Merge branch 'master' of https://github.com/NeuralEnsemble/python-neo into spikegadgets_implementation

Author: samuelgarcia

.circleci/config.yml

@@ -0,0 +1,65 @@
+name: neo.io and neo.rawio tests
+
+on:
+  pull_request:
+    branches: [master, gh_actions_and_datalad]
+    types: [synchronize, opened, reopened, ready_for_review]
+
+jobs:
+  build-and-test:
+    name: Test on (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # "macos-latest", "windows-latest"
+        os: ["ubuntu-latest", ]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          python-version: 3.8
+      - name: Get current year-month
+        id: date
+        run: echo "::set-output name=date::$(date+'%Y-%m')"
+      - uses: actions/cache@v2
+        # the cache for python package is reset:
+        #   * every month
+        #   * when requirements/requirements_testing change
+        id: cache-venv
+        with:
+          path: ~/test_env
+          key: ${{ runner.os }}-venv-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements_testing.txt') }}-${{ steps.date.outputs.date }}
+          restore-keys: |
+            ${{ runner.os }}-venv-
+      - name: Install dependencies
+        run: |
+          # this is for datalad and download testing datasets
+          sudo apt install git git-annex
+          # needed for correct operation of git/git-annex/DataLad
+          git config --global user.email "neo_ci@fake_mail.com"
+          git config --global user.name "neo CI"
+          # create an environment and install everything
+          python -m venv ~/test_env
+          source ~/test_env/bin/activate
+          python -m pip install --upgrade pip
+          # pip install -r requirements.txt
+          pip install -r requirements_testing.txt
+          pip install -e .
+      - name: Get ephy_testing_data current head hash
+        # the key depend on the last comit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git
+        id: vars
+        run: |
+          echo "::set-output name=HASH_EPHY_DATASET::$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)"
+      - uses: actions/cache@v2
+        id: cache-datasets
+        with:
+          path: ~/ephy_testing_data
+          key: ${{ runner.os }}-datasets-${{ steps.vars.outputs.HASH_EPHY_DATASET }}
+          restore-keys: |
+            ${{ runner.os }}-datasets
+      - name: Test with pytest
+        run: |
+          source ~/test_env/bin/activate
+          # only neo.rawio and neo.io
+          pytest --cov=neo neo/test/rawiotest
+          pytest --cov=neo neo/test/iotest

.github/workflows/full-test.yml

@@ -30,6 +30,7 @@ before_install:
   - pip install "numpy==$NUMPY_VERSION"
 install:
   - pip install -r requirements.txt
+  - pip install nose
   - pip install coveralls
   - pip install .
   - pip install pillow

.travis.yml

@@ -56,6 +56,7 @@ and may not be the current affiliation of a contributor.
 * Shashwat Sridhar
 * Alessio Buccino [23]
 * Regimantas Jurkus [13]
+* Steffen Buergers [24]
 
 1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Universite Claude Bernard Lyon 1
 2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
@@ -80,6 +81,7 @@ and may not be the current affiliation of a contributor.
 21. Institut des Neurosciences Paris-Saclay, CNRS UMR 9197 - Université Paris-Sud, Gif-sur-Yvette, France
 22. Neurtex Brain Research Institute, Dallas, TX, USAs
 23. Bio Engineering Laboratory, DBSSE, ETH, Basel, Switzerland
+24. CatalystNeuro
 
 If we've somehow missed you off the list we're very sorry - please let us know.
 

doc/source/authors.rst

@@ -8,7 +8,6 @@
 logging_handler = logging.StreamHandler()
 
 from neo.core import *
-# ~ import neo.rawio
 from neo.io import *
 
 from neo.version import version as __version__

neo/__init__.py

@@ -19,6 +19,7 @@
 * :attr:`AsciiSignalIO`
 * :attr:`AsciiSpikeTrainIO`
 * :attr:`AxographIO`
+* :attr:`AxonaIO`
 * :attr:`AxonIO`
 * :attr:`BCI2000IO`
 * :attr:`BlackrockIO`
@@ -41,8 +42,8 @@
 * :attr:`NeuroScopeIO`
 * :attr:`NeuroshareIO`
 * :attr:`NixIO`
-* :attr:`NSDFIO`
 * :attr:`OpenEphysIO`
+* :attr:`OpenEphysBinaryIO`
 * :attr:`PhyIO`
 * :attr:`PickleIO`
 * :attr:`PlexonIO`
@@ -78,6 +79,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.io.AxonaIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.io.AxonIO
 
     .. autoattribute:: extensions
@@ -170,11 +175,11 @@
 
     .. autoattribute:: extensions
 
-.. autoclass:: neo.io.NSDFIO
+.. autoclass:: neo.io.OpenEphysIO
 
     .. autoattribute:: extensions
 
-.. autoclass:: neo.io.OpenEphysIO
+.. autoclass:: neo.io.OpenEphysBinaryIO
 
     .. autoattribute:: extensions
 
@@ -255,6 +260,7 @@
 from neo.io.asciisignalio import AsciiSignalIO
 from neo.io.asciispiketrainio import AsciiSpikeTrainIO
 from neo.io.axographio import AxographIO
+from neo.io.axonaio import AxonaIO
 from neo.io.axonio import AxonIO
 from neo.io.blackrockio import BlackrockIO
 from neo.io.blkio import BlkIO
@@ -279,8 +285,8 @@
 from neo.io.neuroscopeio import NeuroScopeIO
 from neo.io.nixio import NixIO
 from neo.io.nixio_fr import NixIO as NixIOFr
-from neo.io.nsdfio import NSDFIO
 from neo.io.openephysio import OpenEphysIO
+from neo.io.openephysbinaryio import OpenEphysBinaryIO
 from neo.io.phyio import PhyIO
 from neo.io.pickleio import PickleIO
 from neo.io.plexonio import PlexonIO
@@ -301,6 +307,7 @@
     AsciiSignalIO,
     AsciiSpikeTrainIO,
     AxographIO,
+    AxonaIO,
     AxonIO,
     BCI2000IO,
     BlackrockIO,
@@ -325,8 +332,8 @@
     NeuroExplorerIO,
     NeuroScopeIO,
     NeuroshareIO,
-    NSDFIO,
     OpenEphysIO,
+    OpenEphysBinaryIO,
     PhyIO,
     PickleIO,
     PlexonIO,

neo/io/__init__.py

@@ -0,0 +1,11 @@
+from neo.io.basefromrawio import BaseFromRaw
+from neo.rawio.axonarawio import AxonaRawIO
+
+
+class AxonaIO(AxonaRawIO, BaseFromRaw):
+    name = 'Axona IO'
+    description = "Read raw continuous data (.bin and .set files)"
+
+    def __init__(self, filename):
+        AxonaRawIO.__init__(self, filename=filename)
+        BaseFromRaw.__init__(self, filename)

neo/io/axonaio.py

@@ -198,8 +198,12 @@ def read_spiketrain(self, cluster_id, model,
             w = pq.Quantity(w, raw_data_units)
         else:
             w = None
+        if model.duration > 0.:
+            t_stop = model.duration
+        else:
+            t_stop = np.max(model.spike_times[idx])
         sptr = SpikeTrain(times=model.spike_times[idx],
-                          t_stop=model.duration, waveforms=w, units='s',
+                          t_stop=t_stop, waveforms=w, units='s',
                           sampling_rate=model.sample_rate * pq.Hz,
                           file_origin=self.filename,
                           **{'cluster_id': cluster_id})