Polish CodeQL and do some chores

.github/workflows/benchmarks.yml

@@ -20,11 +20,11 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y ninja-build ccache
       - name: Set up cmake
-        uses: jwlawson/actions-setup-cmake@v1.13
+        uses: jwlawson/actions-setup-cmake@v2.0.0
         with:
           cmake-version: 3.22.x
       - name: Clone w/ submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       # figure out vector extensions for ccache key

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

@@ -17,7 +17,7 @@ jobs:
 
     steps:
       - name: Get Arbor
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Create unique version in pyproject.toml
@@ -38,7 +38,7 @@ jobs:
 
     steps:
       - name: Get Arbor
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Delete pyproject.toml
@@ -69,7 +69,7 @@ jobs:
       - name: Get packages
         run: python3 -m pip install build
       - name: Get Arbor
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Delete pyproject.toml
@@ -118,7 +118,7 @@ jobs:
     needs: [build_binary_wheels, build_sdist]
     steps:
       - name: "Clone w/ submodules"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           submodules: "recursive"

.github/workflows/codeql.yml

@@ -46,13 +46,13 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         submodules: recursive
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -81,6 +81,6 @@ jobs:
     #     ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
       with:
         category: "/language:${{matrix.language}}"

.github/workflows/lint.yml

@@ -11,17 +11,17 @@ jobs:
     strategy:
       fail-fast: false
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
       - name: Get packages
         run: |
           python -m pip install --upgrade pip
           pip install flake8
       - name: Clone w/ submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Python Formatting

.github/workflows/sanitize.yml

@@ -33,11 +33,11 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y ninja-build ccache
       - name: Set up cmake
-        uses: jwlawson/actions-setup-cmake@v1.13
+        uses: jwlawson/actions-setup-cmake@v2.0.0
         with:
           cmake-version: 3.19.x
       - name: Clone w/ submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Update pip

.github/workflows/test-docs.yaml

@@ -18,17 +18,17 @@ jobs:
         python-version: [3.8]
     steps:
       - name: Set up cmake
-        uses: jwlawson/actions-setup-cmake@v1.13
+        uses: jwlawson/actions-setup-cmake@v2.0.0
         with:
           cmake-version: ${{ matrix.config.cmake }}
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Update pip and setup venv
         run: python -m pip install --upgrade pip && python -m venv ~/env && . ~/env/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV
       - name: Clone w/ submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Install Python packages

.github/workflows/test-matrix.yml

@@ -105,19 +105,19 @@ jobs:
         run: |
           brew install openmpi ninja ccache
       - name: Set up cmake
-        uses: jwlawson/actions-setup-cmake@v1.13
+        uses: jwlawson/actions-setup-cmake@v2.0.0
         with:
           cmake-version: ${{ matrix.config.cmake }}
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.config.py }}
       - name: Update pip
         run: python -m pip install --upgrade pip
       - name: Install Python packages
         run:  pip install numpy sphinx svgwrite sphinx-rtd-theme mpi4py pandas seaborn
       - name: Clone w/ submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       # figure out vector extensions for ccache key

.github/workflows/test-pip.yml

@@ -17,11 +17,11 @@ jobs:
         os: [ubuntu-20.04]
         python-version: [3.8]
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Clone w/ submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Update pip and setup venv

.github/workflows/test-spack.yml

@@ -32,7 +32,7 @@ jobs:
           sudo apt-get install -y gfortran libblas-dev
 
       - name: clone arbor
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: arbor
           submodules: recursive

README.md

@@ -5,6 +5,7 @@
 [![gitpod](https://img.shields.io/badge/Gitpod-Ready--to--Code-blue?logo=gitpod)](https://gitpod.io/#https://github.com/arbor-sim/arbor)
 [![docs](https://readthedocs.org/projects/arbor/badge/?version=latest)](https://docs.arbor-sim.org/en/latest/)
 [![gitter](https://badges.gitter.im/arbor-sim/community.svg)](https://gitter.im/arbor-sim/community)
+[![CodeQL](https://github.com/arbor-sim/arbor/actions/workflows/codeql.yml/badge.svg?branch=master)](https://github.com/arbor-sim/arbor/actions/workflows/codeql.yml)
 
