[MAIN] Release 0.14.0 (#599)

* bump version number to 0.14.0 * update title in zenodo.json * update authors for .zenodo.json for 0.14.0 * update codemeta.json for 0.14.0 * added release note to documentation * update release notes in documentation
NeuralEnsemble · Oct 31, 2023 · 9d99c29 · 9d99c29
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diff --git a/.zenodo.json b/.zenodo.json
@@ -10,54 +10,19 @@
             "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": "Köhler, Cristiano"
         },
-        {
-            "orcid": "0000-0003-0789-6279",
-            "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": "0000-0001-7292-1982",
             "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",
             "name": "Kern, Moritz"
         },
-        {
-            "orcid": "0000-0002-9557-1003",
-            "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 0.13.0",
+    "title": "Elephant 0.14.0",
 
     "keywords": [
     "neuroscience",

diff --git a/codemeta.json b/codemeta.json
@@ -6,15 +6,15 @@
     "contIntegration": "https://github.com/NeuralEnsemble/elephant/actions",
     "dateCreated": "2013-17-15",
     "datePublished": "2015-04-08",
-    "dateModified": "2023-07-12",
+    "dateModified": "2023-10-31",
     "downloadUrl": "https://files.pythonhosted.org/packages/aa/e5/a42131ffa1de8e379ba56d67c85824d2471e6fbedcf710283f589c0dd4a4/elephant-0.13.0.tar.gz",
     "issueTracker": "https://github.com/NeuralEnsemble/elephant/issues",
     "name": "Elephant",
-    "version": "0.13.0",
+    "version": "0.14.0",
     "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",
-    "releaseNotes": "https://github.com/NeuralEnsemble/elephant/releases/tag/v0.13.0",
+    "releaseNotes": "https://github.com/NeuralEnsemble/elephant/releases/tag/v0.14.0",
     "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/v0.13.0/requirements"
+        "https://github.com/NeuralEnsemble/elephant/tree/v0.14.0/requirements"
     ],
     "relatedLink": [
         "http://python-elephant.org",
@@ -61,16 +61,6 @@
                 "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/0000-0003-0789-6279",
-            "givenName": "Regimantas",
-            "familyName": "Jurkus",
-            "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",
@@ -81,26 +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/0000-0002-9557-1003",
-            "givenName": "Anno Christopher",
-            "familyName": "Kurth",
-            "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/0000-0001-9170-4422",
-            "givenName": "Junji",
-            "familyName": "Ito",
-            "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/0000-0003-3776-4226",
@@ -110,46 +80,6 @@
                 "@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 +2,37 @@
 Release Notes
 =============
 
+
+Elephant 0.14.0 release notes
+=============================
+
+New functionality and features
+------------------------------
+* Added ASSET class initialization parameter to define the binning rounding error tolerance, allowing users to control the behavior of spike time binning (#585).
+* Enhanced ASSET function output messages and status information by replacing print statements with logging calls, introducing tqdm progress bars for looped steps, and providing control over INFO and DEBUG logging via parameters (#570).
+* Implemented logging instead of warnings in the round_binning_errors() function in elephant/utils.py (#571).
+* Implemented trial handling, providing a unified framework for representing and accessing trial data, supporting diverse trial structures and a common API (#579).
+* Improved `instantaneous_rate` function to support trial data (#579).
+
+Bug fixes
+---------
+* Added example to doc-string, handled one-dimensional arrays as input for x_positions, and added regression unit-tests in CSD.generate_lfp (#594).
+* Modified the check for signal type in z_score when using inplace option to ensure it works correctly with `np.float32` and `np.float64`  (#592).
+
+Documentation
+-------------
+* Fixed documentation build on readthedocs by updating deprecated configuration key `build.image` to `build.os` (#596).
+
+Validations
+-----------
+* Fixed spike time tiling coefficient calculation for unsorted spiketrains. The fix includes sorting the input spiketrains, additional input checks, and a validation test. (#564).
+
+Other changes
+-------------
+* Fixed several typos and grammatical errors in GPFA tutorial notebook (#587)
+* Updated the build_wheels action to use cibuildwheel version 2.13.1, enabling the building of wheels for Python 3.11 (#582).
+
+
 Elephant 0.13.0 release notes
 =============================
 

diff --git a/elephant/VERSION b/elephant/VERSION
@@ -1 +1 @@
-0.14.0b1
+0.14.0