb_mech_param,
     )
 
     # Non-unique mapping to mechanisms
     with pytest.raises(create_acc.CreateAccException):
-        Nrn2ArbParamAdapter.format(
-            mech_param, mechs=["SKv3_1", "1"])
+        Nrn2ArbParamAdapter.format(mech_param, mechs=["SKv3_1", "1"])
 
     # Global property with non-trivial transformation
     global_property = create_acc.Location(name="celsius", value="0")
     mech = None
     arb_global_property = create_acc.Location(
-        name="temperature-kelvin", value="273.14999999999998")
+        name="temperature-kelvin", value="273.14999999999998"
+    )
     # Non-trivial name and value/units transformation
-    assert Nrn2ArbParamAdapter.format(global_property, []) == \
-        (mech, arb_global_property)
+    assert Nrn2ArbParamAdapter.format(global_property, []) == (
+        mech,
+        arb_global_property,
+    )
 
     # Inhomogeneuos mechanism parameter
     apical_region = ArbLabel("region", "apic", "(tag 4)")
     param_scaler = NrnSegmentSomaDistanceScaler(
-        name='soma-distance-scaler',
-        distribution='(-0.8696 + 2.087*math.exp(({distance})*0.0031))*{value}'
+        name="soma-distance-scaler",
+        distribution="(-0.8696 + 2.087*math.exp(({distance})*0.0031))*{value}",
     )
 
     iexpr_param = create_acc.RangeExpr(
         location=apical_region,
         name="gkbar_hh",
         value="0.025",
-        value_scaler=param_scaler
+        value_scaler=param_scaler,
     )
     mech = "hh"
     arb_iexpr_param = create_acc.RangeExpr(
@@ -125,50 +129,56 @@ def test_Nrn2ArbParamAdapter_format():
         value="0.025",
         value_scaler=param_scaler,
     )
-    assert (
-        Nrn2ArbParamAdapter.format(
-            iexpr_param, mechs=[mech])
-        == (mech, arb_iexpr_param)
+    assert Nrn2ArbParamAdapter.format(iexpr_param, mechs=[mech]) == (
+        mech,
+        arb_iexpr_param,
     )
 
     # Point process mechanism parameter
     loc = ephys.locations.ArbLocsetLocation(
-        name='somacenter',
-        locset='(location 0 0.5)')
+        name="somacenter", locset="(location 0 0.5)"
+    )
 
     mech = ephys.mechanisms.NrnMODPointProcessMechanism(
-        name='expsyn',
-        suffix='ExpSyn',
-        locations=[loc])
+        name="expsyn", suffix="ExpSyn", locations=[loc]
+    )
 
     mech_loc = ephys.locations.NrnPointProcessLocation(
-        'expsyn_loc',
-        pprocess_mech=mech)
+        "expsyn_loc", pprocess_mech=mech
+    )
 
     point_expr_param = create_acc.PointExpr(
-        name="tau", value="10", point_loc=[mech_loc])
+        name="tau", value="10", point_loc=[mech_loc]
+    )
 
     arb_point_expr_param = create_acc.PointExpr(
-        name="tau", value="10", point_loc=[mech_loc])
-    assert (
-        Nrn2ArbParamAdapter.format(
-            point_expr_param, mechs=[mech])
-        == (mech, arb_point_expr_param)
+        name="tau", value="10", point_loc=[mech_loc]
+    )
+    assert Nrn2ArbParamAdapter.format(point_expr_param, mechs=[mech]) == (
+        mech,
+        arb_point_expr_param,
     )
 
 
 @pytest.mark.unit
 def test_Nrn2ArbMechGrouper_format_params_and_group_by_mech():
     """Test grouping of parameters by mechanism."""
-    params = [create_acc.Location(name="gSKv3_1bar_SKv3_1", value="1.025"),
-              create_acc.Location(name="ena", value="-30")]
+    params = [
+        create_acc.Location(name="gSKv3_1bar_SKv3_1", value="1.025"),
+        create_acc.Location(name="ena", value="-30"),
+    ]
     mechs = ["SKv3_1"]
-    local_mechs = Nrn2ArbMechGrouper.\
-        _format_params_and_group_by_mech(params, mechs)
-    assert local_mechs == \
-        {None: [create_acc.Location(name="ion-reversal-potential \"na\"",
-                                    value="-30")],
-         "SKv3_1": [create_acc.Location(name="gSKv3_1bar", value="1.025")]}
+    local_mechs = Nrn2ArbMechGrouper._format_params_and_group_by_mech(
+        params, mechs
+    )
+    assert local_mechs == {
+        None: [
+            create_acc.Location(
+                name='ion-reversal-potential "na"', value="-30"
+            )
+        ],
+        "SKv3_1": [create_acc.Location(name="gSKv3_1bar", value="1.025")],
+    }
 
 
 @pytest.mark.unit
@@ -177,10 +187,13 @@ def test_Nrn2ArbMechGrouper_process_global():
     params = {"ki": 3, "v_init": -65}
     global_mechs = Nrn2ArbMechGrouper.process_global(params)
     assert global_mechs == {
-        None: [create_acc.Location(name="ion-internal-concentration \"k\"",
-                                   value="3"),
-               create_acc.Location(name="membrane-potential",
-                                   value="-65")]}
+        None: [
+            create_acc.Location(
+                name='ion-internal-concentration "k"', value="3"
+            ),
+            create_acc.Location(name="membrane-potential", value="-65"),
+        ]
+    }
 
 
 @pytest.mark.unit
@@ -188,22 +201,23 @@ def test_Nrn2ArbMechGrouper_is_global_property():
     """Test adapting local parameters from Neuron to Arbor."""
     all_regions = ArbLabel("region", "all_regions", "(all)")
     param = create_acc.Location(name="axial-resistivity", value="1")
-    assert Nrn2ArbMechGrouper._is_global_property(
-        all_regions, param) is True
+    assert Nrn2ArbMechGrouper._is_global_property(all_regions, param) is True
 
     soma_region = ArbLabel("region", "soma", "(tag 1)")
-    assert Nrn2ArbMechGrouper._is_global_property(
-        soma_region, param) is False
+    assert Nrn2ArbMechGrouper._is_global_property(soma_region, param) is False
 
 
 @pytest.mark.unit
 def test_separate_global_properties():
     """Test separating global properties from label-specific mechs."""
     all_regions = ArbLabel("region", "all_regions", "(all)")
-    mechs = {None: [create_acc.Location(name="axial-resistivity", value="1")],
-             "SKv3_1": [create_acc.Location(name="gSKv3_1bar", value="1.025")]}
-    local_mechs, global_properties = \
+    mechs = {
+        None: [create_acc.Location(name="axial-resistivity", value="1")],
+        "SKv3_1": [create_acc.Location(name="gSKv3_1bar", value="1.025")],
+    }
+    local_mechs, global_properties = (
         Nrn2ArbMechGrouper._separate_global_properties(all_regions, mechs)
+    )
     assert local_mechs == {None: [], "SKv3_1": mechs["SKv3_1"]}
     assert global_properties == {None: mechs[None]}
 
@@ -214,23 +228,28 @@ def test_Nrn2ArbMechGrouper_process_local():
     all_regions = ArbLabel("region", "all_regions", "(all)")
     soma_region = ArbLabel("region", "soma", "(tag 1)")
     params = [
-        (all_regions,
-         [create_acc.Location(name="cm", value="100")]),
-        (soma_region,
-         [create_acc.Location(name="v_init", value="-65"),
-          create_acc.Location(name="gSKv3_1bar_SKv3_1", value="1.025")])
+        (all_regions, [create_acc.Location(name="cm", value="100")]),
+        (
+            soma_region,
+            [
+                create_acc.Location(name="v_init", value="-65"),
+                create_acc.Location(name="gSKv3_1bar_SKv3_1", value="1.025"),
+            ],
+        ),
     ]
     channels = {all_regions: [], soma_region: ["SKv3_1"]}
-    local_mechs, global_properties = \
-        Nrn2ArbMechGrouper.process_local(params, channels)
+    local_mechs, global_properties = Nrn2ArbMechGrouper.process_local(
+        params, channels
+    )
     assert local_mechs.keys() == {all_regions, soma_region}
     assert local_mechs[all_regions] == {None: []}
     assert local_mechs[soma_region] == {
         None: [create_acc.Location(name="membrane-potential", value="-65")],
-        "SKv3_1": [create_acc.Location(name="gSKv3_1bar", value="1.025")]
+        "SKv3_1": [create_acc.Location(name="gSKv3_1bar", value="1.025")],
     }
     assert global_properties == {
-        None: [create_acc.Location(name="membrane-capacitance", value="1")]}
+        None: [create_acc.Location(name="membrane-capacitance", value="1")]
+    }
 
 
 @pytest.mark.unit
@@ -239,8 +258,8 @@ def test_ArbNmodlMechFormatter_load_mech_catalogue_meta():
     nmodl_formatter = ArbNmodlMechFormatter(None)
 
     assert isinstance(nmodl_formatter.cats, dict)
-    assert nmodl_formatter.cats.keys() == {'BBP', 'default', 'allen'}
-    assert "Ca_HVA" in nmodl_formatter.cats['BBP']
+    assert nmodl_formatter.cats.keys() == {"BBP", "default", "allen"}
+    assert "Ca_HVA" in nmodl_formatter.cats["BBP"]
 
 
 @pytest.mark.unit
@@ -261,7 +280,7 @@ def test_ArbNmodlMechFormatter_translate_density():
                 value="0.029999999999999999",
                 scale=(
                     "(add (scalar -0.62109375) (mul (scalar 0.546875) "
-                    "(log (add (mul (distance (region \"soma\"))"
+                    '(log (add (mul (distance (region "soma"))'
                     " (scalar 0.421875) ) (scalar 1.25) ) ) ) )"
                 ),
             ),
@@ -273,7 +292,7 @@ def test_ArbNmodlMechFormatter_translate_density():
                 value="0.029999999999999999",
                 scale=(
                     "(add (scalar -0.62109375) (mul (scalar 0.546875) "
-                    "(log (add (mul (distance (region \"soma\"))"
+                    '(log (add (mul (distance (region "soma"))'
                     " (scalar 0.421875) ) (scalar 1.25) ) ) ) )"
                 ),
             ),
@@ -281,8 +300,7 @@ def test_ArbNmodlMechFormatter_translate_density():
     }
     nmodl_formatter = ArbNmodlMechFormatter(None)
     translated_mechs = nmodl_formatter.translate_density(mechs)
-    assert translated_mechs.keys() == {"default::hh",
-                                       "default::pas/e=0.25"}
+    assert translated_mechs.keys() == {"default::hh", "default::pas/e=0.25"}
     assert translated_mechs["default::hh"] == mechs["hh"]
     assert translated_mechs["default::pas/e=0.25"] == mechs["pas"][1:]
 
@@ -291,21 +309,21 @@ def test_ArbNmodlMechFormatter_translate_density():
 def test_arb_populate_label_dict():
     """Unit test for _populate_label_dict."""
     local_mechs = {ArbLabel("region", "all", "(all)"): {}}
-    local_scaled_mechs = {
-        ArbLabel("region", "first_branch", "(branch 0)"): {}}
+    local_scaled_mechs = {ArbLabel("region", "first_branch", "(branch 0)"): {}}
     pprocess_mechs = {}
 
