python>=3.11, bluepyefe>=2.3.48, scipy>=1.16.1 (#7)

* only get experimental traces

* add requirements to the readme

Author: AurelienJaquier

.github/workflows/test.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v3

README.rst

@@ -46,6 +46,29 @@ Additionally, to cite software used for different steps of the pipeline, please
 
 - Ion Channel Selector: `Me-Features-to-Mo-ID Mapping <https://github.com/openbraininstitute/me-features-to-mo-ID-mapping>`_: paper: `Roussel et al., 2023 <https://doi.org/10.1371/journal.pcbi.1010058>`_
 
+Requirements
+------------
+
+* `Python 3.11+ <https://www.python.org/downloads/release/python-311/>`_
+* numpy
+* scipy >= 1.16.1
+* pandas
+* ipyparallel >= 6.3
+* tqdm
+* pyyaml
+* gitpython
+* bluepyopt >= 1.14.10
+* bluepyefe >= 2.3.48
+* neurom >= 3.0
+* efel >= 5.5.5
+* configparser
+* neuron >= 8.0
+* morph_tool >= 2.8
+* morphio
+* fasteners >= 0.16
+* jinja2 >= 3.0.3
+* currentscape >= 0.0.11
+
 Installation
 ------------
 

bluepyemodel/access_point/forge_access_point.py

@@ -1034,7 +1034,7 @@ def check_resource(
 def get_available_traces(species=None, brain_region=None, access_token=None, forge_path=None):
     """Returns a list of Resources of type Traces from the bbp/lnmce Nexus project"""
 
-    filters = {"type": "Trace", "distribution": {"encodingFormat": "application/nwb"}}
+    filters = {"type": "ExperimentalTrace", "distribution": {"encodingFormat": "application/nwb"}}
 
     if species:
         filters["subject"] = species

pyproject.toml

@@ -10,18 +10,18 @@ authors = [
 description="Blue Brain Python Electrical Modeling Pipeline"
 readme = "README.rst"
 license = {file = "LICENSE.txt"}
-requires-python = ">= 3.9"
+requires-python = ">= 3.11"
 dynamic = ["version"]
 dependencies = [
     "numpy",
-    "scipy",
+    "scipy>=1.16.1",
     "pandas",
     "ipyparallel>=6.3",
     "tqdm",
     "pyyaml",
     "gitpython",
     "bluepyopt>=1.14.10",
-    "bluepyefe>=2.2.0",
+    "bluepyefe>=2.3.48",
     "neurom>=3.0",
     "efel>=5.5.5",
     "configparser",