diff --git a/.github/workflows/test-everything.yml b/.github/workflows/test-everything.yml
index b776bd9dbf4bab70b40ce9951dcaf2bac5135617..59ae3c2cd0bfc99fc1dfe5933e3833b7766a550b 100644
--- a/.github/workflows/test-everything.yml
+++ b/.github/workflows/test-everything.yml
@@ -152,7 +152,7 @@ jobs:
mkdir build
cd build
cmake .. -GNinja -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DARB_WITH_PYTHON=ON -DARB_VECTORIZE=${{ matrix.config.simd }} -DPython3_EXECUTABLE=`which python` -DARB_WITH_MPI=${{ matrix.config.mpi }} -DARB_USE_BUNDLED_LIBS=ON -DARB_WITH_ASSERTIONS=ON
- ninja -j4 tests examples pyarb html
+ ninja -j4 tests examples pyarb
cd -
- if: ${{ matrix.variant == 'shared' }}
name: Build arbor
@@ -161,7 +161,7 @@ jobs:
mkdir build
cd build
cmake .. -GNinja -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DARB_WITH_PYTHON=ON -DARB_VECTORIZE=${{ matrix.config.simd }} -DPython3_EXECUTABLE=`which python` -DARB_WITH_MPI=${{ matrix.config.mpi }} -DARB_USE_BUNDLED_LIBS=ON -DARB_WITH_ASSERTIONS=ON -DBUILD_SHARED_LIBS=ON
- ninja -j4 tests examples pyarb html
+ ninja -j4 tests examples pyarb
cd -
- name: Install arbor
run: |
@@ -224,3 +224,34 @@ jobs:
run: python -m unittest discover -v -s python
- name: Run Python examples
run: scripts/run_python_examples.sh
+ testdocs:
+ name: "Docs build test"
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-20.04]
+ python-version: [3.7]
+ steps:
+ - name: Set up cmake
+ uses: jwlawson/actions-setup-cmake@v1.13
+ with:
+ cmake-version: ${{ matrix.config.cmake }}
+ - name: Set up Python
+ uses: actions/setup-python@v4
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Update pip
+ run: python -m pip install --upgrade pip
+ - name: Clone w/ submodules
+ uses: actions/checkout@v3
+ with:
+ submodules: recursive
+ - name: Install Python packages
+ run: python3 -m pip install -r doc/requirements.txt -U
+ - name: Build Arbor Docs
+ run: |
+ mkdir build
+ cd build
+ cmake .. -DARB_WITH_PYTHON=ON -DPython3_EXECUTABLE=`which python` -DARB_USE_BUNDLED_LIBS=ON
+ make html
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 55405a5ed17c2d6834f3d75067b33b4699371611..a65dad813304d23c8f123d7106b0a3f6aca6294a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
# v0.8.1
-** 2022 12 20 **
+** 2022 12 22 **
A 🎄 holiday release! Not much has changed in a month, but we'd like to share it all the same. Notably, the [Arbor GUI](https://github.com/arbor-sim/gui/) [is co-released](https://github.com/arbor-sim/gui/releases/tag/v0.8) as of Arbor v0.8, and v0.8.1 will be no different.
@@ -22,7 +22,24 @@ A 🎄 holiday release! Not much has changed in a month, but we'd like to share
## Full commit log
-...
+* Post release: add Zenodo entry, add Spack entry, update docs and scripts by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2036
+* BUGFIX: add ARB_CUDA flag to example catalogue by @boeschf in https://github.com/arbor-sim/arbor/pull/2039
+* Additional builtin functions to Arbor's NMODL dialect by @boeschf in https://github.com/arbor-sim/arbor/pull/2035
+* Throw better errors when we cannot look up ion diffusivity by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2040
+* âš¡ Voltage Processes by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2033
+* simplify make catalogue by @boeschf in https://github.com/arbor-sim/arbor/pull/2042
+* spack gpu option by @boeschf in https://github.com/arbor-sim/arbor/pull/2043
+* Remove deprecated spike_detector. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2041
+* make ARB_MODCC functional again by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2029
+* Yank v0.5 from Spack file, it does not build due to change in setting arch by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2037
+* Use pugixml instead of libxml2 by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2048
+* [BUGFIX] a-b-c: actually set compiler, improved default by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2051
+* Sde Tutorial by @boeschf in https://github.com/arbor-sim/arbor/pull/2044
+* Set Python to known version for all CI workflows by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2058
+* consistent mechanism ids by @boeschf in https://github.com/arbor-sim/arbor/pull/2057
+* Fix docs about exprelr. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2064
+* Allow __ in profiler names. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2065
+* CI fixes for wheel building, prep for musllinux, Spack by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2069
# v0.8
diff --git a/CITATION.bib b/CITATION.bib
index eaadd2932480116c45c3dc4877da0930aeba5a00..e2718882071a839671c103e3889c41a4149f47cc 100644
--- a/CITATION.bib
+++ b/CITATION.bib
@@ -8,7 +8,7 @@
doi={10.1109/EMPDP.2019.8671560},
ISSN={2377-5750}}
-@software{nora_abi_akar_2022_7323982,
+@software{nora_abi_akar_2022_7473671,
author = {Nora Abi Akar and
John Biddiscombe and
Benjamin Cumming and
@@ -30,12 +30,13 @@
Fabian Bösch and
Jannik Luboeinski and
Simon Frasch and
- Lukas Drescher},
- title = {Arbor Library v0.8},
+ Lukas Drescher and
+ Lennart Landsmeer},
+ title = {Arbor Library v0.8.1},
month = nov,
year = 2022,
publisher = {Zenodo},
version = {v0.8},
- doi = {10.5281/zenodo.7323982},
- url = {https://doi.org/10.5281/zenodo.7323982}
-}
+ doi = {10.5281/zenodo.7473671},
+ url = {https://doi.org/10.5281/zenodo.7473671}
+}
\ No newline at end of file
diff --git a/VERSION b/VERSION
index 6f4eebdf6f68fc72411793cdb19e3f1715b117f3..b1e9d951056912530cfc048ba13e16441c3a2ede 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.8.1
+0.8.2-dev
diff --git a/doc/concepts/domdec.rst b/doc/concepts/domdec.rst
index bc9ea903d4d0b4832e21ccb10dadc34e73351f22..ee4513acd2c7e70ab23825f23b9c492ea244f8da 100644
--- a/doc/concepts/domdec.rst
+++ b/doc/concepts/domdec.rst
@@ -34,12 +34,6 @@ We define some terms as used in the context of connectivity
.. glossary::
- connection
- Tuple of ``(source, target, weight, delay)`` describing an
- axon/synapse connection as travelling time (`delay`) and attenuation
- (`weight`) between two sites `source = (gid, threshold_detector)` and `target
- = (gid, synapse)` where `threshold_detector` and `synapse` are string labels.
-
cell_group
List of same-kinded cells that share some information. Must not be split
across domains.
diff --git a/doc/dev/cable_cell.rst b/doc/dev/cable_cell.rst
index 945b50788a3e619a8a2e5144672bef2452c12a2e..84b397ad4a439d05fc248a7455210b08182d4ccc 100644
--- a/doc/dev/cable_cell.rst
+++ b/doc/dev/cable_cell.rst
@@ -80,7 +80,7 @@ Discretisation splits the segments described by the morphology into *control
volumes* (CV; sometimes called *compartments*) according to a ``cv_policy``.
This allows us to construct a system of linear equations, the Hines matrix, to
describe the evolution of the CV voltages according to the cable equation. Refer
-to :ref:`Discretisation <discretisation>` and :ref:`Cable equation
+to :ref:`Discretisation <morph-cv-policies>` and :ref:`Cable equation
<cable_equation>`.
Backend-dependent data is stored in ``shared_state`` as per-compartment data and
diff --git a/doc/ecosystem/index.rst b/doc/ecosystem/index.rst
index 2ad07ee41769772e80d983016afcd39062b59040..1494cca56952e634a266307ffdd6dbb4665253d4 100644
--- a/doc/ecosystem/index.rst
+++ b/doc/ecosystem/index.rst
@@ -25,10 +25,10 @@ NSuite
A framework for maintaining and running benchmarks and validation tests for multi-compartment neural network simulations on HPC systems. `NSuite documentation <https://nsuite.readthedocs.io>`_
Arbor GUI
- The Arbor GUI visualizes cable cells and can be used to decorate morphologies. Single cell simulations can be ran (using the Arbor simulator) and output plotted right from the GUI. `Code repository and Readme <https://github.com/arbor-sim/gui>`_
+ The Arbor GUI visualizes cable cells and can be used to decorate morphologies. Single cell simulations can be ran (using the Arbor simulator) and output plotted right from the GUI. `Arbor GUI code repository and readme <https://github.com/arbor-sim/gui>`_
nmlcc
- Arbor has built-in read support for NeuroML morphologies, but not yet for other NeuroML components (mechanisms, networks). `nmlcc` is compiler/translator that aims to generate complete Arbor inputs for any NeuroML file. `Code repository and Readme <https://github.com/thorstenhater/nmlcc/>`_
+ Arbor has built-in read support for NeuroML morphologies, but not yet for other NeuroML components (mechanisms, networks). `nmlcc` is compiler/translator that aims to generate complete Arbor inputs for any NeuroML file. `nmlcc code repository and readme <https://github.com/thorstenhater/nmlcc/>`_
.. figure:: arbor.png
:align: center
diff --git a/doc/index.rst b/doc/index.rst
index 0bcbffbe20b807506ddd72865326c8b748306fd7..f375b97a286a9062c6a85edbabf536eb59e70114 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -6,8 +6,8 @@ Arbor
.. |ci| image:: https://github.com/arbor-sim/arbor/actions/workflows/test-everything.yml/badge.svg
:target: https://github.com/arbor-sim/arbor/actions/workflows/test-everything.yml
-.. |pythonwheels| image:: https://github.com/arbor-sim/arbor/actions/workflows/ciwheel.yml/badge.svg
- :target: https://github.com/arbor-sim/arbor/actions/workflows/ciwheel.yml
+.. |pythonwheels| image:: https://github.com/arbor-sim/arbor/actions/workflows/release.yml/badge.svg
+ :target: https://github.com/arbor-sim/arbor/actions/workflows/release.yml
.. |gitter| image:: https://badges.gitter.im/arbor-sim/community.svg
:target: https://gitter.im/arbor-sim/community
@@ -45,6 +45,9 @@ The Arbor software can be cited by version via Zenodo or via Arbors introductory
Latest version
|zlatest|
+Version 0.8.1
+ |z081|
+
Version 0.8
|z08|
@@ -80,6 +83,9 @@ Cite (Bibtex format)
.. |zlatest| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1459678.svg
:target: https://doi.org/10.5281/zenodo.1459678
+.. |z081| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7473671.svg
+ :target: https://doi.org/10.5281/zenodo.7473671
+
.. |z08| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7323982.svg
:target: https://doi.org/10.5281/zenodo.7323982
diff --git a/doc/install/python.rst b/doc/install/python.rst
index 2f18d59d2486686c4415e81443da9aa7a58484ec..ef223b97f97b56edf610e5d23b2fe6150b046d96 100644
--- a/doc/install/python.rst
+++ b/doc/install/python.rst
@@ -44,7 +44,7 @@ You are now ready to use Arbor! You can continue reading these documentation pag
* Ubuntu/Debian: ``git cmake gcc python3-dev python3-pip``
* Fedora/CentOS/OpenSuse: ``git cmake gcc-c++ python3-devel python3-pip``
- * MacOS: get ``brew`` `here <https://brew.sh>`_ and run ``brew install cmake clang python3``
+ * MacOS: get ``brew`` `at brew.sh <https://brew.sh>`_ and run ``brew install cmake clang python3``
* Windows: the simplest way is to use `WSL <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_ and then follow the instructions for Ubuntu.
