Fix cyclic-import issues

bluepysnap/circuit_ids.py

@@ -17,7 +17,6 @@
 
 """Circuit ids."""
 import abc
-from collections import namedtuple
 
 import numpy as np
 import pandas as pd
@@ -26,9 +25,6 @@
 from bluepysnap._doctools import AbstractDocSubstitutionMeta
 from bluepysnap.exceptions import BluepySnapError
 
-CircuitNodeId = namedtuple("CircuitNodeId", ("population", "id"))
-CircuitEdgeId = namedtuple("CircuitEdgeId", ("population", "id"))
-
 
 class CircuitIds(abc.ABC):
     """High performances CircuitID container.
@@ -324,11 +320,11 @@ def __init__(self, index, sort_index=True):
     def __iter__(self):
         """Iterator on the CircuitNodeIds."""
         for index in self.index:
-            yield CircuitNodeId(*index)
+            yield utils.CircuitNodeId(*index)
 
     def __getitem__(self, item):
         """Getter on the CircuitNodeIds."""
-        return CircuitNodeId(*self.index[item])
+        return utils.CircuitNodeId(*self.index[item])
 
 
 class CircuitEdgeIds(
@@ -353,8 +349,8 @@ def __init__(self, index, sort_index=True):
     def __iter__(self):
         """Iterator on the CircuitEdgeIds."""
         for index in self.index:
-            yield CircuitEdgeId(*index)
+            yield utils.CircuitEdgeId(*index)
 
     def __getitem__(self, item):
         """Getter on the CircuitEdgeIds."""
-        return CircuitEdgeId(*self.index[item])
+        return utils.CircuitEdgeId(*self.index[item])

bluepysnap/circuit_validation.py

@@ -12,6 +12,7 @@
 
 from bluepysnap import schemas
 from bluepysnap.config import Parser
+from bluepysnap.exceptions import BluepySnapValidationError as Error
 from bluepysnap.morph import EXTENSIONS_MAPPING
 from bluepysnap.sonata_constants import DEFAULT_EDGE_TYPE, DEFAULT_NODE_TYPE
 from bluepysnap.utils import load_json
@@ -20,40 +21,6 @@
 MAX_MISSING_FILES_DISPLAY = 10
 
 
-class Error:
-    """Error used for reporting of validation errors."""
-
-    FATAL = "FATAL"
-    WARNING = "WARNING"
-    INFO = "INFO"
-
-    def __init__(self, level, message=None):
-        """Error.
-
-        Args:
-            level (str): error level
-            message (str|None): message
-        """
-        self.level = level
-        self.message = message
-
-    def __str__(self):
-        """Returns only message by default."""
-        return str(self.message)
-
-    __repr__ = __str__
-
-    def __eq__(self, other):
-        """Two errors are equal if inherit from Error and their level, message are equal."""
-        if not isinstance(other, Error):
-            return False
-        return self.level == other.level and self.message == other.message
-
-    def __hash__(self):
-        """Hash. Errors with the same level and message give the same hash."""
-        return hash(self.level) ^ hash(self.message)
-
-
 def fatal(message):
     """Shortcut for a fatal error.
 

bluepysnap/edges/edge_population.py

@@ -26,10 +26,10 @@
 from more_itertools import first
 
 from bluepysnap import query, utils
-from bluepysnap.circuit_ids import CircuitEdgeId, CircuitEdgeIds
+from bluepysnap.circuit_ids import CircuitEdgeIds
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.sonata_constants import DYNAMICS_PREFIX, ConstContainer, Edge
-from bluepysnap.utils import IDS_DTYPE
+from bluepysnap.utils import IDS_DTYPE, CircuitEdgeId
 
 
 def _is_empty(xs):

bluepysnap/edges/edges.py

@@ -20,10 +20,11 @@
 import numpy as np
 
 from bluepysnap._doctools import AbstractDocSubstitutionMeta
-from bluepysnap.circuit_ids import CircuitEdgeIds, CircuitNodeId, CircuitNodeIds
-from bluepysnap.edges import EdgePopulation
+from bluepysnap.circuit_ids import CircuitEdgeIds, CircuitNodeIds
+from bluepysnap.edges.edge_population import EdgePopulation
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.network import NetworkObject
+from bluepysnap.utils import CircuitNodeId
 
 
 class Edges(

bluepysnap/exceptions.py

@@ -27,3 +27,37 @@ class BluepySnapDeprecationError(Exception):
 
