[Main] Release 1.1.0 (NeuralEnsemble#621)

* Change copyright year to 2024 * add version cap for numpy<2 * update .zenodo.json * update codemeta.json * change affiliation in .zenodo.json * update affiliation in authors.rst * update affiliation in .zenodo.json * update affiliation in codemeta.json * undo previous change to authors.rst affiliation * add new IAS-6 affiliation * update affiliation * add new contributor to codemeta.json * add release notes to docs * fix environment.yml * fixed warnings for docs sphinx build * Fix link to neo docs in asset.ipynb * fix link to elephant docs * Fix link to intel docs * Fix formatting for readthedocs build warnings * update CI * fix CI fail on coveralls report * Update doc/release_notes.rst Co-authored-by: Michael Denker <[email protected]> --------- Co-authored-by: Moritz-Alexander-Kern <[email protected]> Co-authored-by: Michael Denker <[email protected]>
INM-6 · Apr 10, 2024 · de4b3dc · de4b3dc
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -42,6 +42,11 @@ on:
     branches:
       - master
 
+# Cancel previous workflows on the same pull request
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 # jobs define the steps that will be executed on the runner
 jobs:
 
@@ -105,7 +110,8 @@ jobs:
 
       - name: Test with pytest
         run: |
-          coverage run --source=elephant -m pytest && coveralls --service=github || echo "Coveralls submission failed"
+          coverage run --source=elephant -m pytest
+          coveralls --service=github || echo "Coveralls submission failed"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
@@ -291,7 +297,8 @@ jobs:
 
       - name: Test with pytest
         run: |
-          mpiexec -n 1 python -m mpi4py -m coverage run --source=elephant -m pytest && coveralls --service=github || echo "Coveralls submission failed"
+          mpiexec -n 1 python -m mpi4py -m coverage run --source=elephant -m pytest
+          coveralls --service=github || echo "Coveralls submission failed"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

diff --git a/.zenodo.json b/.zenodo.json
@@ -2,12 +2,12 @@
     "creators": [
         {
             "orcid": "0000-0003-1255-7300",
-            "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",
+            "affiliation": "Institute for Advanced Simulation (IAS-6), Jülich Research Centre, Jülich, Germany",
             "name": "Denker, Michael"
         },
         {
             "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",
+            "affiliation": "Institute for Advanced Simulation (IAS-6), Jülich Research Centre, Jülich, Germany",
             "name": "Kern, Moritz"
         },
         {
@@ -17,7 +17,7 @@
         }
     ],
 
-    "title": "Elephant 1.0.0",
+    "title": "Elephant 1.1.0",
 
     "keywords": [
     "neuroscience",

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright (c) 2014-2023, Elephant authors and contributors
+Copyright (c) 2014-2024, Elephant authors and contributors
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

diff --git a/README.md b/README.md
@@ -38,7 +38,7 @@ Modified BSD License, see [LICENSE.txt](LICENSE.txt) for details.
 
 #### Copyright
 
-:copyright: 2014-2023 by the [Elephant team](doc/authors.rst).
+:copyright: 2014-2024 by the [Elephant team](doc/authors.rst).
 
