bsb-arbor 6.0.0a15__py3-none-any.whl → 6.0.1__py3-none-any.whl

bsb_arbor/adapter.py

@@ -63,7 +63,20 @@ class SingleReceiverCollection(list):
 
 
 class Population:
+    """
+    Represents a population of cells for the Arbor simulator.
+
+    This class manages a collection of cells from a specific cell model, handling their
+    GID ranges and providing methods to access and manipulate subsets of the population.
+    """
     def __init__(self, simdata, cell_model, offset):
+        """
+        Initialize a population of cells.
+
+        :param simdata: The simulation data container
+        :param cell_model: The cell model for this population
+        :param offset: The GID offset for this population
+        """
         self._model = cell_model
         self._simdata = simdata
         ps = cell_model.get_placement_set(simdata.chunks)
@@ -72,22 +85,61 @@ class Population:
 
     @property
     def model(self):
+        """
+        Get the cell model associated with this population.
+
+        :return: The cell model object
+        """
         return self._model
 
     @property
     def offset(self):
+        """
+        Get the GID offset for this population.
+
+        :return: The GID offset value
+        """
         return self._offset
 
     def __len__(self):
+        """
+        Get the total number of cells in this population.
+
+        :return: The number of cells
+        """
         return sum(stop - start for start, stop in self._ranges)
 
     def __contains__(self, i):
+        """
+        Check if a GID is part of this population.
+
+        :param i: The GID to check
+        :return: True if the GID is in this population, False otherwise
+        """
         return any(start <= i < stop for start, stop in self._ranges)
 
     def copy(self):
+        """
+        Create a copy of this population.
+
+        :return: A new Population instance with the same properties
+        """
         return Population(self._simdata, self._model, self._offset)
 
     def __getitem__(self, item):
+        """
+        Get a subset of the population based on the provided index or mask.
+
+        Supports various indexing methods:
+        - Boolean masking: Select cells based on a boolean mask
+        - Integer indexing: Select specific cells by their indices
+        - Slicing: Select a range of cells
+
+        :param item: The index, slice, or mask to use for selection
+        :return: A new Population instance containing the selected cells
+        :raises ValueError: If the dimensions of the mask don't match the population
+        :raises IndexError: If an index is out of bounds
+        """
         # Boolean masking, kind of
         if getattr(item, "dtype", None) == bool or _all_bools(item):  # noqa: E721
             if len(item) != len(self):
@@ -106,6 +158,14 @@ class Population:
             return self._subpop_one(item)
 
     def _get_ranges(self, chunks, ps, offset):
+        """
+        Calculate the GID ranges for this population based on chunk statistics.
+
+        :param chunks: The simulation chunks to include
+        :param ps: The placement set for the cell model
+        :param offset: The starting GID offset
+        :return: A list of (start, stop) tuples representing GID ranges
+        """
         stats = ps.get_chunk_stats()
         ranges = []
         for chunk, len_ in sorted(
@@ -117,6 +177,15 @@ class Population:
         return ranges
 
     def _subpop_np(self, arr):
+        """
+        Create a subpopulation from a numpy array of indices.
+
+        This method handles array-based indexing, including boolean masks,
+        integer arrays, and slices.
+
+        :param arr: A numpy array of indices to include in the subpopulation
+        :return: A new Population instance containing only the selected cells
+        """
         pop = self.copy()
         if not len(pop):
             return pop
@@ -138,6 +207,13 @@ class Population:
         return pop
 
     def _subpop_one(self, item):
+        """
+        Create a subpopulation containing a single cell.
+
+        :param item: The index of the cell to include
+        :return: A new Population instance containing only the selected cell
+        :raises IndexError: If the index is out of bounds
+        """
         if item >= len(self):
             raise IndexError(f"Index {item} out of bounds for size {len(self)}")
         pop = self.copy()
@@ -150,6 +226,11 @@ class Population:
                 ptr += stop - start
 
     def __iter__(self):
+        """
+        Iterate over all GIDs in this population.
+
+        :yield: Each GID in the population's ranges
+        """
         yield from itertools.chain.from_iterable(range(r[0], r[1]) for r in self._ranges)
 
 

bsb_arbor-6.0.1.dist-info/METADATA

@@ -0,0 +1,29 @@
+Metadata-Version: 2.4
+Name: bsb-arbor
+Version: 6.0.1
+Summary: Arbor simulation adapter for the BSB framework.
+Author-email: Robin De Schepper <robin@alexandria.sc>, Dimitri Rodarie <dimitri.rodarie@unipv.it>
+Requires-Python: >=3.10,<4
+Description-Content-Type: text/markdown
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+License-File: LICENSE
+Requires-Dist: numpy~=1.21
+Requires-Dist: bsb-core~=6.0
+Requires-Dist: arborize~=6.0
+Requires-Dist: arbor~=0.10; sys_platform != 'win32'
+
+[![Build Status](https://github.com/dbbs-lab/bsb/actions/workflows/main.yml/badge.svg)](https://github.com/dbbs-lab/bsb/actions/workflows/main.yml)
+[![Documentation](https://readthedocs.org/projects/bsb-arbor/badge/?version=latest)](https://bsb-arbor.readthedocs.io/en/latest/?badge=latest)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+
+# bsb-arbor
+
+bsb-arbor is a plugin of the [BSB](https://github.com/dbbs-lab/bsb)
+It contains the interfaces and tools to simulate BSB circuits with the 
+[Arbor simulator](https://arbor-sim.org/).
+
+Comprehensive documentation is available at:
+
+* [BSB Documentation](https://bsb.readthedocs.io/en/latest)
+* [bsb-arbor Documentation](https://bsb-arbor.readthedocs.io/en/latest)
+

