Merge remote-tracking branch 'origin/master' into qa/clean-up-load-ba…

…lance

.github/workflows/sanitize.yml

@@ -1,10 +1,18 @@
 name: Sanitize
 
 on:
-  pull_request:
+  push:
     branches: [ master ]
     paths-ignore: 'doc/**'
 
+  schedule:
+    - cron: '0 2 * * 0' # run at 2 AM every sunday
+
+permissions:
+  issues: write
+  pull-requests: write
+  contents: write
+
 jobs:
   build:
     name: "Sanitize"
@@ -58,7 +66,39 @@ jobs:
           cd -
       - name: Run unit tests
         run: |
-          build/bin/unit --gtest_filter=-*DeathTest
-          build/bin/unit-modcc
+          build/bin/unit --gtest_filter=-*DeathTest 2>&1 | tee output.log
+          build/bin/unit-modcc 2>&1 | tee -a output.log
+        shell: bash
       - name: Run examples
-        run: scripts/run_cpp_examples.sh
+        run: scripts/run_cpp_examples.sh 2>&1 | tee -a output.log
+        shell: bash
+      - name: Ouput File
+        if: ${{ failure() && github.event_name == 'schedule' }}
+        run: |
+          FENCE='```'
+          HEADER="$(cat << EOF
+          <details>
+          
+          <summary>output from test runs</summary>
+          
+          ${FENCE}
+          EOF
+          )"
+          FOOTER="$(cat << EOF
+          ${FENCE}
+          
+          </details>
+          EOF
+          )"
+          echo "${HEADER}" > issue.md
+          cat output.log >> issue.md
+          echo "${FOOTER}" >> issue.md
+          echo -e "\nSee also the [corresponding workflow](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})\n" >> issue.md
+      - name: Create Issue From File
+        if: ${{ failure() && github.event_name == 'schedule' }}
+        uses: peter-evans/create-issue-from-file@v4
+        with:
+          title: '[AUTOMATED] Sanitize checks failed'
+          content-filepath: ./issue.md
+          labels: |
+            automated issue

.github/workflows/test-docs.yaml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04]
-        python-version: [3.7]
+        python-version: [3.8]
     steps:
       - name: Set up cmake
         uses: jwlawson/[email protected]

.github/workflows/test-matrix.yml

@@ -20,7 +20,7 @@ jobs:
             os:    "ubuntu-20.04",
             cc:    "gcc-9",
             cxx:   "g++-9",
-            py:    "3.7",
+            py:    "3.8",
             cmake: "3.19.x",
             mpi:   "ON",
             simd:  "OFF"
@@ -30,7 +30,7 @@ jobs:
             os:    "ubuntu-20.04",
             cc:    "clang-9",
             cxx:   "clang++-9",
-            py:    "3.7",
+            py:    "3.8",
             cmake: "3.19.x",
             mpi:   "ON",
             simd:  "OFF"
@@ -40,7 +40,7 @@ jobs:
             os:    "macos-11",
             cc:    "clang",
             cxx:   "clang++",
-            py:    "3.7",
+            py:    "3.8",
             cmake: "3.19.x",
             mpi:   "ON",
             simd:  "OFF"

.github/workflows/test-pip.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04]
-        python-version: [3.7]
+        python-version: [3.8]
     steps:
       - uses: actions/setup-python@v4
         with:

.readthedocs.yml

@@ -13,11 +13,10 @@ sphinx:
 formats: []
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.7"
+    python: "3.11"
 
 python:
-  system_packages: true
   install:
-    - requirements: doc/requirements.txt
+    - requirements: doc/requirements.txt

CHANGELOG.md

@@ -103,7 +103,7 @@ After much more delay than anticipated, we are very happy to present a new Arbor
 ## New Contributors
 * @musicinmybrain made their first contribution in https://github.com/arbor-sim/arbor/pull/2080
 
-**Full Changelog**: https://github.com/arbor-sim/arbor/compare/v0.8...v0.9.0-rc
+**Full Changelog**: https://github.com/arbor-sim/arbor/compare/v0.8.1...v0.9.0
 
