Release 0.13.0 (#577)

* bump version number to 0.13.0 * update .zendodo.json * update .codemeta.json * add release notes to docs
NeuralEnsemble · Jul 13, 2023 · 5a56c31 · 5a56c31
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diff --git a/.zenodo.json b/.zenodo.json
@@ -15,11 +15,6 @@
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
             "name": "Jurkus, Regimantas"
         },
-        {
-            "orcid": "0000-0002-9302-5893",
-            "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
-            "name": "Kramer, Maximilian"
-        },
         {
             "orcid": "0000-0001-7292-1982",
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
@@ -30,14 +25,39 @@
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
             "name": "Kurth, Anno Christopher"
         },
+        {
+            "orcid": "0000-0003-3776-4226",
+            "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
+            "name": "Kleinjohann, Alexander"
+        },
+        {
+            "orcid": "0000-0003-2498-0536",
+            "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
+            "name": "Bouss, Peter"
+        },
+        {
+            "orcid": "0000-0002-4793-7541",
+            "affiliation": "Institut des Neurosciences Paris-Saclay (NeuroPSI), Département de Neurosciences Intégratives et Computationnelles (ICN), Université Paris-Saclay, France",
+            "name": "Davison, Andrew"
+        },
+        {
+            "orcid": "0000-0002-2403-928X",
+            "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
+            "name": "Morales-Gregorio, Aitor"
+        },
+        {
+            "orcid": "0000-0002-9302-5893",
+            "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
+            "name": "Kramer, Maximilian"
+        },
         {
             "orcid": "0000-0001-9170-4422",
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
             "name": "Ito, Junji"
         }
     ],
 
-    "title": "Elephant 0.12.0",
+    "title": "Elephant 0.13.0",
 
     "keywords": [
     "neuroscience",

diff --git a/codemeta.json b/codemeta.json
@@ -6,11 +6,11 @@
     "contIntegration": "https://github.com/NeuralEnsemble/elephant/actions",
     "dateCreated": "2013-17-15",
     "datePublished": "2015-04-08",
-    "dateModified": "2023-02-24",
+    "dateModified": "2023-07-12",
     "downloadUrl": "https://files.pythonhosted.org/packages/73/ef/e5308696a3e7fda842f58363a9db6690d42f30a7ebf818e15cc28014bf87/elephant-0.12.0.tar.gz",
     "issueTracker": "https://github.com/NeuralEnsemble/elephant/issues",
     "name": "Elephant",
-    "version": "0.12.0",
+    "version": "0.13.0",
     "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",
@@ -34,7 +34,7 @@
         "MacOS"
     ],
     "softwareRequirements": [
-        "https://github.com/NeuralEnsemble/elephant/tree/v0.12.0/requirements"
+        "https://github.com/NeuralEnsemble/elephant/tree/v0.13.0/requirements"
     ],
     "relatedLink": [
         "http://python-elephant.org",
@@ -71,16 +71,6 @@
                 "name": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany"
             }
         },
-        {
-            "@type": "Person",
-            "@id": "https://orcid.org/0000-0002-9302-5893",
-            "givenName": "Maximilian",
-            "familyName": "Kramer",
-            "affiliation": {
-                "@type": "Organization",
-                "name": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany"
-            }
-        },
         {
             "@type": "Person",
             "@id": "https://orcid.org/0000-0001-7292-1982",
@@ -110,6 +100,56 @@
                 "@type": "Organization",
                 "name": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany"
             }
+        },
+        {
+            "@type": "Person",
+            "@id": "https://orcid.org/0000-0003-3776-4226",
+            "givenName": "Alexander",
+            "familyName": "Kleinjohann",
+            "affiliation": {
+                "@type": "Organization",
+                "name": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany"
+            }
+        },
+        {
+            "@type": "Person",
+            "@id": "https://orcid.org/0000-0003-2498-0536",
+            "givenName": "Peter",
+            "familyName": "Bouss",
+            "affiliation": {
+                "@type": "Organization",
+                "name": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany"
+            }
+        },
+        {
+            "@type": "Person",
+            "@id": "https://orcid.org/0000-0002-4793-7541",
+            "givenName": "Andrew",
+            "familyName": "Davison",
+            "affiliation": {
+                "@type": "Organization",
+                "name": "Institut des Neurosciences Paris-Saclay (NeuroPSI), Département de Neurosciences Intégratives et Computationnelles (ICN), Université Paris-Saclay, France"
+            }
+        },
+        {
+            "@type": "Person",
+            "@id": "https://orcid.org/0000-0002-2403-928X",
+            "givenName": "Aitor",
+            "familyName": "Morales-Gregorio",
+            "affiliation": {
+                "@type": "Organization",
+                "name": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany"
+            }
+        },
+        {
+            "@type": "Person",
+            "@id": "https://orcid.org/0000-0002-9302-5893",
+            "givenName": "Maximilian",
+            "familyName": "Kramer",
+            "affiliation": {
+                "@type": "Organization",
+                "name": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany"
+            }
         }
     ]
 }
diff --git a/doc/release_notes.rst b/doc/release_notes.rst
@@ -2,6 +2,46 @@
 Release Notes
 =============
 
