Copyright (#1)

* update copyright and repo links

* use trusted publisher instead of secrets in pypi workflow

* remove ebrains mirroring workflow

* fix isi log slope tests with numpy 2

* use python 3.12 to run cibuildwheel

* use macos-13 with cibuildwheel

---------

Co-authored-by: Aurélien Jaquier

.github/workflows/build-wheels.yml

@@ -10,11 +10,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, macos-12, windows-latest]
+        os: [ubuntu-22.04, macos-13, windows-latest]
         python: [cp39, cp310, cp311, cp312]
         arch: [x86_64, amd64]
         exclude:
-          - os: macos-12
+          - os: macos-13
             arch: amd64
           - os: ubuntu-22.04
             arch: amd64
@@ -30,7 +30,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9 # This might need to be dynamic based on the matrix
+          python-version: 3.12 # This might need to be dynamic based on the matrix
       - name: Install cibuildwheel
         run: pip install cibuildwheel
       - name: Build wheels

.github/workflows/publish.yml

@@ -76,6 +76,11 @@ jobs:
     name: Release and Publish on PyPI
     runs-on: ubuntu-22.04
     needs: [call-test-workflow, tag, wheels, tarball]
+    environment:  # needed for pypi publication
+      name: pypi
+      url: https://pypi.org/p/efel
+    permissions:  # needed for pypi publication
+      id-token: write
     steps:
       - uses: actions/checkout@v4
         with:
@@ -97,6 +102,3 @@ jobs:
 
       - name: Publish package to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_PASSWORD }}

README.md

@@ -1,4 +1,4 @@
-<img src="https://raw.githubusercontent.com/BlueBrain/eFEL/master/docs/source/logo/eFELBanner.png" alt="eFEL banner" />
+<img src="https://raw.githubusercontent.com/openbraininstitute/eFEL/master/docs/source/logo/eFELBanner.png" alt="eFEL banner" />
 
 <table>
 <tr>
@@ -20,31 +20,31 @@
 <tr>
   <td>License</td>
   <td>
-    <a href="https://github.com/BlueBrain/efel/blob/master/LICENSE.txt">
+    <a href="https://github.com/openbraininstitute/efel/blob/master/LICENSE.txt">
     <img src="https://img.shields.io/pypi/l/efel.svg" alt="license" />
     </a>
 </td>
 </tr>
 <tr>
   <td>Build Status</td>
   <td>
-    <a href="https://github.com/BlueBrain/eFEL/actions">
-    <img src="https://github.com/BlueBrain/eFEL/workflows/Build/badge.svg?branch=master" alt="actions build status" />
+    <a href="https://github.com/openbraininstitute/eFEL/actions">
+    <img src="https://github.com/openbraininstitute/eFEL/workflows/Build/badge.svg" alt="actions build status" />
     </a>
   </td>
 </tr>
 <tr>
   <td>Coverage</td>
   <td>
-    <a href="https://codecov.io/gh/BlueBrain/efel">
-    <img src="https://codecov.io/github/BlueBrain/eFEL/coverage.svg?branch=master" alt="coverage" />
+    <a href="https://codecov.io/gh/openbraininstitute/efel">
+    <img src="https://codecov.io/github/openbraininstitute/eFEL/coverage.svg?branch=master" alt="coverage" />
     </a>
   </td>
 </tr>
 <tr>
     <td>Gitter</td>
     <td>
-        <a href="https://gitter.im/bluebrain/efel">
+        <a href="https://gitter.im/openbraininstitute/efel">
         <img src="https://badges.gitter.im/Join%20Chat.svg" />
     </a>
     </td>
@@ -121,7 +121,7 @@ pip install efel
 If you want to install straight from the github repository you can use
 
 ```bash
-pip install git+git://github.com/BlueBrain/eFEL
+pip install git+git://github.com/openbraininstitute/eFEL
 ```
 
 Quick Start
@@ -139,7 +139,7 @@ To get a list with all the available feature names
 efel.get_feature_names()
 ```
 
-Note that the extra-cellular features, the bpap_attenuation feature and the check_ais_initiation feature are not listed above because they have to be used in a special way, as described [here](https://github.com/BlueBrain/eFEL/blob/master/examples/extracellular/extrafeats_example.ipynb) for extra-cellular features, [here](https://github.com/BlueBrain/eFEL/blob/master/docs/source/eFeatures.rst#bpap_attenuation) for bpap_attenuation feature and [here](https://github.com/BlueBrain/eFEL/blob/master/docs/source/eFeatures.rst#check_ais_initiation) for check_ais_initiation feature.
+Note that the extra-cellular features, the bpap_attenuation feature and the check_ais_initiation feature are not listed above because they have to be used in a special way, as described [here](https://github.com/openbraininstitute/eFEL/blob/master/examples/extracellular/extrafeats_example.ipynb) for extra-cellular features, [here](https://github.com/openbraininstitute/eFEL/blob/master/docs/source/eFeatures.rst#bpap_attenuation) for bpap_attenuation feature and [here](https://github.com/openbraininstitute/eFEL/blob/master/docs/source/eFeatures.rst#check_ais_initiation) for check_ais_initiation feature.
 
 To change the spike detection threshold setting (default is -20 mV)
 
@@ -151,7 +151,7 @@ For a full list of available settings, please refer to the [Setting class](./efe
 The python function to extract features is get_feature_values(...).
 Below is a short example on how to use this function. The code and example
 trace are available
-[here](https://github.com/BlueBrain/eFEL/blob/master/examples/basic/basic_example1.py)
+[here](https://github.com/openbraininstitute/eFEL/blob/master/examples/basic/basic_example1.py)
 
 ```python
 """Basic example 1 for eFEL"""
@@ -239,4 +239,4 @@ This project/research was supported by funding to the Blue Brain Project, a rese
 Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.
 
 Copyright (c) 2009-2024 Blue Brain Project/EPFL
-
+Copyright (c) 2025 Open Brain Institute

tests/test_isi.py

@@ -39,6 +39,7 @@ def test_ISIs_single_spike():
 def test_isi_log_slope_core_exception():
     """Test that _isi_log_slope_core handles np.polyfit raising a LinAlgError."""
     # Mock np.polyfit to raise a LinAlgError
+    tmp = np.polyfit
     np.polyfit = MagicMock(side_effect=np.linalg.LinAlgError("Singular matrix"))
 
     # Call _isi_log_slope_core with some dummy data
@@ -50,7 +51,7 @@ def test_isi_log_slope_core_exception():
     assert result is None
 
     # Reset np.polyfit to its original state
-    np.polyfit = np.lib.polynomial.polyfit
+    np.polyfit = tmp
 
 
 class TestRegularISI: