Remove deprecations (#1026)

Remove deprecated modules and deprecation warning. viewer module was not included to be treated separately

neurom/__init__.py

@@ -61,7 +61,6 @@
 
 from neurom.features import get
 from neurom.io.utils import MorphLoader, load_morphology, load_morphologies
-from neurom.io.utils import load_neuron, load_neurons
 from neurom.exceptions import NeuroMDeprecationWarning
 
 APICAL_DENDRITE = NeuriteType.apical_dendrite

neurom/check/runner.py

@@ -35,9 +35,8 @@
 
 from neurom import load_morphology
 from neurom.check import check_wrapper
-from neurom.exceptions import ConfigError
+from neurom.exceptions import ConfigError, NeuroMError
 from neurom.io import utils
-from neurom.utils import warn_deprecated
 
 L = logging.getLogger(__name__)
 
@@ -147,10 +146,10 @@ def _sanitize_config(config):
             checks = config['checks']
             if 'morphology_checks' not in checks:
                 checks['morphology_checks'] = []
-            if 'neuron_checks' in checks:
-                warn_deprecated('"neuron_checks" is deprecated, use "morphology_checks" instead '
-                                'for the config of `neurom.check`')  # pragma: no cover
-                checks['morphology_checks'] = config['neuron_checks']  # pragma: no cover
+            if 'neuron_checks' in checks:  # pragma: no cover
+                raise NeuroMError(
+                    "'neuron_checks' is not supported. Please rename it into 'morphology_checks'"
+                )
         else:
             raise ConfigError('Need to have "checks" in the config')
 

neurom/core/__init__.py

@@ -30,5 +30,5 @@
 
 # those imports here for backward compatibility
 from neurom.core.soma import Soma
-from neurom.core.morphology import Section, Neurite, Morphology, Neuron
+from neurom.core.morphology import Section, Neurite, Morphology
 from neurom.core.population import Population

neurom/core/morphology.py

@@ -38,7 +38,7 @@
 from neurom.core.dataformat import COLS
 from neurom.core.types import NeuriteIter, NeuriteType
 from neurom.core.population import Population
-from neurom.utils import flatten, warn_deprecated
+from neurom.utils import flatten
 
 
 class Section:
@@ -420,13 +420,6 @@ def graft_morphology(section):
     return Morphology(m)
 
 
-def graft_neuron(section):
-    """Deprecated in favor of ``graft_morphology``."""
-    warn_deprecated('`neurom.core.neuron.graft_neuron` is deprecated in favor of '
-                    '`neurom.core.morphology.graft_morphology`')  # pragma: no cover
-    return graft_morphology(section)  # pragma: no cover
-
-
 class Neurite:
     """Class representing a neurite tree."""
 
@@ -588,12 +581,3 @@ def __repr__(self):
         """Return a string representation."""
         return 'Morphology <soma: %s, n_neurites: %d>' % \
             (self.soma, len(self.neurites))
-
-
-class Neuron(Morphology):
-    """Deprecated ``Neuron`` class. Use ``Morphology`` instead."""
-    def __init__(self, filename, name=None):
-        """Dont use me."""
-        super().__init__(filename, name)  # pragma: no cover
-        warn_deprecated('`neurom.core.neuron.Neuron` is deprecated in favor of '
-                        '`neurom.core.morphology.Morphology`')  # pragma: no cover

neurom/io/utils.py

@@ -41,7 +41,6 @@
 from neurom.core.morphology import Morphology
 from neurom.core.population import Population
 from neurom.exceptions import NeuroMError
-from neurom.utils import warn_deprecated
 
 L = logging.getLogger(__name__)
 
@@ -165,13 +164,6 @@ def load_morphology(morph, reader=None):
     return Morphology(morph, Path(morph).name)
 
 
-def load_neuron(morph, reader=None):
-    """Deprecated in favor of ``load_morphology``."""
-    warn_deprecated('`neurom.io.utils.load_neuron` is deprecated in favor of '
-                    '`neurom.io.utils.load_morphology`')  # pragma: no cover
-    return load_morphology(morph, reader)  # pragma: no cover
-
-
 def load_morphologies(morphs,
                       name=None,
                       ignored_exceptions=(),
@@ -199,10 +191,3 @@ def load_morphologies(morphs,
         files = morphs
         name = name or 'Population'
     return Population(files, name, ignored_exceptions, cache)
-
-
-def load_neurons(morphs, name=None, ignored_exceptions=(), cache=False):
-    """Deprecated in favor of ``load_morphologies``."""
-    warn_deprecated('`neurom.io.utils.load_neurons` is deprecated in favor of '
-                    '`neurom.io.utils.load_morphologies`')  # pragma: no cover
-    return load_morphologies(morphs, name, ignored_exceptions, cache)  # pragma: no cover