Merged master.

Merge remote-tracking branch 'upstream/master' into spack_improvements

.github/workflows/benchmarks.yml

@@ -3,6 +3,7 @@ name: Benchmarks
 on:
   pull_request:
     branches: [ master ]
+    paths-ignore: 'doc/**'
 
 jobs:
   build:

.github/workflows/lint.yml

@@ -7,14 +7,15 @@ on:
 jobs:
   build:
     name: Lint
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
     steps:
+      - uses: actions/checkout@v3
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: '3.10'
       - name: Get packages
         run: |
           python -m pip install --upgrade pip

.github/workflows/sanitize.yml

@@ -3,6 +3,7 @@ name: Sanitize
 on:
   pull_request:
     branches: [ master ]
+    paths-ignore: 'doc/**'
 
 jobs:
   build:

.github/workflows/test-docs.yaml

@@ -0,0 +1,41 @@
+name: Test docs
+
+on:
+  push:
+    branches: [ master ]
+    paths: 'doc/**'
+  pull_request:
+    branches: [ master ]
+    paths: 'doc/**'
+
+jobs:
+  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: ${{ matrix.python-version }}
+      - name: Update pip and setup venv
+        run: python -m pip install --upgrade pip && python -m venv ~/env && . ~/env/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV
+      - name: Clone w/ submodules
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+      - name: Install Python packages
+        run: python -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

.github/workflows/test-everything.yml → .github/workflows/test-matrix.yml

@@ -1,10 +1,12 @@
-name: Test Everything
+name: Test Matrix
 
 on:
   push:
     branches: [ master ]
+    paths-ignore: 'doc/**'
   pull_request:
     branches: [ master ]
+    paths-ignore: 'doc/**'
 
 jobs:
   testallconfigs:
@@ -191,67 +193,3 @@ jobs:
       #   run: scripts/run_python_examples.sh
       - name: Test executables
         run: ./scripts/test_executables.sh
-  testpip:
-    name: "Pip build test + Python examples test"
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-20.04]
-        python-version: [3.7]
-    steps:
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Clone w/ submodules
-        uses: actions/checkout@v3
-        with:
-          submodules: recursive
-      - name: Update pip and setup venv
-        run: python -m pip install --upgrade pip && python -m venv ~/env && . ~/env/bin/activate && echo PATH=$PATH >> $GITHUB_ENV
-      - name: Debug info Python
-        run: |
-          which python
-          python --version
-          pip --version
-      - name: Build and install Arbor using pip + build flags
-        run: CMAKE_ARGS="-DARB_VECTORIZE=ON -DARB_ARCH=native" pip install . --user
-      - name: Check that build flags match
-        run: |
-          python -c "import arbor; print(arbor.config())" | grep -q "'arch': 'native'"
-      - name: Run Python tests
-        run: python -m unittest discover -v -s python
-      - name: Run Python examples
-        run: scripts/run_python_examples.sh
-      - name: Test executables
-        run: scripts/test_executables.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: ${{ matrix.python-version }}
-      - name: Update pip and setup venv
-        run: python -m pip install --upgrade pip && python -m venv ~/env && . ~/env/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV
-      - name: Clone w/ submodules
-        uses: actions/checkout@v3
-        with:
-          submodules: recursive
-      - name: Install Python packages
-        run: python -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
-        

.github/workflows/test-pip.yaml

@@ -0,0 +1,44 @@
+name: Test pip
+
+on:
+  push:
+    branches: [ master ]
+    paths-ignore: 'doc/**'
+  pull_request:
+    branches: [ master ]
+    paths-ignore: 'doc/**'
+
+jobs:
+  testpip:
+    name: "Pip build test + Python examples test"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04]
+        python-version: [3.7]
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Clone w/ submodules
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+      - name: Update pip and setup venv
+        run: python -m pip install --upgrade pip && python -m venv ~/env && . ~/env/bin/activate && echo PATH=$PATH >> $GITHUB_ENV
+      - name: Debug info Python
+        run: |
+          which python
+          python --version
+          pip --version
+      - name: Build and install Arbor using pip + build flags
+        run: CMAKE_ARGS="-DARB_VECTORIZE=ON -DARB_ARCH=native" pip install . --user
+      - name: Check that build flags match
+        run: |
+          python -c "import arbor; print(arbor.config())" | grep -q "'arch': 'native'"
+      - name: Run Python tests
+        run: python -m unittest discover -v -s python
+      - name: Run Python examples
+        run: scripts/run_python_examples.sh
+      - name: Test executables
+        run: scripts/test_executables.sh

