Merge branch 'master' into support_numpy_2

Author: Moritz-Alexander-Kern

.github/workflows/CI.yml

@@ -88,7 +88,7 @@ jobs:
         run: |
             echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/elephant-data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
 
-      - uses: actions/cache/restore@v4.0.2
+      - uses: actions/cache/restore@v4.2.2
         # Loading cache of elephant-data
         id: cache-datasets
         with:
@@ -148,7 +148,7 @@ jobs:
         run: |
             echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/elephant-data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
 
-      - uses: actions/cache/restore@v4.0.2
+      - uses: actions/cache/restore@v4.2.2
         # Loading cache of elephant-data
         id: cache-datasets
         with:
@@ -213,7 +213,7 @@ jobs:
         run: |
             echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/elephant-data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
 
-      - uses: actions/cache/restore@v4.0.2
+      - uses: actions/cache/restore@v4.2.2
         # Loading cache of elephant-data
         id: cache-datasets
         with:
@@ -279,7 +279,7 @@ jobs:
         run: |
             echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/elephant-data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
 
-      - uses: actions/cache/restore@v4.0.2
+      - uses: actions/cache/restore@v4.2.2
         # Loading cache of elephant-data
         id: cache-datasets
         with:
@@ -346,7 +346,7 @@ jobs:
           echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
 
       - name: Cache pip
-        uses: actions/cache@v4
+        uses: actions/cache@v4.2.2
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
 
@@ -357,7 +357,7 @@ jobs:
         run: |
             echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/elephant-data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
 
-      - uses: actions/cache/restore@v4.0.2
+      - uses: actions/cache/restore@v4.2.2
         # Loading cache of elephant-data
         id: cache-datasets
         with:
@@ -431,7 +431,7 @@ jobs:
           echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
 
       - name: Cache pip
-        uses: actions/cache@v4
+        uses: actions/cache@v4.2.2
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
           # Look to see if there is a cache hit for the corresponding requirements files
@@ -497,7 +497,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Cache test_env
-        uses: actions/cache@v4
+        uses: actions/cache@v4.2.2
         with:
           path: ~/test_env
           # Look to see if there is a cache hit for the corresponding requirements files

.github/workflows/cache_elephant_data.yml

@@ -23,7 +23,7 @@ jobs:
         run: |
             echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/elephant-data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
 
-      - uses: actions/cache@v4.0.2
+      - uses: actions/cache@v4.2.2
         # Loading cache of elephant-data
         id: cache-datasets
         with:

.zenodo.json

@@ -17,7 +17,7 @@
         }
     ],
 
-    "title": "Elephant 1.1.0",
+    "title": "Elephant 1.1.1",
 
     "keywords": [
     "neuroscience",

README.md

@@ -9,7 +9,7 @@
 [![tests](https://github.com/NeuralEnsemble/elephant/actions/workflows/CI.yml/badge.svg)](https://github.com/NeuralEnsemble/elephant/actions/workflows/CI.yml)
 [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/6191/badge)](https://bestpractices.coreinfrastructure.org/projects/6191)
 [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
-[![Twitter](https://img.shields.io/twitter/follow/PyElephant?style=social)](https://twitter.com/pyelephant)
+[![Follow me on Bluesky](https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff&label=Follow%20me%20on&color=0285FF)](https://bsky.app/profile/pyelephant.bsky.social)
 [![Fosstodon](https://img.shields.io/badge/@elephant-6364FF?logo=mastodon&logoColor=fff&style=flat)](https://fosstodon.org/@elephant)
 
 

codemeta.json

@@ -6,15 +6,15 @@
     "contIntegration": "https://github.com/NeuralEnsemble/elephant/actions",
     "dateCreated": "2022-03-14",
     "datePublished": "2015-04-08",
-    "dateModified": "2024-03-19",
-    "downloadUrl": "https://files.pythonhosted.org/packages/cb/b5/893fadd5505e638a4c8788bf0a2f5a211f59f45203f3dfa3919469e83ed4/elephant-1.0.0.tar.gz",
+    "dateModified": "2024-10-28",
+    "downloadUrl": "https://files.pythonhosted.org/packages/83/2e/479328a34751bb6cd626beadca334f267763fe940706a0236979efd7301c/elephant-1.1.1.tar.gz",
     "issueTracker": "https://github.com/NeuralEnsemble/elephant/issues",
     "name": "Elephant",
-    "version": "1.1.0",
+    "version": "1.1.1",
     "identifier": "https://doi.org/10.5281/zenodo.1186602",
     "description": "Elephant (Electrophysiology Analysis Toolkit) is an open-source, community centered library for the analysis of electrophysiological data in the Python programming language. The focus of Elephant is on generic analysis functions for spike train data and time series recordings from electrodes, such as the local field potentials (LFP) or intracellular voltages.In addition to providing a common platform for analysis code from different laboratories, the Elephant project aims to provide a consistent and homogeneous analysis framework that is built on a modular foundation. \nElephant is the direct successor to Neurotools and maintains ties to complementary projects such as OpenElectrophy and spykeviewer.",
     "applicationCategory": "library",
-    "releaseNotes": "https://github.com/NeuralEnsemble/elephant/releases/tag/v1.1.0",
+    "releaseNotes": "https://github.com/NeuralEnsemble/elephant/releases/tag/v1.1.1",
     "funding": "EU Grant 604102 (HBP), EU Grant 720270(HBP), EU Grant 785907(HBP), EU Grant 945539(HBP)",
     "developmentStatus": "active",
     "keywords": [
@@ -34,7 +34,7 @@
         "MacOS"
     ],
     "softwareRequirements": [
-        "https://github.com/NeuralEnsemble/elephant/tree/v1.1.0/requirements"
+        "https://github.com/NeuralEnsemble/elephant/tree/v1.1.1/requirements"
     ],
     "relatedLink": [
         "http://python-elephant.org",
@@ -72,4 +72,4 @@
             }
         }
     ]
-}
+}

doc/release_notes.rst

@@ -3,6 +3,24 @@ Release Notes
 =============
 
 
+Release 1.1.1
+=============
+Bug fixes
+---------
+- Resolved deprecated `.A` attribute in `scipy.sparse` matrices (scipy >=1.14.0).
+  Replaced usage of the deprecated `.A` attribute with `.toarray()` in SPADE, ensuring compatibility with SciPy 1.14.0 (https://github.com/NeuralEnsemble/elephant/pull/636).
+
+- Modified tests to accommodate Neo 0.13.1, where adding the same object multiple times to a container is no longer permitted. These changes fix the generation of test data without affecting Elephant’s core functionality (https://github.com/NeuralEnsemble/elephant/pull/634).
+
+- Fixed deprecated `copy` method for `neo` objects (neo >=0.13.4), updated Elephant to handle the removal of the `copy` method from `neo` objects in version 0.13.4 (https://github.com/NeuralEnsemble/elephant/pull/646).
+
+Selected dependency changes
+---------------------------
+- SciPy >= 1.14.0
+- Neo >= 0.13.1
+- Numpy < 2.0.0
+
+
 Release 1.1.0
 =============
 New functionality and features