.. _in_python_custom:
@@ -100,7 +100,7 @@ The following flags can be used to configure the installation:
documented below, may also have to be set appropriately to generated
vectorized code. See :ref:`install-architecture` for details.
* ``ARB_ARCH=<native|*>``: CPU micro-architecture to target. The advised
- default is ``native``. See `here
+ default is ``native``. See `the GNU GCC documentation
<https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html>`_ for a full list of
options.
diff --git a/doc/scripts/divio_docs_theme/layout.html b/doc/scripts/divio_docs_theme/layout.html
index f13c2c154d69caced76c3cf7f689d8f57c77a4c3..d6cee7855b955936f1add7063ea73436f9d7d1da 100755
--- a/doc/scripts/divio_docs_theme/layout.html
+++ b/doc/scripts/divio_docs_theme/layout.html
@@ -131,7 +131,7 @@
<div class="header-title-wrap">
<a class="header-title" href="{{ pathto(master_doc) }}">{{ project }}</a>{% if READTHEDOCS %} v: {{ current_version }}{% endif %}
</div>
- <a class="logo-link" target="_blank" href="{{ pathto(master_doc) }}"><img src="{{ pathto('_static/' + logo, 1) }}" class="logo" alt="{{ project }}"/></a>
+ <a class="logo-link" target="_blank" href="{{ pathto(master_doc) }}"><img src="{{ pathto(logo_url,1) }}" class="logo" alt="{{ project }}"/></a>
</div>
{% include "breadcrumbs.html" %}
diff --git a/doc/tutorial/probe_lfpykit.rst b/doc/tutorial/probe_lfpykit.rst
index 3faa6e8612a0315bbde244de955c32233b4e9d3d..5d25710010e859cbcc91e796f5a603c7e4b475f7 100644
--- a/doc/tutorial/probe_lfpykit.rst
+++ b/doc/tutorial/probe_lfpykit.rst
@@ -125,20 +125,20 @@ and returns the corresponding :class:`~arbor.place_pwlin` and :class:`~arbor.cab
.. literalinclude:: ../../python/example/probe_lfpykit.py
:language: python
- :lines: 72-116
+ :lines: 72-114
Store the function output:
.. literalinclude:: ../../python/example/probe_lfpykit.py
:language: python
- :lines: 119-120
+ :lines: 117-118
Next, we instantiate :class:`Recipe`, and execute the model for a few hundred ms,
sampling the different signals every 1 ms:
.. literalinclude:: ../../python/example/probe_lfpykit.py
:language: python
- :lines: 122-135
+ :lines: 120-133
Extract recorded membrane voltages, electrode and transmembrane currents.
Note that membrane voltages at branch points and intersections between CVs are dropped as
@@ -146,14 +146,14 @@ we only illustrate membrane voltages of segments with finite lengths.
.. literalinclude:: ../../python/example/probe_lfpykit.py
:language: python
- :lines: 137-152
+ :lines: 135-150
Finally we sum the stimulation and transmembrane currents, allowing the stimuli to mimic a synapse
current embedded in the membrane itself rather than an intracellular electrode current:
.. literalinclude:: ../../python/example/probe_lfpykit.py
:language: python
- :lines: 154-160
+ :lines: 152-158
.. _tutorial_lfpykit-lfpykit:
@@ -171,21 +171,21 @@ Starting with a class inherited from :class:`lfpykit.CellGeometry`:
.. literalinclude:: ../../python/example/probe_lfpykit.py
:language: python
- :lines: 170-202
+ :lines: 168-200
Then, a class inherited from :class:`lfpykit.LineSourcePotential`.