-    label_dict = create_acc._arb_populate_label_dict(local_mechs,
-                                                     local_scaled_mechs,
-                                                     pprocess_mechs)
+    label_dict = create_acc._arb_populate_label_dict(
+        local_mechs, local_scaled_mechs, pprocess_mechs
+    )
     assert label_dict.keys() == {"all", "first_branch"}
 
     with pytest.raises(create_acc.CreateAccException):
         other_pprocess_mechs = {
-            ArbLabel("region", "first_branch", "(branch 1)"): {}}
-        create_acc._arb_populate_label_dict(local_mechs,
-                                            local_scaled_mechs,
-                                            other_pprocess_mechs)
+            ArbLabel("region", "first_branch", "(branch 1)"): {}
+        }
+        create_acc._arb_populate_label_dict(
+            local_mechs, local_scaled_mechs, other_pprocess_mechs
+        )
 
 
 @pytest.mark.unit
@@ -314,11 +332,16 @@ def test_create_acc():
     mech = utils.make_mech()
     parameters = utils.make_parameters()
 
-    acc = create_acc.create_acc([mech, ], parameters,
-                                morphology='CCell.swc',
-                                template_name='CCell')
+    acc = create_acc.create_acc(
+        [
+            mech,
+        ],
+        parameters,
+        morphology="CCell.swc",
+        template_name="CCell",
+    )
 
-    ref_dir = testdata_dir / 'acc/CCell'
+    ref_dir = testdata_dir / "acc/CCell"
     cell_json = "CCell.json"
     decor_acc = "CCell_decor.acc"
     label_dict_acc = "CCell_label_dict.acc"
@@ -326,22 +349,22 @@ def test_create_acc():
     # Testing keys
     assert cell_json in acc
     cell_json_dict = json.loads(acc[cell_json])
-    assert 'cell_model_name' in cell_json_dict
-    assert 'produced_by' in cell_json_dict
-    assert 'morphology' in cell_json_dict
-    assert 'label_dict' in cell_json_dict
-    assert 'decor' in cell_json_dict
+    assert "cell_model_name" in cell_json_dict
+    assert "produced_by" in cell_json_dict
+    assert "morphology" in cell_json_dict
+    assert "label_dict" in cell_json_dict
+    assert "decor" in cell_json_dict
     # Testing values
     with open(ref_dir / cell_json) as f:
         ref_cell_json = json.load(f)
     for k in ref_cell_json:
-        if k != 'produced_by':
+        if k != "produced_by":
             assert ref_cell_json[k] == cell_json_dict[k]
 
     # Testing building blocks
     assert decor_acc in acc
-    assert acc[decor_acc].startswith('(arbor-component')
-    assert '(decor' in acc[decor_acc]
+    assert acc[decor_acc].startswith("(arbor-component")
+    assert "(decor" in acc[decor_acc]
     # Testing values
     with open(ref_dir / decor_acc) as f:
         ref_decor = f.read()
@@ -349,19 +372,20 @@ def test_create_acc():
 
     # Testing building blocks
     assert label_dict_acc in acc
-    assert acc[label_dict_acc].startswith('(arbor-component')
-    assert '(label-dict' in acc[label_dict_acc]
-    matches = re.findall(r'\(region-def "(?P<loc>\w+)" \(tag (?P<tag>\d+)\)\)',
-                         acc[label_dict_acc])
+    assert acc[label_dict_acc].startswith("(arbor-component")
+    assert "(label-dict" in acc[label_dict_acc]
+    matches = re.findall(
+        r'\(region-def "(?P<loc>\w+)" \(tag (?P<tag>\d+)\)\)',
+        acc[label_dict_acc],
+    )
     for pos, loc_tag in enumerate(DEFAULT_ARBOR_REGION_ORDER):
         assert matches[pos][0] == loc_tag[0]
         assert matches[pos][1] == str(loc_tag[1])
     # Testing values
-    ref_labels = arbor.load_component(
-        ref_dir / label_dict_acc).component
+    ref_labels = arbor.load_component(ref_dir / label_dict_acc).component
     with tempfile.TemporaryDirectory() as test_dir:
         test_labels_filename = pathlib.Path(test_dir).joinpath(label_dict_acc)
-        with open(test_labels_filename, 'w') as f:
+        with open(test_labels_filename, "w") as f:
             f.write(acc[label_dict_acc])
         test_labels = arbor.load_component(test_labels_filename).component
     assert dict(ref_labels.items()) == dict(test_labels.items())
@@ -375,41 +399,46 @@ def test_create_acc_filename():
     custom_param_val = str(__file__)
 
     acc = create_acc.create_acc(
-        [mech, ],
-        parameters, morphology='CCell.asc',
-        template_name='CCell',
-        template_filename='acc/templates/*_template.jinja2',
+        [
+            mech,
+        ],
+        parameters,
+        morphology="CCell.asc",
+        template_name="CCell",
+        template_filename="acc/templates/*_template.jinja2",
         template_dir=testdata_dir,
-        custom_jinja_params={
-            'custom_param': custom_param_val})
+        custom_jinja_params={"custom_param": custom_param_val},
+    )
     cell_json = "CCell_cell.json"
     decor_acc = "CCell_decor.acc"
     label_dict_acc = "CCell_label_dict.acc"
 
     assert cell_json in acc
     cell_json_dict = json.loads(acc[cell_json])
-    assert 'cell_model_name' in cell_json_dict
-    assert 'produced_by' in cell_json_dict
-    assert 'morphology' in cell_json_dict
-    assert 'label_dict' in cell_json_dict
-    assert 'decor' in cell_json_dict
+    assert "cell_model_name" in cell_json_dict
+    assert "produced_by" in cell_json_dict
+    assert "morphology" in cell_json_dict
+    assert "label_dict" in cell_json_dict
+    assert "decor" in cell_json_dict
 
     assert decor_acc in acc
-    assert acc[decor_acc].startswith('(arbor-component')
-    assert '(decor' in acc[decor_acc]
+    assert acc[decor_acc].startswith("(arbor-component")
+    assert "(decor" in acc[decor_acc]
 
     assert label_dict_acc in acc
-    assert acc[label_dict_acc].startswith('(arbor-component')
-    assert '(label-dict' in acc[label_dict_acc]
-    matches = re.findall(r'\(region-def "(?P<loc>\w+)" \(tag (?P<tag>\d+)\)\)',
-                         acc[label_dict_acc])
+    assert acc[label_dict_acc].startswith("(arbor-component")
+    assert "(label-dict" in acc[label_dict_acc]
+    matches = re.findall(
+        r'\(region-def "(?P<loc>\w+)" \(tag (?P<tag>\d+)\)\)',
+        acc[label_dict_acc],
+    )
     for pos, loc_tag in enumerate(DEFAULT_ARBOR_REGION_ORDER):
         assert matches[pos][0] == loc_tag[0]
         assert matches[pos][1] == str(loc_tag[1])
 
     assert '(meta-data (info "test-decor"))' in acc[decor_acc]
     assert '(meta-data (info "test-label-dict"))' in acc[label_dict_acc]
-    assert custom_param_val in cell_json_dict['produced_by']
+    assert custom_param_val in cell_json_dict["produced_by"]
 
 
 @pytest.mark.unit
@@ -426,60 +455,76 @@ def test_create_acc_replace_axon():
             latest_seg,
             arbor.mpoint(prox_x, 0, 0, 0.5),
             arbor.mpoint(dist_x, 0, 0, 0.5),
-            ArbFileMorphology.tags['axon']
+            ArbFileMorphology.tags["axon"],
         )
 
     replace_axon = arbor.morphology(replace_axon_st)
 
     try:
-        acc = create_acc.create_acc([mech, ], parameters,
-                                    morphology_dir=testdata_dir,
-                                    morphology='simple.swc',
-                                    template_name='CCell',
-                                    replace_axon=replace_axon)
+        acc = create_acc.create_acc(
+            [
+                mech,
+            ],
+            parameters,
+            morphology_dir=testdata_dir,
+            morphology="simple.swc",
+            template_name="CCell",
+            replace_axon=replace_axon,
+        )
     except Exception as e:  # fail with an older Arbor version
         assert isinstance(e, NotImplementedError)
-        assert len(e.args) == 1 and e.args[0] == \
-            "Need a newer version of Arbor for axon replacement."
+        assert (
+            len(e.args) == 1
+            and e.args[0]
+            == "Need a newer version of Arbor for axon replacement."
+        )
         return
 
     cell_json = "CCell.json"
     cell_json_dict = json.loads(acc[cell_json])
-    assert 'replace_axon' in cell_json_dict['morphology']
+    assert "replace_axon" in cell_json_dict["morphology"]
 
-    with open(testdata_dir / 'acc/CCell/simple_axon_replacement.acc') as f:
+    with open(testdata_dir / "acc/CCell/simple_axon_replacement.acc") as f:
         replace_axon_ref = f.read()
 
-    assert acc[cell_json_dict['morphology']['replace_axon']] == \
-        replace_axon_ref
+    assert (
+        acc[cell_json_dict["morphology"]["replace_axon"]] == replace_axon_ref
+    )
 
 
 def make_cell(replace_axon):
-    morph_filename = testdata_dir / 'simple_ax2.swc'
-    morph = ephys.morphologies.NrnFileMorphology(morph_filename,
-                                                 do_replace_axon=replace_axon)
+    morph_filename = testdata_dir / "simple_ax2.swc"
+    morph = ephys.morphologies.NrnFileMorphology(
+        morph_filename, do_replace_axon=replace_axon
+    )
     somatic_loc = ephys.locations.NrnSeclistLocation(
-        'somatic', seclist_name='somatic')
-    mechs = [ephys.mechanisms.NrnMODMechanism(
-        name='hh', suffix='hh', locations=[somatic_loc])]
-    gkbar_hh_scaler = '(-0.62109375 + 0.546875*math.log(' \
-                      '({distance})*0.421875 + 1.25))*{value}'
+        "somatic", seclist_name="somatic"
+    )
+    mechs = [
+        ephys.mechanisms.NrnMODMechanism(
+            name="hh", suffix="hh", locations=[somatic_loc]
+        )
+    ]
+    gkbar_hh_scaler = (
+        "(-0.62109375 + 0.546875*math.log("
+        "({distance})*0.421875 + 1.25))*{value}"
+    )
     params = [
         ephys.parameters.NrnSectionParameter(
-            name='gnabar_hh',
-            param_name='gnabar_hh',
-            locations=[somatic_loc]),
+            name="gnabar_hh", param_name="gnabar_hh", locations=[somatic_loc]
+        ),
         ephys.parameters.NrnRangeParameter(
-            name='gkbar_hh',
-            param_name='gkbar_hh',
+            name="gkbar_hh",
+            param_name="gkbar_hh",
             value_scaler=ephys.parameterscalers.NrnSegmentSomaDistanceScaler(
-                distribution=gkbar_hh_scaler),
-            locations=[somatic_loc])]
+                distribution=gkbar_hh_scaler
+            ),
+            locations=[somatic_loc],
+        ),
+    ]
     return ephys.models.CellModel(
-        'simple_ax2',
-        morph=morph,
-        mechs=mechs,
-        params=params)
+        "simple_ax2", morph=morph, mechs=mechs, params=params
+    )
 
 
 def run_short_sim(cable_cell):
@@ -487,9 +532,9 @@ def run_short_sim(cable_cell):
     arb_cell_model = arbor.single_cell_model(cable_cell)
     arb_cell_model.properties.catalogue = arbor.catalogue()
     arb_cell_model.properties.catalogue.extend(
-        arbor.default_catalogue(), "default::")
-    arb_cell_model.properties.catalogue.extend(
-        arbor.bbp_catalogue(), "BBP::")
+        arbor.default_catalogue(), "default::"
+    )
+    arb_cell_model.properties.catalogue.extend(arbor.bbp_catalogue(), "BBP::")
 
