Merge pull request #191 from h-mayorquin/format_black

Move to src structure and pre-commit format

.github/workflows/full_tests.yml

@@ -31,4 +31,4 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true
-        file: ./coverage.xml
+        file: ./coverage.xml

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

@@ -12,9 +12,9 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: "3.10"
     - name: Install Tools
       run: |
         python -m pip install --upgrade pip

.gitignore

@@ -23,4 +23,4 @@ doc/examples/*
 
 dev_*
 .coverage
-cov.xml
+cov.xml

.readthedocs.yaml

@@ -5,7 +5,7 @@ build:
 
 sphinx:
   configuration: doc/conf.py
-    
+
 python:
   version: 3.8
   install:

README.md

@@ -79,4 +79,3 @@ Target users/projet :
 
 
  Author: Samuel Garcia
-

doc/api.rst

@@ -10,12 +10,12 @@ Probe
 
     .. autoclass:: probeinterface.Probe
         :members:
-    
+
 ProbeGroup
 ----------
 
 .. automodule:: probeinterface
-    
+
     .. autoclass:: probeinterface.ProbeGroup
         :members:
 
@@ -27,19 +27,19 @@ Import/export to formats
     .. autofunction:: read_probeinterface
 
     .. autofunction:: write_probeinterface
-    
+
     .. autofunction:: read_prb
-    
+
     .. autofunction:: write_prb
-    
+
     .. autofunction:: read_csv
-    
+
     .. autofunction:: write_csv
-    
+
     .. autofunction:: read_spikeglx
-    
+
     .. autofunction:: read_mearec
-    
+
     .. autofunction:: read_nwb
 
 
@@ -49,13 +49,13 @@ Probe generators
 .. automodule:: probeinterface.generator
 
     .. autofunction:: generate_dummy_probe
-    
+
     .. autofunction:: generate_dummy_probe_group
-    
+
     .. autofunction:: generate_tetrode
-    
+
     .. autofunction:: generate_multi_columns_probe
-    
+
     .. autofunction:: generate_linear_probe
 
 Plotting
@@ -64,7 +64,7 @@ Plotting
 .. automodule:: probeinterface.plotting
 
     .. autofunction:: plot_probe
-    
+
     .. autofunction:: plot_probe_group
 
 Library
@@ -73,4 +73,3 @@ Library
 .. automodule:: probeinterface.library
 
     .. autofunction:: get_probe
-

doc/index.rst

@@ -17,19 +17,19 @@ The :code:`probeinterface` package also provides:
   * basic plotting functions with matplotlib
   * input/output functions to several formats (PRB, NWB, CSV, MEArec, SpikeGLX, ...)
 
-Here is a schema for the naming used in the package:  
+Here is a schema for the naming used in the package:
 
 .. image:: img/probeinterface_naming.png
     :width: 400 px
 
 
-  
+
 .. include:: examples/index.rst
-   
+
 .. toctree::
    :caption: Contents:
    :maxdepth: 1
-   
+
    overview
    examples/index.rst
    format_spec

doc/library.rst

@@ -28,6 +28,3 @@ TODO: explain with more details
   5. Ask for an account
   6. Push to a branch with gin client
   7. Make a pull request on the gin portal (like a github PR)
-
-
-

doc/overview.rst

@@ -58,7 +58,7 @@ This package also provide:
   * generator functions to create user-defined probes
 
 
-Goal 1 
+Goal 1
 ---------
 
 This common interface could be used by several projects for spike sorting and electrophysiology analysis:

doc/release_notes.rst

@@ -5,7 +5,7 @@ Release notes
 
 .. toctree::
    :maxdepth: 1
-   
+
    releases/0.2.16.rst
    releases/0.2.15.rst
    releases/0.2.14.rst

doc/releases/0.1.0.rst

@@ -4,4 +4,3 @@ probeinterface 0.1.0
 11th jan 2021
 
 Initial release.
-

doc/releases/0.2.0.rst

@@ -4,4 +4,3 @@ probeinterface 0.2.0
 March, 2 2021
 
 Format improvement with all ids in str.
-

doc/releases/0.2.1.rst

@@ -7,4 +7,3 @@ March, 24 2021
 * to_numpy()/from_numpy()
 * to_dataframe()/from_dataframe()
 * read_mearec
-

doc/releases/0.2.10.rst

@@ -10,4 +10,4 @@ September, 1st 2022
 * implement read_imro() / write_imro()
 * Add new wiring : 'ASSY-77>Adpt.A64-Om32_2x-sm>two_RHD2132'
 * Handle OpenEphys NPIX with multiple probes
-* Add cross-checked ASSY-116>RHD2132 mapping 
+* Add cross-checked ASSY-116>RHD2132 mapping

doc/releases/0.2.14.rst

@@ -7,12 +7,12 @@ October, 27th 2022
 * Fix a **important bug** in :code:`read_spikeglx()` / :code:`read_imro()` that was leading
   to wrong contact locations when the Imec Readout Table (aka imRo)
   was set with complex multi-bank patterns.
-  The bug was introduced with version **0.2.10**, released on September 1st 2022, and it is also present in these 
+  The bug was introduced with version **0.2.10**, released on September 1st 2022, and it is also present in these
   versions: **0.2.10**, **0.2.11**, **0.2.12**, and **0.2.13**.
 
