Release v0.10.0 (#2380)

# v0.10.0 (*08.08.2024*)

## Major Changes since v0.9.0
* Automatic network generation from high-level specifications.
* Units at the user interface including scaling and conversion.
* Morphologies are loaded through a unified interface; which produces a bundle of morphology, metadata, and segment tree.

## Internal Updates

* Documentation overhaul
* Python bindings offer type stubs; giving auto-completion and inline documentation in some editors/IDEs.
* Performance improvements
  - Label resolution uses hashes instead of strings, saving memory, network traffic, and time.
  - Spike delivery is up to 30% faster leading to 10% end-to-end improvements in some cases (e.g. `example/brunel`) 
  - Load balancing is faster and doesn't rely on MPI, leading to shorter setup times for large networks.
* Fixes
  - Better support for source builds on MacOS (aarch64)
  - `modcc` no longer allows internal variables (`v`, `celsius`, ...) as `ASSIGNED`
  - Better support for raw (C++) mechanisms
* MC cells renamed cable cells.
  
## Breaking changes
* Return values of all morphology loaders have changed.
* Raw (segment tree) loaders removed.
* Support for Python 3.8 removed.
* C++: Removed `simulation::inject_events`, use a generator instead. 
  
## New Contributors
* @ErbB4 made their first contribution in #2271

**Full Changelog**: v0.9.0...v0.10.0

.github/workflows/build-pip-wheels.yml

@@ -121,7 +121,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-          submodules: "recursive"
+          submodules: recursive
           path: arbor
       - name: Make full tarball
         run: |

CHANGELOG.md

@@ -1,3 +1,35 @@
+# v0.10.0 (*08.08.2024*)
+
+## Major Changes since v0.9.0
+* Automatic network generation from high-level specifications.
+* Units at the user interface including scaling and conversion.
+* Morphologies are loaded through a unified interface; which produces a bundle of morphology, metadata, and segment tree.
+
+## Internal Updates
+
+* Documentation overhaul
+* Python bindings offer type stubs; giving auto-completion and inline documentation in some editors/IDEs.
+* Performance improvements
+  - Label resolution uses hashes instead of strings, saving memory, network traffic, and time.
+  - Spike delivery is up to 30% faster leading to 10% end-to-end improvements in some cases (e.g. `example/brunel`) 
+  - Load balancing is faster and doesn't rely on MPI, leading to shorter setup times for large networks.
+* Fixes
+  - Better support for source builds on MacOS (aarch64)
+  - `modcc` no longer allows internal variables (`v`, `celsius`, ...) as `ASSIGNED`
+  - Better support for raw (C++) mechanisms
+* MC cells renamed cable cells.
+
+## Breaking changes
+* Return values of all morphology loaders have changed.
+* Raw (segment tree) loaders removed.
+* Support for Python 3.8 removed.
+* C++: Removed `simulation::inject_events`, use a generator instead. 
+
+## New Contributors
+* @ErbB4 made their first contribution in https://github.com/arbor-sim/arbor/pull/2271
+
+**Full Changelog**: https://github.com/arbor-sim/arbor/compare/v0.9.0...v0.10.0
+
 # v0.9.0
 
 ** 2023 08 09 **

VERSION

@@ -1 +1 @@
-0.9.1-dev
+0.10.0

cmake/GitSubmodule.cmake

@@ -18,7 +18,12 @@ function(check_git_submodule name path)
             "Or download submodules recursively when checking out:\n"
             "    git clone --recursive https://github.com/arbor-sim/arbor.git\n"
         )
-
+        get_filename_component(dotgit "${path}/" ABSOLUTE)
+        file(GLOB RESULT "${path}/*")
+        list(LENGTH RESULT RES_LEN)
+        if(NOT RES_LEN EQUAL 0)
+            message("However, the directory contains some ($RES_LEN) files. Possibly .git was omitted?")
+        endif()
         # if the repository was not available, and git failed, set AVAIL to false
         set(${success_var} OFF PARENT_SCOPE)
     endif()

doc/contrib/release.rst

@@ -43,13 +43,13 @@ Update tags/versions and test
    - README.md, ATTRIBUTIONS.md, CONTRIBUTING.md, CHANGELOG.md. For autogenerated CHANGELOG, see below.
    - Verify MANIFEST.in (required for PyPI sdist).
    - Double-check that all examples/tutorials/etc are covered by CI.
-   - Check Python/pip/PyPi metadata and scripts, e.g., ``setup.py``, ``pyproject.toml``.
+   - Check Python/pip/PyPi metadata and scripts, e.g., ``pyproject.toml``.
 
 #. Create new temp-branch ending in ``-rc``. E.g. ``v0.9.0-rc``
 #. Bump the ``VERSION`` file:
 
-   - For as long as `scikit-build-core` does not support loading fields from external files, also bump in `pyproject.toml`
-   - See also :ref:`dev-version`
+   - For as long as ``scikit-build-core`` does not support loading fields from external files, also bump in ```pyproject.toml``
+   - See also :ref:``dev-version``
    - Append ``-rc``. (Make sure there's no ``-dev``)
 
 #. Create a **draft PR**. Tag and push with ``-rc``. E.g. ``v0.9.0-rc``

doc/cpp/interconnectivity.rst

@@ -31,7 +31,7 @@ Interconnectivity
         The weight delivered to the target synapse.
         The weight is dimensionless, and its interpretation is
         specific to the synapse type of the target. For example,
-        the `expsyn` synapse interprets it as a conductance
+        the ``expsyn`` synapse interprets it as a conductance
         with units μS (micro-Siemens).
 
