Another minimal change (#1643)

* the change

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/actions/build-test-environment/action.yml

@@ -8,13 +8,13 @@ inputs:
   os:
     description: 'Operating system to set up'
     required: false
-    
+
 runs:
   using: "composite"
   steps:
     - name: Install dependencies
       run: |
-        sudo apt install git 
+        sudo apt install git
         git config --global user.email "[email protected]"
         git config --global user.name "CI Almighty"
         python -m venv ${{ github.workspace }}/test_env # Environment used in the caching step
@@ -42,4 +42,4 @@ runs:
         wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz
         tar xvzf git-annex-standalone-amd64.tar.gz
         echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH
-      shell: bash
+      shell: bash

.github/actions/show-test-environment/action.yml

@@ -20,4 +20,4 @@ runs:
         if [ -d "$HOME/spikeinterface_datasets" ]; then
           find $HOME/spikeinterface_datasets
         fi
-      shell: bash
+      shell: bash

.github/build_job_summary.py

@@ -1,5 +1,5 @@
 """
-This function builds a summary from the pytest output in markdown to be used by GITHUB_STEP_SUMMARY. 
+This function builds a summary from the pytest output in markdown to be used by GITHUB_STEP_SUMMARY.
 The input file is the output of the following command:
 pytest -vv --durations=0 --durations-min=0.001 > report.txt
 """
@@ -37,7 +37,7 @@
 data_frame_to_display = data_frame[["test_name", "type", "test_time", "%of_total_time", "%cum_total_time", "long_name"]]
 data_frame_header_markdown = data_frame_to_display.head(10).to_markdown()
 data_frame_markdown = data_frame_to_display.to_markdown()
-    
+
 # Build GITHUB_STEP_SUMMARY markdown file
 sys.stdout.write("## Pytest summary")
 sys.stdout.write("\n \n")
@@ -60,4 +60,4 @@
 sys.stdout.write(data_frame_markdown)
 sys.stdout.write("\n \n")
 sys.stdout.write("</details>")
-sys.stdout.write("\n \n")
+sys.stdout.write("\n \n")

.github/import_test.py

@@ -30,7 +30,7 @@
                 f"import_statement = '{import_statement}' \n"
                 f"time_taken = timeit.timeit(import_statement, number=1) \n"
                 f"print(time_taken) \n"
-               ) 
+               )
 
         result = subprocess.run(["python", "-c", script_to_execute], capture_output=True, text=True)
 
@@ -54,4 +54,4 @@
     raise Exception("\n".join(exceptions))
 
 # This is displayed to GITHUB_STEP_SUMMARY
-print(markdown_output)
+print(markdown_output)

.github/is_spikeinterface_dev.py

@@ -3,4 +3,4 @@
 package_name = "spikeinterface"
 version = importlib.metadata.version(package_name)
 if version.endswith("dev0"):
-    print(True)
+    print(True)

.github/run_tests.sh

@@ -6,4 +6,4 @@ source $GITHUB_WORKSPACE/test_env/bin/activate
 pytest -m "$MARKER" -vv -ra --durations=0 --durations-min=0.001 | tee report.txt; test ${PIPESTATUS[0]} -eq 0 || exit 1
 echo "# Timing profile of ${MARKER}" >> $GITHUB_STEP_SUMMARY
 python $GITHUB_WORKSPACE/.github/build_job_summary.py report.txt >> $GITHUB_STEP_SUMMARY
-rm report.txt
+rm report.txt

.github/workflows/caches_cron_job.yml

@@ -1,6 +1,6 @@
 name: Create caches for gin ecephys data and virtual env
 
-on: 
+on:
   workflow_dispatch:
   push:  # When someting is pushed into main this checks if caches need to re-created
     branches:
@@ -9,9 +9,9 @@ on:
     - cron: "0 12 * * *"  # Daily at noon UTC
 
 jobs:
-
 
-
+
+
   create-virtual-env-cache-if-missing:
     name: Caching virtual env
     runs-on: "ubuntu-latest"
@@ -35,13 +35,13 @@ jobs:
           key: ${{ runner.os }}-venv-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
       - name: Cache found?
         run: echo "Cache-hit == ${{steps.cache-venv.outputs.cache-hit == 'true'}}"
-      - name: Create the virtual environment to be cached 
+      - name: Create the virtual environment to be cached
         if: steps.cache-venv.outputs.cache-hit != 'true'
         uses: ./.github/actions/build-test-environment
-  
-  
-  
-  
+
+
+
+
   create-gin-data-cache-if-missing:
     name: Caching data env
     runs-on: "ubuntu-latest"
@@ -54,10 +54,10 @@ jobs:
           mkdir --parents --verbose $HOME/spikeinterface_datasets/ephy_testing_data/
           chmod -R 777 $HOME/spikeinterface_datasets
           ls -l $HOME/spikeinterface_datasets
-      - name: Get current hash (SHA) of the ephy_testing_data repo 
+      - name: Get current hash (SHA) of the ephy_testing_data repo
         id: repo_hash
         run: |
-          echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" 
+          echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)"
           echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
       - uses: actions/cache@v3
         id: cache-datasets
@@ -87,7 +87,7 @@ jobs:
       - name: Show size of the cache to assert data is downloaded
         run: |
           cd $HOME
-          pwd 
+          pwd
           du -hs spikeinterface_datasets
           cd spikeinterface_datasets
           pwd

