update branch

Author: alejoe91

.github/workflows/core-test.yml

@@ -9,8 +9,6 @@ on:
   push:
     branches: [master]
 
-
-
 jobs:
   multi-os-python-numpy:
     runs-on: ${{ matrix.os }}
@@ -20,27 +18,27 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
-        python-version: ['3.7', '3.8', '3.9', '3.10']
-        numpy-version: ['1.18.5', '1.19.5', '1.20.3', '1.21.6', '1.22.4', '1.23.0']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        numpy-version: ['1.19.5', '1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1']
         exclude:
-           - python-version: '3.7'
-             numpy-version: '1.22.4'
-           - python-version: '3.7'
-             numpy-version: '1.23.0'
-           - python-version: '3.10'
-             numpy-version: '1.18.5'
            - python-version: '3.10'
              numpy-version: '1.19.5'
            - python-version: '3.10'
              numpy-version: '1.20.3'
+           - python-version: '3.11'
+             numpy-version: '1.19.5'
+           - python-version: '3.11'
+             numpy-version: '1.20.3'
+           - python-version: '3.11'
+             numpy-version: '1.21.6'
     steps:
         - name: Set up Python ${{ matrix.python-version }}
-          uses: actions/setup-python@v2
+          uses: actions/setup-python@v4
           with:
             python-version: ${{ matrix.python-version }}
 
         - name: Checkout repository
-          uses: actions/checkout@v2
+          uses: actions/checkout@v3
 
         - name: Install numpy ${{ matrix.numpy-version }}
           run: |

.github/workflows/ebrains.yml

@@ -0,0 +1,30 @@
+name: Mirror to EBRAINS
+
+# Configure the events that are going to trigger tha automated update of the mirror
+on:
+  push:
+    branches: [ master ]
+
+# Configure what will be updated
+jobs:
+  # set the job name
+  to_ebrains:
+    runs-on: ubuntu-latest
+    steps:
+      # this task will push the master branch of the source_repo (github) to the
+      # destination_repo (ebrains gitlab)
+      - name: syncmaster
+        uses: wei/git-sync@v3
+        with:
+          source_repo: https://github.com/NeuralEnsemble/python-neo
+          source_branch: "master"
+          destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/NeuralEnsemble/neo.git"
+          destination_branch: "main"
+      # this task will push all tags from the source_repo to the destination_repo
+      - name: synctags
+        uses: wei/git-sync@v3
+        with:
+          source_repo: https://github.com/NeuralEnsemble/python-neo
+          source_branch: "refs/tags/*"
+          destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/NeuralEnsemble/neo.git"
+          destination_branch: "refs/tags/*"

.github/workflows/io-test.yml

@@ -27,24 +27,24 @@ jobs:
     steps:
 
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Get current year-month
         id: date
-        run: echo "::set-output name=date::$(date +'%Y-%m')"
+        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
 
       - name: Get ephy_testing_data current head hash
         # the key depend on the last commit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git
-        id: vars
+        id: ephy_testing_data_hash
         run: |
-          echo "::set-output name=HASH_EPHY_DATASET::$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)"
+          echo "latest_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> GITHUB_OUTPUT
 
       - uses: actions/cache@v3
         # Loading cache of ephys_testing_dataset
         id: cache-datasets
         with:
           path: ~/ephy_testing_data
-          key: ${{ runner.os }}-datasets-${{ steps.vars.outputs.HASH_EPHY_DATASET }}
+          key: ${{ runner.os }}-datasets-${{ steps.ephy_testing_data_hash.outputs.latest_hash }}
 
       - uses: conda-incubator/setup-miniconda@v2
         with:

doc/source/developers_guide.rst

@@ -38,8 +38,8 @@ a GitHub account and then set to watch the repository at `GitHub Repository`_
 Requirements
 ------------
 
-    * Python_ 3.7 or later
-    * numpy_ >= 1.11.0
+    * Python_ 3.8 or later
+    * numpy_ >= 1.19.5
     * quantities_ >= 0.12.1
     * nose_ >= 1.1.2 (for running tests)
     * Sphinx_ (for building documentation)
@@ -193,15 +193,15 @@ open a pull request on GitHub
 Python version
 --------------
 
-Neo should work with Python 3.7 or newer. If you need support for Python 2.7,
+Neo should work with Python 3.8 or newer. If you need support for Python 2.7,
 use Neo v0.8.0 or earlier.
 
 
 Coding standards and style
 --------------------------
 
 All code should conform as much as possible to `PEP 8`_, and should run with
-Python 3.7 or newer.
+Python 3.8 or newer.
 
