Upgrade to zarr v3

Author: alejoe91

.github/workflows/full_tests.yml

@@ -28,7 +28,8 @@ jobs:
     - name: Install package
       run: |
         python -m pip install --upgrade pip
-        pip install .[test]
+        pip install .
+        pip install --group test
     - name: Pytest
       run: |
         pytest -m "not library" -v

.github/workflows/full_tests_codecov.yml

@@ -20,7 +20,8 @@ jobs:
     - name: Install package
       run: |
         python -m pip install --upgrade pip
-        pip install .[test]
+        pip install .
+        pip install --group test
     - name: Pytest
       run: |
         pytest --cov=probeinterface --cov-report xml:./coverage.xml

.gitignore

@@ -27,3 +27,4 @@ cov.xml
 
 
 neuropixel_library_generated/*
+uv.lock

.pre-commit-config.yaml

@@ -6,13 +6,13 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.12.0
+    rev: 26.3.1
     hooks:
     -   id: black
         files: ^src/|^tests/
 - repo: https://github.com/codespell-project/codespell
   # Configuration for codespell is in .pre-commit-config.yaml
-  rev: v2.4.1
+  rev: v2.4.2
   hooks:
   -    id: codespell
        additional_dependencies:

.readthedocs.yaml

@@ -1,16 +1,14 @@
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
     python: "3.10"
+  jobs:
+    install:
+      - pip install -U pip
+      - pip install .
+      - pip install --group docs
 
 sphinx:
   configuration: doc/conf.py
-
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs

doc/api.rst

@@ -65,7 +65,7 @@ Plotting
 
     .. autofunction:: plot_probe
 
-    .. autofunction:: plot_probe_group
+    .. autofunction:: plot_probegroup
 
 Library
 -------

doc/generate_format_example.py

@@ -6,7 +6,7 @@
 import matplotlib.pyplot as plt
 
 from probeinterface import Probe, ProbeGroup, combine_probes, write_probeinterface
-from probeinterface.plotting import plot_probe, plot_probe_group
+from probeinterface.plotting import plot_probe, plot_probegroup
 
 from probeinterface import generate_tetrode
 

examples/ex_03_generate_probe_group.py

@@ -13,7 +13,7 @@
 import matplotlib.pyplot as plt
 
 from probeinterface import Probe, ProbeGroup
-from probeinterface.plotting import plot_probe_group
+from probeinterface.plotting import plot_probegroup
 from probeinterface import generate_dummy_probe
 
 ##############################################################################
@@ -39,11 +39,11 @@
 ##############################################################################
 #  We can now plot all probes in the same axis:
 
-plot_probe_group(probegroup, same_axes=True)
+plot_probegroup(probegroup, same_axes=True)
 
 ##############################################################################
 #  or in separate axes:
 
-plot_probe_group(probegroup, same_axes=False, with_contact_id=True)
+plot_probegroup(probegroup, same_axes=False, with_contact_id=True)
 
 plt.show()

examples/ex_05_device_channel_indices.py

@@ -17,7 +17,7 @@
 import matplotlib.pyplot as plt
 
 from probeinterface import Probe, ProbeGroup
-from probeinterface.plotting import plot_probe, plot_probe_group
+from probeinterface.plotting import plot_probe, plot_probegroup
 from probeinterface import generate_multi_columns_probe
 
 ##############################################################################
@@ -85,6 +85,6 @@
 # The indices of the probe group can also be plotted:
 
 fig, ax = plt.subplots()
-plot_probe_group(probegroup, with_contact_id=True, same_axes=True, ax=ax)
+plot_probegroup(probegroup, with_contact_id=True, same_axes=True, ax=ax)
 
 plt.show()

examples/ex_06_import_export_to_file.py

@@ -24,7 +24,7 @@
 import matplotlib.pyplot as plt
 
 from probeinterface import Probe, ProbeGroup
-from probeinterface.plotting import plot_probe, plot_probe_group
+from probeinterface.plotting import plot_probe, plot_probegroup
 from probeinterface import generate_dummy_probe
 from probeinterface import write_probeinterface, read_probeinterface
 from probeinterface import write_prb, read_prb
@@ -48,7 +48,7 @@
 write_probeinterface('my_two_probe_setup.json', probegroup)
 
 probegroup2 = read_probeinterface('my_two_probe_setup.json')
-plot_probe_group(probegroup2)
+plot_probegroup(probegroup2)
 
 ##############################################################################
 # The format looks like this:
@@ -98,6 +98,6 @@
     f.write(prb_two_tetrodes)
 
 two_tetrode = read_prb('two_tetrodes.prb')
-plot_probe_group(two_tetrode, same_axes=False, with_contact_id=True)
+plot_probegroup(two_tetrode, same_axes=False, with_contact_id=True)
 
 plt.show()