     # Run a very short simulation to test mechanism instantiation
     arb_cell_model.run(tfinal=0.1)
@@ -499,26 +544,29 @@ def run_short_sim(cable_cell):
 def test_cell_model_write_and_read_acc():
     """ephys.create_acc: Test write_acc and read_acc w/o axon replacement"""
     cell = make_cell(replace_axon=False)
-    param_values = {'gnabar_hh': 0.1,
-                    'gkbar_hh': 0.03}
+    param_values = {"gnabar_hh": 0.1, "gkbar_hh": 0.03}
 
     with tempfile.TemporaryDirectory() as acc_dir:
         cell.write_acc(acc_dir, param_values)
-        cell_json, arb_morph, arb_decor, arb_labels = \
-            create_acc.read_acc(
-                pathlib.Path(acc_dir).joinpath(cell.name + '.json'))
-    assert 'replace_axon' not in cell_json['morphology']
-
-    cable_cell = arbor.cable_cell(morphology=arb_morph,
-                                  decor=arb_decor,
-                                  labels=arb_labels)
+        cell_json, arb_morph, arb_decor, arb_labels = create_acc.read_acc(
+            pathlib.Path(acc_dir).joinpath(cell.name + ".json")
+        )
+    assert "replace_axon" not in cell_json["morphology"]
+
+    cable_cell = arbor.cable_cell(
+        morphology=arb_morph, decor=arb_decor, labels=arb_labels
+    )
     assert isinstance(cable_cell, arbor.cable_cell)
     assert len(cable_cell.cables('"soma"')) == 1
     assert len(cable_cell.cables('"axon"')) == 1
-    assert len(arb_morph.branch_segments(
-        cable_cell.cables('"soma"')[0].branch)) == 5
-    assert len(arb_morph.branch_segments(
-        cable_cell.cables('"axon"')[0].branch)) == 5
+    assert (
+        len(arb_morph.branch_segments(cable_cell.cables('"soma"')[0].branch))
+        == 5
+    )
+    assert (
+        len(arb_morph.branch_segments(cable_cell.cables('"axon"')[0].branch))
+        == 5
+    )
 
     run_short_sim(cable_cell)
 
@@ -527,40 +575,50 @@ def test_cell_model_write_and_read_acc():
 def test_cell_model_write_and_read_acc_replace_axon():
     """ephys.create_acc: Test write_acc and read_acc w/ axon replacement"""
     cell = make_cell(replace_axon=True)
-    param_values = {'gnabar_hh': 0.1,
-                    'gkbar_hh': 0.03}
+    param_values = {"gnabar_hh": 0.1, "gkbar_hh": 0.03}
 
     with tempfile.TemporaryDirectory() as acc_dir:
         try:
             nrn_sim = ephys.simulators.NrnSimulator()
-            cell.write_acc(acc_dir, param_values,
-                           sim=nrn_sim)
+            cell.write_acc(acc_dir, param_values, sim=nrn_sim)
         except Exception as e:  # fail with an older Arbor version
             assert isinstance(e, NotImplementedError)
-            assert len(e.args) == 1 and e.args[0] == \
-                "Need a newer version of Arbor for axon replacement."
+            assert (
+                len(e.args) == 1
+                and e.args[0]
+                == "Need a newer version of Arbor for axon replacement."
+            )
             return
 
         # Axon replacement implemented in installed Arbor version
-        cell_json, arb_morph, arb_decor, arb_labels = \
-            create_acc.read_acc(
-                pathlib.Path(acc_dir).joinpath(cell.name + '.json'))
-
-    assert 'replace_axon' in cell_json['morphology']
-    cable_cell = arbor.cable_cell(morphology=arb_morph,
-                                  decor=arb_decor,
-                                  labels=arb_labels)
+        cell_json, arb_morph, arb_decor, arb_labels = create_acc.read_acc(
+            pathlib.Path(acc_dir).joinpath(cell.name + ".json")
+        )
+
+    assert "replace_axon" in cell_json["morphology"]
+    cable_cell = arbor.cable_cell(
+        morphology=arb_morph, decor=arb_decor, labels=arb_labels
+    )
     assert isinstance(cable_cell, arbor.cable_cell)
     assert len(cable_cell.cables('"soma"')) == 1
     assert len(cable_cell.cables('"axon"')) == 1
-    assert len(arb_morph.branch_segments(
-        cable_cell.cables('"soma"')[0].branch)) == 6
-    assert len(arb_morph.branch_segments(
-        cable_cell.cables('"axon"')[0].branch)) == 6
-    assert cable_cell.cables('"soma"')[0].prox == 0.
-    assert abs(cable_cell.cables('"soma"')[0].dist -
-               cable_cell.cables('"axon"')[0].prox) < 1e-6
-    assert cable_cell.cables('"axon"')[0].dist == 1.
+    assert (
+        len(arb_morph.branch_segments(cable_cell.cables('"soma"')[0].branch))
+        == 6
+    )
+    assert (
+        len(arb_morph.branch_segments(cable_cell.cables('"axon"')[0].branch))
+        == 6
+    )
+    assert cable_cell.cables('"soma"')[0].prox == 0.0
+    assert (
+        abs(
+            cable_cell.cables('"soma"')[0].dist
+            - cable_cell.cables('"axon"')[0].prox
+        )
+        < 1e-6
+    )
+    assert cable_cell.cables('"axon"')[0].dist == 1.0
 
     run_short_sim(cable_cell)
 
@@ -569,37 +627,37 @@ def test_cell_model_write_and_read_acc_replace_axon():
 def test_cell_model_create_acc_replace_axon_without_instantiate():
     """ephys.create_acc: Test write_acc and read_acc w/ axon replacement"""
     cell = make_cell(replace_axon=True)
-    param_values = {'gnabar_hh': 0.1,
-                    'gkbar_hh': 0.03}
-
-    with pytest.raises(ValueError,
-                       match='Need an instance of NrnSimulator in sim'
-                             ' to instantiate morphology in order to'
-                             ' create JSON/ACC-description with'
-                             ' axon replacement.'):
+    param_values = {"gnabar_hh": 0.1, "gkbar_hh": 0.03}
+
+    with pytest.raises(
+        ValueError,
+        match="Need an instance of NrnSimulator in sim"
+        " to instantiate morphology in order to"
+        " create JSON/ACC-description with"
+        " axon replacement.",
+    ):
         cell.create_acc(param_values)
 
 
 def check_acc_dir(test_dir, ref_dir):
-    assert os.listdir(ref_dir) == os.listdir(test_dir)
+    assert sorted(os.listdir(ref_dir)) == sorted(os.listdir(test_dir))
 
-    ref_dir_ver_suffix = '_py' + ''.join(sys.version.split('.')[:2])
+    ref_dir_ver_suffix = "_py" + "".join(sys.version.split(".")[:2])
     ref_dir_ver = ref_dir.parent / (ref_dir.name + ref_dir_ver_suffix)
 
     for file in os.listdir(ref_dir):
-
         if (ref_dir_ver / file).exists():
             ref_dir_file = ref_dir_ver
         else:
             ref_dir_file = ref_dir
 
-        if file.endswith('.json'):
+        if file.endswith(".json"):
             with open(os.path.join(test_dir, file)) as f:
                 cell_json_dict = json.load(f)
             with open(ref_dir_file / file) as f:
                 ref_cell_json = json.load(f)
             for k in ref_cell_json:
-                if k != 'produced_by':
+                if k != "produced_by":
                     assert ref_cell_json[k] == cell_json_dict[k]
         else:
             with open(os.path.join(test_dir, file)) as f:
@@ -611,17 +669,21 @@ def check_acc_dir(test_dir, ref_dir):
 
 @pytest.mark.unit
 def test_write_acc_simple():
-    SIMPLECELL_PATH = str((pathlib.Path(__file__).parent /
-                          '../../../examples/simplecell').resolve())
+    SIMPLECELL_PATH = str(
+        (
+            pathlib.Path(__file__).parent / "../../../examples/simplecell"
+        ).resolve()
+    )
     sys.path.insert(0, SIMPLECELL_PATH)
-    ref_dir = (testdata_dir / 'acc/simplecell').resolve()
+    ref_dir = (testdata_dir / "acc/simplecell").resolve()
     old_cwd = os.getcwd()
     try:
         os.chdir(SIMPLECELL_PATH)
         import simplecell_model
+
         param_values = {
-            'gnabar_hh': 0.10299326453483033,
-            'gkbar_hh': 0.027124836082684685
+            "gnabar_hh": 0.10299326453483033,
+            "gkbar_hh": 0.027124836082684685,
         }
 
         cell = simplecell_model.create(do_replace_axon=True)
@@ -629,16 +691,20 @@ def test_write_acc_simple():
         cell.instantiate_morphology_3d(nrn_sim)
 
         with tempfile.TemporaryDirectory() as test_dir:
-            cell.write_acc(test_dir,
-                           param_values,
-                           # ext_catalogues=ext_catalogues,
-                           create_mod_morph=True)
+            cell.write_acc(
+                test_dir,
+                param_values,
+                # ext_catalogues=ext_catalogues,
+                create_mod_morph=True,
+            )
 
             check_acc_dir(test_dir, ref_dir)
-    except Exception as e:  # fail with an older Arbor version
-        assert isinstance(e, NotImplementedError)
-        assert len(e.args) == 1 and e.args[0] == \
-            "Need a newer version of Arbor for axon replacement."
+    except NotImplementedError as e:  # fail with an older Arbor version
+        assert (
+            len(e.args) == 1
+            and e.args[0]
+            == "Need a newer version of Arbor for axon replacement."
+        )
     finally:
         cell.destroy(nrn_sim)
         os.chdir(old_cwd)
@@ -647,34 +713,36 @@ def test_write_acc_simple():
 
