Merge branch 'master' of https://github.com/BlueBrain/BluePyOpt into test-py311

Conflicts:
	.github/workflows/test.yml

Author: Jaquier Aurélien Tristan

.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

@@ -11,8 +11,11 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest]
         python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        include:
+          - os: macos-latest
+            python-version: "3.10"
 
     steps:
     - uses: actions/checkout@v2

MANIFEST.in

@@ -1,6 +1,10 @@
 include versioneer.py
 include bluepyopt/_version.py
+include bluepyopt/ephys/static/arbor_mechanisms.json
 include bluepyopt/ephys/templates/cell_template.jinja2
+include bluepyopt/ephys/templates/acc/_json_template.jinja2
+include bluepyopt/ephys/templates/acc/decor_acc_template.jinja2
+include bluepyopt/ephys/templates/acc/label_dict_acc_template.jinja2
 
 include.txt
 include AUTHORS.txt

Makefile

@@ -15,7 +15,11 @@ l5pc_nbconvert: jupyter
 	cd examples/l5pc && \
 		jupyter nbconvert --to python L5PC.ipynb && \
 		sed '/get_ipython/d;/plt\./d;/plot_responses/d;/import matplotlib/d;/neurom/d;/axes/d;/fig/d;/for index/d' L5PC.py >L5PC.tmp && \
-		mv L5PC.tmp L5PC.py
+		mv L5PC.tmp L5PC.py && \
+		python l5pc_validate_neuron_arbor_pm.py --prepare-only --regions somatic --param-values ../../bluepyopt/tests/testdata/l5pc_validate_neuron_arbor/param_values.json && \
+		jupyter nbconvert --to python l5pc_validate_neuron_arbor_somatic.ipynb && \
+		sed '/get_ipython/d;/plt\./d;/import matplotlib/d;/from IPython.display/d;/multiprocessing/d;s/pool.map/map/g;s/# test_l5pc: insert //g;/# test_l5pc: skip/d' l5pc_validate_neuron_arbor_somatic.py >l5pc_validate_neuron_arbor_somatic.tmp && \
+		mv l5pc_validate_neuron_arbor_somatic.tmp l5pc_validate_neuron_arbor_somatic.py
 l5pc_nrnivmodl:
 	cd examples/l5pc && nrnivmodl mechanisms
 l5pc_zip:
@@ -28,7 +32,11 @@ sc_prepare: jupyter
 	cd examples/simplecell && \
 		jupyter nbconvert --to python simplecell.ipynb && \
 		sed '/get_ipython/d;/plt\./d;/plot_responses/d;/import matplotlib/d' simplecell.py >simplecell.tmp && \
-		mv simplecell.tmp simplecell.py
+		mv simplecell.tmp simplecell.py && \
+		jupyter nbconvert --to python simplecell_arbor.ipynb && \
+		sed '/get_ipython/d;/plt\./d;/plot_responses/d;/import matplotlib/d' simplecell_arbor.py >simplecell_arbor.tmp && \
+		mv simplecell_arbor.tmp simplecell_arbor.py
+
 meta_prepare: jupyter
 	cd examples/metaparameters && \
 		jupyter nbconvert --to python metaparameters.ipynb && \
@@ -41,6 +49,8 @@ coverage_test: test
 jupyter:
 	pip install jupyter
 	pip install ipython --upgrade
+	pip install papermill
+	pip install scipy
 install_test_requirements:
 	pip install -q $(TEST_REQUIREMENTS) --upgrade
 test: clean unit functional
@@ -65,6 +75,8 @@ clean:
 	rm -rf bluepyopt/tests/coverage.xml
 	rm -rf bluepyopt/tests/coverage_html
 	rm -rf examples/l5pc/L5PC.py
+	rm -rf examples/l5pc/l5pc_validate_neuron_arbor_somatic.ipynb
+	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

README.rst

@@ -107,6 +107,9 @@ We are providing support using a chat channel on `Gitter <https://gitter.im/Blue
 
 News
 ====
+- 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.
@@ -139,6 +142,11 @@ 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 following line instead to install bluepyopt.
+
+.. code-block:: bash
+
+    pip install bluepyopt[arbor]
 
 Cloud infrastructure
 ====================
@@ -156,7 +164,8 @@ Single compartmental model
 An iPython notebook with an introductory optimisation of a one compartmental
 model with 2 HH channels can be found at
 
-https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell.ipynb
+https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell.ipynb (NEURON)
+https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell_arbor.ipynb (Arbor)
 
 
 |landscape_example|
@@ -171,7 +180,8 @@ Scripts for a more complex neocortical L5PC are in
 
 With a notebook:
 
-https://github.com/BlueBrain/BluePyOpt/blob/master/examples/l5pc/L5PC.ipynb
+https://github.com/BlueBrain/BluePyOpt/blob/master/examples/l5pc/L5PC.ipynb (NEURON)
+https://github.com/BlueBrain/BluePyOpt/blob/master/examples/l5pc/L5PC_arbor.ipynb (Arbor)
 
 Thalamocortical Cells
 ---------------------
@@ -193,6 +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

@@ -201,7 +201,7 @@ def setup_deap(self):
         # import deap_efel_eval1
         self.toolbox.register(
             "evaluate",
-            self.evaluator.set_neuron_variables_and_evaluate_with_lists
+            self.evaluator.init_simulator_and_evaluate_with_lists
         )
 
         # Register the mate operator

bluepyopt/deapext/optimisationsCMA.py

@@ -213,7 +213,7 @@ def setup_deap(self):
         # Register the evaluation function for the individuals
         self.toolbox.register(
             "evaluate",
-            self.evaluator.set_neuron_variables_and_evaluate_with_lists
+            self.evaluator.init_simulator_and_evaluate_with_lists
         )
 
         import copyreg

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/acc.py

@@ -0,0 +1,57 @@
+'''Dependencies of Arbor simulator backend'''
+
+try:
+    import arbor
+except ImportError as e:
+    class arbor:
+        def __getattribute__(self, _):
+            raise ImportError("Exporting cell models to ACC/JSON, loading"
+                              " them or optimizing them with the Arbor"
+                              " simulator requires missing dependency arbor."
+                              " To install BluePyOpt with arbor,"
+                              " run 'pip install bluepyopt[arbor]'.")
+
+
+class ArbLabel:
+    """Arbor label"""
+
+    def __init__(self, type, name, s_expr):
+        if type not in ['locset', 'region', 'iexpr']:
+            raise ValueError('Invalid Arbor label type %s' % type)
+        self._type = type
+        self._name = name
+        self._s_expr = s_expr
+
+    @property
+    def defn(self):
+        """Label definition for label-dict"""
+        return '(%s-def "%s" %s)' % (self._type, self._name, self._s_expr)
+
+    @property
+    def ref(self):
+        """Reference to label defined in label-dict"""
+        return '(%s "%s")' % (self._type, self._name)
+
+    @property
+    def name(self):
+        """Name of the label"""
+        return self._name
+
+    @property
+    def loc(self):
+        """S-expression defining the location of the label"""
+        return self._s_expr
+
+    def __eq__(self, other):
+        if other is None:
+            return False
+        elif not isinstance(other, ArbLabel):
+            raise TypeError('%s is not an ArbLabel' % str(other))
+        else:
+            return self._s_expr == other._s_expr
+
+    def __hash__(self):
+        return hash(self._s_expr)
+
+    def __repr__(self):
+        return self.defn