 class BluepySnapDeprecationWarning(DeprecationWarning):
     """SNAP deprecation warning."""
+
+
+class BluepySnapValidationError:
+    """Error used for reporting of validation errors."""
+
+    FATAL = "FATAL"
+    WARNING = "WARNING"
+    INFO = "INFO"
+
+    def __init__(self, level, message=None):
+        """Error.
+
+        Args:
+            level (str): error level
+            message (str|None): message
+        """
+        self.level = level
+        self.message = message
+
+    def __str__(self):
+        """Returns only message by default."""
+        return str(self.message)
+
+    __repr__ = __str__
+
+    def __eq__(self, other):
+        """Two errors are equal if inherit from Error and their level, message are equal."""
+        if not isinstance(other, BluepySnapValidationError):
+            return False
+        return self.level == other.level and self.message == other.message
+
+    def __hash__(self):
+        """Hash. Errors with the same level and message give the same hash."""
+        return hash(self.level) ^ hash(self.message)

bluepysnap/input.py

@@ -17,7 +17,7 @@
 """Simulation input access."""
 import libsonata
 
-from bluepysnap import BluepySnapError
+from bluepysnap.exceptions import BluepySnapError
 
 
 class SynapseReplay:

bluepysnap/nodes/node_population.py

@@ -68,7 +68,7 @@
 from more_itertools import first
 
 from bluepysnap import query, utils
-from bluepysnap.circuit_ids import CircuitNodeId, CircuitNodeIds
+from bluepysnap.circuit_ids import CircuitNodeIds
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.node_sets import NodeSet
 from bluepysnap.sonata_constants import DYNAMICS_PREFIX, ConstContainer, Node
@@ -429,7 +429,7 @@ def ids(self, group=None, limit=None, sample=None, raise_missing_property=True):
         else:
             result = utils.ensure_list(group)
             # test if first value is a CircuitNodeId all values are all CircuitNodeId
-            if isinstance(first(result, None), CircuitNodeId):
+            if isinstance(first(result, None), utils.CircuitNodeId):
                 try:
                     result = [cid.id for cid in result if cid.population == self.name]
                 except AttributeError as e:
@@ -526,7 +526,7 @@ def get(self, group=None, properties=None, raise_missing_property=True):
         if group is not None:
             if isinstance(group, (int, np.integer)):
                 self._check_id(group)
-            elif isinstance(group, CircuitNodeId):
+            elif isinstance(group, utils.CircuitNodeId):
                 group = self.ids(group, raise_missing_property=raise_missing_property)[0]
             else:
                 group = self.ids(group, raise_missing_property=raise_missing_property)

bluepysnap/nodes/nodes.py

@@ -23,7 +23,7 @@
 from bluepysnap.circuit_ids import CircuitNodeIds
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.network import NetworkObject
-from bluepysnap.nodes import NodePopulation
+from bluepysnap.nodes.node_population import NodePopulation
 
 
 class Nodes(

bluepysnap/schemas/schemas.py

@@ -8,6 +8,8 @@
 import referencing
 import yaml
 
+from bluepysnap.exceptions import BluepySnapValidationError as Error
+
 DEFINITIONS = "definitions"
 
 
@@ -45,7 +47,6 @@ def _wrap_errors(filepath, schema_errors, join_str):
     """
     # NOTE: would probably make more sense to have different parser for circuit,
     # as datatype and attributes only exists in the case of h5 files.
-    from bluepysnap.circuit_validation import Error
 
     warnings = []
     errors = []

bluepysnap/utils.py

@@ -19,11 +19,11 @@
 
 import json
 import warnings
+from collections import namedtuple
 from collections.abc import Iterable
 
 import numpy as np
 
-from bluepysnap.circuit_ids import CircuitEdgeId, CircuitNodeId
 from bluepysnap.exceptions import (
     BluepySnapDeprecationError,
     BluepySnapDeprecationWarning,
@@ -36,6 +36,9 @@
 # all returned node or edge ids.
 IDS_DTYPE = np.int64
 
+CircuitNodeId = namedtuple("CircuitNodeId", ("population", "id"))
+CircuitEdgeId = namedtuple("CircuitEdgeId", ("population", "id"))
+
 
 class Deprecate:
     """Class for the deprecations in BluepySnap."""

tests/test_circuit_ids.py

@@ -9,7 +9,7 @@
 
 import bluepysnap.circuit_ids as test_module
 from bluepysnap.exceptions import BluepySnapError
-from bluepysnap.utils import IDS_DTYPE
+from bluepysnap.utils import IDS_DTYPE, CircuitEdgeId, CircuitNodeId
 
 from utils import setup_tempdir
 
@@ -18,40 +18,14 @@ def _multi_index():
     return pd.MultiIndex.from_arrays([["a", "a", "b", "a"], [0, 1, 0, 2]])
 
 
-class TestCircuitNodeId:
-    def setup_method(self):
-        self.test_obj = test_module.CircuitNodeId("pop", 1)
-
-    def test_init(self):
-        assert isinstance(self.test_obj, test_module.CircuitNodeId)
-        assert isinstance(self.test_obj, tuple)
-
-    def test_accessors(self):
-        assert self.test_obj.population == "pop"
-        assert self.test_obj.id == 1
-
-
-class TestCircuitEdgeId:
-    def setup_method(self):
-        self.test_obj = test_module.CircuitEdgeId("pop", 1)
-
-    def test_init(self):
-        assert isinstance(self.test_obj, test_module.CircuitEdgeId)
-        assert isinstance(self.test_obj, tuple)
-
-    def test_accessors(self):
-        assert self.test_obj.population == "pop"
-        assert self.test_obj.id == 1
-
-
 class TestCircuitNodeIds:
     @property
     def ids_cls(self):
         return test_module.CircuitNodeIds
 