 @pytest.mark.unit
 def test_write_acc_l5pc():
-    L5PC_PATH = str((pathlib.Path(__file__).parent /
-                    '../../../examples/l5pc').resolve())
+    L5PC_PATH = str(
+        (pathlib.Path(__file__).parent / "../../../examples/l5pc").resolve()
+    )
     sys.path.insert(0, L5PC_PATH)
-    ref_dir = (testdata_dir / 'acc/l5pc').resolve()
+    ref_dir = (testdata_dir / "acc/l5pc").resolve()
     old_cwd = os.getcwd()
     try:
         import l5pc_model
+
         param_values = {
-            'gNaTs2_tbar_NaTs2_t.apical': 0.026145,
-            'gSKv3_1bar_SKv3_1.apical': 0.004226,
-            'gImbar_Im.apical': 0.000143,
-            'gNaTa_tbar_NaTa_t.axonal': 3.137968,
-            'gK_Tstbar_K_Tst.axonal': 0.089259,
-            'gamma_CaDynamics_E2.axonal': 0.002910,
-            'gNap_Et2bar_Nap_Et2.axonal': 0.006827,
-            'gSK_E2bar_SK_E2.axonal': 0.007104,
-            'gCa_HVAbar_Ca_HVA.axonal': 0.000990,
-            'gK_Pstbar_K_Pst.axonal': 0.973538,
-            'gSKv3_1bar_SKv3_1.axonal': 1.021945,
-            'decay_CaDynamics_E2.axonal': 287.198731,
-            'gCa_LVAstbar_Ca_LVAst.axonal': 0.008752,
-            'gamma_CaDynamics_E2.somatic': 0.000609,
-            'gSKv3_1bar_SKv3_1.somatic': 0.303472,
-            'gSK_E2bar_SK_E2.somatic': 0.008407,
-            'gCa_HVAbar_Ca_HVA.somatic': 0.000994,
-            'gNaTs2_tbar_NaTs2_t.somatic': 0.983955,
-            'decay_CaDynamics_E2.somatic': 210.485284,
-            'gCa_LVAstbar_Ca_LVAst.somatic': 0.000333,
+            "gNaTs2_tbar_NaTs2_t.apical": 0.026145,
+            "gSKv3_1bar_SKv3_1.apical": 0.004226,
+            "gImbar_Im.apical": 0.000143,
+            "gNaTa_tbar_NaTa_t.axonal": 3.137968,
+            "gK_Tstbar_K_Tst.axonal": 0.089259,
+            "gamma_CaDynamics_E2.axonal": 0.002910,
+            "gNap_Et2bar_Nap_Et2.axonal": 0.006827,
+            "gSK_E2bar_SK_E2.axonal": 0.007104,
+            "gCa_HVAbar_Ca_HVA.axonal": 0.000990,
+            "gK_Pstbar_K_Pst.axonal": 0.973538,
+            "gSKv3_1bar_SKv3_1.axonal": 1.021945,
+            "decay_CaDynamics_E2.axonal": 287.198731,
+            "gCa_LVAstbar_Ca_LVAst.axonal": 0.008752,
+            "gamma_CaDynamics_E2.somatic": 0.000609,
+            "gSKv3_1bar_SKv3_1.somatic": 0.303472,
+            "gSK_E2bar_SK_E2.somatic": 0.008407,
+            "gCa_HVAbar_Ca_HVA.somatic": 0.000994,
+            "gNaTs2_tbar_NaTs2_t.somatic": 0.983955,
+            "decay_CaDynamics_E2.somatic": 210.485284,
+            "gCa_LVAstbar_Ca_LVAst.somatic": 0.000333,
         }
 
         cell = l5pc_model.create(do_replace_axon=True)
@@ -682,16 +750,21 @@ def test_write_acc_l5pc():
         cell.instantiate_morphology_3d(nrn_sim)
 
         with tempfile.TemporaryDirectory() as test_dir:
-            cell.write_acc(test_dir,
-                           param_values,
-                           # ext_catalogues=ext_catalogues,
-                           create_mod_morph=True)
+            cell.write_acc(
+                test_dir,
+                param_values,
+                # ext_catalogues=ext_catalogues,
+                create_mod_morph=True,
+            )
 
             check_acc_dir(test_dir, ref_dir)
     except Exception as e:  # fail with an older Arbor version
         assert isinstance(e, NotImplementedError)
-        assert len(e.args) == 1 and e.args[0] == \
-            "Need a newer version of Arbor for axon replacement."
+        assert (
+            len(e.args) == 1
+            and e.args[0]
+            == "Need a newer version of Arbor for axon replacement."
+        )
     finally:
         cell.destroy(nrn_sim)
         os.chdir(old_cwd)
@@ -700,22 +773,26 @@ def test_write_acc_l5pc():
 
 @pytest.mark.unit
 def test_write_acc_expsyn():
-    EXPSYN_PATH = str((pathlib.Path(__file__).parent /
-                      '../../../examples/expsyn').resolve())
+    EXPSYN_PATH = str(
+        (pathlib.Path(__file__).parent / "../../../examples/expsyn").resolve()
+    )
     sys.path.insert(0, EXPSYN_PATH)
-    ref_dir = (testdata_dir / 'acc/expsyn').resolve()
+    ref_dir = (testdata_dir / "acc/expsyn").resolve()
     old_cwd = os.getcwd()
     try:
         import expsyn
-        param_values = {'expsyn_tau': 10.0}
 
-        cell = expsyn.create_model(sim='arb', do_replace_axon=False)
+        param_values = {"expsyn_tau": 10.0}
+
+        cell = expsyn.create_model(sim="arb", do_replace_axon=False)
 
         with tempfile.TemporaryDirectory() as test_dir:
-            cell.write_acc(test_dir,
-                           param_values,
-                           # ext_catalogues=ext_catalogues,
-                           create_mod_morph=True)
+            cell.write_acc(
+                test_dir,
+                param_values,
+                # ext_catalogues=ext_catalogues,
+                create_mod_morph=True,
+            )
 
             check_acc_dir(test_dir, ref_dir)
     finally:
diff --git a/bluepyopt/tests/test_ephys/test_locations.py b/bluepyopt/tests/test_ephys/test_locations.py
index 28868742..cef6c78b 100644
--- a/bluepyopt/tests/test_ephys/test_locations.py
+++ b/bluepyopt/tests/test_ephys/test_locations.py
@@ -21,8 +21,8 @@
 
 # pylint:disable=W0612, W0201
 import json
-import numpy as np
 
+import numpy as np
 import pytest
 
 from bluepyopt import ephys
@@ -33,27 +33,24 @@
 def test_location_init():
     """ephys.locations: test if Location works"""
 
-    loc = ephys.locations.Location('test')
+    loc = ephys.locations.Location("test")
     assert isinstance(loc, ephys.locations.Location)
-    assert loc.name == 'test'
+    assert loc.name == "test"
 
 
 @pytest.mark.unit
 class TestNrnSectionCompLocation(object):
-
     """Test class for NrnSectionCompLocation"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.loc = ephys.locations.NrnSectionCompLocation(
-            name='test',
-            sec_name='soma[0]',
-            comp_x=0.5)
+            name="test", sec_name="soma[0]", comp_x=0.5
+        )
         self.loc_dend = ephys.locations.NrnSectionCompLocation(
-            name='test',
-            sec_name='dend[1]',
-            comp_x=0.5)
-        assert self.loc.name == 'test'
+            name="test", sec_name="dend[1]", comp_x=0.5
+        )
+        assert self.loc.name == "test"
         self.sim = ephys.simulators.NrnSimulator()
 
     def test_instantiate(self):
@@ -61,13 +58,14 @@ def test_instantiate(self):
 
         # Create a little test class with a soma and two dendritic sections
         class Cell(object):
-
             """Cell class"""
+
             pass
+
         cell = Cell()
         soma = self.sim.neuron.h.Section()
-        dend1 = self.sim.neuron.h.Section(name='dend1')
-        dend2 = self.sim.neuron.h.Section(name='dend2')
+        dend1 = self.sim.neuron.h.Section(name="dend1")
+        dend2 = self.sim.neuron.h.Section(name="dend2")
 
         cell.soma = [soma]
         cell.dend = [dend1, dend2]
@@ -81,22 +79,17 @@ class Cell(object):
 
 @pytest.mark.unit
 class TestNrnSeclistCompLocation(object):
-
     """Test class for NrnSectionCompLocation"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.loc = ephys.locations.NrnSeclistCompLocation(
-            name='test',
-            seclist_name='somatic',
-            sec_index=0,
-            comp_x=0.5)
+            name="test", seclist_name="somatic", sec_index=0, comp_x=0.5
+        )
         self.loc_dend = ephys.locations.NrnSeclistCompLocation(
-            name='test',
-            seclist_name='basal',
-            sec_index=1,
-            comp_x=0.5)
-        assert self.loc.name == 'test'
+            name="test", seclist_name="basal", sec_index=1, comp_x=0.5
+        )
+        assert self.loc.name == "test"
         self.sim = ephys.simulators.NrnSimulator()
 
     def test_instantiate(self):
@@ -105,12 +98,13 @@ def test_instantiate(self):
         # Create a little test class with a soma and two dendritic sections
         class Cell(object):
             """Cell class"""
+
             pass
 
         cell = Cell()
         soma = self.sim.neuron.h.Section()
-        dend1 = self.sim.neuron.h.Section(name='dend1')
-        dend2 = self.sim.neuron.h.Section(name='dend2')
+        dend1 = self.sim.neuron.h.Section(name="dend1")
+        dend2 = self.sim.neuron.h.Section(name="dend2")
 
         cell.somatic = self.sim.neuron.h.SectionList()
         cell.somatic.append(soma)
@@ -130,20 +124,17 @@ class Cell(object):
 
 @pytest.mark.unit
 class TestNrnSeclistSecLocation(object):
-
     """Test class for NrnSeclistSecLocation"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.loc = ephys.locations.NrnSeclistSecLocation(
-            name='test',
-            seclist_name='somatic',
-            sec_index=0)
+            name="test", seclist_name="somatic", sec_index=0
+        )
         self.loc_dend = ephys.locations.NrnSeclistSecLocation(
-            name='test',
-            seclist_name='basal',
-            sec_index=1)
-        assert self.loc.name == 'test'
+            name="test", seclist_name="basal", sec_index=1
+        )
+        assert self.loc.name == "test"
         self.sim = ephys.simulators.NrnSimulator()
 
     def test_instantiate(self):
@@ -152,12 +143,13 @@ def test_instantiate(self):
         # Create a little test class with a soma and two dendritic sections
         class Cell(object):
             """Cell class"""
+
             pass
 
         cell = Cell()
         soma = self.sim.neuron.h.Section()
-        dend1 = self.sim.neuron.h.Section(name='dend1')
-        dend2 = self.sim.neuron.h.Section(name='dend2')
+        dend1 = self.sim.neuron.h.Section(name="dend1")
+        dend2 = self.sim.neuron.h.Section(name="dend2")
 
         cell.somatic = self.sim.neuron.h.SectionList()
         cell.somatic.append(soma)
@@ -174,16 +166,14 @@ class Cell(object):
 
 @pytest.mark.unit
 class TestNrnSomaDistanceCompLocation(object):
-
     """Test class for NrnSomaDistanceCompLocation"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.loc = ephys.locations.NrnSomaDistanceCompLocation(
-            'test',
-            125,
-            'testdend')
-        assert self.loc.name == 'test'
+            "test", 125, "testdend"
+        )
+        assert self.loc.name == "test"
         self.sim = ephys.simulators.NrnSimulator()
 
     def test_instantiate(self):
@@ -191,23 +181,26 @@ def test_instantiate(self):
 
         # Create a little test class with a soma and two dendritic sections
         class Cell(object):
-
             """Cell class"""
+
             pass
+
         cell = Cell()
         soma = self.sim.neuron.h.Section()
         cell.soma = [soma]
         cell.testdend = self.sim.neuron.h.SectionList()
-        dend1 = self.sim.neuron.h.Section(name='dend1')
-        dend2 = self.sim.neuron.h.Section(name='dend2')
+        dend1 = self.sim.neuron.h.Section(name="dend1")
+        dend2 = self.sim.neuron.h.Section(name="dend2")
 
         cell.testdend.append(sec=dend1)
         cell.testdend.append(sec=dend2)
 
-        pytest.raises(ephys.locations.EPhysLocInstantiateException,
-                      self.loc.instantiate,
-                      sim=self.sim,
-                      icell=cell)
+        pytest.raises(
+            ephys.locations.EPhysLocInstantiateException,
+            self.loc.instantiate,
+            sim=self.sim,
+            icell=cell,
+        )
 
         dend1.connect(soma(0.5), 0.0)
         dend2.connect(dend1(1.0), 0.0)
@@ -218,22 +211,17 @@ class Cell(object):
 