 You can use the `pep8`_ program to check the code for PEP 8 conformity.
 You can also use `flake8`_, which combines pep8 and pyflakes.

doc/source/install.rst

@@ -11,8 +11,8 @@ Installing from the Python Package Index
 Dependencies
 ------------
 
-    * Python_ >= 3.7
-    * numpy_ >= 1.18.5
+    * Python_ >= 3.8
+    * numpy_ >= 1.19.5
     * quantities_ >= 0.12.1
 
 You can install the latest published version of Neo and its dependencies using::

doc/source/releases/0.11.1.rst

@@ -0,0 +1,47 @@
+========================
+Neo 0.11.1 release notes
+========================
+
+21st October 2022
+
+.. currentmodule:: neo.io
+
+Bug fixes and improvements in IO modules
+----------------------------------------
+
+Bug fixes and/or improvements have been made to
+:class:`OpenEphysBinaryIO`, :class:`BlackrockIO`, :class:`NWBIO`, :class:`PhyIO`, :class:`NeuralynxIO`
+
+
+Supported format versions
+-------------------------
+
+:class:`BlackrockIO` now supports file version 3.0
+
+
+Other changes
+-------------
+
+New installation mode
+
+- Neo can now be installed including all optional dependencies via *pip install neo[all]*
+
+Faster import
+
+- Dependency imports have been optimized for faster import of Neo
+
+Epoch durations
+
+- Epoch durations of epochs can now be of type float
+
+See all `pull requests`_ included in this release and the `list of closed issues`_.
+
+Acknowledgements
+----------------
+
+Thanks to Andrew Davison, Julia Sprenger, Chadwick Boulay, Alessio Buccino, Elodie Legouée, Samuel Garcia for their contributions to this release.
+
+.. generated with git shortlog --since=2022-09-01 -sne then checking Github for PRs merged since the last release but with commits before then
+
+.. _`list of closed issues`: https://github.com/NeuralEnsemble/python-neo/issues?q=is%3Aissue+milestone%3A0.11.1+is%3Aclosed
+.. _`pull requests`: https://github.com/NeuralEnsemble/python-neo/pulls?q=is%3Apr+is%3Aclosed+merged%3A%3E2022-09-01+milestone%3A0.11.1

doc/source/whatisnew.rst

@@ -6,6 +6,7 @@ Release notes
 .. toctree::
    :maxdepth: 1
 
+   releases/0.11.1.rst
    releases/0.11.0.rst
    releases/0.10.2.rst
    releases/0.10.1.rst

neo/core/epoch.py

@@ -175,7 +175,14 @@ def __repr__(self):
         return '<Epoch: %s>' % ', '.join(objs)
 
     def _repr_pretty_(self, pp, cycle):
-        super()._repr_pretty_(pp, cycle)
+        labels = ""
+        if self._labels is not None:
+            labels = " with labels"
+        pp.text(f"{self.__class__.__name__} containing {self.size} epochs{labels}; "
+        f"time units {self.units.dimensionality.string}; datatype {self.dtype} ")
+        if self._has_repr_pretty_attrs_():
+            pp.breakable()
+            self._repr_pretty_attrs_(pp, cycle)
 
     def rescale(self, units):
         '''

neo/core/event.py

@@ -148,7 +148,14 @@ def __repr__(self):
         return '<Event: %s>' % ', '.join(objs)
 
     def _repr_pretty_(self, pp, cycle):
-        super()._repr_pretty_(pp, cycle)
+        labels = ""
+        if self._labels is not None:
+            labels = " with labels"
+        pp.text(f"{self.__class__.__name__} containing {self.size} events{labels}; "
+        f"time units {self.units.dimensionality.string}; datatype {self.dtype} ")
+        if self._has_repr_pretty_attrs_():
+            pp.breakable()
+            self._repr_pretty_attrs_(pp, cycle)
 
     def rescale(self, units):
         '''

neo/core/spiketrain.py

@@ -346,7 +346,21 @@ def __init__(self, times, t_stop, units=None, dtype=None, copy=True,
                             array_annotations=array_annotations, **annotations)
 
     def _repr_pretty_(self, pp, cycle):
-        super()._repr_pretty_(pp, cycle)
+        waveforms = ""
+        if self.waveforms:
+            waveforms = "with waveforms"
+        pp.text(f"{self.__class__.__name__} containing {self.size} spikes{waveforms}; "
+                f"units {self.units.dimensionality.string}; datatype {self.dtype} ")
+        if self._has_repr_pretty_attrs_():
+            pp.breakable()
+            self._repr_pretty_attrs_(pp, cycle)
+
+        def _pp(line):
+            pp.breakable()
+            with pp.group(indent=1):
+                pp.text(line)
+
+        _pp(f"time: {self.t_start} to {self.t_stop}")
 
     def rescale(self, units):
         '''