 
 # v0.8.1

CITATION.bib

@@ -8,7 +8,7 @@ @INPROCEEDINGS{
     doi={10.1109/EMPDP.2019.8671560},
     ISSN={2377-5750}}
     
-@software{nora_abi_akar_2022_7473671,
+@software{nora_abi_akar_2023_8233847,
   author       = {Nora Abi Akar and
                   John Biddiscombe and
                   Benjamin Cumming and
@@ -32,11 +32,11 @@ @software{nora_abi_akar_2022_7473671
                   Simon Frasch and
                   Lukas Drescher and
                   Lennart Landsmeer},
-  title        = {Arbor Library v0.8.1},
+  title        = {Arbor Library v0.9.0},
   month        = nov,
-  year         = 2022,
+  year         = 2023,
   publisher    = {Zenodo},
-  version      = {v0.8},
-  doi          = {10.5281/zenodo.7473671},
-  url          = {https://doi.org/10.5281/zenodo.7473671}
-}
+  version      = {v0.9.0},
+  doi          = {10.5281/zenodo.8233847},
+  url          = {https://doi.org/10.5281/zenodo.8233847}
+}

CMakeLists.txt

@@ -359,7 +359,7 @@ endif()
 #----------------------------------------------------------
 
 # The minimum version of Python supported by Arbor.
-set(arb_py_version 3.7.0)
+set(arb_py_version 3.8.0)
 
 if(DEFINED PYTHON_EXECUTABLE)
     set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})

VERSION

@@ -1 +1 @@
-0.9.0
+0.9.1-dev

arbor/CMakeLists.txt

@@ -26,7 +26,7 @@ set(arbor_sources
     io/serialize_hex.cpp
     label_resolution.cpp
     lif_cell_group.cpp
-    mc_cell_group.cpp
+    cable_cell_group.cpp
     mechcat.cpp
     mechinfo.cpp
     memory/gpu_wrappers.cpp

arbor/backends/event_delivery.md

@@ -20,7 +20,7 @@ Target handles are used by the lowered cell implementation to identify a particu
 instance that can receive events — ultimately via `net_receive` — and corresponding simulated
 cell. The cell information is given as an index into the cell group collection of cells.
 
-Target handles are represented by the `target_handle` struct, opaque to `mc_cell_group`,
+Target handles are represented by the `target_handle` struct, opaque to `cable_cell_group`,
 but created in the `fvm_multicell` for each point mechanism (synapse) in the cell group.
 
 ### Deliverable events

arbor/mc_cell_group.cpp → arbor/cable_cell_group.cpp

@@ -15,7 +15,7 @@
 #include "cell_group.hpp"
 #include "fvm_lowered_cell.hpp"
 #include "label_resolution.hpp"
-#include "mc_cell_group.hpp"
+#include "cable_cell_group.hpp"
 #include "profile/profiler_macro.hpp"
 #include "sampler_map.hpp"
 #include "util/filter.hpp"
@@ -26,7 +26,7 @@
 
 namespace arb {
 
-mc_cell_group::mc_cell_group(const std::vector<cell_gid_type>& gids,
+cable_cell_group::cable_cell_group(const std::vector<cell_gid_type>& gids,
                              const recipe& rec,
                              cell_label_range& cg_sources,
                              cell_label_range& cg_targets,
@@ -68,7 +68,7 @@ mc_cell_group::mc_cell_group(const std::vector<cell_gid_type>& gids,
     spike_sources_.shrink_to_fit();
 }
 
-void mc_cell_group::reset() {
+void cable_cell_group::reset() {
     spikes_.clear();
 
     for (auto &entry: sampler_map_) {
@@ -92,9 +92,9 @@ struct sampler_call_info {
     sample_size_type end_offset;
 };
 
-void mc_cell_group::t_serialize(serializer& ser,
+void cable_cell_group::t_serialize(serializer& ser,
                               const std::string& k) const { serialize(ser, k, *this); }
-void mc_cell_group::t_deserialize(serializer& ser,
+void cable_cell_group::t_deserialize(serializer& ser,
                                 const std::string& k) { deserialize(ser, k, *this); }
 
 // Working space for computing and collating data for samplers.
@@ -382,7 +382,7 @@ void run_samples(
     std::visit([&](auto& x) {run_samples(x, sc, raw_times, raw_samples, sample_records, scratch); }, sc.pdata_ptr->info);
 }
 
-void mc_cell_group::advance(epoch ep, time_type dt, const event_lane_subrange& event_lanes) {
+void cable_cell_group::advance(epoch ep, time_type dt, const event_lane_subrange& event_lanes) {
     time_type tstart = lowered_->time();
 
     // Bin and collate deliverable events from event lanes.
@@ -510,7 +510,7 @@ void mc_cell_group::advance(epoch ep, time_type dt, const event_lane_subrange& e
     }
 }
 
