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Merge pull request #191 from h-mayorquin/format_black
Move to src structure and pre-commit format
2 parents cedafaa + 60bdf3f commit 2dfc737

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‎.github/workflows/full_tests.yml

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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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fail_ci_if_error: true
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file: ./coverage.xml
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file: ./coverage.xml

‎.github/workflows/publish-to-pypi.yml

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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.8
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uses: actions/setup-python@v2
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uses: actions/setup-python@v4
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with:
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python-version: 3.8
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python-version: "3.10"
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- name: Install Tools
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run: |
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python -m pip install --upgrade pip

‎.gitignore

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dev_*
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.coverage
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cov.xml
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cov.xml

‎.readthedocs.yaml

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sphinx:
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configuration: doc/conf.py
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python:
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version: 3.8
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install:

‎README.md

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Author: Samuel Garcia
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‎doc/api.rst

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.. autoclass:: probeinterface.Probe
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:members:
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ProbeGroup
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----------
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.. automodule:: probeinterface
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.. autoclass:: probeinterface.ProbeGroup
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:members:
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.. autofunction:: read_probeinterface
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.. autofunction:: write_probeinterface
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.. autofunction:: read_prb
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.. autofunction:: write_prb
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.. autofunction:: read_csv
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.. autofunction:: write_csv
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.. autofunction:: read_spikeglx
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.. autofunction:: read_mearec
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.. autofunction:: read_nwb
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.. automodule:: probeinterface.generator
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.. autofunction:: generate_dummy_probe
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.. autofunction:: generate_dummy_probe_group
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.. autofunction:: generate_tetrode
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.. autofunction:: generate_multi_columns_probe
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.. autofunction:: generate_linear_probe
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Plotting
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.. automodule:: probeinterface.plotting
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.. autofunction:: plot_probe
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.. autofunction:: plot_probe_group
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Library
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.. automodule:: probeinterface.library
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.. autofunction:: get_probe
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‎doc/index.rst

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* basic plotting functions with matplotlib
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* input/output functions to several formats (PRB, NWB, CSV, MEArec, SpikeGLX, ...)
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Here is a schema for the naming used in the package:
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Here is a schema for the naming used in the package:
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.. image:: img/probeinterface_naming.png
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:width: 400 px
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.. include:: examples/index.rst
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.. toctree::
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:caption: Contents:
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:maxdepth: 1
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overview
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examples/index.rst
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format_spec

‎doc/library.rst

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5. Ask for an account
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6. Push to a branch with gin client
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7. Make a pull request on the gin portal (like a github PR)
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‎doc/overview.rst

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* generator functions to create user-defined probes
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Goal 1
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Goal 1
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---------
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This common interface could be used by several projects for spike sorting and electrophysiology analysis:

‎doc/release_notes.rst

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.. toctree::
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:maxdepth: 1
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releases/0.2.16.rst
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releases/0.2.15.rst
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releases/0.2.14.rst

‎doc/releases/0.1.0.rst

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11th jan 2021
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Initial release.
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‎doc/releases/0.2.0.rst

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March, 2 2021
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Format improvement with all ids in str.
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‎doc/releases/0.2.1.rst

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* to_numpy()/from_numpy()
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* to_dataframe()/from_dataframe()
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* read_mearec
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‎doc/releases/0.2.10.rst

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* implement read_imro() / write_imro()
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* Add new wiring : 'ASSY-77>Adpt.A64-Om32_2x-sm>two_RHD2132'
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* Handle OpenEphys NPIX with multiple probes
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* Add cross-checked ASSY-116>RHD2132 mapping
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* Add cross-checked ASSY-116>RHD2132 mapping

‎doc/releases/0.2.14.rst

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* Fix a **important bug** in :code:`read_spikeglx()` / :code:`read_imro()` that was leading
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to wrong contact locations when the Imec Readout Table (aka imRo)
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was set with complex multi-bank patterns.
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The bug was introduced with version **0.2.10**, released on September 1st 2022, and it is also present in these
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The bug was introduced with version **0.2.10**, released on September 1st 2022, and it is also present in these
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versions: **0.2.10**, **0.2.11**, **0.2.12**, and **0.2.13**.
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**If you used spikeinterface/probeinterface with SpikeGLX data using one of these versions, we recommend you
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to check your contact positions (if they are non-standard - using the probe tip) and re-run your spike-sorting
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**If you used spikeinterface/probeinterface with SpikeGLX data using one of these versions, we recommend you
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to check your contact positions (if they are non-standard - using the probe tip) and re-run your spike-sorting
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analysis if they are wrong.**
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A big thanks to Tom Bugnon and Graham Findlay for
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A big thanks to Tom Bugnon and Graham Findlay for
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`spotting the bug <https://github.com/SpikeInterface/probeinterface/issues/141>`_.

‎doc/releases/0.2.2.rst

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* write_prb handle group_mode
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* add wriring RDH2164
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* doc improvement
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‎doc/releases/0.2.3.rst

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* add a pathway
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* show_channel_on_click
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* debug read_mearec()
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‎doc/releases/0.2.4.rst

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* expose read_maxwell function
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* vector annotations
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* changes to BIDS format
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‎doc/releases/0.2.5.rst

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* vector annotations added to numpy representation
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* add "electrode" to annotations from read_maxwell
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‎doc/releases/0.2.6.rst

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* documention improvement
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* spikeglx neuropixel2 integration
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* plotting improvement
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‎doc/releases/0.2.7.rst

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* add read_3brain to io
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* annotate spikeGLX with probe version
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* annotate spikeGLX with probe version

‎doc/releases/0.2.8.rst

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* expose function select_dimensions (2d>3d and 3d>2d)
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* add to_dict/from_dict in ProbeGroup
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* Add "text_on_contact" in plot_probe()
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* Add read_openephys function for Neuropux-PXI plugin
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* Add read_openephys function for Neuropux-PXI plugin

‎examples/README.rst

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---------------
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Start here with a tutorial showing probeinterface.
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‎examples/ex_02_probe_2d_probe_3d.py

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##############################################################################
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# Let's transform it into a 3d probe.
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#
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#
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# Here the axes are 'xz' so y will be 0 for all contacts.
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# The shape of probe_3d.contact_positions is now (n_elec, 3)
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‎examples/ex_03_generate_probe_group.py

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##############################################################################
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# Generate 2 dummy `Probe` objects with the utils function:
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#
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probe0 = generate_dummy_probe(elec_shapes='square')
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probe1 = generate_dummy_probe(elec_shapes='circle')

‎examples/ex_06_import_export_to_file.py

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* PRB (.prb) : used by klusta/spyking-circus/tridesclous
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* CSV (.csv): 2 or 3 columns locations in text file
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* mearec (.h5) : mearec handles the geometry
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* mearec (.h5) : mearec handles the geometry
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* spikeglx (.meta) : spikeglx also handles the geometry
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"""

‎examples/ex_07_probe_generator.py

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##############################################################################
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# Generate 4 tetrodes:
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# Generate a linear probe:
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##############################################################################
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‎examples/ex_11_automatic_wiring.py

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##############################################################################
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# We can "wire" this probe to a recording device.
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# Imagine we connect this Neuronexus probe with an Omnetic to an Intan RHD headstage.
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# using the `probe.set_device_channel_indices()` function:
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‎probeinterface/__init__.py

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‎pyproject.toml

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package-dir = {"probeinterface" = "src/probeinterface"}
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[project.optional-dependencies]
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omit = [
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]
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[tool.black]
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line-length = 120

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