.github/workflows/spack.yml → .github/workflows/test-spack.yml

@@ -3,8 +3,10 @@ name: Spack
 on:
   push:
     branches: [ master ]
+    paths-ignore: 'doc/**'
   pull_request:
     branches: [ master ]
+    paths-ignore: 'doc/**'
 
 jobs:
   build:

CMakeLists.txt

@@ -19,11 +19,13 @@ set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
 # Have LTO where possible, ie add -flto
 check_ipo_supported(RESULT HAVE_LTO OUTPUT ERR_LTO)
-if(HAVE_LTO AND NOT DEFINED CMAKE_INTERPROCEDURAL_OPTIMIZATION)
-  message (STATUS "LTO support found, enabling")
-  set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
-else()
-  message(STATUS "No LTO: ${ERR_LTO}")
+if(NOT DEFINED CMAKE_INTERPROCEDURAL_OPTIMIZATION)
+  if(HAVE_LTO)
+    message (STATUS "LTO support found, enabling")
+    set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
+  else()
+    message(STATUS "No LTO: ${ERR_LTO}")
+  endif()
 endif()
 
 # Turn on this option to force the compilers to produce color output when output is

README.md

@@ -1,5 +1,7 @@
-[![ci](https://github.com/arbor-sim/arbor/actions/workflows/test-everything.yml/badge.svg)](https://github.com/arbor-sim/arbor/actions/workflows/test-everything.yml)
-[![pythonwheels](https://github.com/arbor-sim/arbor/actions/workflows/release.yml/badge.svg)](https://github.com/arbor-sim/arbor/actions/workflows/release.yml)
+[![ci](https://github.com/arbor-sim/arbor/actions/workflows/test-matrix.yml/badge.svg)](https://github.com/arbor-sim/arbor/actions/workflows/test-matrix.yml)
+[![spack](https://github.com/arbor-sim/arbor/actions/workflows/test-spack.yml/badge.svg)](https://github.com/arbor-sim/arbor/actions/workflows/test-spack.yml)
+[![pip](https://github.com/arbor-sim/arbor/actions/workflows/test-pip.yml/badge.svg)](https://github.com/arbor-sim/arbor/actions/workflows/test-pip.yml)
+[![pythonwheels](https://github.com/arbor-sim/arbor/actions/workflows/build-pip-wheels.yml/badge.svg)](https://github.com/arbor-sim/arbor/actions/workflows/build-pip-wheels.yml)
 [![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)

arbor/backends/gpu/forest.hpp

@@ -58,6 +58,8 @@ struct ARB_ARBOR_API forest {
 
 
 struct level_iterator {
+    constexpr static unsigned npos = unsigned(-1);
+
     level_iterator(tree* t, unsigned level) {
         tree_ = t;
         only_on_level = level;
@@ -94,16 +96,15 @@ struct level_iterator {
                 next_children = index + 1;
             } else {
                 // we are done with the iteration
-                current_level = -1;
-                current_node  = -1;
-                next_children = -1;
+                current_level = npos;
+                current_node  = npos;
+                next_children = npos;
             }
 
         }
     }
 
     unsigned next() {
-        constexpr unsigned npos = unsigned(-1);
         if (!valid()) {
             // we are done
             return npos;

arbor/backends/gpu/shared_state.cpp

@@ -43,8 +43,7 @@ std::pair<arb_value_type, arb_value_type> minmax_value_impl(arb_size_type n, con
 
 // Ion state methods:
 
-ion_state::ion_state(int charge,
-                     const fvm_ion_config& ion_data,
+ion_state::ion_state(const fvm_ion_config& ion_data,
                      unsigned, // alignment/padding ignored.
                      solver_ptr ptr):
     write_eX_(ion_data.revpot_written),
@@ -62,7 +61,7 @@ ion_state::ion_state(int charge,
     reset_Xi_(make_const_view(ion_data.reset_iconc)),
     reset_Xo_(make_const_view(ion_data.reset_econc)),
     init_eX_(make_const_view(ion_data.init_revpot)),
-    charge(1u, charge),
+    charge(1u, static_cast<arb_value_type>(ion_data.charge)),
     solver(std::move(ptr)) {
     arb_assert(node_index_.size()==init_Xi_.size());
     arb_assert(node_index_.size()==init_Xo_.size());

arbor/backends/gpu/shared_state.hpp

@@ -64,11 +64,9 @@ struct ARB_ARBOR_API ion_state {
 
     ion_state() = default;
 