Other use cases may inherit from any other parent class defined in :mod:`lfpykit.models` in a similar manner:
.. literalinclude:: ../../python/example/probe_lfpykit.py
:language: python
- :lines: 205-253
+ :lines: 202-251
With these two classes one may then compute extracellular potentials from transmembrane
currents in space with a few lines of code:
.. literalinclude:: ../../python/example/probe_lfpykit.py
:language: python
- :lines: 256-278
+ :lines: 254-276
.. _tutorial_lfpykit-illustration:
diff --git a/doc/tutorial/single_cell_allen.rst b/doc/tutorial/single_cell_allen.rst
index 292e2afca44b300ba666efb07ebd6184c2a50e89..b1fae81fafdd41a7a34b94dee08f1cc787a4b94a 100644
--- a/doc/tutorial/single_cell_allen.rst
+++ b/doc/tutorial/single_cell_allen.rst
@@ -154,7 +154,7 @@ Then, we extract Arbor's output, accessible after the simulation ran at
The careful observer notices that this trace does not match the experimental data shown on the Allen website
(or in the ``488683423.nwb`` file). Sweep 35 clearly has 5 spikes, not 4. That is because in the Allen SDK,
the axon in the ``swc`` file is replaced with a stub, see
- `here <https://www.biorxiv.org/content/10.1101/2020.04.09.030239v1.full>`_ and `here <https://github.com/AllenInstitute/AllenSDK/issues/1683>`_.
+ `this paper <https://www.biorxiv.org/content/10.1101/2020.04.09.030239v1.full>`_ and `this AllenSDK Issue <https://github.com/AllenInstitute/AllenSDK/issues/1683>`_.
However, that adapted morphology is not exportable back to a modified ``swc`` file. When we tried to mimic
the procedure, we did not obtain the experimental trace.
diff --git a/scripts/check-all-tags.sh b/scripts/check-all-tags.sh
index dbb0907001548327c4821bb983805d48a29c96f5..57e9553aae013442f6e8979e0262c1020b1156a1 100755
--- a/scripts/check-all-tags.sh
+++ b/scripts/check-all-tags.sh
@@ -13,7 +13,7 @@ PREFIX="${1:-} `pwd`/build/bin"
cxx=/usr/local/opt/llvm/bin/clang++
cc=/usr/local/opt/llvm/bin/clang
-for tag in v0.4 v0.5.2 v0.6 v0.7 v0.8
+for tag in v0.4 v0.5.2 v0.6 v0.7 v0.8 v0.8.1
do
echo "Version=$tag"
rm -rf ext/*
@@ -54,7 +54,7 @@ check () {
fi
}
-for tag in "v0.4-79855b66" "v0.5.2-51e35898" "v0.6-930c23eb" "v0.7-d0e424b4" "v0.8-8e82ec1"
+for tag in "v0.4-79855b66" "v0.5.2-51e35898" "v0.6-930c23eb" "v0.7-d0e424b4" "v0.8-8e82ec1" "v0.8.1-c683a1f"
do
echo "Version=$tag"
for simd in ON OFF
diff --git a/spack/package.py b/spack/package.py
index 2cf738397b1e4979b241d94d69fe81675b6db282..34a30425b85d0185301a52855a1786444ab8e264 100644
--- a/spack/package.py
+++ b/spack/package.py
@@ -12,10 +12,15 @@ class Arbor(CMakePackage, CudaPackage):
homepage = "https://arbor-sim.org"
git = "https://github.com/arbor-sim/arbor.git"
- url = "https://github.com/arbor-sim/arbor/releases/download/v0.8/arbor-v0.8-full.tar.gz"
+ url = "https://github.com/arbor-sim/arbor/releases/download/v0.8.1/arbor-v0.8.1-full.tar.gz"
maintainers = ["bcumming", "brenthuisman", "haampie", "schmitts"]
version("master", branch="master", submodules=True)
+ version(
+ "0.8.1",
+ sha256="caebf96676ace6a9c50436541c420ca4bb53f0639dcab825de6fa370aacf6baa",
+ url="https://github.com/arbor-sim/arbor/releases/download/v0.8.1/arbor-v0.8.1-full.tar.gz",
+ )
version(
"0.8",
sha256="18df5600308841616996a9de93b55a105be0f59692daa5febd3a65aae5bc2c5d",