SimulationConfig: Adds "represents_physical_electrode" field in "inpu…

…ts" section (#354)

* SimulationConfig: Adds "represents_physical_electrode" field in "inputs" section

.github/workflows/publish-sdist-wheels.yml

@@ -45,7 +45,6 @@ jobs:
           path: src-cache/
           key: ${{ runner.os }}-build-${{ env.cache-name }}
 
-
       - name: Build wheels on Linux
         if: runner.os == 'Linux'
         env:
@@ -60,7 +59,7 @@ jobs:
         run: |
           # used by setup.py to decide if to set `FindHDF5` to use static hdf5 libraries
           export STATIC_HDF5=True
-          export CMAKE_PREFIX_PATH=/opt/hdf5-static/install-/install/
+          export CMAKE_PREFIX_PATH=/opt/hdf5-static/install-x86_64/install/
 
           CIBW_MANYLINUX_X86_64_IMAGE=manylinux2014 python -m cibuildwheel --output-dir dist
           CIBW_MANYLINUX_X86_64_IMAGE=manylinux_2_28 python -m cibuildwheel --output-dir dist

.github/workflows/run-tests.yml

@@ -97,10 +97,7 @@ jobs:
     name: Run tests on macos
     runs-on: macos-latest
     env:
-      CIBW_ARCHS_MACOS: "x86_64"
-      CMAKE_OSX_ARCHITECTURES: "x86_64"
       UNIXY_HDF5_VERSION: 1.14.3
-      MACOSX_DEPLOYMENT_TARGET: "11.0"
 
     steps:
       - name: Checkout repository
@@ -124,10 +121,18 @@ jobs:
             ln -s $PWD/src-cache /Users/runner/work/src-cache
             bash ci/hdf5-build.sh /Users/runner/work/src-cache
 
-      - name: Build and run unittests
+      - name: Build and run unittests C++ tests
         run: |
+            : "${CIBW_ARCHS_MACOS:=$(uname -m)}"
             export CMAKE_PREFIX_PATH=/Users/runner/work/src-cache/install-$CIBW_ARCHS_MACOS/install
             export STATIC_HDF5=True
 
             ./ci/cpp_test.sh
+
+      - name: Build and run unittests python tests
+        run: |
+            : "${CIBW_ARCHS_MACOS:=$(uname -m)}"
+            export CMAKE_PREFIX_PATH=/Users/runner/work/src-cache/install-$CIBW_ARCHS_MACOS/install
+            export STATIC_HDF5=True
+
             ./ci/python_test.sh

ci/hdf5-build.sh

@@ -1,11 +1,12 @@
 #!/bin/bash
 set -e -x
 
+: "${UNIXY_HDF5_VERSION:=1.14.3}"
+: "${CIBW_ARCHS_MACOS:=$(uname -m)}"
 
 export INPUT=$(cd $(dirname "$1") && pwd -P)/$(basename "$1")
 export OUTPUT="$INPUT/install-$CIBW_ARCHS_MACOS"
 
-: "${UNIXY_HDF5_VERSION:=1.14.3}"
 
 function download_unpack_hdf5 {
     pushd "$INPUT"

ci/python_test.sh

@@ -15,8 +15,13 @@ source $BIN/activate
 set -u
 
 $BIN/pip -v install --upgrade pip setuptools wheel
+
+which python
+which pip
+pip debug
+
 $BIN/pip -v install --force .
 
