Merge branch 'master' into fix-broken-example

Author: zm711

.github/workflows/caches_cron_job.yml

@@ -10,57 +10,57 @@ on:
 
 jobs:
 
-  create-conda-env-cache-if-missing:
-    name: Caching conda env
-    runs-on: "ubuntu-latest"
-    strategy:
-      fail-fast: true
-    defaults:
-      # by default run in bash mode (required for conda usage)
-      run:
-        shell: bash -l {0}
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Get current year-month
-        id: date
-        run: |
-          echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
-
-      - name: Get current dependencies hash
-        id: dependencies
-        run: |
-          echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
-
-      - uses: actions/cache@v3
-        # the cache for python package is reset:
-        #   * every month
-        #   * when package dependencies change
-        id: cache-conda-env
-        with:
-          path: /usr/share/miniconda/envs/neo-test-env
-          key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
-
-      - name: Cache found?
-        run: echo "Cache-hit == ${{steps.cache-conda-env.outputs.cache-hit == 'true'}}"
-
-      # activate environment if not restored from cache
-      - uses: conda-incubator/[email protected]
-        if: steps.cache-conda-env.outputs.cache-hit != 'true'
-        with:
-          activate-environment: neo-test-env
-          environment-file: environment_testing.yml
-          python-version: 3.9
-
-      - name: Create the conda environment to be cached
-        if: steps.cache-conda-env.outputs.cache-hit != 'true'
-        # create conda env, configure git and install pip, neo and test dependencies from master
-        # for PRs that change dependencies, this environment will be updated in the test workflow
-        run: |
-          git config --global user.email "neo_ci@fake_mail.com"
-          git config --global user.name "neo CI"
-          python -m pip install -U pip  # Official recommended way
-          pip install --upgrade -e .[test]
+  # create-conda-env-cache-if-missing:
+  #   name: Caching conda env
+  #   runs-on: "ubuntu-latest"
+  #   strategy:
+  #     fail-fast: true
+  #   defaults:
+  #     # by default run in bash mode (required for conda usage)
+  #     run:
+  #       shell: bash -l {0}
+  #   steps:
+  #     - uses: actions/checkout@v3
+
+  #     - name: Get current year-month
+  #       id: date
+  #       run: |
+  #         echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
+
+  #     - name: Get current dependencies hash
+  #       id: dependencies
+  #       run: |
+  #         echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
+
+  #     - uses: actions/cache@v3
+  #       # the cache for python package is reset:
+  #       #   * every month
+  #       #   * when package dependencies change
+  #       id: cache-conda-env
+  #       with:
+  #         path: /usr/share/miniconda/envs/neo-test-env
+  #         key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
+
+  #     - name: Cache found?
+  #       run: echo "Cache-hit == ${{steps.cache-conda-env.outputs.cache-hit == 'true'}}"
+
+  #     # activate environment if not restored from cache
+  #     - uses: conda-incubator/[email protected]
+  #       if: steps.cache-conda-env.outputs.cache-hit != 'true'
+  #       with:
+  #         activate-environment: neo-test-env
+  #         environment-file: environment_testing.yml
+  #         python-version: 3.9
+
+      # - name: Create the conda environment to be cached
+      #   if: steps.cache-conda-env.outputs.cache-hit != 'true'
+      #   # create conda env, configure git and install pip, neo and test dependencies from master
+      #   # for PRs that change dependencies, this environment will be updated in the test workflow
+      #   run: |
+      #     git config --global user.email "neo_ci@fake_mail.com"
+      #     git config --global user.name "neo CI"
+      #     python -m pip install -U pip  # Official recommended way
+      #     pip install --upgrade -e .[test]
 
   create-data-cache-if-missing:
     name: Caching data env

.github/workflows/io-test.yml

@@ -76,10 +76,25 @@ jobs:
         # restore-key hits should result in `cache-hit` == 'false'
         #if: steps.cache-conda-env.outputs.cache-hit != 'true'
         run: |
-          conda install datalad pip numpy=${{ matrix.numpy-version }} -c conda-forge
+          conda install pip numpy=${{ matrix.numpy-version }} -c conda-forge
         # this command is for updating cache. We are resting removal.
         # conda env update --name neo-test-env-${{ matrix.python-version }} --file environment_testing.yml --prune
 
+      - name: Install git-annex
+        # this is the trick from the spikeinterface repo for getting git-annex to work with datalad
+        shell: bash
+        run: |
+          pip install datalad-installer
+          wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz
+          mkdir /home/runner/work/installation
+          mv git-annex-standalone-amd64.tar.gz /home/runner/work/installation/
+          workdir=$(pwd)
+          cd /home/runner/work/installation
+          tar xvzf git-annex-standalone-amd64.tar.gz
+          echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH
+          cd $workdir
+          git config --global filter.annex.process "git-annex filter-process"  # recommended for efficiency
+
       - name: Configure git
         run: |
           git config --global user.email "neo_ci@fake_mail.com"

doc/source/authors.rst

@@ -90,8 +90,11 @@ and may not be the current affiliation of a contributor.
 * Xin Niu
 * Nikhil Chandra [40]
 * Luigi Petrucco [42]
+* Tommaso Lambresa [43]
+* Nina Kudryashova [37]
+* Rémi Proville [44]
 
-1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Universite Claude Bernard Lyon 1
+1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Université Claude Bernard Lyon 1
 2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
 3. University of California, Berkeley
 4. Laboratoire de Neurosciences Intégratives et Adaptatives, CNRS UMR 6149 - Université de Provence, Marseille, France
@@ -133,6 +136,8 @@ and may not be the current affiliation of a contributor.
 40. Plexon Inc.
 41. Paris Brain Institute
 42. Istituto Italiano di Tecnologia (IIT), Italy
+43. University of Genoa, Italy
+44. AquiNeuro, SAS
 
