Merge branch 'master' into arbor_integration

Author: lukasgd

.github/workflows/keep-alive.yml

@@ -23,14 +23,14 @@ jobs:
           echo "datelimit=$datethen" >> $GITHUB_ENV
 
       - name: setup git config
-        if: github.event.base.repo.updated_at <= env.datelimit
+        if: github.event.repository.pushed_at <= env.datelimit
         run: |
           # setup the username and email.
           git config user.name "Github Actions Keepalive Bot"
           git config user.email "<>"
 
       - name: commit IF last commit is older than 50 days
-        if: github.event.base.repo.updated_at <= env.datelimit
+        if: github.event.repository.pushed_at <= env.datelimit
         run: |
           git commit -m "Empty commit to keep the gihub workflows alive" --allow-empty
           git push origin master

.github/workflows/test.yml

@@ -7,10 +7,15 @@ on:
 
 jobs:
   test:
-    runs-on: ubuntu-latest
+    name: Test for python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        os: [ubuntu-latest]
         python-version: ["3.7", "3.8", "3.9", "3.10"]
+        include:
+          - os: macos-latest
+            python-version: "3.10"
 
     steps:
     - uses: actions/checkout@v2

AUTHORS.txt

@@ -6,3 +6,4 @@ Giuseppe Chindemi @ BBP
 Tanguy Damart @ BBP
 Elisabetta Iavarone @ BBP
 Anil Tuncel @ BBP
+Aurelien Jaquier @ BBP

Makefile

@@ -79,8 +79,20 @@ clean:
 	rm -rf examples/l5pc/l5pc_validate_neuron_arbor_somatic.py
 	rm -rf examples/l5pc/x86_64
 	rm -rf examples/stochkv/x86_64
+	rm -rf x86_64
 	rm -rf .coverage
 	rm -rf coverage.xml
+	rm -rf channels
+	rm -rf LEMS_l5pc.xml
+	rm -rf LEMS_l5pc_nrn.py
+	rm -rf l5pc.Pop_l5pc_0_0.v.dat
+	rm -rf time.dat
+	rm -rf l5pc.hoc
+	rm -rf l5pc.net.nml
+	rm -rf l5pc_0_0.cell.nml
+	rm -rf l5pc_0_0.hoc
+	rm -rf loadcell.hoc
+	rm -rf *.mod
 	find . -name "*.pyc" -exec rm -rf {} \;
 l5pc_start: install
 	cd examples/l5pc && \

README.rst

@@ -107,7 +107,9 @@ We are providing support using a chat channel on `Gitter <https://gitter.im/Blue
 
 News
 ====
-- 2022/10/31: BluePyOpt now supports Arbor simulator.
+- 2023/01: BluePyOpt now supports the Arbor simulator.
+- 2022/12: Support for LFPy models merged into master. Examples and preprint: https://github.com/alejoe91/multimodalfitting, https://www.biorxiv.org/content/10.1101/2022.08.03.502468v1.full
+- 2022/12: BluePyOpt now has the ability to write out NeuroML files: https://github.com/BlueBrain/BluePyOpt/tree/master/bluepyopt/neuroml
 - 2021/08/30: BluePyOpt dropped Python 2.7 support.
 - 2017/01/04: BluePyOpt is now considered compatible with Python 3.6+.
 - 2016/11/10: BluePyOpt now supports NEURON point processes. This means we can fit parameters of Adex/GIF/Izhikevich models, and also synapse models.
@@ -140,7 +142,7 @@ And then bluepyopt itself:
 
     pip install bluepyopt
 
-Support for simulators other than NEURON is optional and not installed by default. If you want to use [Arbor](https://arbor-sim.org/) to run your models, use the followig line instead to install bluepyopt.
+Support for simulators other than NEURON is optional and not installed by default. If you want to use [Arbor](https://arbor-sim.org/) to run your models, use the following line instead to install bluepyopt.
 
 .. code-block:: bash
 
@@ -201,6 +203,14 @@ With 2 notebooks:
 https://github.com/BlueBrain/BluePyOpt/blob/master/examples/tsodyksmarkramstp/tsodyksmarkramstp.ipynb
 https://github.com/BlueBrain/BluePyOpt/blob/master/examples/tsodyksmarkramstp/tsodyksmarkramstp_multiplefreqs.ipynb
 
+Exporting cell in neuroml format
+--------------------------------
+An iPython notebook showing how to export a BluePyOpt cell in the neuroml format, how to create a LEMS simulation,
+and how to run the LEMS simulation with the neuroml cell can be found at:
+
+https://github.com/BlueBrain/BluePyOpt/blob/master/examples/neuroml/neuroml.ipynb
+
+
 API documentation
 =================
 The API documentation can be found on `ReadTheDocs <http://bluepyopt.readthedocs.io/en/latest/>`_.

bluepyopt/deapext/optimisations.py

@@ -199,7 +199,10 @@ def setup_deap(self):
 
         # Register the evaluation function for the individuals
         # import deap_efel_eval1
-        self.toolbox.register("evaluate", self.evaluator.evaluate_with_lists)
+        self.toolbox.register(
+            "evaluate",
+            self.evaluator.init_simulator_and_evaluate_with_lists
+        )
 
         # Register the mate operator
         self.toolbox.register(

bluepyopt/deapext/optimisationsCMA.py

@@ -211,7 +211,10 @@ def setup_deap(self):
         )
 
         # Register the evaluation function for the individuals
-        self.toolbox.register("evaluate", self.evaluator.evaluate_with_lists)
+        self.toolbox.register(
+            "evaluate",
+            self.evaluator.init_simulator_and_evaluate_with_lists
+        )
 
         import copyreg
         import types

bluepyopt/deapext/tools/selIBEA.py

@@ -63,7 +63,7 @@ def _calc_fitness_components(population, kappa):
     population_matrix = numpy.fromiter(
         iter(-x for individual in population
              for x in individual.fitness.wvalues),
-        dtype=numpy.float)
+        dtype=numpy.float64)
     pop_len = len(population)
     feat_len = len(population[0].fitness.wvalues)
     population_matrix = population_matrix.reshape((pop_len, feat_len))

bluepyopt/ephys/create_hoc.py

@@ -157,6 +157,11 @@ def _generate_parameters(parameters, location_order, loc_desc):
         if loc not in param_locations:
             continue
         for param in param_locations[loc]:
+            if not isinstance(param.param_dependencies, list) or \
+                    len(param.param_dependencies) > 0:
+                raise CreateHocException(  # also an ACC exception
+                    'Exporting models with parameters that have'
+                    ' param_dependencies is not yet supported.')
             if isinstance(param, NrnRangeParameter):
                 if isinstance(
                         param.value_scaler,