Merge branch 'master' into slds-wt

Author: nrnhines

.github/workflows/coverage.yml

@@ -66,7 +66,7 @@ jobs:
       - name: Setup cmake
         uses: jwlawson/actions-setup-cmake@v2
         with:
-          cmake-version : '3.19'
+          cmake-version : '3.20'
 
       - name: Setup Caliper profiler
         run: |

.github/workflows/neuron-ci.yml

@@ -36,8 +36,8 @@ jobs:
       SDK_ROOT: $(xcrun --sdk macosx --show-sdk-path)
       SKIP_WHEELHOUSE_REPAIR: true
       BUILD_TYPE: Release
-      DESIRED_CMAKE_VERSION: 3.19
-      DYNAMIC_PYTHON_CMAKE_VERSION: 3.19
+      DESIRED_CMAKE_VERSION: '3.20'
+      DYNAMIC_PYTHON_CMAKE_VERSION: '3.20'
       PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.10' }}
       PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.14' }}
       MUSIC_INSTALL_DIR: /opt/MUSIC

.github/workflows/release.yml

@@ -159,7 +159,7 @@ jobs:
       - name: Setup cmake
         uses: jwlawson/actions-setup-cmake@v2
         with:
-          cmake-version : '3.19'
+          cmake-version : '3.20'
 
       - name: Set up Python
         id: setup-python

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.19 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.20 FATAL_ERROR)
 # Note that this needs to happen **before** the call to project(...). This is because CMake reads
 # the CRAYPE_LINK_TYPE environment variable inside the call to project(...) and sets various flags
 # and properties based on its value. Because we are so early in the CMake processing, we have to
@@ -39,7 +39,7 @@ if(POLICY CMP0177)
   cmake_policy(SET CMP0177 NEW)
 endif()
 
-# customizable install path to Python components. Mostly useful for Spack builds
+# customizable install path to Python components. Mostly useful for Spack & venv builds
 set(NRN_INSTALL_PYTHON_PREFIX
     "lib/python/neuron/"
     CACHE STRING
@@ -65,6 +65,11 @@ else()
   set(NRN_INSTALL_DATA_PREFIX)
 endif()
 
+# Make python install path relative to CMAKE_INSTALL_PREFIX
+if(IS_ABSOLUTE "${NRN_INSTALL_PYTHON_PREFIX}")
+  cmake_path(RELATIVE_PATH NRN_INSTALL_PYTHON_PREFIX BASE_DIRECTORY "${CMAKE_INSTALL_PREFIX}")
+endif()
+
 # =============================================================================
 # CMake common project settings
 # =============================================================================

docs/capi.rst

@@ -905,9 +905,10 @@ Functions, objects, and the stack
         
         // Create current clamp at soma
         Symbol* iclamp_sym = nrn_symbol("IClamp");
-        nrn_object_push((Object*)soma);  // Push soma as object
+        nrn_section_push(soma);          // specify the section separately
         nrn_double_push(0.0);            // Push location (0.0)
         Object* iclamp = nrn_object_new(iclamp_sym, 2);
+        nrn_section_pop();
 
     **Python Equivalent:**
 
@@ -1966,8 +1967,10 @@ Here we stimulate the cell with a :class:`IClamp` at time 1 ms.
         nrn_mechanism_insert(soma, nrn_symbol("hh"));
 
         // current clamp at soma(0.5)
+        nrn_section_push(soma);          // specify the section separately
         nrn_double_push(0.5);
         Object* iclamp = nrn_object_new(nrn_symbol("IClamp"), 1);
+        nrn_section_pop();
         for (const auto& [property, value] : {pair{"amp", 0.3}, pair{"del", 1.0}, pair{"dur", 0.1}}) {
             nrn_property_set(iclamp, property, value);
         }
@@ -2051,4 +2054,4 @@ This displays the following image:
 .. image:: progref/images/hh_sim_cpp.png
    :alt: Hodgkin-Huxley simulation driven by a current clamp at 1ms showing an action potential
    :width: 75%
-   :align: center
+   :align: center

docs/cmake_doc/options.rst

@@ -306,6 +306,30 @@ NRN_ENABLE_PYTHON:BOOL=ON
   Enable Python interpreter support
   (default python, fallback to python3, but see PYTHON_EXECUTABLE below)
 