.github/workflows/core-test.yml

@@ -27,19 +27,19 @@ jobs:
         run: |
           git config --global user.email "[email protected]"
           git config --global user.name "CI Almighty"
-          python -m pip install -U pip  # Official recommended way 
+          python -m pip install -U pip  # Official recommended way
           pip install -e .[test_core]
       - name: Test core with pytest
         run: |
           pytest -vv -ra --durations=0 --durations-min=0.001 src/spikeinterface/core | tee report.txt; test ${PIPESTATUS[0]} -eq 0 || exit 1
         shell: bash  # Necessary for pipeline to work on windows
       - name: Build test summary
-        run: | 
+        run: |
           pip install pandas
           pip install tabulate
-          echo "# Timing profile of core tests in ${{matrix.os}}" >> $GITHUB_STEP_SUMMARY 
+          echo "# Timing profile of core tests in ${{matrix.os}}" >> $GITHUB_STEP_SUMMARY
           # Outputs markdown summary to standard output
-          python ./.github/build_job_summary.py report.txt >> $GITHUB_STEP_SUMMARY 
-          cat $GITHUB_STEP_SUMMARY 
+          python ./.github/build_job_summary.py report.txt >> $GITHUB_STEP_SUMMARY
+          cat $GITHUB_STEP_SUMMARY
           rm report.txt
-        shell: bash  # Necessary for pipeline to work on windows
+        shell: bash  # Necessary for pipeline to work on windows

.github/workflows/full-test-with-codecov.yml

@@ -58,8 +58,8 @@ jobs:
         run: |
           source ${{ github.workspace }}/test_env/bin/activate
           pytest -m "not sorters_external" --cov=./ --cov-report xml:./coverage.xml -vv -ra --durations=0 | tee report_full.txt; test ${PIPESTATUS[0]} -eq 0 || exit 1
-          echo "# Timing profile of full tests" >> $GITHUB_STEP_SUMMARY 
-          python ./.github/build_job_summary.py report_full.txt >> $GITHUB_STEP_SUMMARY 
+          echo "# Timing profile of full tests" >> $GITHUB_STEP_SUMMARY
+          python ./.github/build_job_summary.py report_full.txt >> $GITHUB_STEP_SUMMARY
           cat $GITHUB_STEP_SUMMARY
           rm report_full.txt
       - uses: codecov/codecov-action@v3

.github/workflows/full-test.yml

@@ -5,7 +5,7 @@ on:
     types: [synchronize, opened, reopened]
     branches:
       - main
-      
+
 concurrency:  # Cancel previous workflows on the same pull request
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true

.github/workflows/test_imports.yml

@@ -27,24 +27,23 @@ jobs:
         run: |
           git config --global user.email "[email protected]"
           git config --global user.name "CI Almighty"
-          python -m pip install -U pip  # Official recommended way 
+          python -m pip install -U pip  # Official recommended way
           pip install -e .  # This should install core only
       - name: Profile Imports
         run: |
           echo "## OS: ${{ matrix.os }}" >> $GITHUB_STEP_SUMMARY
           echo "---" >> $GITHUB_STEP_SUMMARY
           echo "### Import times when only installing only core dependencies " >> $GITHUB_STEP_SUMMARY
-          python ./.github/import_test.py >> $GITHUB_STEP_SUMMARY 
+          python ./.github/import_test.py >> $GITHUB_STEP_SUMMARY
         shell: bash  # Necessary for pipeline to work on windows
       - name: Install in full mode
         run: |
-          python -m pip install -U pip  # Official recommended way 
+          python -m pip install -U pip  # Official recommended way
           pip install -e .[full]
       - name: Profile Imports with full
         run: |
           # Add a header to separate the two profiles
           echo "---" >> $GITHUB_STEP_SUMMARY
           echo "### Import times when installing full dependencies in " >> $GITHUB_STEP_SUMMARY
-          python ./.github/import_test.py >> $GITHUB_STEP_SUMMARY 
+          python ./.github/import_test.py >> $GITHUB_STEP_SUMMARY
         shell: bash  # Necessary for pipeline to work on windows
-

.gitignore

@@ -187,4 +187,4 @@ examples/modules/toolkit/tmp_*
 test_folder/
 
 # Mac OS
-.DS_Store
+.DS_Store

README.md

@@ -71,7 +71,7 @@ Detailed documentation for spikeinterface can be found [here](https://spikeinter
 
 Several tutorials to get started can be found in [spiketutorials](https://github.com/SpikeInterface/spiketutorials).
 
