move to src layout. remove get_bridge_instance.

Author: benoitmartin88

setup.py

@@ -29,7 +29,7 @@
 
 import os
 
-from setuptools import setup
+from setuptools import setup, find_packages
 
 
 def find_version(*file_paths):
@@ -51,7 +51,7 @@ def readme():
         return f.read()
 
 
-version = find_version("deisa", "__version__.py")
+version = find_version("src/deisa/dask", "__version__.py")
 
 setup(name='deisa',
       version=version,
@@ -74,14 +74,21 @@ def readme():
 
       keywords='deisa in-situ',
 
-      packages=['deisa'],
+      package_dir={'': 'src'},
+      packages=find_packages(where="src"),
 
       install_requires=[
-          "dask",
+          'dask',
           'distributed'
       ],
 
-      tests_require=["pytest", "numpy"],
+      extras_require={
+          "test": [
+              "pytest",
+              "numpy",
+              "deisa-common @ git+https://github.com/deisa-project/common@main"
+          ]
+      },
       test_suite='test',
 
       classifiers=[

deisa/__init__.py src/deisa/dask/__init__.pydeisa/__init__.py renamed to src/deisa/dask/__init__.py

@@ -3,4 +3,4 @@
 # SPDX-License-Identifier: MIT
 ###################################################################################################
 
-from deisa.deisa import *
+from .deisa import *

deisa/__version__.py src/deisa/dask/__version__.pydeisa/__version__.py renamed to src/deisa/dask/__version__.py

@@ -44,29 +44,6 @@
 from distributed import Client, Future
 
 
-def get_bridge_instance(dask_scheduler_address: str | Client, mpi_comm_size: int, mpi_rank: int,
-                        arrays_metadata: dict[str, dict], **kwargs):
-    """
-    Get an instance of the Bridge class to establish a connection between MPI and Dask.
-
-    This function facilitates the creation of a `Bridge` instance that acts as
-    a communication layer between the MPI processes and the Dask scheduler. It
-    requires MPI-related parameters, Dask scheduler address, and metadata about
-    the arrays being utilized.
-
-    :param dask_scheduler_address: Address of the Dask scheduler or an instance
-        of dask.distributed.Client to connect to.
-    :param mpi_comm_size: Size of the MPI communicator.
-    :param mpi_rank: Rank of the MPI process within the communicator.
-    :param arrays_metadata: Metadata for arrays managed in the bridge. It should
-        indicate characteristics and configuration details about the arrays.
-    :param kwargs: Additional optional arguments to configure the Bridge instance.
-    :return: An instance of Bridge configured to mediate communication between MPI
-        and Dask.
-    """
-    return Bridge(dask_scheduler_address, mpi_comm_size, mpi_rank, arrays_metadata, **kwargs)
-
-
 class Bridge:
     def __init__(self, dask_scheduler_address: str | Client, mpi_comm_size: int, mpi_rank: int,
                  arrays_metadata: dict[str, dict], **kwargs):
@@ -163,7 +140,7 @@ def publish_data(self, array_name: str, data: np.ndarray, iteration: int):
         # TODO: what to do if error ?
 
 
-class Deisa(object):
+class Deisa:
     SLIDING_WINDOW_THREAD_PREFIX = "deisa_sliding_window_callback_"
 
     def __init__(self, dask_scheduler_address: str | Client, mpi_comm_size: int, nb_workers: int):

deisa/deisa.py src/deisa/dask/deisa.pydeisa/deisa.py renamed to src/deisa/dask/deisa.py

@@ -26,11 +26,12 @@
 # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 # =============================================================================
+
 import numpy as np
+from deisa.common import BridgeInterface
+from deisa.dask import Bridge
 from distributed import Client
 
-from deisa import get_bridge_instance
-
 
 class TestSimulation:
     __test__ = False
@@ -47,8 +48,8 @@ def __init__(self, client: Client, global_grid_size: tuple, mpi_parallelism: tup
         assert global_grid_size[1] % mpi_parallelism[1] == 0, "cannot compute local grid size for y dimension"
 
         self.nb_mpi_ranks = mpi_parallelism[0] * mpi_parallelism[1]
-        self.bridges = [get_bridge_instance(client, self.nb_mpi_ranks, rank, arrays_metadata) for rank in
-                        range(self.nb_mpi_ranks)]
+        self.bridges: list[BridgeInterface] = [Bridge(client, self.nb_mpi_ranks, rank, arrays_metadata) for rank in
+                                               range(self.nb_mpi_ranks)]
 
     def __gen_data(self, noise_level: int = 0) -> np.ndarray:
         # Create coordinate grid

test/TestSimulator.py

@@ -39,7 +39,7 @@
 from distributed import Client, LocalCluster, Queue, Variable
 
 from TestSimulator import TestSimulation
-from deisa.deisa import Deisa
+from deisa.dask import Deisa
 
 
 @pytest.mark.parametrize('global_shape', [(32, 32), (32, 16), (16, 32)])
@@ -155,7 +155,7 @@ def test_deisa_ctor_scheduler_file_error(self):
 
 
 class TestUsingDaskCluster:
-    @pytest.fixture(scope="class")
+    @pytest.fixture(scope="function")
     def env_setup(self):
         cluster = LocalCluster(n_workers=2, threads_per_worker=1, processes=False)
         client = Client(cluster)
@@ -240,7 +240,6 @@ def test_get_dask_array(self, global_grid_size: tuple, mpi_parallelism: tuple, n
 
         client, cluster = env_setup
 
-        scheduler_address = cluster.scheduler_address
         nb_mpi_ranks = mpi_parallelism[0] * mpi_parallelism[1]
         nb_workers = len(cluster.workers)
 
@@ -485,7 +484,7 @@ def window_callback(window: list[da.Array], timestep: int):
 
         def exception_handler(array_name, e):
             print(f"exception_handler. array_name={array_name}, e={e}", flush=True, file=sys.stderr)
-            # pytest.fail(str(e))
+            # pytest.fail(str(e))   # TODO
 
         deisa.register_sliding_window_callback("my_array", window_callback,
                                                window_size=1,