+NRN_INSTALL_PYTHON_PREFIX:STRING="lib/python/neuron/"
+-----------------------------------------------------
+  Path where NEURON Python components will be installed, relative to CMAKE_INSTALL_PREFIX. Must end with a directory named "neuron"
+
+  Environment variable PYTHONPATH must contain the real path to NRN_INSTALL_PYTHON_PREFIX in order for python to find neuron.
+
+  This path must end with a directory named "neuron"
+
+  For venv's, configure cmake with:
+
+  .. code-block:: shell
+
+    -DCMAKE_INSTALL_PREFIX=$(python -c "import sysconfig; print(sysconfig.get_path('data', 'venv'))") \
+    -DNRN_INSTALL_PYTHON_PREFIX=$(python -c "import sysconfig; print(sysconfig.get_path('platlib', 'venv') + '/neuron')")
+
+  To install to your home directory, configure cmake with:
+
+  .. code-block:: shell
+
+    -DCMAKE_INSTALL_PREFIX=$(python3 -m site --user-base) \
+    -DNRN_INSTALL_PYTHON_PREFIX=$(python3 -m site --user-site)/neuron
+
+  This option is ignored when building a wheel, in which case the value is forced to "neuron/"
+
 .. _cmake_nrn_enable_python_dynamic:
 NRN_ENABLE_PYTHON_DYNAMIC:BOOL=OFF
 ----------------------------------
@@ -544,7 +568,7 @@ NRN_ENABLE_TESTS:BOOL=OFF
     python3 -m pytest test_currents.py
 
 NRN_ENABLE_COVERAGE:BOOL=OFF
----------------------------
+----------------------------
   Enable code coverage
 
   Requires ``lcov`` (e.g. ``sudo apt install lcov``).
@@ -677,7 +701,7 @@ NRN_ENABLE_DIGEST:BOOL=OFF
   Requires libcrypto
 
 NRN_ENABLE_ARCH_INDEP_EXP_POW:BOOL=OFF
----------------------------------
+--------------------------------------
   Provides \ :func:`use_exp_pow_precision` function so that exp and pow produce
   same results on all platforms.
 

src/coreneuron/apps/main1.cpp

@@ -561,7 +561,11 @@ extern "C" int run_solve_core(int argc, char** argv) {
 
         // register all reports with libsonata
         double min_report_dt = INT_MAX;
+        size_t lfp_report_counter = 0;
         for (size_t i = 0; i < configs.size(); i++) {
+            if (configs[i].type == ReportType::LFP) {
+                configs[i].lfp_report_index = lfp_report_counter++;
+            }
             std::unique_ptr<ReportHandler> report_handler = create_report_handler(configs[i],
                                                                                   spikes_info);
             if (report_handler) {

src/coreneuron/io/nrn2core_direct.h

@@ -106,7 +106,7 @@ extern void (*nrn2core_get_dat3_secmapping_)(int i_c,
                                              int& nsec,
                                              int& nseg,
                                              size_t& total_lfp_factors,
-                                             int& n_electrodes,
+                                             std::vector<size_t>& electrode_offsets,
                                              std::vector<int>& data_sec,
                                              std::vector<int>& data_seg,
                                              std::vector<double>& data_lfp);

src/coreneuron/io/nrn_filehandler.hpp

@@ -10,6 +10,7 @@
 
 #include <iostream>
 #include <fstream>
+#include <sstream>
 #include <vector>
 #include <cmath>
 #include <sys/stat.h>
@@ -118,18 +119,27 @@ class FileHandler {
                           NrnThreadMappingInfo* ntmapping,
                           std::shared_ptr<CellMapping> cmap,
                           const NrnThread& nt) {
-        int nsec, nseg, n_scan;
-        size_t total_lfp_factors;
-        int num_electrodes;
-        char line_buf[max_line_length], name[max_line_length];
-
-        F.getline(line_buf, sizeof(line_buf));
-        n_scan = sscanf(
-            line_buf, "%s %d %d %zd %d", name, &nsec, &nseg, &total_lfp_factors, &num_electrodes);
-
-        nrn_assert(n_scan == 5);
+        std::string line;
+        std::getline(F, line);
+
+        std::istringstream iss(line);
+        std::string name_str;
+        int nsec = 0;
+        int nseg = 0;
+        size_t total_lfp_factors = 0;
+        int offset_count = 0;
+        iss >> name_str >> nsec >> nseg >> total_lfp_factors >> offset_count;
+        nrn_assert(!iss.fail());
+
+        if (offset_count > 0) {
+            cmap->electrode_offsets.resize(offset_count);
+            for (int k = 0; k < offset_count; k++) {
+                iss >> cmap->electrode_offsets[k];
+            }
+            nrn_assert(!iss.fail());
+        }
 