 
 #### Acknowledgments

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": "2023-11-10",
+    "dateModified": "2024-19-03",
     "downloadUrl": "https://files.pythonhosted.org/packages/cb/b5/893fadd5505e638a4c8788bf0a2f5a211f59f45203f3dfa3919469e83ed4/elephant-1.0.0.tar.gz",
     "issueTracker": "https://github.com/NeuralEnsemble/elephant/issues",
     "name": "Elephant",
-    "version": "1.0.0",
+    "version": "1.1.0",
     "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/v1.0.0",
+    "releaseNotes": "https://github.com/NeuralEnsemble/elephant/releases/tag/v1.1.0",
     "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/v1.0.0/requirements"
+        "https://github.com/NeuralEnsemble/elephant/tree/v1.1.0/requirements"
     ],
     "relatedLink": [
         "http://python-elephant.org",
@@ -48,7 +48,7 @@
             "familyName": "Denker",
             "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"
+                "name": "Institute for Advanced Simulation (IAS-6), Jülich Research Centre, Jülich, Germany"
             }
         },
         {
@@ -58,7 +58,17 @@
             "familyName": "Kern",
             "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"
+                "name": "Institute for Advanced Simulation (IAS-6), Jülich Research Centre, Jülich, Germany"
+            }
+        },
+        {
+            "@type": "Person",
+            "@id": "https://orcid.org/0009-0003-9352-9826",
+            "givenName": "Felician",
+            "familyName": "Richter",
+            "affiliation": {
+                "@type": "Organization",
+                "name": "BioMEMS Lab, University of Applied Sciences Aschaffenburg, Germany"
             }
         }
     ]

diff --git a/doc/authors.rst b/doc/authors.rst
@@ -17,8 +17,8 @@ contribution, and may not be the current affiliation of a contributor.
 * Jan Gosmann [6, 8]
 * Julia Sprenger [1]
 * Junji Ito [1]
-* Michael Denker [1]
-* Moritz Kern [1]
+* Michael Denker [1, 14]
+* Moritz Kern [1, 14]
 * Paul Chorley [1]
 * Pierre Yger [2]
 * Pietro Quaglio [1]
@@ -66,5 +66,6 @@ contribution, and may not be the current affiliation of a contributor.
 11. Case Western Reserve University (CWRU), Cleveland, OH, USA
 12. BioMEMS Lab, TH Aschaffenburg University of applied sciences, Germany
 13. Cognitronics and Sensor Systems, CITEC, Bielefeld University, Bielefeld, Germany
+14. Institute for Advanced Simulation (IAS-6), Jülich Research Centre, Jülich, Germany
 
 If we've somehow missed you off the list we're very sorry - please let us know.
diff --git a/doc/install.rst b/doc/install.rst
@@ -202,9 +202,9 @@ You can have one, both, or none installed in your system.
         .. note::
 
             Make sure you've disabled GPU Hangcheck as described in the
-            `Intel GPU developers documentation <https://software.intel.com/
-            content/www/us/en/develop/documentation/get-started-with-intel-
-            oneapi-base-linux/top/before-you-begin.html>`_. Do it with caution -
+            `Intel GPU developers documentation <https://www.intel.com/content/
+            www/us/en/docs/oneapi/installation-guide-linux/2023-1/
+            gpu-disable-hangcheck.html>`_. Do it with caution -
             using your graphics card to perform computations may make the system
             unresponsive until the compute program terminates.
 

diff --git a/doc/release_notes.rst b/doc/release_notes.rst
@@ -3,6 +3,32 @@ Release Notes
 =============
 
