Refactor discretization. (#2415)

This PR rectifies a long-standing issue since the introduction of
`decor`:
CV discretization was treated as a defaultable value instead of a cell
property, along with bio-physical properties.

This lead to some awkward facts:
- Intermingling of bio-physics and numerical settings
- Discretization is treated like a default without override.
- Discretization cannot be changed once set, e.g. if read from `.acc`,
requiring the copy+update of a decor instead

Thus:
- Discretization can now be set during `cable_cell` construction
- It can be read and updated later
- Refactor `cv_policy` to use type erasure like other, similar
constructions, e.g. schedules.
- Hide internal `cv_policy` constructors.

⚠️ Breaks `.acc` by upgrading from 0.9 to 0.10 ⚠️ 

Closes #1408

---------

Co-authored-by: boeschf <[email protected]>

.github/workflows/sanitize.yml

@@ -19,16 +19,16 @@ permissions:
 jobs:
   build:
     name: "Sanitize"
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     strategy:
       fail-fast: false
       matrix:
         name:      ["Sanitize"]
         sanitizer: ["address", "undefined", "thread"]
         simd:      ["ON", "OFF"]
     env:
-        CC:           clang-14
-        CXX:          clang++-14
+        CC:           clang-18
+        CXX:          clang++-18
         ASAN_OPTIONS: detect_leaks=1
     steps:
       - name: Get build dependencies
@@ -43,8 +43,6 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-      - name: Update pip
-        run: python -m pip install --upgrade pip
       # figure out vector extensions for ccache key
       - name: Check vector extensions
         run: |

.github/workflows/test-matrix.yml

@@ -29,8 +29,8 @@ jobs:
         - {
             name:  "Linux Min Clang",
             os:    "ubuntu-22.04",
-            cc:    "clang-12",
-            cxx:   "clang++-12",
+            cc:    "clang-13",
+            cxx:   "clang++-13",
             py:    "3.9",
             cmake: "3.19.x",
             mpi:   "ON",

CMakeLists.txt

@@ -274,7 +274,7 @@ install(FILES mechanisms/BuildModules.cmake DESTINATION ${ARB_INSTALL_DATADIR})
 
 # First make ourselves less chatty
 set(_saved_CMAKE_MESSAGE_LOG_LEVEL ${CMAKE_MESSAGE_LOG_LEVEL})
-set(CMAKE_MESSAGE_LOG_LEVEL WARNING)
+set(CMAKE_MESSAGE_LOG_LEVEL STATUS)
 
 # in the event we can find hwloc, just add it
 find_package(hwloc QUIET)
@@ -341,6 +341,8 @@ CPMAddPackage(NAME fmt
               VERSION 10.0.0
               GIT_TAG 10.0.0)
 
+add_library(ext-gtest INTERFACE)
+add_library(ext-bench INTERFACE)
 if (BUILD_TESTING)
     CPMAddPackage(NAME benchmark
                   GITHUB_REPOSITORY google/benchmark
@@ -351,6 +353,18 @@ if (BUILD_TESTING)
                   GIT_TAG release-1.12.1
                   VERSION 1.12.1
                   OPTIONS "INSTALL_GTEST OFF" "BUILD_GMOCK OFF")
+    if(benchmark_ADDED)
+        target_link_libraries(ext-bench INTERFACE benchmark)
+    else()
+        find_package(benchmark REQUIRED)
+        target_link_libraries(ext-bench INTERFACE benchmark::benchmark)
+    endif()
+    if(googletest_ADDED)
+        target_link_libraries(ext-gtest INTERFACE )
+    else()
+        find_package(googletest REQUIRED)
+        target_link_libraries(ext-gtest INTERFACE gtest gtest_main)
+    endif()
 endif()
 
 CPMAddPackage(NAME units

arbor/cable_cell.cpp

@@ -83,18 +83,22 @@ struct cable_cell_impl {
     // The decorations on the cell.
     decor decorations;
 
+    // Discretization
+    std::optional<cv_policy> discretization_;
+
     // The placeable label to lid_range map
     dynamic_typed_map<constant_type<std::unordered_multimap<hash_type, lid_range>>::type> labeled_lid_ranges;
 
-    cable_cell_impl(const arb::morphology& m, const label_dict& labels, const decor& decorations):
+    cable_cell_impl(const arb::morphology& m, const label_dict& labels, const decor& decorations, const std::optional<cv_policy>& cvp):
         provider(m, labels),
         dictionary(labels),
-        decorations(decorations)
+        decorations(decorations),
+        discretization_{cvp}
     {
         init();
     }
 
-    cable_cell_impl(): cable_cell_impl({},{},{}) {}
+    cable_cell_impl(): cable_cell_impl({}, {}, {}, {}) {}
 
     cable_cell_impl(const cable_cell_impl& other) = default;
 
@@ -203,6 +207,10 @@ struct cable_cell_impl {
     }
 };
 
+const std::optional<cv_policy>& cable_cell::discretization() const { return impl_->discretization_; }
+void cable_cell::discretization(cv_policy cvp) { impl_->discretization_ = std::move(cvp); }
+
+
 using impl_ptr = std::unique_ptr<cable_cell_impl, void (*)(cable_cell_impl*)>;
 impl_ptr make_impl(cable_cell_impl* c) {
     return impl_ptr(c, [](cable_cell_impl* p){delete p;});
@@ -232,8 +240,8 @@ void cable_cell_impl::init() {
     }
 }
 
-cable_cell::cable_cell(const arb::morphology& m, const decor& decorations, const label_dict& dictionary):
-    impl_(make_impl(new cable_cell_impl(m, dictionary, decorations)))
+cable_cell::cable_cell(const arb::morphology& m, const decor& decorations, const label_dict& dictionary, const std::optional<cv_policy>& cvp):
+    impl_(make_impl(new cable_cell_impl(m, dictionary, decorations, cvp)))
 {}
 
 cable_cell::cable_cell(): impl_(make_impl(new cable_cell_impl())) {}

arbor/cable_cell_param.cpp

@@ -105,11 +105,6 @@ std::vector<defaultable> cable_cell_parameter_set::serialize() const {
     for (const auto& [name, mech]: reversal_potential_method) {
         D.push_back(ion_reversal_potential_method{name, mech});
     }
-
-    if (discretization) {
-        D.push_back(*discretization);
-    }
-
     return D;
 }
 
@@ -163,9 +158,6 @@ decor& decor::set_default(defaultable what) {
                 else if constexpr (std::is_same_v<ion_reversal_potential_method, T>) {
                     defaults_.reversal_potential_method[p.ion] = p.method;
                 }
-                else if constexpr (std::is_same_v<cv_policy, T>) {
-                    defaults_.discretization = std::forward<cv_policy>(p);
-                }
                 else if constexpr (std::is_same_v<ion_diffusivity, T>) {
                     if (p.scale.type() != iexpr_type::scalar) throw cable_cell_error{"Default values cannot have a scale."};
                     auto s = p.scale.get_scalar();