-    ion_state(
-        int charge,
-        const fvm_ion_config& ion_data,
-        unsigned align,
-        solver_ptr ptr);
+    ion_state(const fvm_ion_config& ion_data,
+              unsigned align,
+              solver_ptr ptr);
 
     // Set ion concentrations to weighted proportion of default concentrations.
     void init_concentration();

arbor/communication/communicator.cpp

@@ -36,21 +36,21 @@ communicator::communicator(const recipe& rec,
 constexpr inline
 bool is_external(cell_gid_type c) {
     // index of the MSB of cell_gid_type in bits
-    constexpr auto msb = 1 << (std::numeric_limits<cell_gid_type>::digits - 1);
+    constexpr auto msb = static_cast<cell_gid_type>(1 << (std::numeric_limits<cell_gid_type>::digits - 1));
     // If set, we are external
     return bool(c & msb);
 }
 
 constexpr inline
 cell_member_type global_cell_of(const cell_remote_label_type& c) {
-    constexpr auto msb = 1 << (std::numeric_limits<cell_gid_type>::digits - 1);
+    constexpr auto msb = static_cast<cell_gid_type>(1 << (std::numeric_limits<cell_gid_type>::digits - 1));
     // set the MSB
     return {c.rid | msb, c.index};
 }
 
 constexpr inline
 cell_member_type global_cell_of(const cell_member_type& c) {
-    constexpr auto msb = 1 << (std::numeric_limits<cell_gid_type>::digits - 1);
+    constexpr auto msb = static_cast<cell_gid_type>(1 << (std::numeric_limits<cell_gid_type>::digits - 1));
     // set the MSB
     return {c.gid | msb, c.index};
 }

arbor/cv_policy.cpp

@@ -57,7 +57,7 @@ struct cv_policy_bar_: cv_policy_base {
     }
 
     locset cv_boundary_points(const cable_cell& c) const override {
-        return unique_sum(ls::restrict(lhs_.cv_boundary_points(c), complement(rhs_.domain())), rhs_.cv_boundary_points(c));
+        return unique_sum(ls::restrict_to(lhs_.cv_boundary_points(c), complement(rhs_.domain())), rhs_.cv_boundary_points(c));
     }
 
     region domain() const override { return join(lhs_.domain(), rhs_.domain()); }
@@ -82,7 +82,7 @@ locset cv_policy_explicit::cv_boundary_points(const cable_cell& cell) const {
         ls::support(
             util::foldl(
                 [this](locset l, const auto& comp) {
-                    return sum(std::move(l), ls::restrict(locs_, comp));
+                    return sum(std::move(l), ls::restrict_to(locs_, comp));
                 },
                 ls::boundary(domain_),
                 components(cell.morphology(), thingify(domain_, cell.provider()))));
@@ -190,7 +190,7 @@ locset cv_policy_every_segment::cv_boundary_points(const cable_cell& cell) const
 
     return unique_sum(
                 ls::cboundary(domain_),
-                ls::restrict(ls::segment_boundaries(), domain_));
+                ls::restrict_to(ls::segment_boundaries(), domain_));
 }
 cv_policy_base_ptr cv_policy_every_segment::clone() const {
     return cv_policy_base_ptr(new cv_policy_every_segment(*this));

arbor/fvm_lowered_cell.hpp

@@ -185,7 +185,9 @@ struct probe_association_map {
     }
 
     // Return range of fvm_probe_data values associated with probeset_id.
-    auto data_on(cell_member_type probeset_id) const {
+    // Trailing return type added here to avoid warnings about ODR violations when building shared
+    // lib together with LTO - needs to be re-checked in the future
+    auto data_on(cell_member_type probeset_id) const -> decltype(util::transform_view(util::make_range(data.equal_range(probeset_id)), util::second)) {
         return util::transform_view(util::make_range(data.equal_range(probeset_id)), util::second);
     }
 };