 # Arbor Library
 

arbor/cable_cell_group.cpp

@@ -1,6 +1,3 @@
-#include <functional>
-#include <optional>
-#include <unordered_set>
 #include <variant>
 #include <vector>
 
@@ -18,8 +15,6 @@
 #include "cable_cell_group.hpp"
 #include "profile/profiler_macro.hpp"
 #include "sampler_map.hpp"
-#include "util/filter.hpp"
-#include "util/maputil.hpp"
 #include "util/partition.hpp"
 #include "util/range.hpp"
 #include "util/span.hpp"
@@ -215,9 +210,9 @@ void run_samples(
     fvm_probe_scratch& scratch)
 {
     const sample_size_type n_raw_per_sample = p.raw_handles.size();
-    sample_size_type n_sample = (sc.end_offset-sc.begin_offset)/n_raw_per_sample;
-    arb_assert((sc.end_offset-sc.begin_offset)==n_sample*n_raw_per_sample);
-    arb_assert((unsigned)n_raw_per_sample==p.weight.size());
+    sample_size_type n_sample = (sc.end_offset - sc.begin_offset)/n_raw_per_sample;
+    arb_assert((sc.end_offset - sc.begin_offset)==n_sample*n_raw_per_sample);
+    arb_assert((unsigned)n_raw_per_sample == p.weight.size());
 
     auto& sample_ranges = std::get<std::vector<cable_sample_range>>(scratch);
     sample_ranges.clear();
@@ -249,14 +244,12 @@ void run_samples(
     sc.sampler({sc.probeset_id, sc.index, p.get_metadata_ptr()}, n_sample, sample_records.data());
 }
 
-void run_samples(
-    const fvm_probe_interpolated_multi& p,
-    const sampler_call_info& sc,
-    const arb_value_type* raw_times,
-    const arb_value_type* raw_samples,
-    std::vector<sample_record>& sample_records,
-    fvm_probe_scratch& scratch)
-{
+void run_samples(const fvm_probe_interpolated_multi& p,
+                 const sampler_call_info& sc,
+                 const arb_value_type* raw_times,
+                 const arb_value_type* raw_samples,
+                 std::vector<sample_record>& sample_records,
+                 fvm_probe_scratch& scratch) {
     const sample_size_type n_raw_per_sample = p.raw_handles.size();
     const sample_size_type n_interp_per_sample = n_raw_per_sample/2;
     sample_size_type n_sample = (sc.end_offset-sc.begin_offset)/n_raw_per_sample;

arbor/communication/dry_run_context.cpp

@@ -1,12 +1,10 @@
-#include <algorithm>
 #include <string>
 #include <vector>
 
 #include <arbor/spike.hpp>
 
 #include "distributed_context.hpp"
 #include "label_resolution.hpp"
-#include "threading/threading.hpp"
 #include "util/rangeutil.hpp"
 
 namespace arb {
@@ -26,7 +24,7 @@ struct dry_run_context_impl {
         count_type local_size = local_spikes.size();
 
         std::vector<spike> gathered_spikes;
-        gathered_spikes.reserve(local_size*num_ranks_);
+        gathered_spikes.reserve(std::size_t{local_size}*num_ranks_);
 
         for (count_type i = 0; i < num_ranks_; i++) {
             util::append(gathered_spikes, local_spikes);
@@ -49,25 +47,24 @@ struct dry_run_context_impl {
     void remote_ctrl_send_done() const {}
     gathered_vector<cell_gid_type>
     gather_gids(const std::vector<cell_gid_type>& local_gids) const {
-        using count_type = typename gathered_vector<cell_gid_type>::count_type;
-
-        count_type local_size = local_gids.size();
+        size_t local_size = local_gids.size();
 
         std::vector<cell_gid_type> gathered_gids;
         gathered_gids.reserve(local_size*num_ranks_);
 