 @pytest.mark.unit
 class TestNrnSecSomaDistanceCompLocation(object):
-
     """Test class for NrnSecSomaDistanceCompLocation"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.loc = ephys.locations.NrnSecSomaDistanceCompLocation(
-            'test',
-            125,
-            1,
-            'testdend')
+            "test", 125, 1, "testdend"
+        )
         self.loc_other = ephys.locations.NrnSecSomaDistanceCompLocation(
-            'test',
-            250,
-            4,
-            'testdend')
-        assert self.loc.name == 'test'
+            "test", 250, 4, "testdend"
+        )
+        assert self.loc.name == "test"
         self.sim = ephys.simulators.NrnSimulator()
 
     def test_instantiate(self):
@@ -241,18 +229,19 @@ def test_instantiate(self):
 
         # Create a little test class with a soma and two dendritic sections
         class Cell(object):
-
             """Cell class"""
+
             pass
+
         cell = Cell()
         soma = self.sim.neuron.h.Section(name="soma[0]")
         cell.soma = [soma]
         cell.testdend = self.sim.neuron.h.SectionList()
-        dend1 = self.sim.neuron.h.Section(name='dend[0]')
-        dend2 = self.sim.neuron.h.Section(name='dend[1]')
-        dend3 = self.sim.neuron.h.Section(name='dend[2]')
-        dend4 = self.sim.neuron.h.Section(name='dend[3]')
-        dend5 = self.sim.neuron.h.Section(name='dend[4]')
+        dend1 = self.sim.neuron.h.Section(name="dend[0]")
+        dend2 = self.sim.neuron.h.Section(name="dend[1]")
+        dend3 = self.sim.neuron.h.Section(name="dend[2]")
+        dend4 = self.sim.neuron.h.Section(name="dend[3]")
+        dend5 = self.sim.neuron.h.Section(name="dend[4]")
 
         cell.testdend.append(sec=dend1)
         cell.testdend.append(sec=dend2)
@@ -274,21 +263,18 @@ class Cell(object):
 
 @pytest.mark.unit
 class TestNrnTrunkSomaDistanceCompLocation(object):
-
     """Test class for NrnTrunkSomaDistanceCompLocation"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.loc = ephys.locations.NrnTrunkSomaDistanceCompLocation(
-            'test',
-            soma_distance=150,
-            seclist_name='testdend')
+            "test", soma_distance=150, seclist_name="testdend"
+        )
         self.loc_other = ephys.locations.NrnTrunkSomaDistanceCompLocation(
-            'test',
-            soma_distance=350,
-            seclist_name='testdend')
+            "test", soma_distance=350, seclist_name="testdend"
+        )
 
-        assert self.loc.name == 'test'
+        assert self.loc.name == "test"
         self.sim = ephys.simulators.NrnSimulator()
 
     def test_instantiate(self):
@@ -296,18 +282,19 @@ def test_instantiate(self):
 
         # Create a little test class with a soma and two dendritic sections
         class Cell(object):
-
             """Cell class"""
+
             pass
+
         cell = Cell()
         soma = self.sim.neuron.h.Section(name="soma[0]")
         cell.soma = [soma]
         cell.testdend = self.sim.neuron.h.SectionList()
-        dend1 = self.sim.neuron.h.Section(name='dend[0]')
-        dend2 = self.sim.neuron.h.Section(name='dend[1]')
-        dend3 = self.sim.neuron.h.Section(name='dend[2]')
-        dend4 = self.sim.neuron.h.Section(name='dend[3]')
-        dend5 = self.sim.neuron.h.Section(name='dend[4]')
+        dend1 = self.sim.neuron.h.Section(name="dend[0]")
+        dend2 = self.sim.neuron.h.Section(name="dend[1]")
+        dend3 = self.sim.neuron.h.Section(name="dend[2]")
+        dend4 = self.sim.neuron.h.Section(name="dend[3]")
+        dend5 = self.sim.neuron.h.Section(name="dend[4]")
 
         cell.testdend.append(sec=dend1)
         cell.testdend.append(sec=dend2)
@@ -348,18 +335,22 @@ def test_serialize():
         NrnSeclistCompLocation,
         NrnSeclistLocation,
         NrnSeclistSecLocation,
-        NrnSomaDistanceCompLocation)
+        NrnSomaDistanceCompLocation,
+    )
 
-    seclist_name, sec_index, comp_x, soma_distance = 'somatic', 0, 0.5, 800
+    seclist_name, sec_index, comp_x, soma_distance = "somatic", 0, 0.5, 800
     locations = (
-        NrnSeclistCompLocation('NrnSeclistCompLocation',
-                               seclist_name, sec_index, comp_x),
-        NrnSeclistLocation(
-            'NrnSeclistLocation', seclist_name),
+        NrnSeclistCompLocation(
+            "NrnSeclistCompLocation", seclist_name, sec_index, comp_x
+        ),
+        NrnSeclistLocation("NrnSeclistLocation", seclist_name),
         NrnSeclistSecLocation(
-            'NrnSeclistSecLocation', seclist_name, sec_index),
+            "NrnSeclistSecLocation", seclist_name, sec_index
+        ),
         NrnSomaDistanceCompLocation(
-            'NrnSomaDistanceCompLocation', soma_distance, seclist_name),)
+            "NrnSomaDistanceCompLocation", soma_distance, seclist_name
+        ),
+    )
 
     for loc in locations:
         serialized = loc.to_dict()
diff --git a/bluepyopt/tests/test_ephys/test_simulators.py b/bluepyopt/tests/test_ephys/test_simulators.py
index f35fd006..4e4203f5 100644
--- a/bluepyopt/tests/test_ephys/test_simulators.py
+++ b/bluepyopt/tests/test_ephys/test_simulators.py
@@ -22,13 +22,12 @@
 # pylint:disable=W0612
 
 import os
+import pathlib
 import types
-
-import pytest
-import numpy
-
 from unittest import mock
+
 import numpy
+import pytest
 
 import bluepyopt.ephys as ephys
 import bluepyopt.ephys.examples as examples
@@ -46,7 +45,7 @@ def test_nrnsimulator_init():
 def test_nrnsimulator_init_windows():
     """ephys.simulators: test if NrnSimulator constructor works on Windows"""
 
-    with mock.patch('platform.system', mock.MagicMock(return_value="Windows")):
+    with mock.patch("platform.system", mock.MagicMock(return_value="Windows")):
         neuron_sim = ephys.simulators.NrnSimulator()
         assert isinstance(neuron_sim, ephys.simulators.NrnSimulator)
         assert not neuron_sim.disable_banner
@@ -69,9 +68,9 @@ def test_nrnsimulator_cvode_minstep():
 
     # Check default minstep before and after run
     neuron_sim = ephys.simulators.NrnSimulator(cvode_minstep=0.01)
-    assert neuron_sim.cvode.minstep() == 0.
+    assert neuron_sim.cvode.minstep() == 0.0
     neuron_sim.run(tstop=10)
-    assert neuron_sim.cvode.minstep() == 0.
+    assert neuron_sim.cvode.minstep() == 0.0
 
     # Check with that minstep is set back to the original value after run
     neuron_sim = ephys.simulators.NrnSimulator(cvode_minstep=0.0)
@@ -82,20 +81,26 @@ def test_nrnsimulator_cvode_minstep():
 
     # Check that the minstep is effective
     cvode_minstep = 0.012
-    params = {'gnabar_hh': 0.10299326453483033,
-              'gkbar_hh': 0.027124836082684685}
+    params = {
+        "gnabar_hh": 0.10299326453483033,
+        "gkbar_hh": 0.027124836082684685,
+    }
     simplecell = examples.simplecell.SimpleCell()
     evaluator = simplecell.cell_evaluator
     evaluator.cell_model.unfreeze(params.keys())
     evaluator.sim = ephys.simulators.NrnSimulator(cvode_minstep=cvode_minstep)
     responses = evaluator.run_protocols(
-        protocols=evaluator.fitness_protocols.values(),
-        param_values=params)
+        protocols=evaluator.fitness_protocols.values(), param_values=params
+    )
     ton = list(evaluator.fitness_protocols.values())[0].stimuli[0].step_delay
-    toff = ton + list(evaluator.fitness_protocols.values())[0].stimuli[
-        0].step_duration
-    t_series = numpy.array(responses['Step1.soma.v']['time'])
-    t_series = t_series[((ton + 1.) < t_series) & (t_series < (toff - 1.))]
+    toff = (
+        ton
+        + list(evaluator.fitness_protocols.values())[0]
+        .stimuli[0]
+        .step_duration
+    )
+    t_series = numpy.array(responses["Step1.soma.v"]["time"])
+    t_series = t_series[((ton + 1.0) < t_series) & (t_series < (toff - 1.0))]
     min_dt = numpy.min(numpy.ediff1d(t_series))
     assert (min_dt >= cvode_minstep) == 1
     evaluator.cell_model.freeze(params)
@@ -105,6 +110,7 @@ def test_nrnsimulator_cvode_minstep():
 def test_neuron_import():
     """ephys.simulators: test if bluepyopt.neuron import was successful"""
     from bluepyopt import ephys  # NOQA
+
     neuron_sim = ephys.simulators.NrnSimulator()
     assert isinstance(neuron_sim.neuron, types.ModuleType)
 
@@ -114,6 +120,7 @@ def test_nrnsim_run_dt_exception():
     """ephys.simulators: test if run return exception when dt was changed"""
 
     from bluepyopt import ephys  # NOQA
+
     neuron_sim = ephys.simulators.NrnSimulator()
     neuron_sim.neuron.h.dt = 1.0
     pytest.raises(Exception, neuron_sim.run, 10, cvode_active=False)
@@ -124,18 +131,20 @@ def test_nrnsim_run_cvodeactive_dt_exception():
     """ephys.simulators: test if run return exception cvode and dt both used"""
 
     from bluepyopt import ephys  # NOQA
+
     neuron_sim = ephys.simulators.NrnSimulator()
     neuron_sim.neuron.h.dt = 1.0
     pytest.raises(ValueError, neuron_sim.run, 10, dt=0.1, cvode_active=True)
 
 
 @pytest.mark.unit
-@mock.patch('glob.glob')
+@mock.patch.object(pathlib.Path, "glob")
 def test_disable_banner_exception(mock_glob):
     """ephys.simulators: test if disable_banner raises exception"""
     mock_glob.return_value = []
 
     import warnings
+
     with warnings.catch_warnings(record=True) as warnings_record:
         ephys.simulators.NrnSimulator._nrn_disable_banner()
         assert len(warnings_record) == 1
@@ -154,7 +163,7 @@ def test_lfpysimulator_init():
 def test_lfpyimulator_init_windows():
     """ephys.simulators: test if LFPySimulator constructor works on Windows"""
 
