Merge pull request #227 from SpikeInterface/prepare_release

Prepare 0.2.18 release

README.md

@@ -45,37 +45,68 @@
 
 A Python package to handle the layout, geometry, and wiring of silicon probes for extracellular electrophysiology experiments.
 
-Documentation : https://probeinterface.readthedocs.io/
+Please [Star](https://github.com/SpikeInterface/probeinterface/stargazers) the project to support us and [Watch](https://github.com/SpikeInterface/probeinterface/subscription) to always stay up-to-date!
 
 
 ## Goals
 
-Make a lightweight package to handle:
+ProbeInterface aims to provide a common framework to handle probe information across neuroscience experiments.
+
+ProbeInterface is used by the [SpikeInterface](https://github.com/SpikeInterface/spikeinterface) package to attach probe information to a recording object.
+You can find detailed documentation in the [SpikeInterface documentation](https://spikeinterface.readthedocs.io/en/latest/modules/core.html#handling-probes).
+
+In practice, ProbeInterface is a lightweight package to handle:
 
   * probe contact geometry (both 2D and 3D layouts)
-  * probe shape (contour of the probe, shape of channel contact, ...)
-  * probe wiring to device (the physical layout often doesn't match the channel ordering)
-  * combining several probes into a device with global geometry + global wiring
-  * exporting probe geometry data into JSON files
-  * loading existing probe geometry files (Neuronexus, imec, Cambridge Neurotech...) [Started here](https://gin.g-node.org/spikeinterface/probeinterface_library)
+  * probe shape (contour of the probe, shape of channel contacts, etc.)
+  * probe wiring to a device (the physical layout often doesn't match the channel ordering)
+  * combining several probes into a device, with probe groups and a global wiring
+  * exporting probe data into a common JSON file format
+  * loading existing probe geometry files (Cambridge Neurotech, NeuroNexus, etc.) from the [probeinterface_library](https://github.com/SpikeInterface/probeinterface_library)
+
+In addition, ProbeInterface also offers the following features:
+
+  * `matplotlib`-based plotting functions
+  * loading/saving probes using common formats (PRB, CSV, NWB, ...)
+  * correctly handling SI units (um, mm)
+
+
+## Documentation
+
+Detailed documentation of the latest PyPI release of ProbeInterface can be found [here](https://probeinterface.readthedocs.io/en/0.2.18).
+
+Detailed documentation of the development version of ProbeInterface can be found [here](https://probeinterface.readthedocs.io/en/latest).
+
+## How to install probeinterface
+
+You can install the latest version of `probeinterface` version with pip:
 
-Bonus :
+```bash
+pip install probeinterface
+```
 
-  * optional plotting (based on `matplotlib`)
-  * load/save geometry using common formats (PRB, CSV, NWB, ...)
-  * handle SI length units correctly um/mm/...
+To get the latest updates, you can install `probeinterface` from source:
 
+```bash
+git clone https://github.com/SpikeInterface/probeinterface.git
+cd probeinterface
+pip install -e .
+cd ..
+```
 
-Target users/projet :
 
-  * spikeinterface team : integrate this into spikeextractor for channel location
-  * neo team : handle array_annotations for AnalogSignal
-  * spikeforest team : use this package for ploting probe activity
-  * phy team: integrate for probe display
-  * spyking-circus team : handle probe with this package
-  * kilosort team : handle probe with this package
-  * tridesclous team : handle probe with this package
-  * open ephys team : automatically generate channel map configuration files
+## Citation
 
+If you find ProbeInterface useful in your research, please cite:
 
- Author: Samuel Garcia
+```bibtex
+@article{garcia2022probeinterface,
+  title={ProbeInterface: a unified framework for probe handling in extracellular electrophysiology},
+  author={Garcia, Samuel and Sprenger, Julia and Holtzman, Tahl and Buccino, Alessio P},
+  journal={Frontiers in Neuroinformatics},
+  volume={16},
+  pages={823056},
+  year={2022},
+  publisher={Frontiers Media SA}
+}
+```

doc/release_notes.rst

@@ -6,6 +6,7 @@ Release notes
 .. toctree::
    :maxdepth: 1
 
+   releases/0.2.18.rst
    releases/0.2.17.rst
    releases/0.2.16.rst
    releases/0.2.15.rst

doc/releases/0.2.18.rst

@@ -0,0 +1,30 @@
+probeinterface 0.2.18
+---------------------
+
+Oct, 30th 2023
+
+
+Features
+^^^^^^^^
+
+* Extend probe constructor (name, serial_number, manufacturer, model_name) (#206)
+* Extend available NP2 probe types to commercial types (20** series) (#217)
+* Remove :code:`with_channel_index` argument from :code:`plot_probe` (#229)
+* Remove checker for unique contact ids in probe group (#229)
+* Unify usage of "contact" and remove "channel" notation (except for "device_channel_index") (#229)
+
+
+Bug fixes
+^^^^^^^^^
+
+* Fix shank_pitch to NP-2.4 in SpikeGLX (#205)
+* Fix y_shift_per_column docs and add assertion (#212)
+* Change np.in1d to np.isin as the former will be deprecated (#220)
+* Fix contour of NP2.0 for Open Ephys Neuropixels (#224)
+
+Docs
+^^^^
+
+* Add available pathways in 'Automatic wiring' docs (#213)
+* Add Typing and Update Docstrings (#214)
+* Add more details to how to contribute (#222)

pyproject.toml

@@ -50,6 +50,7 @@ test = [
 docs = [
     "pillow",
     "sphinx-gallery",
+    "sphinx_rtd_theme",
     "matplotlib==3.2.2",
     "scipy",
     "pandas",