 
+Release 1.1.0
+=============
+New functionality and features
+------------------------------
+* New method "Total spiking probability edges" (TPSE) for inferring functional connectivity (https://github.com/NeuralEnsemble/elephant/pull/560).
+
+Bug fixes
+---------
+* Fixed expired SciPy deprecations and breaking changes related to `sp.sqrt`, ensuring continued compatibility with the latest version of SciPy (https://github.com/NeuralEnsemble/elephant/pull/616).
+* Addressed failing unit tests for `neo_tools` with Neo 0.13.0, ensuring compatibility with the latest Neo release (https://github.com/NeuralEnsemble/elephant/pull/617).
+
+Documentation
+-------------
+* Fixed a bug in the CI docs runner to resolve formatting issues, ensuring documentation build is tested (https://github.com/NeuralEnsemble/elephant/pull/615).
+
+Other changes
+-------------
+* added Python 3.12 CI runner to ensure compatibility with the latest Python language features (https://github.com/NeuralEnsemble/elephant/pull/611).
+* Integrated `Trials` object with GPFA, allowing for a more formal way of specifying trials (https://github.com/NeuralEnsemble/elephant/pull/610).
+
+Selected dependency changes
+---------------------------
+* scipy>=1.10.0
+* Support for Python 3.12
+
+
 Release 1.0.0
 =============
 Elephant's first major release is focused on providing a stable and consistent API consistency that will be maintained over the 1.x series of releases. In order to provide future support, this release will remove all features and API specifications that have been deprecated over the course of the last releases of the 0.x line. While work on the next generation of Elephant will commence, all new analysis capabilities will be consistently back-ported to become available in the 1.x release line.
@@ -339,7 +365,7 @@ Breaking changes
   - now the users can directly access `.sparse_matrix` attribute of BinnedSpikeTrain to do efficient (yet unsafe in general) operations. For this reason, `to_sparse_array()` function, which does not make a copy, as one could think of, is deprecated.
 * `instantaneous_rate` function (https://github.com/NeuralEnsemble/elephant/pull/362):
   - in case of multiple input spike trains, the output of the instantaneous rate function is (always) a 2D matrix of shape `(time, len(spiketrains))` instead of a pseudo 1D array (previous behavior) of shape `(time, 1)` that contained the instantaneous rate summed across input spike trains;
-  - in case of multiple input spike trains, the user needs to manually provide the input kernel instead of `auto`, which is set by default, for the reason that it's currently not clear how to estimate the common kernel for a set of spike trains. If you have an idea how to do this, we`d appreciate if you let us know by [getting in touch with us](https://elephant.readthedocs.io/en/latest/get_in_touch.html).
+  - in case of multiple input spike trains, the user needs to manually provide the input kernel instead of `auto`, which is set by default, for the reason that it's currently not clear how to estimate the common kernel for a set of spike trains. If you have an idea how to do this, we`d appreciate if you let us know by [getting in touch with us](https://elephant.readthedocs.io/en/v0.7.0/get_in_touch.html).
 
 Other changes
 -------------
@@ -618,7 +644,7 @@ API changes
 * Interoperability between Neo 0.5.0 and Elephant
     * Elephant has adapted its functions to the changes in Neo 0.5.0,
       most of the functionality behaves as before
-    * See Neo documentation for recent changes: http://neo.readthedocs.io/en/latest/whatisnew.html
+    * See Neo documentation for recent changes: http://neo.readthedocs.io/en/0.5.2/whatisnew.html
 
 Other changes
 -------------

diff --git a/doc/tutorials/asset.ipynb b/doc/tutorials/asset.ipynb
diff --git a/doc/tutorials/unitary_event_analysis.ipynb b/doc/tutorials/unitary_event_analysis.ipynb
@@ -34,12 +34,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2018-07-18T08:56:30.663173Z",
-     "start_time": "2018-07-18T08:56:29.825521Z"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import random\n",
@@ -66,12 +61,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2018-07-18T08:56:32.142189Z",
-     "start_time": "2018-07-18T08:56:31.420462Z"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# Download data\n",
@@ -92,10 +82,6 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2018-07-18T08:56:32.920355Z",
-     "start_time": "2018-07-18T08:56:32.611208Z"
-    },
     "nbsphinx": "hidden"
    },
    "outputs": [],
@@ -459,12 +445,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2018-07-18T08:56:33.836628Z",
-     "start_time": "2018-07-18T08:56:33.647488Z"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "io = neo.io.NixIO(f\"{filepath}\",'ro')\n",
@@ -486,12 +467,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2018-07-18T08:56:37.042743Z",
-     "start_time": "2018-07-18T08:56:34.926673Z"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "UE = ue.jointJ_window_analysis(\n",

diff --git a/elephant/__init__.py b/elephant/__init__.py
@@ -2,7 +2,7 @@
 """
 Elephant is a package for the analysis of neurophysiology data, based on Neo.
 
