Merge pull request #588 from ICB-DCM/develop

* Ignore B027 empty method in an abstract base class (#587)

* Ignore B027 empty method in an abstract base class

* Refactor EPSMixin

* Fix EPSMixin for ConcurrentFutureSampler

* restrict distributed, see dask/distributed#7227

* tmp add bokeh for tests to avoid restrictions

* version+releasenotes 0.12.7

.flake8

@@ -11,6 +11,8 @@ extend-ignore =
   E203
   # Don't be crazy if line too long
   E501
+  # Empty method in an abstract base class
+  B027
 
 per-file-ignores =
   # Imported but unused

CHANGELOG.rst

@@ -8,6 +8,16 @@ Release Notes
 ...........
 
 
+0.12.7 (2022-10-30)
+-------------------
+
+Minor:
+
+* Ignore B027 empty method in an abstract base class
+* Refactor EPSMixin
+* Fix EPSMixin for ConcurrentFutureSampler
+* Temporarily add bokeh to test due to dask error
+
 0.12.6 (2022-08-30)
 -------------------
 

pyabc/population.py

@@ -104,9 +104,10 @@ def __init__(self, particles: List[Particle]):
             raise AssertionError(
                 "A population should only consist of accepted particles"
             )
-        if not np.isclose(sum(p.weight for p in particles), 1):
+
+        if not np.isclose(total_weight := sum(p.weight for p in particles), 1):
             raise AssertionError(
-                "The population total weight is not normalized."
+                f"The population total weight {total_weight} is not normalized."
             )
 
         self.calculate_model_probabilities()

pyabc/sampler/concurrent_future.py

@@ -1,3 +1,5 @@
+"""Sample via the python concurrent futures executor interface."""
+
 from .base import Sampler
 from .eps_mixin import EPSMixin
 
@@ -11,66 +13,49 @@ class ConcurrentFutureSampler(EPSMixin, Sampler):
 
     Parameters
     ----------
-
-    cfuture_executor: concurrent.futures.Executor, required
+    cfuture_executor: "concurrent.futures.Executor"
         Configured object that implements the concurrent.futures.Executor
         interface
-
     client_max_jobs:
         Maximum number of jobs that can submitted to the client at a time.
         If this value is smaller than the maximum number of cores provided by
         the distributed infrastructure, the infrastructure will not be utilized
         fully.
-
     default_pickle:
         Specify if the sampler uses pythons default pickle function to
         communicate the submit function to python; if this is the case, a
         cloud-pickle based workaround is used to pickle the simulate and
         evaluate functions. This allows utilization of locally defined
         functions, which can not be pickled using default pickle, at the cost
         of an additional pickling overhead.
-
-    batch_size: int, optional
+    batch_size:
         Number of parameter samples that are evaluated in one remote execution
         call. Batch submission can be used to reduce the communication overhead
         for fast (ms-s) model evaluations. Large batch sizes can result in un-
         necessary model evaluations. By default, batch_size=1, i.e. no batching
         is done.
-
     """
 
     def __init__(
         self,
         cfuture_executor=None,
-        client_max_jobs=200,
-        default_pickle=True,
-        batch_size=1,
+        client_max_jobs: int = 200,
+        default_pickle: bool = True,
+        batch_size: int = 1,
     ):
-        super().__init__()
-
-        # Assign Client
-        self.my_client = cfuture_executor
-
-        # Client options
-        self.client_max_jobs = client_max_jobs
-
-        # Job state
-        self.jobs_queued = 0
-
-        # Empty functions
-        self.simulate_one = None
-        self.accept_one = None
-
-        # Option pickling
-        self.default_pickle = default_pickle
-
-        # Batchsize
-        self.batch_size = batch_size
+        EPSMixin.__init__(
+            self,
+            client=cfuture_executor,
+            client_max_jobs=client_max_jobs,
+            default_pickle=default_pickle,
+            batch_size=batch_size,
+        )
+        Sampler.__init__(self)
 
     def __getstate__(self):
         d = dict(self.__dict__)
-        del d['my_client']
+        del d['client']
         return d
 
-    def client_cores(self):
+    def client_cores(self) -> int:
         return self.client_max_jobs

pyabc/sampler/dask_sampler.py

@@ -1,3 +1,5 @@
+"""Sample via dask."""
+
 import numpy as np
 from dask.distributed import Client
 
@@ -13,7 +15,7 @@ class DaskDistributedSampler(EPSMixin, Sampler):
 
     Parameters
     ----------
-    dask_client: dask.Client, optional
+    dask_client:
         The configured dask Client.
         If none is provided, then a local dask distributed cluster is created.
     client_max_jobs:
@@ -22,14 +24,14 @@ class DaskDistributedSampler(EPSMixin, Sampler):
         the distributed infrastructure, the infrastructure will not be utilized
         fully.
     default_pickle:
-        Specify if the sampler uses pythons default pickle function to
+        Specify if the sampler uses python's default pickle function to
         communicate the submit function to python; if this is the case, a
         cloud-pickle based workaround is used to pickle the simulate and
         evaluate functions. This allows utilization of locally defined
         functions, which can not be pickled using default pickle, at the cost
         of an additional pickling overhead. For dask, this workaround should
         not be necessary and it should be save to use default_pickle=false.
-    batch_size: int, optional
+    batch_size:
         Number of parameter samples that are evaluated in one remote execution
         call. Batchsubmission can be used to reduce the communication overhead
         for fast (ms-s) model evaluations. Large batch sizes can result in un-
@@ -39,41 +41,35 @@ class DaskDistributedSampler(EPSMixin, Sampler):
 
     def __init__(
         self,
-        dask_client=None,
-        client_max_jobs=np.inf,
-        default_pickle=False,
-        batch_size=1,
+        dask_client: Client = None,
+        client_max_jobs: int = np.inf,
+        default_pickle: bool = False,
+        batch_size: int = 1,
     ):
-        super().__init__()
-
         # Assign Client
         if dask_client is None:
             dask_client = Client()
-        self.my_client = dask_client
-
-        # Client options
-        self.client_max_jobs = client_max_jobs
-
-        # Job state
-        self.jobs_queued = 0
-
-        # For dask, we use cloudpickle by default
-        self.default_pickle = default_pickle
 
-        # Batchsize
-        self.batch_size = batch_size
+        EPSMixin.__init__(
+            self,
+            client=dask_client,
+            client_max_jobs=client_max_jobs,
+            default_pickle=default_pickle,
+            batch_size=batch_size,
+        )
+        Sampler.__init__(self)
 
     def __getstate__(self):
         d = dict(self.__dict__)
-        del d['my_client']
+        del d['client']
         return d
 
-    def client_cores(self):
-        return sum(self.my_client.ncores().values())
+    def client_cores(self) -> int:
+        return sum(self.client.ncores().values())
 
     def shutdown(self):
         """Shutdown the dask client.
         If it was started without arguments, the
         local cluster that was started at the same time is also closed.
         """
-        self.my_client.close()
+        self.client.close()