     @property
     def id_cls(self):
-        return test_module.CircuitNodeId
+        return CircuitNodeId
 
     @property
     def id_name(self):
@@ -335,7 +309,7 @@ def ids_cls(self):
 
     @property
     def id_cls(self):
-        return test_module.CircuitEdgeId
+        return CircuitEdgeId
 
     @property
     def id_name(self):

tests/test_edge_population.py

@@ -12,10 +12,10 @@
 import bluepysnap.edges.edge_population as test_module
 from bluepysnap.bbp import Synapse
 from bluepysnap.circuit import Circuit
-from bluepysnap.circuit_ids import CircuitEdgeId, CircuitEdgeIds, CircuitNodeIds
+from bluepysnap.circuit_ids import CircuitEdgeIds, CircuitNodeIds
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.sonata_constants import DEFAULT_EDGE_TYPE, Edge
-from bluepysnap.utils import IDS_DTYPE
+from bluepysnap.utils import IDS_DTYPE, CircuitEdgeId
 
 from utils import PICKLED_SIZE_ADJUSTMENT, TEST_DATA_DIR, copy_test_data, edit_config
 

tests/test_edges.py

@@ -11,9 +11,9 @@
 import bluepysnap.edges as test_module
 from bluepysnap.bbp import Synapse
 from bluepysnap.circuit import Circuit
-from bluepysnap.circuit_ids import CircuitEdgeId, CircuitEdgeIds, CircuitNodeId, CircuitNodeIds
+from bluepysnap.circuit_ids import CircuitEdgeIds, CircuitNodeIds
 from bluepysnap.exceptions import BluepySnapError
-from bluepysnap.utils import IDS_DTYPE
+from bluepysnap.utils import IDS_DTYPE, CircuitEdgeId, CircuitNodeId
 
 from utils import PICKLED_SIZE_ADJUSTMENT, TEST_DATA_DIR
 

tests/test_frame_report.py

@@ -8,10 +8,10 @@
 
 import bluepysnap.frame_report as test_module
 from bluepysnap.bbp import Cell
-from bluepysnap.circuit_ids import CircuitNodeId, CircuitNodeIds
+from bluepysnap.circuit_ids import CircuitNodeIds
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.simulation import Simulation
-from bluepysnap.utils import IDS_DTYPE
+from bluepysnap.utils import IDS_DTYPE, CircuitNodeId
 
 from utils import TEST_DATA_DIR
 

tests/test_morph.py

@@ -7,9 +7,9 @@
 
 import bluepysnap.morph as test_module
 from bluepysnap.circuit import Circuit
-from bluepysnap.circuit_ids import CircuitNodeId
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.sonata_constants import Node
+from bluepysnap.utils import CircuitNodeId
 
 from utils import TEST_DATA_DIR, copy_test_data, create_node_population, edit_config
 

tests/test_neuron_models.py

@@ -8,9 +8,9 @@
 
 import bluepysnap.neuron_models as test_module
 from bluepysnap.circuit import Circuit, CircuitConfig
-from bluepysnap.circuit_ids import CircuitNodeId
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.sonata_constants import Node
+from bluepysnap.utils import CircuitNodeId
 
 from utils import TEST_DATA_DIR, copy_config, copy_test_data, create_node_population, edit_config
 

tests/test_node_population.py

@@ -14,11 +14,11 @@
 
 from bluepysnap.bbp import Cell
 from bluepysnap.circuit import Circuit
-from bluepysnap.circuit_ids import CircuitNodeId, CircuitNodeIds
+from bluepysnap.circuit_ids import CircuitNodeIds
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.node_sets import NodeSets
 from bluepysnap.sonata_constants import DEFAULT_NODE_TYPE, Node
-from bluepysnap.utils import IDS_DTYPE
+from bluepysnap.utils import IDS_DTYPE, CircuitNodeId
 
 from utils import (
     PICKLED_SIZE_ADJUSTMENT,

tests/test_nodes.py

@@ -10,10 +10,10 @@
 
 import bluepysnap.nodes as test_module
 from bluepysnap.circuit import Circuit
-from bluepysnap.circuit_ids import CircuitNodeId, CircuitNodeIds
+from bluepysnap.circuit_ids import CircuitNodeIds
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.node_sets import NodeSets
-from bluepysnap.utils import IDS_DTYPE
+from bluepysnap.utils import IDS_DTYPE, CircuitNodeId
 
 from utils import PICKLED_SIZE_ADJUSTMENT, TEST_DATA_DIR