{bsb_arbor-6.0.0a15.dist-info → bsb_arbor-6.0.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
 bsb_arbor/__init__.py,sha256=1kJSMSgt1vnjllcKXRUfomu0XTczbqYkkRf-TjSQbP8,437
-bsb_arbor/adapter.py,sha256=2aeDo_znf7_przJMDe7AqfVse9GlRA0WA8qDDJcfEqs,16136
+bsb_arbor/adapter.py,sha256=OJdbfNVQ_74KtFlgQit1MCi4zuoNzf2WOzs-wIzDv00,18996
 bsb_arbor/cell.py,sha256=V4JxsdwS_FNfQ_wRjnJH-kFVLMwipzLSHcYbf-VgP_c,2476
 bsb_arbor/connection.py,sha256=1u3yLA7R0G3Rxxf0Zvw3AcBa242n8XeSVej_r8iXjXY,2446
 bsb_arbor/device.py,sha256=5PD6nujSlTu74BonS5Ojp7LhopusQ4cDVEEAYg1aAMA,1752
@@ -8,8 +8,8 @@ bsb_arbor/devices/__init__.py,sha256=8PgEH4gktvNW7KywuFXIzZXsPuWayWt0BPuKz6sJyPA
 bsb_arbor/devices/poisson_generator.py,sha256=PGcx1YQn6WoZ3yZGXbW0nF1gtDo1fC7KGnmFYaklR3s,1045
 bsb_arbor/devices/probe.py,sha256=Dv0GiWxNUuiKRYg8wCik2xlQLvh5dJBE4e-v3-W2eLg,1732
 bsb_arbor/devices/spike_recorder.py,sha256=xJ720Tg9EO71RIc54ZEN04UqUDNyyI5TliC1ZD5UHWc,1339
-bsb_arbor-6.0.0a15.dist-info/entry_points.txt,sha256=8z5oyflKGOBD2smUKyrUit-_2JqBs85g8rm5YOM8SYg,43
-bsb_arbor-6.0.0a15.dist-info/licenses/LICENSE,sha256=ljOS4DjXvqEo5VzGfdaRwgRZPbNScGBmfwyC8PChvmQ,32422
-bsb_arbor-6.0.0a15.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
-bsb_arbor-6.0.0a15.dist-info/METADATA,sha256=Lu2mGvQBc8furvuB3gjEn40uR7dby3SxuCfAdFokQNg,1602
-bsb_arbor-6.0.0a15.dist-info/RECORD,,
+bsb_arbor-6.0.1.dist-info/entry_points.txt,sha256=8z5oyflKGOBD2smUKyrUit-_2JqBs85g8rm5YOM8SYg,43
+bsb_arbor-6.0.1.dist-info/licenses/LICENSE,sha256=ljOS4DjXvqEo5VzGfdaRwgRZPbNScGBmfwyC8PChvmQ,32422
+bsb_arbor-6.0.1.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+bsb_arbor-6.0.1.dist-info/METADATA,sha256=tINOGljnDSXkfeQBOfjZIdlEDRCeAVBB2GrsdS7YDd4,1347
+bsb_arbor-6.0.1.dist-info/RECORD,,

bsb_arbor-6.0.0a15.dist-info/METADATA

@@ -1,36 +0,0 @@
-Metadata-Version: 2.4
-Name: bsb-arbor
-Version: 6.0.0a15
-Summary: Arbor simulation adapter for the BSB framework.
-Author-email: Robin De Schepper <robin@alexandria.sc>, Dimitri Rodarie <dimitri.rodarie@unipv.it>
-Requires-Python: >=3.10,<4
-Description-Content-Type: text/markdown
-Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
-License-File: LICENSE
-Requires-Dist: numpy~=1.21
-Requires-Dist: bsb-core~=6.0
-Requires-Dist: arborize~=6.0
-Requires-Dist: arbor~=0.10; sys_platform != 'win32'
-Requires-Dist: bsb-arbor[test, docs] ; extra == "dev"
-Requires-Dist: pre-commit~=3.5 ; extra == "dev"
-Requires-Dist: ruff>=0.8.2 ; extra == "dev"
-Requires-Dist: snakeviz~=2.1 ; extra == "dev"
-Requires-Dist: furo~=2024.0 ; extra == "docs"
-Requires-Dist: sphinxext-bsb~=6.0 ; extra == "docs"
-Requires-Dist: bsb-core[parallel] ; extra == "test"
-Requires-Dist: bsb-hdf5~=6.0 ; extra == "test"
-Requires-Dist: bsb-test~=6.0 ; extra == "test"
-Requires-Dist: coverage>=7.3 ; extra == "test"
-Provides-Extra: dev
-Provides-Extra: docs
-Provides-Extra: test
-
-[![Build Status](https://github.com/dbbs-lab/bsb-arbor/actions/workflows/main.yml/badge.svg)](https://github.com/dbbs-lab/bsb-arbor/actions/workflows/main.yml)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-
-# bsb-arbor
-
-bsb-arbor is a plugin of the [BSB](https://github.com/dbbs-lab/bsb) (see also 
-[bsb-core](https://github.com/dbbs-lab/bsb-core)). 
-It contains the interfaces and tools to simulate BSB circuit with the 
-[Arbor simulator](https://arbor-sim.org/).