mpinb · bgmeulem · Apr 23, 2026 · Nov 30, 2025 · Apr 23, 2026 · Apr 23, 2026
diff --git a/.github/workflows/check-version.yml b/.github/workflows/check-version.yml
@@ -4,9 +4,19 @@ on:
   push:
     branches:
       - master
+    paths-ignore:
+      - README.md
+      - CHANGELOG.md
+      - .gitignore
+      - 'CITATION.cff'
   pull_request:
     branches:
       - master
+    paths-ignore:
+      - README.md
+      - CHANGELOG.md
+      - .gitignore
+      - 'CITATION.cff'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

diff --git a/CITATION.cff b/CITATION.cff
@@ -58,5 +58,5 @@ keywords:
   - python
   - neuron
 license: Apache-2.0
-version: 0.7.1-beta
+version: 0.7.2-beta
 date-released: '2026-04-22'
diff --git a/biophysics_fitting/hay/L5tt_parameter_setup.py b/biophysics_fitting/hay/L5tt_parameter_setup.py
@@ -520,7 +520,11 @@ def set_hot_zone(cell_param, min_=None, max_=None, outsidescale_sections=None):
         cell_param (:class:`~single_cell_parser.parameters.NTParameterSet` | dict): The cell parameter dictionary.
         min\_ (float): The minimum distance from the soma.
         max\_ (float): The maximum distance from the soma.
-        outsidescale_sections (list): A list of sections where the channels should be inserted.
+        outsidescale_sections (list): 
+            A list of sections not part of the hot zone, but including calcium channels nonetheless.
+            These sections will get a Ca channel density equal to the :ref:`neuron_parameters_format` key ``outside_scale``.
+            Usually, this is less than the hot zone density.
+            See :ref:`~single_cell_parser.cell_parser.insert_range_mechanisms` for more information on channel density during neuron model creation.
 
     Returns:
         :class:`~single_cell_parser.parameters.NTParameterSet` | dict: The updated cell_param.

diff --git a/getting_started/example_data/simulation_data/biophysics/89/db/42/metadata.json b/getting_started/example_data/simulation_data/biophysics/89/db/42/metadata.json
@@ -1 +1 @@
-{"dumper": "just_create_isf_db", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "just_create_isf_db", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/...tarted/example_data/simulation_data/biophysics/89/db/RW_exploration_example/metadata.json b/...tarted/example_data/simulation_data/biophysics/89/db/RW_exploration_example/metadata.json
@@ -1 +1 @@
-{"dumper": "just_create_folder", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "just_create_folder", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/getting_started/example_data/simulation_data/biophysics/89/db/fixed_params/metadata.json b/getting_started/example_data/simulation_data/biophysics/89/db/fixed_params/metadata.json
@@ -1 +1 @@
-{"dumper": "to_cloudpickle", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "to_cloudpickle", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/getting_started/example_data/simulation_data/biophysics/89/db/get_Combiner/metadata.json b/getting_started/example_data/simulation_data/biophysics/89/db/get_Combiner/metadata.json
@@ -1 +1 @@
-{"dumper": "to_cloudpickle", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "to_cloudpickle", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/getting_started/example_data/simulation_data/biophysics/89/db/get_Evaluator/metadata.json b/getting_started/example_data/simulation_data/biophysics/89/db/get_Evaluator/metadata.json
@@ -1 +1 @@
-{"dumper": "to_cloudpickle", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "to_cloudpickle", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/getting_started/example_data/simulation_data/biophysics/89/db/get_Simulator/metadata.json b/getting_started/example_data/simulation_data/biophysics/89/db/get_Simulator/metadata.json
@@ -1 +1 @@
-{"dumper": "to_cloudpickle", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "to_cloudpickle", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/getting_started/example_data/simulation_data/biophysics/89/db/get_fixed_params/metadata.json b/getting_started/example_data/simulation_data/biophysics/89/db/get_fixed_params/metadata.json
@@ -1 +1 @@
-{"dumper": "to_cloudpickle", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "to_cloudpickle", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/getting_started/example_data/simulation_data/biophysics/89/db/morphology/metadata.json b/getting_started/example_data/simulation_data/biophysics/89/db/morphology/metadata.json
@@ -1 +1 @@
-{"dumper": "just_create_folder", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "just_create_folder", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/getting_started/example_data/simulation_data/biophysics/89/db/params/metadata.json b/getting_started/example_data/simulation_data/biophysics/89/db/params/metadata.json
@@ -1 +1 @@
-{"dumper": "pandas_to_pickle", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "pandas_to_pickle", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/getting_started/example_data/simulation_data/biophysics/89/metadata.json b/getting_started/example_data/simulation_data/biophysics/89/metadata.json
@@ -1 +1 @@
-{"dumper": "just_create_isf_db", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "just_create_isf_db", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/getting_started/example_data/simulation_data/biophysics/example_models/metadata.json b/getting_started/example_data/simulation_data/biophysics/example_models/metadata.json
@@ -1 +1 @@
-{"dumper": "to_cloudpickle", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "to_cloudpickle", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/getting_started/example_data/simulation_data/biophysics/simulator/metadata.json b/getting_started/example_data/simulation_data/biophysics/simulator/metadata.json
@@ -1 +1 @@
-{"dumper": "to_cloudpickle", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "to_cloudpickle", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/getting_started/example_data/simulation_data/biophysics/voltage_traces/metadata.json b/getting_started/example_data/simulation_data/biophysics/voltage_traces/metadata.json
@@ -1 +1 @@
-{"dumper": "to_cloudpickle", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
+{"dumper": "to_cloudpickle", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
diff --git a/pyproject.toml b/pyproject.toml
@@ -14,7 +14,7 @@ authors = [
 description = "An In Silico Framework for the generation, simulation and analysis of neuron-network interactions during in vivo conditions."
 name = "ISF"
 requires-python = ">=3.8"
-version = "0.7.1-beta"
+version = "0.7.2-beta"
 