 pushd python/tests
-$BIN/python -m unittest -v 
+$BIN/python -m unittest -v
 popd

include/bbp/sonata/config.h

@@ -460,13 +460,17 @@ class SONATA_API SimulationConfig
         double ampStart{};
         /// The final current when a stimulus concludes (nA)
         double ampEnd{};
+        /// Whether this input represents a physical electrode. Default is false
+        bool representsPhysicalElectrode = false;
     };
 
     struct InputRelativeLinear: public InputBase {
         /// The percentage of a cell's threshold current to inject
         double percentStart{};
         /// The percentage of a cell's threshold current to inject at the end
         double percentEnd{};
+        /// Whether this input represents a physical electrode. Default is false
+        bool representsPhysicalElectrode = false;
     };
 
     struct InputPulse: public InputBase {
@@ -478,14 +482,21 @@ class SONATA_API SimulationConfig
         double width{};
         /// The frequency of pulse trains (Hz)
         double frequency{};
+        /// Whether this input represents a physical electrode. Default is false
+        bool representsPhysicalElectrode = false;
     };
 
     struct InputSubthreshold: public InputBase {
         /// A percentage adjusted from 100 of a cell's threshold current
         double percentLess{};
+        /// Whether this input represents a physical electrode. Default is false
+        bool representsPhysicalElectrode = false;
     };
 
-    struct InputHyperpolarizing: public InputBase {};
+    struct InputHyperpolarizing: public InputBase {
+        /// Whether this input represents a physical electrode. Default is false
+        bool representsPhysicalElectrode = false;
+    };
 
     struct InputSynapseReplay: public InputBase {
         /// The location of the file with the spike info for injection, file extension must be .h5
@@ -507,6 +518,8 @@ class SONATA_API SimulationConfig
         /// State var to track whether the value of injected noise current is mean or
         /// mean_percent
         double variance{};
+        /// Whether this input represents a physical electrode. Default is false
+        bool representsPhysicalElectrode = false;
     };
 
     struct InputShotNoise: public InputBase {
@@ -527,6 +540,8 @@ class SONATA_API SimulationConfig
         /// The variance of gamma-distributed amplitudes in nA^2 (current_clamp) or uS^2
         /// (conductance)
         double ampVar{};
+        /// Whether this input represents a physical electrode. Default is false
+        bool representsPhysicalElectrode = false;
     };
 
     struct InputRelativeShotNoise: public InputBase {
@@ -548,6 +563,8 @@ class SONATA_API SimulationConfig
         /// signal std dev as percentage of a cell’s threshold current (current_clamp) or inverse
         /// input resistance (conductance).
         double sdPercent{};
+        /// Whether this input represents a physical electrode. Default is false
+        bool representsPhysicalElectrode = false;
     };
 
     struct InputAbsoluteShotNoise: public InputBase {
@@ -567,6 +584,8 @@ class SONATA_API SimulationConfig
         double mean{};
         /// signal std dev in nA (current_clamp) or uS (conductance).
         double sigma{};
+        /// Whether this input represents a physical electrode. Default is false
+        bool representsPhysicalElectrode = false;
     };
 
     struct InputOrnsteinUhlenbeck: public InputBase {
@@ -582,6 +601,8 @@ class SONATA_API SimulationConfig
         double mean{};
         /// Signal std dev in nA (current_clamp) or uS (conductance)
         double sigma{};
+        /// Whether this input represents a physical electrode. Default is false
+        bool representsPhysicalElectrode = false;
     };
 
     struct InputRelativeOrnsteinUhlenbeck: public InputBase {
@@ -599,6 +620,8 @@ class SONATA_API SimulationConfig
         /// Signal std dev as percentage of a cell’s threshold current (current_clamp) or inverse
         /// input resistance (conductance)
         double sdPercent{};
+        /// Whether this input represents a physical electrode. Default is false
+        bool representsPhysicalElectrode = false;
     };
 
     using Input = nonstd::variant<InputLinear,

python/bindings.cpp

@@ -823,7 +823,10 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(InputLinear, ampStart))
         .def_readonly("amp_end",
                       &SimulationConfig::InputLinear::ampEnd,
-                      DOC_SIMULATIONCONFIG(InputLinear, ampEnd));
+                      DOC_SIMULATIONCONFIG(InputLinear, ampEnd))
+        .def_readonly("represents_physical_electrode",
+                      &SimulationConfig::InputLinear::representsPhysicalElectrode,
+                      DOC_SIMULATIONCONFIG(InputLinear, representsPhysicalElectrode));
 