-        for (count_type i = 0; i < num_ranks_; i++) {
+        for (size_t i = 0; i < num_ranks_; i++) {
             util::append(gathered_gids, local_gids);
         }
 
-        for (count_type i = 0; i < num_ranks_; i++) {
-            for (count_type j = i*local_size; j < (i+1)*local_size; j++){
+        for (size_t i = 0; i < num_ranks_; i++) {
+            for (size_t j = i*local_size; j < (i+1)*local_size; j++){
                 gathered_gids[j] += num_cells_per_tile_*i;
             }
         }
 
+        using count_type = typename gathered_vector<cell_gid_type>::count_type;
         std::vector<count_type> partition;
-        for (count_type i = 0; i <= num_ranks_; i++) {
+        for (size_t i = 0; i <= num_ranks_; i++) {
             partition.push_back(static_cast<count_type>(i*local_size));
         }
 

arbor/include/arbor/common_types.hpp

@@ -138,8 +138,8 @@ using time_type = double;
 constexpr time_type terminal_time = std::numeric_limits<time_type>::max();
 
 // For holding counts and indexes into generated sample data.
-
-using sample_size_type = std::int32_t;
+using sample_index_type = std::int32_t;
+using sample_size_type  = std::uint32_t;
 
 // Enumeration for execution back-end targets, as specified in domain decompositions.
 

arbor/include/arbor/math.hpp

@@ -101,7 +101,8 @@ template <
 >
 C round_up(T v, U b) {
     C m = v%b;
-    return v-m+signum(m)*impl::abs_if_signed(b, Signed{});
+    C sign = signum(m);
+    return v - m + sign*impl::abs_if_signed(b, Signed{});
 }
 
 // Returns 1/x if x != 0; 0 otherwise

arbor/include/arbor/util/hash_def.hpp

@@ -40,8 +40,9 @@ namespace detail {
 template <typename T>
 inline constexpr std::size_t internal_hash(T&& data) {
     using D = std::decay_t<T>;
-    constexpr std::size_t prime = 0x100000001b3;
-    constexpr std::size_t offset_basis = 0xcbf29ce484222325;
+    // Due to constexpr if we might never use these.
+    [[maybe_unused]] constexpr std::size_t prime = 0x100000001b3;
+    [[maybe_unused]] constexpr std::size_t offset_basis = 0xcbf29ce484222325;
     static_assert(!std::is_pointer_v<D> || std::is_same_v<D, void*> || std::is_convertible_v<T, std::string_view>,
                   "Pointer types except void* will not be hashed.");
     if constexpr (std::is_convertible_v<T, std::string_view>) {

example/generators/generators.cpp

@@ -82,8 +82,6 @@ class generator_recipe: public arb::recipe {
     std::vector<arb::event_generator> event_generators(cell_gid_type gid) const override {
         assert(gid==0); // There is only one cell in the model
 
-        using RNG = std::mt19937_64;
-
         auto hz_to_freq = [](double hz) { return hz*1e-3; };
         time_type t0 = 0;
 

modcc/io/prefixbuf.cpp

@@ -75,11 +75,13 @@ int indent_manip::xindex() {
 
 static void apply_indent_prefix(std::ios& s, int index) {
     if (auto pbuf = dynamic_cast<prefixbuf*>(s.rdbuf())) {
-        indent_stack* stack_ptr = static_cast<indent_stack*>(s.pword(index));
-        unsigned tabwidth = s.iword(index);
-
-        unsigned tabs = (!stack_ptr || stack_ptr->empty())? 0: stack_ptr->top();
-        pbuf->prefix = std::string(tabs*tabwidth, ' ');
+        if (auto ptr = static_cast<indent_stack*>(s.pword(index)); ptr && !ptr->empty()) {
+            unsigned n_tab = ptr->top();
+            unsigned width = s.iword(index);
+            pbuf->prefix = std::string(n_tab*width, ' ');
+        } else {
+            pbuf->prefix = std::string();
+        }
     }
 }