-        mapinfo->type = section_type_from_string(name);
+        mapinfo->type = section_type_from_string(name_str);
 
         if (nseg) {
             auto sec = read_vector<int>(nseg);
@@ -144,20 +154,16 @@ class FileHandler {
                 lfp_factors = read_vector<double>(total_lfp_factors);
             }
 
-            int factor_offset = 0;
             for (int i = 0; i < nseg; i++) {
                 mapinfo->add_segment(sec[i], seg[i]);
                 ntmapping->add_segment_id(seg[i]);
-                int factor_offset = i * num_electrodes;
                 if (total_lfp_factors > 0) {
-                    // Abort if the factors contains a NaN
+                    const auto num_electrodes = cmap->num_electrodes();
                     nrn_assert(count_if(lfp_factors.begin(), lfp_factors.end(), [](double d) {
                                    return std::isnan(d);
                                }) == 0);
-                    std::vector<double> segment_factors(lfp_factors.begin() + factor_offset,
-                                                        lfp_factors.begin() + factor_offset +
-                                                            num_electrodes);
-                    cmap->add_segment_lfp_factor(seg[i], segment_factors);
+                    auto begin = lfp_factors.begin() + i * num_electrodes;
+                    cmap->add_segment_lfp_factor(seg[i], begin, begin + num_electrodes);
                 }
             }
         }

src/coreneuron/io/nrnsection_mapping.hpp

@@ -18,6 +18,7 @@
 #include <vector>
 
 #include "coreneuron/io/reports/nrnreport.hpp"
+#include "coreneuron/utils/nrn_assert.h"
 #include "coreneuron/utils/utils.hpp"
 
 namespace coreneuron {
@@ -73,8 +74,15 @@ struct CellMapping {
     /** list of section lists (like soma, axon, apic) */
     std::vector<std::shared_ptr<SecMapping>> sec_mappings;
 
-    /** map containing segment ids an its respective lfp factors */
-    std::unordered_map<int, std::vector<double>> lfp_factors;
+    /** segment ids for lfp factors (one per compartment with LFP data) */
+    std::vector<int> lfp_segment_ids;
+
+    /** flat array of lfp factors: stride = num_electrodes, indexed as [i * stride + e] */
+    std::vector<double> lfp_factors_flat;
+
+    /** Electrode offsets per LFP report (CSR-style, size = num_reports + 1).
+     *  offsets[i]..offsets[i+1] gives the electrode range for report i. */
+    std::vector<size_t> electrode_offsets;
 
     CellMapping(int g)
         : gid(g) {}
@@ -99,13 +107,9 @@ struct CellMapping {
                                });
     }
 
-    /** @brief return the number of electrodes in the lfp_factors map **/
-    int num_electrodes() const {
-        int num_electrodes = 0;
-        if (!lfp_factors.empty()) {
-            num_electrodes = lfp_factors.begin()->second.size();
-        }
-        return num_electrodes;
+    /** @brief return the total number of electrodes **/
+    size_t num_electrodes() const {
+        return electrode_offsets.empty() ? 0 : electrode_offsets.back();
     }
 
     /** @brief number of section lists */
@@ -148,8 +152,18 @@ struct CellMapping {
     }
 
     /** @brief add the lfp electrode factors of a segment_id */
-    void add_segment_lfp_factor(const int segment_id, std::vector<double>& factors) {
-        lfp_factors.insert({segment_id, factors});
+    void add_segment_lfp_factor(const int segment_id,
+                                std::vector<double>::const_iterator begin,
+                                std::vector<double>::const_iterator end) {
+        const size_t n = std::distance(begin, end);
+        if (n == 0) {
+            return;
+        }
+        const auto curr_n_electrodes = num_electrodes();
+        // All segments must have the same number of electrode factors
+        nrn_assert(curr_n_electrodes == 0 || n == curr_n_electrodes);
+        lfp_segment_ids.push_back(segment_id);
+        lfp_factors_flat.insert(lfp_factors_flat.end(), begin, end);
     }
 };