     py::class_<SimulationConfig::InputRelativeLinear, SimulationConfig::InputBase>(simConf,
                                                                                    "RelativeLinear")
@@ -832,7 +835,10 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(InputRelativeLinear, percentStart))
         .def_readonly("percent_end",
                       &SimulationConfig::InputRelativeLinear::percentEnd,
-                      DOC_SIMULATIONCONFIG(InputRelativeLinear, percentEnd));
+                      DOC_SIMULATIONCONFIG(InputRelativeLinear, percentEnd))
+        .def_readonly("represents_physical_electrode",
+                      &SimulationConfig::InputRelativeLinear::representsPhysicalElectrode,
+                      DOC_SIMULATIONCONFIG(InputRelativeLinear, representsPhysicalElectrode));
 
     py::class_<SimulationConfig::InputPulse, SimulationConfig::InputBase>(simConf, "Pulse")
         .def_readonly("amp_start",
@@ -846,16 +852,25 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(InputPulse, width))
         .def_readonly("frequency",
                       &SimulationConfig::InputPulse::frequency,
-                      DOC_SIMULATIONCONFIG(InputPulse, frequency));
+                      DOC_SIMULATIONCONFIG(InputPulse, frequency))
+        .def_readonly("represents_physical_electrode",
+                      &SimulationConfig::InputPulse::representsPhysicalElectrode,
+                      DOC_SIMULATIONCONFIG(InputPulse, representsPhysicalElectrode));
 
     py::class_<SimulationConfig::InputSubthreshold, SimulationConfig::InputBase>(simConf,
                                                                                  "Subthreshold")
         .def_readonly("percent_less",
                       &SimulationConfig::InputSubthreshold::percentLess,
-                      DOC_SIMULATIONCONFIG(InputSubthreshold, percentLess));
+                      DOC_SIMULATIONCONFIG(InputSubthreshold, percentLess))
+        .def_readonly("represents_physical_electrode",
+                      &SimulationConfig::InputSubthreshold::representsPhysicalElectrode,
+                      DOC_SIMULATIONCONFIG(InputSubthreshold, representsPhysicalElectrode));
 
     py::class_<SimulationConfig::InputHyperpolarizing, SimulationConfig::InputBase>(
-        simConf, "Hyperpolarizing");
+        simConf, "Hyperpolarizing")
+        .def_readonly("represents_physical_electrode",
+                      &SimulationConfig::InputHyperpolarizing::representsPhysicalElectrode,
+                      DOC_SIMULATIONCONFIG(InputHyperpolarizing, representsPhysicalElectrode));
 
     py::class_<SimulationConfig::InputSynapseReplay, SimulationConfig::InputBase>(simConf,
                                                                                   "SynapseReplay")
@@ -880,7 +895,10 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(InputNoise, meanPercent))
         .def_readonly("variance",
                       &SimulationConfig::InputNoise::variance,
-                      DOC_SIMULATIONCONFIG(InputNoise, variance));
+                      DOC_SIMULATIONCONFIG(InputNoise, variance))
+        .def_readonly("represents_physical_electrode",
+                      &SimulationConfig::InputNoise::representsPhysicalElectrode,
+                      DOC_SIMULATIONCONFIG(InputNoise, representsPhysicalElectrode));
 
     py::class_<SimulationConfig::InputShotNoise, SimulationConfig::InputBase>(simConf, "ShotNoise")
         .def_readonly("rise_time",
@@ -906,7 +924,10 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(InputShotNoise, ampMean))
         .def_readonly("amp_var",
                       &SimulationConfig::InputShotNoise::ampVar,
-                      DOC_SIMULATIONCONFIG(InputShotNoise, ampVar));
+                      DOC_SIMULATIONCONFIG(InputShotNoise, ampVar))
+        .def_readonly("represents_physical_electrode",
+                      &SimulationConfig::InputShotNoise::representsPhysicalElectrode,
+                      DOC_SIMULATIONCONFIG(InputShotNoise, representsPhysicalElectrode));
 
