v0.8.1 postrelease

.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
+

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
+* ⚡ 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
 

CITATION.bib

@@ -8,7 +8,7 @@ @INPROCEEDINGS{
     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 @@ @software{nora_abi_akar_2022_7323982
                   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}
+}

VERSION

@@ -1 +1 @@
-0.8.1
+0.8.2-dev

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.

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

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

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
 

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.
 

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" %}

doc/tutorial/probe_lfpykit.rst

@@ -125,35 +125,35 @@ 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
 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:
 

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.
 

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

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",