-void mc_cell_group::add_sampler(sampler_association_handle h, cell_member_predicate probeset_ids,
+void cable_cell_group::add_sampler(sampler_association_handle h, cell_member_predicate probeset_ids,
                                 schedule sched, sampler_function fn)
 {
     std::lock_guard<std::mutex> guard(sampler_mex_);
@@ -524,17 +524,17 @@ void mc_cell_group::add_sampler(sampler_association_handle h, cell_member_predic
     }
 }
 
-void mc_cell_group::remove_sampler(sampler_association_handle h) {
+void cable_cell_group::remove_sampler(sampler_association_handle h) {
     std::lock_guard<std::mutex> guard(sampler_mex_);
     sampler_map_.erase(h);
 }
 
-void mc_cell_group::remove_all_samplers() {
+void cable_cell_group::remove_all_samplers() {
     std::lock_guard<std::mutex> guard(sampler_mex_);
     sampler_map_.clear();
 }
 
-std::vector<probe_metadata> mc_cell_group::get_probe_metadata(cell_member_type probeset_id) const {
+std::vector<probe_metadata> cable_cell_group::get_probe_metadata(cell_member_type probeset_id) const {
     // Probe associations are fixed after construction, so we do not need to grab the mutex.
 
     std::optional<probe_tag> maybe_tag = util::value_by_key(probe_map_.tag, probeset_id);

arbor/mc_cell_group.hpp → arbor/cable_cell_group.hpp

@@ -22,11 +22,11 @@
 
 namespace arb {
 
-class ARB_ARBOR_API mc_cell_group: public cell_group {
+class ARB_ARBOR_API cable_cell_group: public cell_group {
 public:
-    mc_cell_group() = default;
+    cable_cell_group() = default;
 
-    mc_cell_group(const std::vector<cell_gid_type>& gids,
+    cable_cell_group(const std::vector<cell_gid_type>& gids,
                   const recipe& rec,
                   cell_label_range& cg_sources,
                   cell_label_range& cg_targets,
@@ -57,7 +57,7 @@ class ARB_ARBOR_API mc_cell_group: public cell_group {
 
     std::vector<probe_metadata> get_probe_metadata(cell_member_type probeset_id) const override;
 
-    ARB_SERDES_ENABLE(mc_cell_group, gids_, spikes_, lowered_);
+    ARB_SERDES_ENABLE(cable_cell_group, gids_, spikes_, lowered_);
 
     virtual void t_serialize(serializer& ser, const std::string& k) const override;
     virtual void t_deserialize(serializer& ser, const std::string& k) override;

arbor/cell_group_factory.cpp

@@ -9,7 +9,7 @@
 #include "execution_context.hpp"
 #include "fvm_lowered_cell.hpp"
 #include "lif_cell_group.hpp"
-#include "mc_cell_group.hpp"
+#include "cable_cell_group.hpp"
 #include "spike_source_cell_group.hpp"
 
 namespace arb {
@@ -27,7 +27,7 @@ ARB_ARBOR_API cell_group_factory cell_kind_implementation(
     switch (ck) {
     case cell_kind::cable:
         return [bk, ctx, seed](const gid_vector& gids, const recipe& rec, cell_label_range& cg_sources, cell_label_range& cg_targets) {
-            return make_cell_group<mc_cell_group>(gids, rec, cg_sources, cg_targets, make_fvm_lowered_cell(bk, ctx, seed));
+            return make_cell_group<cable_cell_group>(gids, rec, cg_sources, cg_targets, make_fvm_lowered_cell(bk, ctx, seed));
         };
 
     case cell_kind::spike_source:

arbor/fvm_lowered_cell.hpp

@@ -172,7 +172,7 @@ struct fvm_probe_data {
 };
 
 // Samplers are tied to probe ids, but one probe id may
-// map to multiple probe representations within the mc_cell_group.
+// map to multiple probe representations within the cable_cell_group.
 
 struct probe_association_map {
     // Keys are probe id.

doc/concepts/decor.rst

@@ -176,7 +176,7 @@ Take for example the built-in mechanism for passive leaky dynamics:
 .. _cablecell-scaled-mechs:
 
 4. Scaling Mechanism and Membrane Parameters
-~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Mechanism parameters are usually homogeneous along a cell. However, sometimes it
 is useful to scale parameters based on inhomogeneous properties.