Add simplecell example

bluepyemodel/emodel_pipeline/plotting.py

@@ -247,7 +247,11 @@ def evolution_parameters_density(
         max_n_gen = max(max_n_gen, run["generation"])
         genealogies[checkpoint_path] = (run["history"].genealogy_history, seed)
 
-    gen_per_bin = 4
+    if max_n_gen >= 8:
+        gen_per_bin = 4
+    else:
+        gen_per_bin = 1
+
     pop_size = len(run["population"])
     histo_bins = (int(max_n_gen / gen_per_bin), 20)
     normalization_factor = gen_per_bin * pop_size
@@ -1973,6 +1977,10 @@ def plot_models(
             dendritic_feature_plots(mo, "rheobase", dest_leaf, figures_dir)
 
         if plot_currentscape:
+            logger.warning(
+                "If an ion channel mod file lacks RANGE current variable (e.g. RANGE ik, ina), "
+                "no associated current will be plotted for that SUFFIX in Currentscape."
+            )
             config = access_point.pipeline_settings.currentscape_config
             figures_dir_currentscape = figures_dir / "currentscape" / dest_leaf
             currentscape(

examples/README.md

@@ -4,6 +4,8 @@ This directory includes various examples demonstrating how to use BluePyEModel:
 
 - [**L5PC**](./L5PC/README.rst): Provides a guide for setting up and running the E-Model building pipeline locally on a personal computer or on a Slurm cluster. This is an example based on the juvenile (P14) rat somatosensory cortex layer 5 thick-tufted pyramidal cell (L5TPC) e-model optimisation of the [SSCxEModelExamples](https://github.com/BlueBrain/SSCxEModelExamples/tree/main/optimization) repository.
 
+- [**simplecell**](./simplecell/simplecell.ipynb): Demonstrates creating a single-compartment neuron model with two parameters using rheobase independent optimisation.
+
 - [**nexus**](./nexus/README.md): Demonstrates the use of BluePyEModel through the Nexus access point.
 
 - [**others**](./others/README.rst): Contains various examples demonstrating different functionalities and use cases.

examples/simplecell/.gitignore

@@ -0,0 +1,18 @@
+.ipynb_checkpoints/
+run/
+.DS_Store/
+checkpoints/
+logs/
+figures/
+docs/
+notebooks/
+temp/
+.ipython/
+.tmp/
+x86_64/
+core.*
+recordings/
+__pycache__/
+ephys_data/
+myvenv/
+final_tmp.json

examples/simplecell/LICENSE.txt

@@ -0,0 +1,13 @@
+The CC-BY-NC-SA license applies, as indicated by headers in the
+respective source files.
+
+https://creativecommons.org/licenses/by-nc-sa/4.0/
+
+The detailed text is available here
+https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
+
+or in this tarball in the seperate file LICENSE_CC-BY-CA-SA-4.0
+
+The Python code and cell morphology are licensed with the above mentioned CC-BY-NC-SA license.
+
+THIS DATA IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE”.

examples/simplecell/LICENSE_CC-BY-CA-SA-4.0

@@ -0,0 +1,104 @@
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