Fix most mypy errors in the main package.

Add mypy ignores to setup.cfg.

fwdpy11/_functions/data_matrix_from_tables.py

@@ -22,15 +22,15 @@
 import numpy as np
 
 from .._fwdpy11 import _data_matrix_from_tables, _make_data_matrix
-from .._types import DataMatrix
+from .._types import DataMatrix, DiploidPopulation, TableCollection
 
 
 def make_data_matrix(
-    pop: "fwdpy11.DiploidPopulation",
+    pop: DiploidPopulation,
     samples: Union[List, np.ndarray],
     record_neutral: bool,
     record_selected: bool,
-) -> "fwdpy11.DataMatrix":
+) -> DataMatrix:
     """
     Create a :class:`fwdpy11.DataMatrix` from a table collection.
 
@@ -58,15 +58,15 @@ def make_data_matrix(
 
 
 def data_matrix_from_tables(
-    tables: "fwdpy11.TableCollection",
+    tables: TableCollection,
     samples: Union[List, np.ndarray],
     *,
     record_neutral: bool = True,
     record_selected: bool = True,
     include_fixations: bool = False,
     begin: float = 0.0,
     end: Optional[float] = None,
-) -> "fwdpy11.DataMatrix":
+) -> DataMatrix:
     """
     Create a :class:`fwdpy11.DataMatrix` from a table collection.
 

fwdpy11/_types/data_matrix.py

@@ -21,7 +21,7 @@
 
 import numpy as np
 
-from .._fwdpy11 import ll_DataMatrix
+from .._fwdpy11 import ll_DataMatrix, StateMatrix
 
 
 class DataMatrix(ll_DataMatrix):
@@ -55,7 +55,7 @@ def ncol(self) -> int:
         return self._ncol
 
     @property
-    def neutral(self) -> "fwdpy11.StateMatrix":
+    def neutral(self) -> StateMatrix:
         """:class:`fwdpy11.StateMatrix` for neutral variants"""
         return self._neutral
 
@@ -65,7 +65,7 @@ def neutral_keys(self) -> List[int]:
         return self._neutral_keys
 
     @property
-    def selected(self) -> "fwdpy11.StateMatrix":
+    def selected(self) -> StateMatrix:
         """:class:`fwdpy11.StateMatrix` for selected variants"""
         return self._selected
 

fwdpy11/_types/data_matrix_iterator.py

@@ -22,6 +22,7 @@
 import numpy as np
 
 from .._fwdpy11 import ll_DataMatrixIterator
+from .._types import TableCollection
 
 
 class DataMatrixIterator(ll_DataMatrixIterator):
@@ -60,7 +61,7 @@ class DataMatrixIterator(ll_DataMatrixIterator):
 
     def __init__(
         self,
-        tables: "fwdpy11.TableCollection",
+        tables: TableCollection,
         samples: Union[List[int], np.ndarray],
         intervals: List[Tuple[float, float]],
         neutral: bool,

fwdpy11/_types/demography_debugger.py

@@ -18,13 +18,17 @@
 #
 import collections
 import copy
-import typing
 import warnings
+from typing import Dict, List, Optional, Union
 
 import attr
 import fwdpy11
 import numpy as np
 
+from ..demographic_models import DemographicModelDetails
+from ..discrete_demography import DiscreteDemography
+from .diploid_population import DiploidPopulation
+
 
 def _create_event_list(o):
     try:
@@ -86,10 +90,14 @@ class DemographyDebugger(object):
         A list of initial deme sizes is now accepted.
     """
 
-    initial_deme_sizes = attr.ib(converter=_create_initial_deme_sizes)
-    _events = attr.ib(converter=_create_event_list)
-    simlen = attr.ib(converter=_convert_simlen, default=None)
-    deme_labels = attr.ib(default=None)
+    initial_deme_sizes: Union[List[int], DiploidPopulation] = attr.ib(
+        converter=_create_initial_deme_sizes
+    )
+    _events: Union[DiscreteDemography, DemographicModelDetails] = attr.ib(
+        converter=_create_event_list
+    )
+    simlen: int = attr.ib(converter=_convert_simlen, default=None)
+    deme_labels: Optional[Dict] = attr.ib(default=None)
 
     def __attrs_post_init__(self):
         self._validate_migration_rate_change_lengths(self._events)

fwdpy11/_types/diploid_population.py

@@ -1,16 +1,16 @@
 from typing import IO, Dict, Iterable, Iterator, List, Optional, Tuple, Union
 
-import fwdpy11._fwdpy11
 import fwdpy11._types
 import fwdpy11.tskit_tools._dump_tables_to_tskit
 import numpy as np
 import tskit
 
+from .._fwdpy11 import DiploidGenotype, DiploidMetadata, ll_DiploidPopulation
 from .population_mixin import PopulationMixin
 from .table_collection import TableCollection
 
 
-class DiploidPopulation(fwdpy11._fwdpy11.ll_DiploidPopulation, PopulationMixin):
+class DiploidPopulation(ll_DiploidPopulation, PopulationMixin):
     """
     A population of diploid individuals.
 
