Merge branch 'development' into feat/handle-referenced-morphologies

.all-contributorsrc

@@ -181,6 +181,60 @@
         "code",
         "test"
       ]
+    },
+    {
+      "login": "lej0hn",
+      "name": "Giannis Daras",
+      "avatar_url": "https://avatars.githubusercontent.com/u/72049569?v=4",
+      "profile": "https://github.com/lej0hn",
+      "contributions": [
+        "bug",
+        "ideas",
+        "review",
+        "code"
+      ]
+    },
+    {
+      "login": "Dhruvanshu-Joshi",
+      "name": "Dhruvanshu-Joshi",
+      "avatar_url": "https://avatars.githubusercontent.com/u/104030847?v=4",
+      "profile": "https://github.com/Dhruvanshu-Joshi",
+      "contributions": [
+        "bug",
+        "ideas"
+      ]
+    },
+    {
+      "login": "AdityaBITMESRA",
+      "name": "AdityaBITMESRA",
+      "avatar_url": "https://avatars.githubusercontent.com/u/147182147?v=4",
+      "profile": "https://github.com/AdityaBITMESRA",
+      "contributions": [
+        "bug",
+        "ideas",
+        "code",
+        "review"
+      ]
+    },
+    {
+      "login": "YBCS",
+      "name": "Y. Budhachandra",
+      "avatar_url": "https://avatars.githubusercontent.com/u/29734619?v=4",
+      "profile": "https://github.com/YBCS",
+      "contributions": [
+        "code",
+        "test"
+      ]
+    },
+    {
+      "login": "stellaprins",
+      "name": "Stella",
+      "avatar_url": "https://avatars.githubusercontent.com/u/30465823?v=4",
+      "profile": "https://github.com/stellaprins",
+      "contributions": [
+        "code",
+        "ideas"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/ci.yml

@@ -51,3 +51,8 @@ jobs:
         pynml -h
 
         ./test-ghactions.sh -neuron
+
+    - name: Lint with ruff
+      run: |
+        pip install ruff
+        ruff check . --exit-zero

README.md

@@ -12,7 +12,7 @@ pyNeuroML
 [![Twitter Follow](https://img.shields.io/twitter/follow/NeuroML?style=social)](https://twitter.com/NeuroML)
 [![Gitter](https://badges.gitter.im/NeuroML/community.svg)](https://gitter.im/NeuroML/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-12-orange.svg?style=flat-square)](#contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-17-orange.svg?style=flat-square)](#contributors-)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.
@@ -192,6 +192,13 @@ More closely tied to PyNN?
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/andrisecker"><img src="https://avatars.githubusercontent.com/u/13274870?v=4?s=100" width="100px;" alt="András Ecker"/><br /><sub><b>András Ecker</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3Aandrisecker" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=andrisecker" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/RokasSt"><img src="https://avatars.githubusercontent.com/u/12904422?v=4?s=100" width="100px;" alt="Rokas Stanislovas"/><br /><sub><b>Rokas Stanislovas</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3ARokasSt" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=RokasSt" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/robertvi"><img src="https://avatars.githubusercontent.com/u/456100?v=4?s=100" width="100px;" alt="Robert Vickerstaff"/><br /><sub><b>Robert Vickerstaff</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/commits?author=robertvi" title="Code">💻</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=robertvi" title="Tests">⚠️</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/lej0hn"><img src="https://avatars.githubusercontent.com/u/72049569?v=4?s=100" width="100px;" alt="Giannis Daras"/><br /><sub><b>Giannis Daras</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3Alej0hn" title="Bug reports">🐛</a> <a href="#ideas-lej0hn" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/NeuroML/pyNeuroML/pulls?q=is%3Apr+reviewed-by%3Alej0hn" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=lej0hn" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/Dhruvanshu-Joshi"><img src="https://avatars.githubusercontent.com/u/104030847?v=4?s=100" width="100px;" alt="Dhruvanshu-Joshi"/><br /><sub><b>Dhruvanshu-Joshi</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3ADhruvanshu-Joshi" title="Bug reports">🐛</a> <a href="#ideas-Dhruvanshu-Joshi" title="Ideas, Planning, & Feedback">🤔</a></td>
+    </tr>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/AdityaBITMESRA"><img src="https://avatars.githubusercontent.com/u/147182147?v=4?s=100" width="100px;" alt="AdityaBITMESRA"/><br /><sub><b>AdityaBITMESRA</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3AAdityaBITMESRA" title="Bug reports">🐛</a> <a href="#ideas-AdityaBITMESRA" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=AdityaBITMESRA" title="Code">💻</a> <a href="https://github.com/NeuroML/pyNeuroML/pulls?q=is%3Apr+reviewed-by%3AAdityaBITMESRA" title="Reviewed Pull Requests">👀</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/YBCS"><img src="https://avatars.githubusercontent.com/u/29734619?v=4?s=100" width="100px;" alt="Y. Budhachandra"/><br /><sub><b>Y. Budhachandra</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/commits?author=YBCS" title="Code">💻</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=YBCS" title="Tests">⚠️</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/stellaprins"><img src="https://avatars.githubusercontent.com/u/30465823?v=4?s=100" width="100px;" alt="Stella"/><br /><sub><b>Stella</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/commits?author=stellaprins" title="Code">💻</a> <a href="#ideas-stellaprins" title="Ideas, Planning, & Feedback">🤔</a></td>
     </tr>
   </tbody>
   <tfoot>

pyneuroml/__init__.py

@@ -12,7 +12,7 @@
     __version__ = importlib_metadata.version("pyNeuroML")
 
 
-JNEUROML_VERSION = "0.13.2"
+JNEUROML_VERSION = "0.13.3"
 
 # Define a logger for the package
 logging.basicConfig(

pyneuroml/xppaut/__init__.py

@@ -250,10 +250,13 @@ def substitute_functions(expr, functions):
 def to_xpp(data, new_xpp_filename):
     xpp_ode = ""
 
+    from pyneuroml import __version__
+    xpp_ode += "\n## XPP export from pyNeuroML v%s\n"%__version__
+
     xpp_ode += "\n# Parameters\n"
     for k, v in data["parameters"].items():
         if k not in INBUILT.keys():
-            xpp_ode += f"par {k} = {v}\n"
+            xpp_ode += f"par {k}={v}\n"
 
     xpp_ode += "\n# Functions\n"
     for k, v in data["functions"].items():

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pyNeuroML
-version = 1.3.6
+version = 1.3.7
 author = Padraig Gleeson
 author_email = [email protected]
 url = https://github.com/NeuroML/pyNeuroML

tests/utils/test_utils.py

@@ -12,6 +12,7 @@
 import pathlib as pl
 
 import neuroml
+
 from pyneuroml.pynml import read_neuroml2_file, write_neuroml2_file
 from pyneuroml.utils import (
     extract_position_info,