     py::class_<SimulationConfig::InputRelativeShotNoise, SimulationConfig::InputBase>(
         simConf, "RelativeShotNoise")
@@ -933,7 +954,10 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(InputRelativeShotNoise, sdPercent))
         .def_readonly("mean_percent",
                       &SimulationConfig::InputRelativeShotNoise::meanPercent,
-                      DOC_SIMULATIONCONFIG(InputRelativeShotNoise, meanPercent));
+                      DOC_SIMULATIONCONFIG(InputRelativeShotNoise, meanPercent))
+        .def_readonly("represents_physical_electrode",
+                      &SimulationConfig::InputRelativeShotNoise::representsPhysicalElectrode,
+                      DOC_SIMULATIONCONFIG(InputRelativeShotNoise, representsPhysicalElectrode));
 
     py::class_<SimulationConfig::InputAbsoluteShotNoise, SimulationConfig::InputBase>(
         simConf, "AbsoluteShotNoise")
@@ -960,7 +984,10 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(InputAbsoluteShotNoise, mean))
         .def_readonly("sigma",
                       &SimulationConfig::InputAbsoluteShotNoise::sigma,
-                      DOC_SIMULATIONCONFIG(InputAbsoluteShotNoise, sigma));
+                      DOC_SIMULATIONCONFIG(InputAbsoluteShotNoise, sigma))
+        .def_readonly("represents_physical_electrode",
+                      &SimulationConfig::InputAbsoluteShotNoise::representsPhysicalElectrode,
+                      DOC_SIMULATIONCONFIG(InputAbsoluteShotNoise, representsPhysicalElectrode));
 
     py::class_<SimulationConfig::InputOrnsteinUhlenbeck, SimulationConfig::InputBase>(
         simConf, "OrnsteinUhlenbeck")
@@ -981,7 +1008,10 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(InputOrnsteinUhlenbeck, mean))
         .def_readonly("sigma",
                       &SimulationConfig::InputOrnsteinUhlenbeck::sigma,
-                      DOC_SIMULATIONCONFIG(InputOrnsteinUhlenbeck, sigma));
+                      DOC_SIMULATIONCONFIG(InputOrnsteinUhlenbeck, sigma))
+        .def_readonly("represents_physical_electrode",
+                      &SimulationConfig::InputOrnsteinUhlenbeck::representsPhysicalElectrode,
+                      DOC_SIMULATIONCONFIG(InputOrnsteinUhlenbeck, representsPhysicalElectrode));
 
     py::class_<SimulationConfig::InputRelativeOrnsteinUhlenbeck, SimulationConfig::InputBase>(
         simConf, "RelativeOrnsteinUhlenbeck")
@@ -1002,7 +1032,11 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(InputRelativeOrnsteinUhlenbeck, meanPercent))
         .def_readonly("sd_percent",
                       &SimulationConfig::InputRelativeOrnsteinUhlenbeck::sdPercent,
-                      DOC_SIMULATIONCONFIG(InputRelativeOrnsteinUhlenbeck, sdPercent));
+                      DOC_SIMULATIONCONFIG(InputRelativeOrnsteinUhlenbeck, sdPercent))
+        .def_readonly(
+            "represents_physical_electrode",
+            &SimulationConfig::InputRelativeOrnsteinUhlenbeck::representsPhysicalElectrode,
+            DOC_SIMULATIONCONFIG(InputRelativeOrnsteinUhlenbeck, representsPhysicalElectrode));
 
     py::enum_<SimulationConfig::InputBase::Module>(inputBase, "Module")
         .value("linear", SimulationConfig::InputBase::Module::linear)