@@ -29,7 +29,7 @@ def __init__(
         N: Union[int, List[int]],
         length: float,
         *,
-        ll_pop: Optional[fwdpy11._fwdpy11.ll_DiploidPopulation] = None
+        ll_pop: Optional[ll_DiploidPopulation] = None
     ):
         if ll_pop is None:
             super(DiploidPopulation, self).__init__(N, length)
@@ -39,7 +39,7 @@ def __init__(
         self._pytables = TableCollection(self._tables)
 
     @classmethod
-    def create_from_tskit(cls, ts: tskit.TreeSequence) -> "fwdpy11.DiploidPopulation":
+    def create_from_tskit(cls, ts: tskit.TreeSequence):
         """
         Create a new object from an tskit.TreeSequence
 
@@ -63,23 +63,23 @@ def create_from_tskit(cls, ts: tskit.TreeSequence) -> "fwdpy11.DiploidPopulation
             for example.)
 
         """
-        ll = fwdpy11._fwdpy11.ll_DiploidPopulation._create_from_tskit(ts)
+        ll = ll_DiploidPopulation._create_from_tskit(ts)
         return cls(0, 0.0, ll_pop=ll)
 
     @classmethod
-    def load_from_file(cls, filename: str) -> "fwdpy11.DiploidPopulation":
+    def load_from_file(cls, filename: str):
         """
         Load population from the output of
         :func:`fwdpy11.DiploidPopulation.dump_to_file`.
 
         :param filename: A file name
         :type filename: str
         """
-        ll = fwdpy11._fwdpy11.ll_DiploidPopulation._load_from_file(filename)
+        ll = ll_DiploidPopulation._load_from_file(filename)
         return cls(0, 0.0, ll_pop=ll)
 
     @classmethod
-    def load_from_pickle_file(cls, filename: IO) -> "fwdpy11.DiploidPopulation":
+    def load_from_pickle_file(cls, filename: IO):
         """
         Read in a pickled population from a file.
         The file muse have been generated by
@@ -90,7 +90,7 @@ def load_from_pickle_file(cls, filename: IO) -> "fwdpy11.DiploidPopulation":
         .. versionadded: 0.3.0
 
         """
-        ll = fwdpy11._fwdpy11.ll_DiploidPopulation._load_from_pickle_file(filename)
+        ll = ll_DiploidPopulation._load_from_pickle_file(filename)
         return cls(0, 0.0, ll_pop=ll)
 
     @property
@@ -115,17 +115,17 @@ def ancient_sample_nodes(self) -> np.ndarray:
         return self.preserved_nodes
 
     @property
-    def ancient_sample_metadata(self) -> Iterable[fwdpy11.DiploidMetadata]:
+    def ancient_sample_metadata(self) -> Iterable[DiploidMetadata]:
         """Supports buffer protocol"""
         return self._ancient_sample_metadata
 
     @property
-    def diploids(self) -> Iterable[fwdpy11.DiploidGenotype]:
+    def diploids(self) -> Iterable[DiploidGenotype]:
         """Supports buffer protocol"""
         return self._diploids
 
     @property
-    def diploid_metadata(self) -> Iterable[fwdpy11.DiploidMetadata]:
+    def diploid_metadata(self) -> Iterable[DiploidMetadata]:
         """Supports buffer protocol"""
         return self._diploid_metadata
 

fwdpy11/_types/model_params.py

@@ -19,23 +19,15 @@
 import warnings
 
 import attr
-import numpy as np
-
 import fwdpy11
+import numpy as np
 from fwdpy11.class_decorators import (attr_add_asblack,
                                       attr_class_to_from_dict_no_recurse)
 
-_common_attr_attribs = {
-    "kw_only": True,
-    "frozen": True,
-    "slots": True,
-    "repr_ns": "fwdpy11",
-}
-
 