+Elephant 0.13.0 release notes
+=============================
+
+New functionality and features
+------------------------------
+* Implemented non-parametric spectral Granger causality analysis, extending the investigation of signal influence in the spectral domain. (#545)
+* Added functions to extract time bin and neuron information from Spike Sequence Events (SSEs) obtained using ASSET. (#549)
+
+Bug fixes
+---------
+* Resolved issue with old references to the gin repository INM-6/elephant-data, ensuring accurate repository information. (#547)
+* Fixed the usage of deprecated numpy functions, which were removed with numpy 1.25.0. (#568)
+* Rectified a bug in spade, addressing a missing call of `min_neu` to specify the minimum number of neurons in a pattern. Also, added a regression test to verify the fix. (#575)
+* Corrected a bug in the complexity class that resulted in unexpected behavior when binary=False and spread=0. (#554)
+* Resolved a bug in cell assembly detection (CAD) that produced different results compared to the original MATLAB implementation. (#576)
+
+Documentation
+-------------
+* Addressed various formatting issues in docstrings that were causing warnings during documentation builds. (#553)
+* Updated the contributors guide: The guide now includes a step to install Elephant itself by adding a "pip install -e ." command to the instructions for setting up a development environment. (#566)
+
+Validations
+-----------
+* No changes
+
+Other changes
+-------------
+* Added `codemeta.json` for automated publication of Elephant release to ebrains knowledge graph. (#561, #562)
+* Added "howfairis" badge to README.md, indicating Elephant's compliance with fair-software.eu recommendations. (#551)
+* CI: Enhance security of github actions by specifying a particular commit for third party actions, to improve security against re-tagging attacks.  (#565)
+* Separation of the `multitaper_psd()` function into `segmented_multitaper_psd()` and `multitaper_psd()` without segmentation. This restructuring was done to achieve consistency in the spectral module. (#556)
+* Improved reporting in test_multitaper_cohere_perfect_cohere: Updated the unittest to utilize the numpy assert array equal function. This enhancement aims to provide more detailed and informative traceback in case of failures. (#573)
+* Increased tolerance for Weigthed Phase-Lag Index (WPLI) ground truth test to avoid unitest to fail due minor differences in floating point operations (#572)
+* Added shields for twitter and fosstodon to README.md linking to Elephants accounts. (#532)
+
+Selected dependency changes
+---------------------------
+* no changes
+
+
 Elephant 0.12.0 release notes
 =============================
 

diff --git a/elephant/VERSION b/elephant/VERSION
@@ -1 +1 @@
-0.13.0b1
+0.13.0