-:copyright: Copyright 2014-2023 by the Elephant team, see `doc/authors.rst`.
+:copyright: Copyright 2014-2024 by the Elephant team, see `doc/authors.rst`.
 :license: Modified BSD, see LICENSE.txt for details.
 """
 

diff --git a/elephant/asset/asset.py b/elephant/asset/asset.py
@@ -1126,10 +1126,9 @@ def compute(self, u):
                           "the computed joint prob. matrix lie outside of the "
                           f"valid [0, 1] interval:\n{outside_vals}\nIf you're "
                           "using PyOpenCL backend, make sure you've disabled "
-                          "GPU Hangcheck as described here https://"
-                          "software.intel.com/content/www/us/en/develop/"
-                          "documentation/get-started-with-intel-oneapi-"
-                          "base-linux/top/before-you-begin.html\n"
+                          "GPU Hangcheck as described here https://www.intel."
+                          "com/content/www/us/en/docs/oneapi/installation-"
+                          "guide-linux/2023-1/gpu-disable-hangcheck.html \n"
                           "Clipping the output array to 0 and 1.")
             P_total = np.clip(P_total, a_min=0., a_max=1., out=P_total)
 
@@ -2529,11 +2528,11 @@ def joint_probability_matrix(self, pmat, filter_shape, n_largest,
 
            When using PyOpenCL backend, make sure you've disabled GPU Hangcheck
            as described in the `Intel GPU developers documentation
-           <https://software.intel.com/content/www/us/en/develop/
-           documentation/get-started-with-intel-oneapi-base-linux/top/
-           before-you-begin.html>`_. Do it with caution - using your built-in
-           Intel graphics card to perform computations may make the system
-           unresponsive until the compute program terminates.
+           <https://www.intel.com/content/www/us/en/docs/oneapi/installation-
+           guide-linux/2023-1/gpu-disable-hangcheck.html>`_. Do it with
+           caution -using your built-in Intel graphics card to perform
+           computations may make the system unresponsive until the compute
+           program terminates.
 
         """
         l, w = filter_shape

diff --git a/elephant/causality/granger.py b/elephant/causality/granger.py
@@ -75,7 +75,7 @@
    :target: https://mybinder.org/v2/gh/NeuralEnsemble/elephant/master
             ?filepath=doc/tutorials/granger_causality.ipynb
 
-:copyright: Copyright 2014-2023 by the Elephant team, see `doc/authors.rst`.
+:copyright: Copyright 2014-2024 by the Elephant team, see `doc/authors.rst`.
 :license: Modified BSD, see LICENSE.txt for details.
 """
 

diff --git a/elephant/conversion.py b/elephant/conversion.py
@@ -70,7 +70,7 @@
 >>> bst # doctest: +ELLIPSIS
 BinnedSpikeTrain(t_start=0.0 ms, t_stop=9000.0 ms, bin_size=1000.0 ms; ...
 
-:copyright: Copyright 2014-2023 by the Elephant team, see `doc/authors.rst`.
+:copyright: Copyright 2014-2024 by the Elephant team, see `doc/authors.rst`.
 :license: BSD, see LICENSE.txt for details.
 """
 

diff --git a/elephant/cubic.py b/elephant/cubic.py
@@ -39,7 +39,7 @@
 >>> kappa # doctest: +SKIP
 [20.1, 22.656565656565657, 27.674706246134818]
 
-:copyright: Copyright 2014-2023 by the Elephant team, see `doc/authors.rst`.
+:copyright: Copyright 2014-2024 by the Elephant team, see `doc/authors.rst`.
 :license: BSD, see LICENSE.txt for details.
 """
 

diff --git a/elephant/functional_connectivity.py b/elephant/functional_connectivity.py
@@ -23,9 +23,9 @@
 :license: Modified BSD, see LICENSE.txt for details.
 """
 
-from elephant.functional_connectivity_src.total_spiking_probability_edges import (
-    total_spiking_probability_edges,
-)
+from elephant.functional_connectivity_src.total_spiking_probability_edges \
+    import (
+        total_spiking_probability_edges,
+    )
 
 __all__ = ["total_spiking_probability_edges"]
-