 @attr_add_asblack
 @attr_class_to_from_dict_no_recurse
-@attr.s(**_common_attr_attribs)
+@attr.s(kw_only=True, frozen=True, slots=True, repr_ns="fwdpy11")
 class MutationAndRecombinationRates(object):
     """
     Stores and validates the mutation and recombination rate parameters
@@ -107,7 +99,7 @@ def _convert_demography(o):
 
 @attr_add_asblack
 @attr_class_to_from_dict_no_recurse
-@attr.s(**_common_attr_attribs)
+@attr.s(kw_only=True, frozen=True, slots=True, repr_ns="fwdpy11")
 class ModelParams(object):
     """
     This class stores and validates the parameters of a simulation.

fwdpy11/_types/population_mixin.py

@@ -16,12 +16,12 @@
 # You should have received a copy of the GNU General Public License
 # along with fwdpy11.  If not, see <http://www.gnu.org/licenses/>.
 #
-from typing import Dict, Optional, Iterable
+from typing import Dict, Iterable, Optional
 
-import fwdpy11
-import fwdpy11._fwdpy11
 import numpy as np
 
+from .._fwdpy11 import HaploidGenome, Mutation
+
 
 class PopulationMixin(object):
     @property
@@ -35,19 +35,19 @@ def ancient_sample_genetic_values(self) -> np.ndarray:
         ..  versionadded 0.3.0
 
         """
-        return self._ancient_sample_genetic_values
+        return self._ancient_sample_genetic_values  # type: ignore
 
     @property
-    def fixations(self) -> Iterable[fwdpy11.Mutation]:
-        return self._fixations
+    def fixations(self) -> Iterable[Mutation]:
+        return self._fixations  # type: ignore
 
     @property
     def fixation_times(self) -> Iterable[int]:
-        return self._fixation_times
+        return self._fixation_times  # type: ignore
 
     @property
     def generation(self) -> int:
-        return self._generation
+        return self._generation  # type: ignore
 
     @property
     def genetic_values(self) -> np.ndarray:
@@ -59,34 +59,34 @@ def genetic_values(self) -> np.ndarray:
         ..  versionadded 0.3.0
 
         """
-        return self._genetic_values
+        return self._genetic_values  # type: ignore
 
     @property
-    def haploid_genomes(self) -> Iterable[fwdpy11.HaploidGenome]:
-        return self._haploid_genomes
+    def haploid_genomes(self) -> Iterable[HaploidGenome]:
+        return self._haploid_genomes  # type: ignore
 
     @property
     def mcounts(self) -> Iterable[int]:
-        return self._mcounts
+        return self._mcounts  # type: ignore
 
     @property
     def mcounts_ancient_samples(self) -> Iterable[int]:
-        return self._mcounts_ancient_samples
+        return self._mcounts_ancient_samples  # type: ignore
 
     def mutation_indexes(self, pos) -> Optional[np.ndarray]:
         """
         Return indexes in :attr:`fwdpy11.DiploidPopulation.mutations`
         that are mutations at postion `pos`.
         """
-        return self._mutation_indexes(pos)
+        return self._mutation_indexes(pos)  # type: ignore
 
     @property
     def mut_lookup(self) -> Dict:
-        return self._mut_lookup
+        return self._mut_lookup  # type: ignore
 
     @property
-    def mutations(self) -> Iterable[fwdpy11.Mutation]:
-        return self._mutations
+    def mutations(self) -> Iterable[Mutation]:
+        return self._mutations  # type: ignore
 
     @property
     def mutations_ndarray(self) -> np.ndarray:
@@ -100,11 +100,11 @@ def mutations_ndarray(self) -> np.ndarray:
 
         .. versionadded:: 0.4.0
         """
-        return self._mutations_ndarray
+        return self._mutations_ndarray  # type: ignore
 
     @property
     def N(self):
-        return self._N
+        return self._N  # type: ignore
 
     def find_fixation_by_key(self, key, offset=0):
         """
@@ -122,7 +122,7 @@ def find_fixation_by_key(self, key, offset=0):
         .. versionadded:: 0.2.0
 
         """
-        return self._find_fixation_by_key(key, offset)
+        return self._find_fixation_by_key(key, offset)  # type: ignore
 
     def find_mutation_by_key(self, key, offset):
         """
@@ -140,4 +140,4 @@ def find_mutation_by_key(self, key, offset):
         .. versionadded:: 0.2.0
 
         """
-        return self._find_mutation_by_key(key, offset)
+        return self._find_mutation_by_key(key, offset)  # type: ignore