-    with mock.patch('platform.system', mock.MagicMock(return_value="Windows")):
+    with mock.patch("platform.system", mock.MagicMock(return_value="Windows")):
         empty_cell = ephys.models.LFPyCellModel(name="empty_cell")
         neuron_sim = ephys.simulators.LFPySimulator()
         assert isinstance(neuron_sim, ephys.simulators.LFPySimulator)
@@ -171,6 +180,7 @@ def test_lfpyimulator_init_windows():
 def test__lfpysimulator_neuron_import():
     """ephys.simulators: test neuron import from LFPySimulator"""
     from bluepyopt import ephys  # NOQA
+
     empty_cell = ephys.models.LFPyCellModel(name="empty_cell")
     neuron_sim = ephys.simulators.LFPySimulator()
     assert isinstance(neuron_sim.neuron, types.ModuleType)
@@ -181,10 +191,11 @@ def test_lfpysim_run_cvodeactive_dt_exception():
     """ephys.simulators: test if LFPySimulator run returns exception"""
 
     from bluepyopt import ephys  # NOQA
+
     TESTDATA_DIR = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), 'testdata'
+        os.path.dirname(os.path.abspath(__file__)), "testdata"
     )
-    simple_morphology_path = os.path.join(TESTDATA_DIR, 'simple.swc')
+    simple_morphology_path = os.path.join(TESTDATA_DIR, "simple.swc")
     test_morph = ephys.morphologies.NrnFileMorphology(simple_morphology_path)
 
     lfpy_cell = ephys.models.LFPyCellModel(
@@ -196,9 +207,9 @@ def test_lfpysim_run_cvodeactive_dt_exception():
     with pytest.raises(
         ValueError,
         match=(
-            'NrnSimulator: '
-            'Impossible to combine the dt argument when '
-            'cvode_active is True in the NrnSimulator run method'
+            "NrnSimulator: "
+            "Impossible to combine the dt argument when "
+            "cvode_active is True in the NrnSimulator run method"
         ),
     ):
         neuron_sim.run(
@@ -206,19 +217,20 @@ def test_lfpysim_run_cvodeactive_dt_exception():
             dt=0.1,
             cvode_active=True,
             lfpy_cell=lfpy_cell.lfpy_cell,
-            lfpy_electrode=lfpy_cell.lfpy_electrode
+            lfpy_electrode=lfpy_cell.lfpy_electrode,
         )
 
     lfpy_cell.destroy(sim=neuron_sim)
 
 
 @pytest.mark.unit
-@mock.patch('glob.glob')
+@mock.patch.object(pathlib.Path, "glob")
 def test_lfpysimulator_disable_banner_exception(mock_glob):
     """ephys.simulators: test LFPySimulator disable_banner raises exception"""
     mock_glob.return_value = []
 
     import warnings
+
     with warnings.catch_warnings(record=True) as warnings_record:
         ephys.simulators.LFPySimulator._nrn_disable_banner()
         assert len(warnings_record) == 1
diff --git a/bluepyopt/tests/test_l5pc.py b/bluepyopt/tests/test_l5pc.py
index b6e3fc8a..ddc76883 100644
--- a/bluepyopt/tests/test_l5pc.py
+++ b/bluepyopt/tests/test_l5pc.py
@@ -3,8 +3,11 @@
 import json
 import os
 import sys
-
 from contextlib import contextmanager
+
+import bluepyopt
+from bluepyopt import ephys
+
 if sys.version_info[0] < 3:
     from StringIO import StringIO
 else:
@@ -13,45 +16,43 @@
 
 import pytest
 
-L5PC_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__),
-                                         '../../examples/l5pc'))
+L5PC_PATH = os.path.abspath(
+    os.path.join(os.path.dirname(__file__), "../../examples/l5pc")
+)
 SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
 
 sys.path.insert(0, L5PC_PATH)
 
-import bluepyopt
-from bluepyopt import ephys
 
 neuron_sim = ephys.simulators.NrnSimulator()
 
 neuron_sim.neuron.h.nrn_load_dll(
-    os.path.join(
-        L5PC_PATH,
-        'x86_64/.libs/libnrnmech.so'))
+    os.path.join(L5PC_PATH, "x86_64/.libs/libnrnmech.so")
+)
 
 
 # Parameters in release circuit model
 release_parameters = {
-    'gNaTs2_tbar_NaTs2_t.apical': 0.026145,
-    'gSKv3_1bar_SKv3_1.apical': 0.004226,
-    'gImbar_Im.apical': 0.000143,
-    'gNaTa_tbar_NaTa_t.axonal': 3.137968,
-    'gK_Tstbar_K_Tst.axonal': 0.089259,
-    'gamma_CaDynamics_E2.axonal': 0.002910,
-    'gNap_Et2bar_Nap_Et2.axonal': 0.006827,
-    'gSK_E2bar_SK_E2.axonal': 0.007104,
-    'gCa_HVAbar_Ca_HVA.axonal': 0.000990,
-    'gK_Pstbar_K_Pst.axonal': 0.973538,
-    'gSKv3_1bar_SKv3_1.axonal': 1.021945,
-    'decay_CaDynamics_E2.axonal': 287.198731,
-    'gCa_LVAstbar_Ca_LVAst.axonal': 0.008752,
-    'gamma_CaDynamics_E2.somatic': 0.000609,
-    'gSKv3_1bar_SKv3_1.somatic': 0.303472,
-    'gSK_E2bar_SK_E2.somatic': 0.008407,
-    'gCa_HVAbar_Ca_HVA.somatic': 0.000994,
-    'gNaTs2_tbar_NaTs2_t.somatic': 0.983955,
-    'decay_CaDynamics_E2.somatic': 210.485284,
-    'gCa_LVAstbar_Ca_LVAst.somatic': 0.000333
+    "gNaTs2_tbar_NaTs2_t.apical": 0.026145,
+    "gSKv3_1bar_SKv3_1.apical": 0.004226,
+    "gImbar_Im.apical": 0.000143,
+    "gNaTa_tbar_NaTa_t.axonal": 3.137968,
+    "gK_Tstbar_K_Tst.axonal": 0.089259,
+    "gamma_CaDynamics_E2.axonal": 0.002910,
+    "gNap_Et2bar_Nap_Et2.axonal": 0.006827,
+    "gSK_E2bar_SK_E2.axonal": 0.007104,
+    "gCa_HVAbar_Ca_HVA.axonal": 0.000990,
+    "gK_Pstbar_K_Pst.axonal": 0.973538,
+    "gSKv3_1bar_SKv3_1.axonal": 1.021945,
+    "decay_CaDynamics_E2.axonal": 287.198731,
+    "gCa_LVAstbar_Ca_LVAst.axonal": 0.008752,
+    "gamma_CaDynamics_E2.somatic": 0.000609,
+    "gSKv3_1bar_SKv3_1.somatic": 0.303472,
+    "gSK_E2bar_SK_E2.somatic": 0.008407,
+    "gCa_HVAbar_Ca_HVA.somatic": 0.000994,
+    "gNaTs2_tbar_NaTs2_t.somatic": 0.983955,
+    "decay_CaDynamics_E2.somatic": 210.485284,
+    "gCa_LVAstbar_Ca_LVAst.somatic": 0.000333,
 }
 
 
@@ -65,8 +66,8 @@ def load_from_json(filename):
 def dump_to_json(content, filename):
     """Dump structure to json"""
 
-    with open(filename, 'w') as json_file:
-        return json.dump(content, json_file, indent=4, separators=(',', ': '))
+    with open(filename, "w") as json_file:
+        return json.dump(content, json_file, indent=4, separators=(",", ": "))
 
 
 def test_import():
@@ -78,17 +79,16 @@ def test_import():
 
 
 class TestL5PCModel(object):
-
     """Test L5PC model"""
 
-    def setup(self):
+    def setup_method(self):
         """Set up class"""
         sys.path.insert(0, L5PC_PATH)
 
         import l5pc_model  # NOQA
+
         self.l5pc_cell = l5pc_model.create()
-        assert isinstance(self.l5pc_cell,
-                          bluepyopt.ephys.models.CellModel)
+        assert isinstance(self.l5pc_cell, bluepyopt.ephys.models.CellModel)
         self.nrn = ephys.simulators.NrnSimulator()
 
     def test_instantiate(self):
@@ -96,42 +96,45 @@ def test_instantiate(self):
         self.l5pc_cell.freeze(release_parameters)
         self.l5pc_cell.instantiate(sim=self.nrn)
 
-    def teardown(self):
+    def teardown_method(self):
         """Teardown"""
         self.l5pc_cell.destroy(sim=self.nrn)
 
 
 class TestL5PCEvaluator(object):
-
     """Test L5PC evaluator"""
 
-    def setup(self):
+    def setup_method(self):
         """Set up class"""
 
         import l5pc_evaluator  # NOQA
 
         self.l5pc_evaluator = l5pc_evaluator.create()
 
-        assert isinstance(self.l5pc_evaluator,
-                          bluepyopt.ephys.evaluators.CellEvaluator)
+        assert isinstance(
+            self.l5pc_evaluator, bluepyopt.ephys.evaluators.CellEvaluator
+        )
 
     @pytest.mark.slow
     def test_eval(self):
         """L5PC: test evaluation of l5pc evaluator"""
         result = self.l5pc_evaluator.evaluate_with_dicts(
-            param_dict=release_parameters)
+            param_dict=release_parameters
+        )
 
         expected_results = load_from_json(
-            os.path.join(SCRIPT_DIR, 'expected_results.json'))
+            os.path.join(SCRIPT_DIR, "expected_results.json")
+        )
 
         # Use two lines below to update expected result
         # expected_results['TestL5PCEvaluator.test_eval'] = result
         # dump_to_json(expected_results, 'expected_results.json')
 
-        assert set(result.keys(
-        )) == set(expected_results['TestL5PCEvaluator.test_eval'].keys())
+        assert set(result.keys()) == set(
+            expected_results["TestL5PCEvaluator.test_eval"].keys()
+        )
 
-    def teardown(self):
+    def teardown_method(self):
         """Teardown"""
         pass
 