 
 

neo/io/__init__.py

@@ -167,7 +167,7 @@
 .. autoclass:: neo.io.MaxwellIO
 
     .. autoattribute:: extensions
-    
+
 .. autoclass:: neo.io.MedIO
 
     .. autoattribute:: extensions
@@ -280,24 +280,17 @@
 
 import pathlib
 from collections import Counter
+import importlib.util
 
-# try to import the neuroshare library.
+# check if neuroshare library exists
 # if it is present, use the neuroshareapiio to load neuroshare files
 # if it is not present, use the neurosharectypesio to load files
-try:
-    import neuroshare as ns
-except ModuleNotFoundError as err:
-    from neo.io.neurosharectypesio import NeurosharectypesIO as NeuroshareIO
 
-    # print("\n neuroshare library not found, loading data with ctypes" )
-    # print("\n to use the API be sure to install the library found at:")
-    # print("\n www.http://pythonhosted.org/neuroshare/")
-
-else:
+neuroshare_spec = importlib.util.find_spec("neuroshare")
+if neuroshare_spec is not None:
     from neo.io.neuroshareapiio import NeuroshareapiIO as NeuroshareIO
-
-    # print("neuroshare library successfully imported")
-    # print("\n loading with API...")
+else:
+    from neo.io.neurosharectypesio import NeurosharectypesIO as NeuroshareIO
 
 from neo.io.alphaomegaio import AlphaOmegaIO
 from neo.io.asciiimageio import AsciiImageIO

neo/io/baseio.py

@@ -13,11 +13,7 @@
 
 from __future__ import annotations
 from pathlib import Path
-
-try:
-    from collections.abc import Sequence
-except ImportError:
-    from collections import Sequence
+from collections.abc import Sequence
 import logging
 
 from neo import logging_handler

neo/io/neomatlabio.py

@@ -281,6 +281,8 @@ def write_block(self, bl, **kargs):
         """
         Arguments:
             bl: the block to be saved
+            kargs: extra keyword arguments broadcasted to scipy.io.savemat
+
         """
         import scipy.io
 
@@ -307,7 +309,7 @@ def write_block(self, bl, **kargs):
                     else:
                         group_structure[container_name].append(id(child_obj))
 
-        scipy.io.savemat(self.filename, {"block": bl_struct}, oned_as="row")
+        scipy.io.savemat(self.filename, {"block": bl_struct}, oned_as="row", **kargs)
 
     def _get_matlab_value(self, ob, attrname):
         units = None

neo/io/nixio.py

@@ -27,6 +27,8 @@
 from uuid import uuid4
 import warnings
 from packaging.version import Version
+import importlib.util
+import importlib.metadata
 
 import quantities as pq
 import numpy as np
@@ -122,17 +124,15 @@ def dt_from_nix(nixdt, annotype):
 
 
 def check_nix_version():
-    try:
-        import nixio
-    except ImportError:
-        raise Exception(
+    nixio_spec = importlib.util.find_spec("nixio")
+    if nixio_spec is None:
+        raise ImportError(
             "Failed to import NIX. "
             "The NixIO requires the Python package for NIX "
             "(nixio on PyPi). Try `pip install nixio`."
         )
 
-    # nixio version numbers have a 'v' prefix which breaks the comparison
-    nixverstr = nixio.__version__.lstrip("v")
+    nixverstr = importlib.metadata.version("nixio")
     try:
         nixver = Version(nixverstr)
     except ValueError:

neo/io/stimfitio.py

@@ -26,6 +26,8 @@
 08 Feb 2014, C. Schmidt-Hieber, University College London
 """
 
+import importlib.util
+
 import numpy as np
 import quantities as pq
 
@@ -92,7 +94,9 @@ def __init__(self, filename=None):
         """
         # We need this module, so try importing now so that it fails on
         # instantiation rather than read_block
-        import stfio  # noqa
+        stfio_spec = importlib.util.find_spec("stfio")
+        if stfio_spec is None:
+            raise ImportError("stfio must be installed to use StimfitIO")
 
         BaseIO.__init__(self)
 

neo/rawio/axonrawio.py

@@ -23,7 +23,7 @@
 strings section:
 [uModifierNameIndex, uCreatorNameIndex, uProtocolPathIndex, lFileComment, lADCCChannelNames, lADCUnitsIndex
 lDACChannelNameIndex, lDACUnitIndex, lDACFilePath, nLeakSubtractADC]
-['', 'Clampex', '', 'C:/path/protocol.pro', 'some comment', 'IN 0', 'mV', 'IN 1', 'mV', 'Cmd 0', 'pA', 
+['', 'Clampex', '', 'C:/path/protocol.pro', 'some comment', 'IN 0', 'mV', 'IN 1', 'mV', 'Cmd 0', 'pA',
 'Cmd 1', 'pA', 'Cmd 2', 'mV', 'Cmd 3', 'mV']
 
 Information on abf 1 and 2 formats is available here:

neo/rawio/blackrockrawio.py

@@ -979,7 +979,7 @@ def __read_nsx_dataheader_variant_b(
             # use of `int` avoids overflow problem
             data_size = int(dh["nb_data_points"]) * int(self.__nsx_basic_header[nsx_nb]["channel_count"]) * 2
             # define new offset (to possible next data block)
-            offset = data_header[index]["offset_to_data_block"] + data_size
+            offset = int(data_header[index]["offset_to_data_block"]) + data_size
 
             index += 1