-There are also some useful notebooks [on our blog](https://spikeinterface.github.io) that cover advanced benchmarking 
+There are also some useful notebooks [on our blog](https://spikeinterface.github.io) that cover advanced benchmarking
 and sorting components.
 
 You can also have a look at the [spikeinterface-gui](https://github.com/SpikeInterface/spikeinterface-gui).
@@ -85,7 +85,7 @@ You can install the new `spikeinterface` version with pip:
 pip install spikeinterface[full]
 ```
 
-The `[full]` option installs all the extra dependencies for all the different sub-modules. 
+The `[full]` option installs all the extra dependencies for all the different sub-modules.
 
 To install all interactive widget backends, you can use:
 

conftest.py

@@ -29,10 +29,10 @@ def pytest_sessionstart(session):
 def pytest_collection_modifyitems(config, items):
     """
     This function marks (in the pytest sense) the tests according to their name and file_path location
-    Marking them in turn allows the tests to be run by using the pytest -m marker_name option.    
+    Marking them in turn allows the tests to be run by using the pytest -m marker_name option.
     """
 
-    
+
     # python 3.4/3.5 compat: rootdir = pathlib.Path(str(config.rootdir))
     rootdir = Path(config.rootdir)
 

doc/api.rst

@@ -49,7 +49,7 @@ spikeinterface.core
     .. autofunction:: get_template_extremum_channel_peak_shift
     .. autofunction:: get_template_extremum_amplitude
 
-.. 
+..
     .. autofunction:: read_binary
     .. autofunction:: read_zarr
     .. autofunction:: append_recordings
@@ -78,7 +78,7 @@ NEO-based
 ~~~~~~~~~
 
 .. automodule:: spikeinterface.extractors
- 
+
     .. autofunction:: read_alphaomega
     .. autofunction:: read_alphaomega_event
     .. autofunction:: read_axona
@@ -241,7 +241,7 @@ spikeinterface.comparison
 
     .. autoclass:: MultiSortingComparison
         :members:
-    
+
     .. autoclass:: CollisionGTComparison
     .. autoclass:: CorrelogramGTComparison
     .. autoclass:: CollisionGTStudy
@@ -356,4 +356,3 @@ Template Matching
 .. automodule:: spikeinterface.sortingcomponents.matching
 
     .. autofunction:: find_spikes_from_templates
-

doc/authors.rst

@@ -13,7 +13,7 @@ Current core team
 * `Alessio Paolo Buccino <https://github.com/alejoe91>`_ [1]
 * `Samuel Garcia <https://github.com/samuelgarcia>`_ [2]
 
-For any inquiries, please contact Alessio Buccino ([email protected]) or Samuel Garcia 
+For any inquiries, please contact Alessio Buccino ([email protected]) or Samuel Garcia
 ([email protected]), or just write an issue (preferred)!
 
 

doc/conf.py

@@ -40,7 +40,7 @@
     '../examples/modules_gallery/qualitymetrics/waveforms_mearec',
     '../examples/modules_gallery/qualitymetrics/wfs_mearec',
     '../examples/modules_gallery/widgets/waveforms_mearec',
-    
+
 ]
 
 for folder in folders:
@@ -69,7 +69,7 @@
     "sphinx.ext.extlinks",
 ]
 
-numpydoc_show_class_members = False 
+numpydoc_show_class_members = False
 
 
 # Add any paths that contain templates here, relative to this directory.
@@ -133,4 +133,4 @@
 
 extlinks = {
     "probeinterface": ("https://probeinterface.readthedocs.io/%s", None),
-}
+}

doc/development/development.rst

@@ -20,7 +20,7 @@ We use a forking workflow <https://www.atlassian.com/git/tutorials/comparing-wor
 * Create a new branch (e.g., :code:git switch -c my-contribution).
 * Modify the code, commit, and push changes to your fork.
 * Open a pull request from the "Pull Requests" tab of your fork to :code:spikeinterface/main.
-* By following this process, we can review the code and even make changes as necessary. 
+* By following this process, we can review the code and even make changes as necessary.
 
 While we appreciate all the contributions please be mindful of the cost of reviewing pull requests <https://rgommers.github.io/2019/06/the-cost-of-an-open-source-contribution/>_ .
 
