bsb-arbor 6.0.0a18__tar.gz → 6.0.2__tar.gz

bsb_arbor-6.0.2/PKG-INFO

@@ -0,0 +1,29 @@
+Metadata-Version: 2.4
+Name: bsb-arbor
+Version: 6.0.2
+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-6.0.2/README.md

@@ -0,0 +1,14 @@
+[![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-6.0.0a18 → bsb_arbor-6.0.2}/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-6.0.0a18 → bsb_arbor-6.0.2}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "bsb-arbor"
-version = "6.0.0-a18"
+version = "6.0.2"
 readme = "README.md"
 requires-python = ">=3.10,<4"
 dynamic = [ "description" ]
@@ -31,30 +31,16 @@ dependencies = [
   [project.license]
   file = "LICENSE"
 
-  [project.optional-dependencies]
-  test = [
-  "bsb-core[parallel]",
-  "bsb-hdf5~=6.0",
-  "bsb-test~=6.0",
-  "coverage>=7.3"
-]
-  docs = [ "furo~=2024.0", "sphinxext-bsb~=6.0" ]
-  dev = [
-  "bsb-arbor[test,docs]",
-  "pre-commit~=3.5",
-  "ruff>=0.8.2",
-  "snakeviz~=2.1"
-]
-
 [project.entry-points."bsb.simulation_backends"]
 arbor = "bsb_arbor"
 
-[tool.flit.module]
-name = "bsb_arbor"
-
 [tool.uv]
+default-groups = [ "dev", "docs", "test" ]
 sources = { }
 
+[tool.flit.module]
+name = "bsb_arbor"
+
 [tool.coverage.run]
 branch = true
 source = [ "bsb_arbor" ]

bsb_arbor-6.0.0a18/PKG-INFO

@@ -1,36 +0,0 @@
-Metadata-Version: 2.4
-Name: bsb-arbor
-Version: 6.0.0a18
-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/).

bsb_arbor-6.0.0a18/README.md

@@ -1,9 +0,0 @@
-[![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/).