-  **If you used spikeinterface/probeinterface with SpikeGLX data using one of these versions, we recommend you 
-  to check your contact positions (if they are non-standard - using the probe tip) and re-run your spike-sorting 
+  **If you used spikeinterface/probeinterface with SpikeGLX data using one of these versions, we recommend you
+  to check your contact positions (if they are non-standard - using the probe tip) and re-run your spike-sorting
   analysis if they are wrong.**
 
-  A big thanks to Tom Bugnon and Graham Findlay for 
+  A big thanks to Tom Bugnon and Graham Findlay for
   `spotting the bug <https://github.com/SpikeInterface/probeinterface/issues/141>`_.

doc/releases/0.2.2.rst

@@ -7,4 +7,3 @@ April, 4 2021
 * write_prb handle group_mode
 * add wriring RDH2164
 * doc improvement
-

doc/releases/0.2.3.rst

@@ -6,5 +6,3 @@ May, 21 2021
 * add a pathway
 * show_channel_on_click
 * debug read_mearec()
-
-

doc/releases/0.2.4.rst

@@ -6,4 +6,3 @@ July, 30 2021
 * expose read_maxwell function
 * vector annotations
 * changes to BIDS format
-

doc/releases/0.2.5.rst

@@ -5,4 +5,3 @@ September, 14 2021
 
 * vector annotations added to numpy representation
 * add "electrode" to annotations from read_maxwell
-

doc/releases/0.2.6.rst

@@ -6,5 +6,3 @@ November, 26 2021
 * documention improvement
 * spikeglx neuropixel2 integration
 * plotting improvement
-
-

doc/releases/0.2.7.rst

@@ -5,6 +5,4 @@ probeinterface 0.2.7
 March, 1 2022
 
 * add read_3brain to io
-* annotate spikeGLX with probe version 
-
-
+* annotate spikeGLX with probe version

doc/releases/0.2.8.rst

@@ -8,7 +8,4 @@ March, 23rd 2022
 * expose function select_dimensions (2d>3d and 3d>2d)
 * add to_dict/from_dict in ProbeGroup
 * Add "text_on_contact" in plot_probe()
-* Add read_openephys function for Neuropux-PXI plugin 
-
-
-
+* Add read_openephys function for Neuropux-PXI plugin

examples/README.rst

@@ -2,6 +2,3 @@ Examples
 ---------------
 
 Start here with a tutorial showing probeinterface.
-
-
-

examples/ex_02_probe_2d_probe_3d.py

@@ -32,7 +32,7 @@
 
 ##############################################################################
 # Let's transform it into a 3d probe.
-# 
+#
 # Here the axes are 'xz' so y will be 0 for all contacts.
 # The shape of probe_3d.contact_positions is now (n_elec, 3)
 

examples/ex_03_generate_probe_group.py

@@ -18,7 +18,7 @@
 
 ##############################################################################
 # Generate 2 dummy `Probe` objects with the utils function:
-# 
+#
 
 probe0 = generate_dummy_probe(elec_shapes='square')
 probe1 = generate_dummy_probe(elec_shapes='circle')

examples/ex_06_import_export_to_file.py

@@ -12,7 +12,7 @@
 
   * PRB (.prb) : used by klusta/spyking-circus/tridesclous
   * CSV (.csv): 2 or 3 columns locations in text file
-  * mearec (.h5) : mearec handles the geometry 
+  * mearec (.h5) : mearec handles the geometry
   * spikeglx (.meta) : spikeglx also handles the geometry
 
 """

examples/ex_07_probe_generator.py

@@ -21,7 +21,7 @@
 
 ##############################################################################
 # Generate 4 tetrodes:
-# 
+#
 
 from probeinterface import generate_tetrode
 
@@ -39,7 +39,7 @@
 
 ##############################################################################
 # Generate a linear probe:
-# 
+#
 
 from probeinterface import generate_linear_probe
 
@@ -48,7 +48,7 @@
 
 ##############################################################################
 # Generate a multi-column probe:
-# 
+#
 
 from probeinterface import generate_multi_columns_probe
 
@@ -61,7 +61,7 @@
 
 ##############################################################################
 # Generate a square probe:
-# 
+#
 
 square_probe = generate_multi_columns_probe(num_columns=12,
                                             num_contact_per_column=12,

examples/ex_11_automatic_wiring.py

@@ -26,11 +26,11 @@
 ##############################################################################
 # We can "wire"  this probe to a recording device.
 # Imagine we connect this Neuronexus probe with an Omnetic to an Intan RHD headstage.
-# 
+#
 # Using the wiring documentation from these two sites:
 # https://neuronexus.com/wp-content/uploads/2018/09/Wiring_H32.pdf
 # http://intantech.com/RHD_headstages.html?tabSelect=RHD32ch&yPos=0
-# 
+#
 # After a long headache we can figure out the wiring to the device manually and set it
 # using the `probe.set_device_channel_indices()` function:
 

pyproject.toml

@@ -33,7 +33,7 @@ build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
 packages = ["probeinterface"]
-package-dir = {"probeinterface" = "probeinterface"}
+package-dir = {"probeinterface" = "src/probeinterface"}
 
 
 [project.optional-dependencies]
@@ -58,4 +58,8 @@ docs = [
 [tool.coverage.run]
 omit = [
     "tests/*",
-]
+]
+
+
+[tool.black]
+line-length = 120