@@ -52,7 +52,7 @@ If you want to run a specific test in a specific file, you can use the following
 
     pytest pytest src/spikeinterface/core/tests/test_baserecording.py::specific_test_in_this_module
 
-We also mantain pytest markers to run specific tests. For example, if you want to run only the tests 
+We also mantain pytest markers to run specific tests. For example, if you want to run only the tests
 for the :code:`spikeinterface.extractors` module, you can use the following command:
 
 .. code-block:: bash
@@ -69,7 +69,7 @@ Note that you should install the package before running the tests. You can do th
 
 You can change the :code:`[test,extractors,full]` to install only the dependencies you need. The dependencies are specified in the :code:`pyproject.toml` file in the root of the repository.
 
-The specific environment for the CI is specified in the :code:`.github/actions/build-test-environment/action.yml` and you can 
+The specific environment for the CI is specified in the :code:`.github/actions/build-test-environment/action.yml` and you can
 find the full tests in the :code:`.github/workflows/full_test.yml` file.
 
 The extractor tests require datalad for some of the tests. Here are instructions for installing datalad:
@@ -156,22 +156,22 @@ Note, however, that the running time of the command above will be slow. If you w
 Implement a new extractor
 -------------------------
 
-SpikeInterface already supports over 30 file formats, but the acquisition system you use might not be among the 
-supported formats list (***ref***). Most of the extractord rely on the `NEO <https://github.com/NeuralEnsemble/python-neo>`_ 
+SpikeInterface already supports over 30 file formats, but the acquisition system you use might not be among the
+supported formats list (***ref***). Most of the extractord rely on the `NEO <https://github.com/NeuralEnsemble/python-neo>`_
 package to read information from files.
 Therefore, to implement a new extractor to handle the unsupported format, we recommend make a new `neo.rawio `_ class.
-Once that is done, the new class can be easily wrapped into SpikeInterface as an extension of the 
-:py:class:`~spikeinterface.extractors.neoextractors.neobaseextractors.NeoBaseRecordingExtractor` 
-(for :py:class:`~spikeinterface.core.BaseRecording` objects) or 
-:py:class:`~spikeinterface.extractors.neoextractors.neobaseextractors.NeoBaseRecordingExtractor` 
-(for py:class:`~spikeinterface.core.BaseSorting` objects) or with a few lines of 
-code (e.g., see reader for `SpikeGLX <https://github.com/SpikeInterface/spikeinterface/blob/0.96.1/spikeinterface/extractors/neoextractors/spikeglx.py>`_ 
-or `Neuralynx <https://github.com/SpikeInterface/spikeinterface/blob/0.96.1/spikeinterface/extractors/neoextractors/neuralynx.py>`_). 
-
-**NOTE:** implementing a `neo.rawio` Class is not required, but recommended. Several extractors (especially) for Sorting 
+Once that is done, the new class can be easily wrapped into SpikeInterface as an extension of the
+:py:class:`~spikeinterface.extractors.neoextractors.neobaseextractors.NeoBaseRecordingExtractor`
+(for :py:class:`~spikeinterface.core.BaseRecording` objects) or
+:py:class:`~spikeinterface.extractors.neoextractors.neobaseextractors.NeoBaseRecordingExtractor`
+(for py:class:`~spikeinterface.core.BaseSorting` objects) or with a few lines of
+code (e.g., see reader for `SpikeGLX <https://github.com/SpikeInterface/spikeinterface/blob/0.96.1/spikeinterface/extractors/neoextractors/spikeglx.py>`_
+or `Neuralynx <https://github.com/SpikeInterface/spikeinterface/blob/0.96.1/spikeinterface/extractors/neoextractors/neuralynx.py>`_).
+
+**NOTE:** implementing a `neo.rawio` Class is not required, but recommended. Several extractors (especially) for Sorting
 objects are implemented directly in SpikeInterface and inherit from the base classes.
-As examples, see the `CompressedBinaryIblExtractor <https://github.com/SpikeInterface/spikeinterface/blob/0.96.1/spikeinterface/extractors/cbin_ibl.py>`_ 
-for a :py:class:`~spikeinterface.core.BaseRecording` object, or the `SpykingCircusSortingExtractor <https://github.com/SpikeInterface/spikeinterface/blob/0.96.1/spikeinterface/extractors/spykingcircusextractors.py>`_ 
+As examples, see the `CompressedBinaryIblExtractor <https://github.com/SpikeInterface/spikeinterface/blob/0.96.1/spikeinterface/extractors/cbin_ibl.py>`_
+for a :py:class:`~spikeinterface.core.BaseRecording` object, or the `SpykingCircusSortingExtractor <https://github.com/SpikeInterface/spikeinterface/blob/0.96.1/spikeinterface/extractors/spykingcircusextractors.py>`_
 for a a :py:class:`~spikeinterface.core.BaseSorting` object.
 
 
@@ -309,4 +309,3 @@ but we recommend testing the implementation locally.
 After this you need to add a block in doc/sorters_info.rst
 
 Finally, make a pull request to the spikesorters repo, so we can review the code and merge it to the spikesorters!
-