Import ABC from collections.abc instead of collections for Python 3.9…

… compatibility. (#485)

* Import ABC from collections.abc instead of collections for Python 3.9 compatibility.

pysb/bng.py

@@ -14,6 +14,7 @@
 from warnings import warn
 import shutil
 import collections
+from collections.abc import Sequence
 import pysb.pathfinder as pf
 import tokenize
 from pysb.logging import get_logger, EXTENDED_DEBUG
@@ -120,7 +121,7 @@ def _bng_param(cls, param):
             return '"%s"' % param
         elif isinstance(param, bool):
             return 1 if param else 0
-        elif isinstance(param, (collections.Sequence, numpy.ndarray)):
+        elif isinstance(param, (Sequence, numpy.ndarray)):
             return list(param)
         return param
 

pysb/core.py

@@ -12,6 +12,7 @@
 import numpy as np
 import scipy.sparse
 import networkx as nx
+from collections.abc import Iterable, Mapping, Sequence, Set
 
 try:
     reload
@@ -284,7 +285,7 @@ def __init__(self, name, sites=None, site_states=None, _export=True):
 
         # ensure sites is some kind of list (presumably of strings) but not a
         # string itself
-        if not isinstance(sites, collections.Iterable) or \
+        if not isinstance(sites, Iterable) or \
                isinstance(sites, basestring):
             raise ValueError("sites must be a list of strings")
 
@@ -2220,7 +2221,7 @@ def __init__(self):
         )
 
 
-class ComponentSet(collections.Set, collections.Mapping, collections.Sequence):
+class ComponentSet(Set, Mapping, Sequence):
     """
     An add-and-read-only container for storing model Components.
 
@@ -2428,7 +2429,7 @@ def __and__(self, other):
         # We require other to be a ComponentSet too so we know it will support
         # "in" efficiently.
         if not isinstance(other, ComponentSet):
-            return collections.Set.__and__(self, other)
+            return Set.__and__(self, other)
         return ComponentSet(value for value in self if value in other)
 
     def __rand__(self, other):
@@ -2452,7 +2453,7 @@ def rename(self, c, new_name):
             del m[c.name]
 
 
-class OdeView(collections.Sequence):
+class OdeView(Sequence):
     """Compatibility shim for the Model.odes property."""
 
     # This is necessarily coupled pretty tightly with Model. Note that we
@@ -2478,7 +2479,7 @@ def __len__(self):
         return len(self.model.species)
 
 
-class InitialConditionsView(collections.Sequence):
+class InitialConditionsView(Sequence):
     """Compatibility shim for the Model.initial_conditions property."""
 
     def __init__(self, model):

pysb/importers/json.py

@@ -6,6 +6,7 @@
 from pysb.annotation import Annotation
 import sympy
 import collections
+from collections.abc import Mapping
 import json
 import re
 from sympy.parsing.sympy_parser import parse_expr
@@ -37,7 +38,7 @@ def _modelget(self, name):
         return self.b.model.components[name]
 
     def decode_state_value(self, sv):
-        if isinstance(sv, collections.Mapping) and '__object__' in sv:
+        if isinstance(sv, Mapping) and '__object__' in sv:
             if sv['__object__'] == '__multistate__':
                 return MultiState(*sv['sites'])
             if sv['__object__'] == 'ANY':
@@ -46,7 +47,7 @@ def decode_state_value(self, sv):
                 return WILD
         try:
             if len(sv) == 2 and isinstance(sv[0], basestring) \
-                    and isinstance(sv[1], (int, collections.Mapping)):
+                    and isinstance(sv[1], (int, Mapping)):
                 return sv[0], self.decode_state_value(sv[1])
         except TypeError:
             pass

pysb/pattern.py

@@ -1,4 +1,5 @@
 import collections
+from collections.abc import Iterable
 from .core import ComplexPattern, MonomerPattern, Monomer, \
     ReactionPattern, ANY, as_complex_pattern, DanglingBondError, \
     ReusedBondError, Rule
@@ -191,7 +192,7 @@ def _get_bonds_in_monomer_pattern(mp):
             if isinstance(sc, int):
                 bonds_used.append(sc)
             elif not isinstance(sc, basestring) and \
-                    isinstance(sc, collections.Iterable):
+                    isinstance(sc, Iterable):
                 [bonds_used.append(b) for b in sc if isinstance(b, int)]
 
     if pat is None:

pysb/simulator/base.py

@@ -3,6 +3,7 @@
 import itertools
 import sympy
 import collections
+from collections.abc import Mapping, Sequence
 import numbers
 from pysb.core import MonomerPattern, ComplexPattern, as_complex_pattern, \
                       Parameter, Expression, Model, ComponentSet
@@ -168,7 +169,7 @@ def initials_length(self):
                 return len(self.param_values)
 
     def _update_initials_dict(self, initials_dict, initials_source, subs=None):
-        if isinstance(initials_source, collections.Mapping):
+        if isinstance(initials_source, Mapping):
             # Can't just use .update() as we need to test
             # equality with .is_equivalent_to()
             for cp, value_obj in initials_source.items():
@@ -177,7 +178,7 @@ def _update_initials_dict(self, initials_dict, initials_source, subs=None):
                        for existing_cp in initials_dict):
                     continue
 
-                if isinstance(value_obj, (collections.Sequence, np.ndarray))\
+                if isinstance(value_obj, (Sequence, np.ndarray))\
                         and all(isinstance(v, numbers.Number) for v in value_obj):
                     value = value_obj
                 elif isinstance(value_obj, Expression):
@@ -277,17 +278,17 @@ def initials(self):
 
         # Check potential quick return options
         if self._run_initials is not None:
-            if not isinstance(self._run_initials, collections.Mapping) and \
+            if not isinstance(self._run_initials, Mapping) and \
                     self._initials is None:
                 return self._run_initials
-        elif not isinstance(self._initials, collections.Mapping) and \
+        elif not isinstance(self._initials, Mapping) and \
                 self._initials is not None:
             return self._initials
 
         # At this point (after dimensionality check), we can return
         # self._run_initials if it's not a dictionary and not None
         if self._run_initials is not None and not isinstance(
-                self._run_initials, collections.Mapping):
+                self._run_initials, Mapping):
             return self._run_initials
 
         n_sims_initials = self._check_run_initials_vs_base_initials_length()
@@ -331,7 +332,7 @@ def _process_incoming_initials(self, new_initials):
                                      'MonomerPattern or ComplexPattern' %
                                      repr(cplx_pat))
                 # if val is a number, convert it to a single-element array
-                if not isinstance(val, (collections.Sequence, np.ndarray)):
+                if not isinstance(val, (Sequence, np.ndarray)):
                     val = [val]
                     new_initials[cplx_pat] = np.array(val)
                 # otherwise, check whether simulator supports multiple
@@ -468,7 +469,7 @@ def _process_incoming_params(self, new_params):
                     raise IndexError("new_params dictionary has unknown "
                                      "parameter name (%s)" % key)
                 # if val is a number, convert it to a single-element array
-                if not isinstance(val, collections.Sequence):
+                if not isinstance(val, Sequence):
                     val = [val]
                     new_params[key] = np.array(val)
                 # Check all elements are the same length

pysb/simulator/bng.py

@@ -6,9 +6,9 @@
 from pysb.core import as_complex_pattern, Parameter, \
     InvalidComplexPatternException
 import collections
+from collections.abc import Iterable
 import os
 
-
 class BngSimulator(Simulator):
     """ Simulate a model using BioNetGen """
     _supports = {
@@ -111,7 +111,7 @@ def run(self, tspan=None, initials=None, param_values=None, n_runs=1,
 
         if method == 'nf':
             if population_maps is not None and (not isinstance(
-                    population_maps, collections.Iterable) or
+                    population_maps, Iterable) or
                     any(not isinstance(pm, PopulationMap) for pm in
                         population_maps)):
                 raise ValueError('population_maps should be a list of '

pysb/simulator/cupsoda.py

@@ -15,6 +15,7 @@
 from pysb.pathfinder import get_path
 import sympy
 import collections
+from collections.abc import Iterable
 try:
     import pandas as pd
 except ImportError:
@@ -168,7 +169,7 @@ def __init__(self, model, tspan=None, initials=None, param_values=None,
                                                param_values=param_values,
                                                verbose=verbose, **kwargs)
         self.gpu = kwargs.pop('gpu', (0, ))
-        if not isinstance(self.gpu, collections.Iterable):
+        if not isinstance(self.gpu, Iterable):
             self.gpu = [self.gpu]
         self._obs_species_only = kwargs.pop('obs_species_only', True)
         self._cleanup = kwargs.pop('cleanup', True)