 [tool.pixi.workspace]
 channels = ["conda-forge"]

diff --git a/singlecell_input_mapper/__init__.py b/singlecell_input_mapper/__init__.py
@@ -32,7 +32,7 @@
 
 ISF currently implements the following workflows to generate :ref:`syn_file_format` and :ref:`conf_file_format` files:
 
-- :mod:`udvary2022`
+- :mod:`~singlecell_input_mapper.udvary2022`
 
 .. hint::
    If you work on a model system that does not have the required input data for these workflows, we recommend to infer

diff --git a/singlecell_input_mapper/udvary2022/__init__.py b/singlecell_input_mapper/udvary2022/__init__.py
@@ -18,14 +18,6 @@
 of the rat barrel cortex, based on methods and data presented in 
 :cite:t:`Udvary_Harth_Macke_Hege_De_Kock_Sakmann_Oberlaender_2022` and :cite:t:`Egger_Dercksen_Udvary_Hege_Oberlaender_2014`.
 
-This runfile assumes you have downloaded and extracted the barrel cortex model data from
-https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/JZPULNa.
-If this is not the case, please consult ``installer/download_bc_model`` and extract.
-
-Attention:
-    This file is specific to the barrel cortex model data. If you want to use it for other data,
-    you need to adapt the paths to the data accordingly. This runfile can serve as a template.
-
 Inputs:
 
 - Morphology of the postsynaptic neuron
@@ -34,13 +26,6 @@
 - Connections spreadsheet containing Post-Synaptic Targets (PSTs) per unit of length and area
 - Bouton locations of individual axon tracings per presynaptic cell type.
 
-Attention:
-    This runfile has default values for the barrel cortex, and so assumes that you have downloaded 
-    and extracted the barrel cortex model data from
-    https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/JZPULNa.
-    If this is not the case, please consult ``installer/download_bc_model`` and extract,
-    or adapt the paths in this file to your data.
-
 This module then uses :class:`~singlecell_input_mapper.singlecell_input_mapper.network_embedding.NetworkMapper`
 to assign synapses to a single post-synaptic cell morphology, based on the inputs mentioned above.
 This happens according to the following pipeline:
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"dumper": "just_create_isf_db", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
		{"dumper": "just_create_isf_db", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"dumper": "just_create_folder", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
		{"dumper": "just_create_folder", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"dumper": "to_cloudpickle", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
		{"dumper": "to_cloudpickle", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"dumper": "pandas_to_pickle", "time": [2025, 3, 11, 10, 8, 10, 1, 70, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}
		{"dumper": "pandas_to_pickle", "time": [2026, 4, 6, 14, 43, 52, 0, 96, -1], "metadata_creation_time": "post_hoc", "version": "unknown"}