@@ -152,7 +155,8 @@ def stdout_redirector(stream):
 def test_exec():
     """L5PC Notebook: test execution"""
     import numpy
-    numpy.seterr(all='raise')
+
+    numpy.seterr(all="raise")
     old_cwd = os.getcwd()
     output = StringIO()
     try:
@@ -162,14 +166,14 @@ def test_exec():
             # Probably because multiprocessing doesn't work correctly during
             # import
             if sys.version_info[0] < 3:
-                execfile('L5PC.py')  # NOQA
+                execfile("L5PC.py")  # NOQA
             else:
-                with open('L5PC.py') as l5pc_file:
-                    exec(compile(l5pc_file.read(), 'L5PC.py', 'exec'))  # NOQA
+                with open("L5PC.py") as l5pc_file:
+                    exec(compile(l5pc_file.read(), "L5PC.py", "exec"))  # NOQA
         stdout = output.getvalue()
         # first and last values of optimal individual
-        assert '0.001017834439738432' in stdout
-        assert '202.18814057682334' in stdout
+        assert "0.001017834439738432" in stdout
+        assert "202.18814057682334" in stdout
         assert "'gamma_CaDynamics_E2.somatic': 0.03229357096515606" in stdout
     finally:
         os.chdir(old_cwd)
@@ -180,7 +184,8 @@ def test_exec():
 def test_l5pc_validate_neuron_arbor():
     """L5PC Neuron/Arbor validation Notebook: test execution"""
     import numpy
-    numpy.seterr(all='raise')
+
+    numpy.seterr(all="raise")
     old_cwd = os.getcwd()
     output = StringIO()
     try:
@@ -190,19 +195,28 @@ def test_l5pc_validate_neuron_arbor():
             # Probably because multiprocessing doesn't work correctly during
             # import
             if sys.version_info[0] < 3:
-                execfile('l5pc_validate_neuron_arbor_somatic.py')  # NOQA
+                execfile("l5pc_validate_neuron_arbor_somatic.py")  # NOQA
             else:
-                with open('l5pc_validate_neuron_arbor_somatic.py') \
-                        as l5pc_file:
+                with open(
+                    "l5pc_validate_neuron_arbor_somatic.py"
+                ) as l5pc_file:
                     l5pc_globals = {}
-                    exec(compile(l5pc_file.read(),
-                                 'l5pc_validate_neuron_arbor_somatic.py',
-                                 'exec'), l5pc_globals, l5pc_globals)  # NOQA
+                    exec(
+                        compile(
+                            l5pc_file.read(),
+                            "l5pc_validate_neuron_arbor_somatic.py",
+                            "exec",
+                        ),
+                        l5pc_globals,
+                        l5pc_globals,
+                    )  # NOQA
         stdout = output.getvalue()
         # mean relative L1-deviation between Arbor and Neuron below tolerance
-        assert 'Default dt ({:,.3g}): test_l5pc OK!'.format(0.025) + \
-            ' The mean relative Arbor-Neuron L1-deviation and error' \
+        assert (
+            "Default dt ({:,.3g}): test_l5pc OK!".format(0.025)
+            + " The mean relative Arbor-Neuron L1-deviation and error"
             in stdout
+        )
     finally:
         os.chdir(old_cwd)
         output.close()
diff --git a/bluepyopt/tests/test_lfpy.py b/bluepyopt/tests/test_lfpy.py
index c141e7f6..746b4bb3 100644
--- a/bluepyopt/tests/test_lfpy.py
+++ b/bluepyopt/tests/test_lfpy.py
@@ -2,13 +2,11 @@
 
 import os
 import sys
+
 import pytest
 
 L5PC_LFPY_PATH = os.path.abspath(
-    os.path.join(
-        os.path.dirname(__file__),
-        '../../examples/l5pc_lfpy'
-    )
+    os.path.join(os.path.dirname(__file__), "../../examples/l5pc_lfpy")
 )
 SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
 
@@ -30,10 +28,10 @@ def test_lfpy_evaluator():
 
     responses = evaluator.run_protocols(
         protocols=evaluator.fitness_protocols.values(),
-        param_values=release_params
+        param_values=release_params,
     )
     values = evaluator.fitness_calculator.calculate_values(responses)
 
     assert len(values) == 21
-    assert abs(values['Step1.soma.AP_height'] - 27.85963902931001) < 1e-5
-    assert len(responses['Step1.MEA.v']["voltage"]) == 40
+    assert abs(values["Step1.soma.AP_height"] - 27.85963902931001) < 1e-5
+    assert len(responses["Step1.MEA.v"]["voltage"]) == 40
diff --git a/bluepyopt/tests/test_simplecell.py b/bluepyopt/tests/test_simplecell.py
index 93a6c564..394a9fbc 100644
--- a/bluepyopt/tests/test_simplecell.py
+++ b/bluepyopt/tests/test_simplecell.py
@@ -1,40 +1,38 @@
 """Simple cell example test class"""
 
-import sys
 import os
+import sys
 
-SIMPLECELL_PATH = os.path.abspath(os.path.join(
-    os.path.dirname(__file__),
-    '../../examples/simplecell'))
+SIMPLECELL_PATH = os.path.abspath(
+    os.path.join(os.path.dirname(__file__), "../../examples/simplecell")
+)
 
 # sys.path.insert(0, SIMPLECELL_PATH)
 
 
 class TestSimpleCellClass(object):
-
     """Simple cell example test class for NEURON"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.old_cwd = os.getcwd()
         self.old_stdout = sys.stdout
 
         os.chdir(SIMPLECELL_PATH)
-        sys.stdout = open(os.devnull, 'w')
+        sys.stdout = open(os.devnull, "w")
 
-    @staticmethod
-    def test_exec():
+    def test_exec(self):
         """Simplecell NEURON: test execution"""
         # When using import instead of execfile this doesn't work
         # Probably because multiprocessing doesn't work correctly during
         # import
         if sys.version_info[0] < 3:
-            execfile('simplecell.py')  # NOQA
+            execfile("simplecell.py")  # NOQA
         else:
-            with open('simplecell.py') as sc_file:
-                exec(compile(sc_file.read(), 'simplecell.py', 'exec'))  # NOQA
+            with open("simplecell.py") as sc_file:
+                exec(compile(sc_file.read(), "simplecell.py", "exec"))  # NOQA
 
-    def teardown(self):
+    def teardown_method(self):
         """Tear down"""
 
         sys.stdout = self.old_stdout
@@ -42,31 +40,28 @@ def teardown(self):
 
 
 class TestSimpleCellArborClass(object):
-
     """Simple cell example test class for Arbor"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.old_cwd = os.getcwd()
         self.old_stdout = sys.stdout
 
         os.chdir(SIMPLECELL_PATH)
-        sys.stdout = open(os.devnull, 'w')
+        sys.stdout = open(os.devnull, "w")
 
-    @staticmethod
-    def test_exec():
+    def test_exec(self):
         """Simplecell Arbor: test execution"""
         # When using import instead of execfile this doesn't work
         # Probably because multiprocessing doesn't work correctly during
         # import
         if sys.version_info[0] < 3:
-            execfile('simplecell_arbor.py')  # NOQA
+            execfile("simplecell_arbor.py")  # NOQA
         else:
-            with open('simplecell_arbor.py') as sc_file:
-                exec(compile(sc_file.read(),
-                    'simplecell_arbor.py', 'exec'))  # NOQA
+            with open("simplecell_arbor.py") as sc_file:
+                exec(compile(sc_file.read(), "simplecell_arbor.py", "exec"))  # NOQA
 
-    def teardown(self):
+    def teardown_method(self):
         """Tear down"""
 
         sys.stdout = self.old_stdout
diff --git a/versioneer.py b/versioneer.py
index f11c1fee..3dd263e9 100644
--- a/versioneer.py
+++ b/versioneer.py
@@ -1,4 +1,3 @@
-
 # Version: 0.18
 
 """The Versioneer - like a rocketeer, but for versions.
@@ -277,6 +276,7 @@
 """
 
 from __future__ import print_function
+
 try:
     import configparser
 except ImportError:
@@ -308,11 +308,13 @@ def get_root():
         setup_py = os.path.join(root, "setup.py")
         versioneer_py = os.path.join(root, "versioneer.py")
     if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
-        err = ("Versioneer was unable to run the project root directory. "
-               "Versioneer requires setup.py to be executed from "
-               "its immediate directory (like 'python setup.py COMMAND'), "
-               "or in a way that lets it use sys.argv[0] to find the root "
-               "(like 'python path/to/setup.py COMMAND').")
+        err = (
+            "Versioneer was unable to run the project root directory. "
+            "Versioneer requires setup.py to be executed from "
+            "its immediate directory (like 'python setup.py COMMAND'), "
+            "or in a way that lets it use sys.argv[0] to find the root "
+            "(like 'python path/to/setup.py COMMAND')."
+        )
         raise VersioneerBadRootError(err)
     try:
         # Certain runtime workflows (setup.py install/develop in a setuptools
@@ -325,8 +327,10 @@ def get_root():
         me_dir = os.path.normcase(os.path.splitext(me)[0])
         vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0])
         if me_dir != vsr_dir:
-            print("Warning: build in %s is using versioneer.py from %s"
-                  % (os.path.dirname(me), versioneer_py))
+            print(
+                "Warning: build in %s is using versioneer.py from %s"
+                % (os.path.dirname(me), versioneer_py)
+            )
     except NameError:
         pass
     return root
@@ -339,15 +343,16 @@ def get_config_from_root(root):
     # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
     # the top of versioneer.py for instructions on writing your setup.cfg .
     setup_cfg = os.path.join(root, "setup.cfg")
-    parser = configparser.SafeConfigParser()
+    parser = configparser.ConfigParser()
     with open(setup_cfg, "r") as f:
-        parser.readfp(f)
+        parser.read_file(f)
     VCS = parser.get("versioneer", "VCS")  # mandatory
 
     def get(parser, name):
         if parser.has_option("versioneer", name):
             return parser.get("versioneer", name)
         return None
+
     cfg = VersioneerConfig()
     cfg.VCS = VCS
     cfg.style = get(parser, "style") or ""
@@ -372,17 +377,20 @@ class NotThisMethod(Exception):
 
 def register_vcs_handler(vcs, method):  # decorator
     """Decorator to mark a method as the handler for a particular VCS."""
+
     def decorate(f):
         """Store f in HANDLERS[vcs][method]."""
         if vcs not in HANDLERS:
             HANDLERS[vcs] = {}
         HANDLERS[vcs][method] = f
         return f
+
     return decorate
 
 
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
-                env=None):
+def run_command(
+    commands, args, cwd=None, verbose=False, hide_stderr=False, env=None
+):
     """Call the given command(s)."""
     assert isinstance(commands, list)
     p = None
@@ -390,10 +398,13 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
         try:
             dispcmd = str([c] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
-                                 stdout=subprocess.PIPE,
-                                 stderr=(subprocess.PIPE if hide_stderr
-                                         else None))
+            p = subprocess.Popen(
+                [c] + args,
+                cwd=cwd,
+                env=env,
+                stdout=subprocess.PIPE,
+                stderr=(subprocess.PIPE if hide_stderr else None),
+            )
             break
         except EnvironmentError:
             e = sys.exc_info()[1]
@@ -418,7 +429,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
     return stdout, p.returncode
 
 
-LONG_VERSION_PY['git'] = '''
+LONG_VERSION_PY["git"] = '''
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -1011,7 +1022,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
+    tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)])
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %d
@@ -1020,7 +1031,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r'\d', r)])
+        tags = set([r for r in refs if re.search(r"\d", r)])
         if verbose:
             print("discarding '%s', no digits" % ",".join(refs - tags))
     if verbose:
@@ -1028,19 +1039,26 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix):]
+            r = ref[len(tag_prefix) :]
             if verbose:
                 print("picking %s" % r)
-            return {"version": r,
-                    "full-revisionid": keywords["full"].strip(),
-                    "dirty": False, "error": None,
-                    "date": date}
+            return {
+                "version": r,
+                "full-revisionid": keywords["full"].strip(),
+                "dirty": False,
+                "error": None,
+                "date": date,
+            }
     # no suitable tags, so version is "0+unknown", but full hex is still there
     if verbose:
         print("no suitable tags, using unknown + full revision id")
-    return {"version": "0+unknown",
-            "full-revisionid": keywords["full"].strip(),
-            "dirty": False, "error": "no suitable tags", "date": None}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": keywords["full"].strip(),
+        "dirty": False,
+        "error": "no suitable tags",
+        "date": None,
+    }
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
@@ -1055,8 +1073,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
 
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
-                          hide_stderr=True)
+    out, rc = run_command(
+        GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True
+    )
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
@@ -1064,10 +1083,19 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
-                                          "--always", "--long",
-                                          "--match", "%s*" % tag_prefix],
-                                   cwd=root)
+    describe_out, rc = run_command(
+        GITS,
+        [
+            "describe",
+            "--tags",
+            "--dirty",
+            "--always",
+            "--long",
+            "--match",
+            "%s*" % tag_prefix,
+        ],
+        cwd=root,
+    )
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
@@ -1090,17 +1118,18 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     dirty = git_describe.endswith("-dirty")
     pieces["dirty"] = dirty
     if dirty:
-        git_describe = git_describe[:git_describe.rindex("-dirty")]
+        git_describe = git_describe[: git_describe.rindex("-dirty")]
 