     .. cpp:member:: units::quantity delay
@@ -54,12 +54,14 @@ Interconnectivity
 
         - global id, uniquely identifying the source object inside the remote simulation,
         - local id, uniquely identifying the location of the source on the source object,
-        - selection policy, how to map sources `(gid, lid)` to the targets in Arbor.
+        - selection policy, how to map sources ``(gid, lid)`` to the targets in Arbor.
 
     .. Note::
-    The tuple ``(gid, lid)`` must be unique for each source. This addressing scheme follows Arbor's model of multiple
-    sources (threshold detectors) per cell. If the remote simulation does not provide multiple items per
-    source object, ``lid`` can be ignored and set to zero.
+
+       The tuple ``(gid, lid)`` must be unique for each source. This addressing
+       scheme follows Arbor's model of multiple sources (threshold detectors) per
+       cell. If the remote simulation does not provide multiple items per source
+       object, ``lid`` can be ignored and set to zero.
 
 
     .. cpp:member:: cell_local_label_type target

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "arbor"
-version = "0.9.1-dev" # TODO: make dependent on VERSION file. Blocked by https://github.com/scikit-build/scikit-build-core/issues/230
+version = "0.10.0" # TODO: make dependent on VERSION file. Blocked by https://github.com/scikit-build/scikit-build-core/issues/230
 readme = {file = "README.md", content-type = "text/markdown"}
 license = {file = "LICENSE"}
 description = "High performance simulation of networks of multicompartment neurons."
@@ -36,6 +36,7 @@ cmake.args = [
         "-DARB_WITH_PYTHON=ON",
         "-DARB_USE_BUNDLED_LIBS=ON",
 ]
+sdist.include = ["ext/*/.git"]
 wheel.install-dir = "arbor"
 wheel.packages = []
 

python/stubs/arbor/__init__.pyi

@@ -109,6 +109,8 @@ from arbor._arbor import poisson_schedule
 from arbor._arbor import print_config
 from arbor._arbor import probe
 from arbor._arbor import proc_allocation
+from arbor._arbor import profiler_initialize
+from arbor._arbor import profiler_summary
 from arbor._arbor import recipe
 from arbor._arbor import regular_schedule
 from arbor._arbor import reversal_potential
@@ -247,6 +249,8 @@ __all__ = [
     "print_config",
     "probe",
     "proc_allocation",
+    "profiler_initialize",
+    "profiler_summary",
     "recipe",
     "regular_schedule",
     "reversal_potential",
@@ -279,21 +283,21 @@ __config__: dict = {
     "mpi4py": False,
     "gpu": None,
     "vectorize": True,
-    "profiling": False,
+    "profiling": True,
     "neuroml": True,
     "bundled": True,
     "version": "0.9.1-dev",
-    "source": "2024-03-01T14:59:23+01:00 dcdfe101f389cb4854ac3d0a067feeb280600c88 modified",
-    "build_config": "DEBUG",
+    "source": "2024-04-11T13:13:43+02:00 8dac3a25b35f3e73f7ad50c27bd06d018e10bb6f modified",
+    "build_config": "RELEASE",
     "arch": "native",
     "prefix": "/usr/local",
-    "python_lib_path": "/usr/local/lib/python3.12/site-packages",
+    "python_lib_path": "/opt/homebrew/lib/python3.12/site-packages",
     "binary_path": "bin",
     "lib_path": "lib",
     "data_path": "share",
     "CXX": "/opt/homebrew/bin/clang++",
     "pybind-version": "2.11.1",
-    "timestamp": "Mar  4 2024 20:56:20",
+    "timestamp": "Apr 11 2024 20:38:51",
 }
 __version__: str = "0.9.1-dev"
 mnpos: int = 4294967295

python/stubs/arbor/_arbor/__init__.pyi

@@ -119,6 +119,8 @@ __all__ = [
     "print_config",
     "probe",
     "proc_allocation",
+    "profiler_initialize",
+    "profiler_summary",
     "recipe",
     "regular_schedule",
     "reversal_potential",
@@ -2046,6 +2048,40 @@ class morphology:
     A cell morphology.
     """
 
+    def __init__(self, arg0: segment_tree) -> None: ...
+    def __str__(self) -> str: ...
+    def branch_children(self, i: int) -> list[int]:
+        """
+        The child branches of branch i.
+        """
+
+    def branch_parent(self, i: int) -> int:
+        """
+        The parent branch of branch i.
+        """
+
+    def branch_segments(self, i: int) -> list[msegment]:
+        """
+        A list of the segments in branch i, ordered from proximal to distal ends of the branch.
+        """
+
+    def to_segment_tree(self) -> segment_tree:
+        """
+        Convert this morphology to a segment_tree.
+        """
+
+    @property
+    def empty(self) -> bool:
+        """
+        Whether the morphology is empty.
+        """
+
+    @property
+    def num_branches(self) -> int:
+        """
+        The number of branches in the morphology.
+        """
+
 class morphology_provider:
     def __init__(self, morphology: morphology) -> None:
         """
@@ -3277,6 +3313,12 @@ def print_config() -> None:
     Print Arbor's configuration.
     """
 
+def profiler_initialize(arg0: context) -> None: ...
+def profiler_summary(limit: float = 0.0) -> str:
+    """
+    Show summary of the profile; printing contributions above `limit` percent. Defaults to showing all.
+    """
+
 def stochastic_catalogue() -> catalogue: ...
 @typing.overload
 def write_component(