     # now we have TAG-NUM-gHEX or HEX
 
     if "-" in git_describe:
         # TAG-NUM-gHEX
-        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
         if not mo:
             # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = ("unable to parse git-describe output: '%s'"
-                               % describe_out)
+            pieces["error"] = (
+                "unable to parse git-describe output: '%s'" % describe_out
+            )
             return pieces
 
         # tag
@@ -1109,10 +1138,12 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
-                               % (full_tag, tag_prefix))
+            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
+                full_tag,
+                tag_prefix,
+            )
             return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix):]
+        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
 
         # distance: number of commits since tag
         pieces["distance"] = int(mo.group(2))
@@ -1123,13 +1154,15 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     else:
         # HEX: no tags
         pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
-                                    cwd=root)
+        count_out, rc = run_command(
+            GITS, ["rev-list", "HEAD", "--count"], cwd=root
+        )
         pieces["distance"] = int(count_out)  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"],
-                       cwd=root)[0].strip()
+    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[
+        0
+    ].strip()
     pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
 
     return pieces
@@ -1185,16 +1218,22 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     for i in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
-            return {"version": dirname[len(parentdir_prefix):],
-                    "full-revisionid": None,
-                    "dirty": False, "error": None, "date": None}
+            return {
+                "version": dirname[len(parentdir_prefix) :],
+                "full-revisionid": None,
+                "dirty": False,
+                "error": None,
+                "date": None,
+            }
         else:
             rootdirs.append(root)
             root = os.path.dirname(root)  # up a level
 
     if verbose:
-        print("Tried directories %s but none started with prefix %s" %
-              (str(rootdirs), parentdir_prefix))
+        print(
+            "Tried directories %s but none started with prefix %s"
+            % (str(rootdirs), parentdir_prefix)
+        )
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
 
@@ -1223,11 +1262,17 @@ def versions_from_file(filename):
             contents = f.read()
     except EnvironmentError:
         raise NotThisMethod("unable to read _version.py")
-    mo = re.search(r"version_json = '''\n(.*)'''  # END VERSION_JSON",
-                   contents, re.M | re.S)
+    mo = re.search(
+        r"version_json = '''\n(.*)'''  # END VERSION_JSON",
+        contents,
+        re.M | re.S,
+    )
     if not mo:
-        mo = re.search(r"version_json = '''\r\n(.*)'''  # END VERSION_JSON",
-                       contents, re.M | re.S)
+        mo = re.search(
+            r"version_json = '''\r\n(.*)'''  # END VERSION_JSON",
+            contents,
+            re.M | re.S,
+        )
     if not mo:
         raise NotThisMethod("no version_json in _version.py")
     return json.loads(mo.group(1))
@@ -1236,8 +1281,9 @@ def versions_from_file(filename):
 def write_to_version_file(filename, versions):
     """Write the given version number to the given _version.py file."""
     os.unlink(filename)
-    contents = json.dumps(versions, sort_keys=True,
-                          indent=1, separators=(",", ": "))
+    contents = json.dumps(
+        versions, sort_keys=True, indent=1, separators=(",", ": ")
+    )
     with open(filename, "w") as f:
         f.write(SHORT_VERSION_PY % contents)
 
@@ -1269,8 +1315,7 @@ def render_pep440(pieces):
                 rendered += ".dirty"
     else:
         # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
-                                          pieces["short"])
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
@@ -1291,6 +1336,7 @@ def render_pep440_pre(pieces):
         rendered = "0.post.dev%d" % pieces["distance"]
     return rendered
 
+
 def render_pep440_minor(pieces):
     # TAG[.DISTANCE] . No -dirty
 
@@ -1307,7 +1353,6 @@ def render_pep440_minor(pieces):
     return rendered
 
 
-
 def render_pep440_post(pieces):
     """TAG[.postDISTANCE[.dev0]+gHEX] .
 
@@ -1400,11 +1445,13 @@ def render_git_describe_long(pieces):
 def render(pieces, style):
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
-        return {"version": "unknown",
-                "full-revisionid": pieces.get("long"),
-                "dirty": None,
-                "error": pieces["error"],
-                "date": None}
+        return {
+            "version": "unknown",
+            "full-revisionid": pieces.get("long"),
+            "dirty": None,
+            "error": pieces["error"],
+            "date": None,
+        }
 
     if not style or style == "default":
         style = "pep440"  # the default
@@ -1426,9 +1473,13 @@ def render(pieces, style):
     else:
         raise ValueError("unknown style '%s'" % style)
 
-    return {"version": rendered, "full-revisionid": pieces["long"],
-            "dirty": pieces["dirty"], "error": None,
-            "date": pieces.get("date")}
+    return {
+        "version": rendered,
+        "full-revisionid": pieces["long"],
+        "dirty": pieces["dirty"],
+        "error": None,
+        "date": pieces.get("date"),
+    }
 
 
 class VersioneerBadRootError(Exception):
@@ -1451,8 +1502,9 @@ def get_versions(verbose=False):
     handlers = HANDLERS.get(cfg.VCS)
     assert handlers, "unrecognized VCS '%s'" % cfg.VCS
     verbose = verbose or cfg.verbose
-    assert cfg.versionfile_source is not None, \
-        "please set versioneer.versionfile_source"
+    assert (
+        cfg.versionfile_source is not None
+    ), "please set versioneer.versionfile_source"
     assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix"
 
     versionfile_abs = os.path.join(root, cfg.versionfile_source)
@@ -1506,9 +1558,13 @@ def get_versions(verbose=False):
     if verbose:
         print("unable to compute version")
 
-    return {"version": "0+unknown", "full-revisionid": None,
-            "dirty": None, "error": "unable to compute version",
-            "date": None}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": None,
+        "dirty": None,
+        "error": "unable to compute version",
+        "date": None,
+    }
 
 
 def get_version():
@@ -1557,6 +1613,7 @@ def run(self):
             print(" date: %s" % vers.get("date"))
             if vers["error"]:
                 print(" error: %s" % vers["error"])
+
     cmds["version"] = cmd_version
 
     # we override "build_py" in both distutils and setuptools
@@ -1589,10 +1646,12 @@ def run(self):
             # now locate _version.py in the new build/ directory and replace
             # it with an updated value
             if cfg.versionfile_build:
-                target_versionfile = os.path.join(self.build_lib,
-                                                  cfg.versionfile_build)
+                target_versionfile = os.path.join(
+                    self.build_lib, cfg.versionfile_build
+                )
                 print("UPDATING %s" % target_versionfile)
                 write_to_version_file(target_versionfile, versions)
+
     cmds["build_py"] = cmd_build_py
 
     if "cx_Freeze" in sys.modules:  # cx_freeze enabled?
@@ -1617,17 +1676,21 @@ def run(self):
                 os.unlink(target_versionfile)
                 with open(cfg.versionfile_source, "w") as f:
                     LONG = LONG_VERSION_PY[cfg.VCS]
-                    f.write(LONG %
-                            {"DOLLAR": "$",
-                             "STYLE": cfg.style,
-                             "TAG_PREFIX": cfg.tag_prefix,
-                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                             })
+                    f.write(
+                        LONG
+                        % {
+                            "DOLLAR": "$",
+                            "STYLE": cfg.style,
+                            "TAG_PREFIX": cfg.tag_prefix,
+                            "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                            "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                        }
+                    )
+
         cmds["build_exe"] = cmd_build_exe
         del cmds["build_py"]
 
-    if 'py2exe' in sys.modules:  # py2exe enabled?
+    if "py2exe" in sys.modules:  # py2exe enabled?
         try:
             from py2exe.distutils_buildexe import py2exe as _py2exe  # py3
         except ImportError:
@@ -1646,13 +1709,17 @@ def run(self):
                 os.unlink(target_versionfile)
                 with open(cfg.versionfile_source, "w") as f:
                     LONG = LONG_VERSION_PY[cfg.VCS]
-                    f.write(LONG %
-                            {"DOLLAR": "$",
-                             "STYLE": cfg.style,
-                             "TAG_PREFIX": cfg.tag_prefix,
-                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                             })
+                    f.write(
+                        LONG
+                        % {
+                            "DOLLAR": "$",
+                            "STYLE": cfg.style,
+                            "TAG_PREFIX": cfg.tag_prefix,
+                            "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                            "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                        }
+                    )
+
         cmds["py2exe"] = cmd_py2exe
 
     # we override different "sdist" commands for both environments
@@ -1679,8 +1746,10 @@ def make_release_tree(self, base_dir, files):
             # updated value
             target_versionfile = os.path.join(base_dir, cfg.versionfile_source)
             print("UPDATING %s" % target_versionfile)
-            write_to_version_file(target_versionfile,
-                                  self._versioneer_generated_versions)
+            write_to_version_file(
+                target_versionfile, self._versioneer_generated_versions
+            )
+
     cmds["sdist"] = cmd_sdist
 
     return cmds
@@ -1735,11 +1804,15 @@ def do_setup():
     root = get_root()
     try:
         cfg = get_config_from_root(root)
-    except (EnvironmentError, configparser.NoSectionError,
-            configparser.NoOptionError) as e:
+    except (
+        EnvironmentError,
+        configparser.NoSectionError,
+        configparser.NoOptionError,
+    ) as e:
         if isinstance(e, (EnvironmentError, configparser.NoSectionError)):
-            print("Adding sample versioneer config to setup.cfg",
-                  file=sys.stderr)
+            print(
+                "Adding sample versioneer config to setup.cfg", file=sys.stderr
+            )
             with open(os.path.join(root, "setup.cfg"), "a") as f:
                 f.write(SAMPLE_CONFIG)
         print(CONFIG_ERROR, file=sys.stderr)
@@ -1748,15 +1821,18 @@ def do_setup():
     print(" creating %s" % cfg.versionfile_source)
     with open(cfg.versionfile_source, "w") as f:
         LONG = LONG_VERSION_PY[cfg.VCS]
-        f.write(LONG % {"DOLLAR": "$",
-                        "STYLE": cfg.style,
-                        "TAG_PREFIX": cfg.tag_prefix,
-                        "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                        "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                        })
-
-    ipy = os.path.join(os.path.dirname(cfg.versionfile_source),
-                       "__init__.py")
+        f.write(
+            LONG
+            % {
+                "DOLLAR": "$",
+                "STYLE": cfg.style,
+                "TAG_PREFIX": cfg.tag_prefix,
+                "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                "VERSIONFILE_SOURCE": cfg.versionfile_source,
+            }
+        )
+
+    ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py")
     if os.path.exists(ipy):
         try:
             with open(ipy, "r") as f:
@@ -1798,8 +1874,10 @@ def do_setup():
     else:
         print(" 'versioneer.py' already in MANIFEST.in")
     if cfg.versionfile_source not in simple_includes:
-        print(" appending versionfile_source ('%s') to MANIFEST.in" %
-              cfg.versionfile_source)
+        print(
+            " appending versionfile_source ('%s') to MANIFEST.in"
+            % cfg.versionfile_source
+        )
         with open(manifest_in, "a") as f:
             f.write("include %s\n" % cfg.versionfile_source)
     else: