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kushalbakshikushalbakshi
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Merge branch 'datajoint:main' into main
2 parents fd5e9fa + 9299142 commit 41e4d6d

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16 files changed

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‎.github/workflows/release.yaml‎

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@@ -4,14 +4,6 @@ on:
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jobs:
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make_github_release:
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uses: datajoint/.github/.github/workflows/make_github_release.yaml@main
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pypi_release:
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needs: make_github_release
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uses: datajoint/.github/.github/workflows/pypi_release.yaml@main
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secrets:
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TWINE_USERNAME: ${{secrets.TWINE_USERNAME}}
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TWINE_PASSWORD: ${{secrets.TWINE_PASSWORD}}
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with:
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UPLOAD_URL: ${{needs.make_github_release.outputs.release_upload_url}}
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mkdocs_release:
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uses: datajoint/.github/.github/workflows/mkdocs_release.yaml@main
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permissions:

‎CHANGELOG.md‎

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Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
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[Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
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## [0.3.4] - 2024-03-22
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+ Add - pytest
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+ Update - Ephys schema changed from `ephys_acute` to `ephys_no_curation` in `tutorial.ipynb`
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## [0.3.3] - 2024-01-24
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+ Update - remove PyPi release from `release.yml` since it will fail after the new `setup.py`
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## [0.3.2] - 2024-01-12
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+ Fix - `probe_geometry` bugfix for incorrect handling of probes with staggered electrode positions
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## [0.3.1] - 2023-11-28
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+ Update - Flowchart borders for consistency with other DataJoint Elements
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+ Fix - `dj.config()` setup moved to `tutorial_pipeline.py` instead of `__init__.py`
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+ Update - Elements installed directly from GitHub instead of PyPI
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+ Update - Structure of the tutorial notebook
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## [0.3.0] - 2023-10-25
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+ Add - DevContainer for codespaces

‎docs/src/.overrides/assets/stylesheets/extra.css‎

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@@ -92,21 +92,6 @@ html a[title="YouTube"].md-social__link svg {
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/* --md-footer-fg-color: var(--dj-white); */
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}
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table {
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border-collapse: collapse;
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}
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tr {
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border-left: 1px solid var(--dj-black);
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border-right: 1px solid var(--dj-black);
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}
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td, th {
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border-top: 1px solid var(--dj-black);
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border-bottom: 1px solid var(--dj-black);
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}
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[data-md-color-scheme="slate"] td, th {
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background-color: var(--dj-white);
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[data-md-color-scheme="slate"] .jupyter-wrapper .Table Td {
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color: var(--dj-black);
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}

‎element_array_ephys/ephys_acute.py‎

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@@ -1049,9 +1049,11 @@ def make(self, key):
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spike_time_key = (
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"spike_times_sec_adj"
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if "spike_times_sec_adj" in kilosort_dataset.data
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else "spike_times_sec"
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if "spike_times_sec" in kilosort_dataset.data
1054-
else "spike_times"
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else (
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"spike_times_sec"
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if "spike_times_sec" in kilosort_dataset.data
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else "spike_times"
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)
10551057
)
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spike_times = kilosort_dataset.data[spike_time_key]
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kilosort_dataset.extract_spike_depths()
@@ -1086,11 +1088,13 @@ def make(self, key):
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"spike_sites": spike_sites[
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kilosort_dataset.data["spike_clusters"] == unit
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],
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"spike_depths": spike_depths[
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kilosort_dataset.data["spike_clusters"] == unit
1091-
]
1092-
if spike_depths is not None
1093-
else None,
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"spike_depths": (
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spike_depths[
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kilosort_dataset.data["spike_clusters"] == unit
1094+
]
1095+
if spike_depths is not None
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else None
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),
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}
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)
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‎element_array_ephys/ephys_chronic.py‎

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@@ -973,9 +973,11 @@ def make(self, key):
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spike_time_key = (
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"spike_times_sec_adj"
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if "spike_times_sec_adj" in kilosort_dataset.data
976-
else "spike_times_sec"
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if "spike_times_sec" in kilosort_dataset.data
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else "spike_times"
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else (
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"spike_times_sec"
978+
if "spike_times_sec" in kilosort_dataset.data
979+
else "spike_times"
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)
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)
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spike_times = kilosort_dataset.data[spike_time_key]
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kilosort_dataset.extract_spike_depths()
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"spike_sites": spike_sites[
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kilosort_dataset.data["spike_clusters"] == unit
10121014
],
1013-
"spike_depths": spike_depths[
1014-
kilosort_dataset.data["spike_clusters"] == unit
1015-
]
1016-
if spike_depths is not None
1017-
else None,
1015+
"spike_depths": (
1016+
spike_depths[
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kilosort_dataset.data["spike_clusters"] == unit
1018+
]
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if spike_depths is not None
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else None
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),
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}
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)
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‎element_array_ephys/ephys_no_curation.py‎

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@@ -988,9 +988,11 @@ def make(self, key):
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spike_time_key = (
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"spike_times_sec_adj"
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if "spike_times_sec_adj" in kilosort_dataset.data
991-
else "spike_times_sec"
992-
if "spike_times_sec" in kilosort_dataset.data
993-
else "spike_times"
991+
else (
992+
"spike_times_sec"
993+
if "spike_times_sec" in kilosort_dataset.data
994+
else "spike_times"
995+
)
994996
)
995997
spike_times = kilosort_dataset.data[spike_time_key]
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kilosort_dataset.extract_spike_depths()

‎element_array_ephys/ephys_precluster.py‎

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@@ -962,9 +962,11 @@ def make(self, key):
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spike_time_key = (
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"spike_times_sec_adj"
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if "spike_times_sec_adj" in kilosort_dataset.data
965-
else "spike_times_sec"
966-
if "spike_times_sec" in kilosort_dataset.data
967-
else "spike_times"
965+
else (
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"spike_times_sec"
967+
if "spike_times_sec" in kilosort_dataset.data
968+
else "spike_times"
969+
)
968970
)
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spike_times = kilosort_dataset.data[spike_time_key]
970972
kilosort_dataset.extract_spike_depths()
@@ -999,11 +1001,13 @@ def make(self, key):
9991001
"spike_sites": spike_sites[
10001002
kilosort_dataset.data["spike_clusters"] == unit
10011003
],
1002-
"spike_depths": spike_depths[
1003-
kilosort_dataset.data["spike_clusters"] == unit
1004-
]
1005-
if spike_depths is not None
1006-
else None,
1004+
"spike_depths": (
1005+
spike_depths[
1006+
kilosort_dataset.data["spike_clusters"] == unit
1007+
]
1008+
if spike_depths is not None
1009+
else None
1010+
),
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}
10081012
)
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‎element_array_ephys/ephys_report.py‎

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fig_prefix = (
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"-".join(
7777
[
78-
v.strftime("%Y%m%d%H%M%S")
79-
if isinstance(v, datetime.datetime)
80-
else str(v)
78+
(
79+
v.strftime("%Y%m%d%H%M%S")
80+
if isinstance(v, datetime.datetime)
81+
else str(v)
82+
)
8183
for v in key.values()
8284
]
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)

‎element_array_ephys/probe.py‎

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"""
22
Neuropixels Probes
33
"""
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import datajoint as dj
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from .readers import probe_geometry

‎element_array_ephys/readers/probe_geometry.py‎

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@@ -188,7 +188,7 @@ def build_electrode_layouts(
188188
row_offset = np.zeros_like(x_coords)
189189
else:
190190
assert len(row_offset) == row_count
191-
row_offset = np.tile(row_offset, col_count_per_shank)
191+
row_offset = np.repeat(row_offset, col_count_per_shank)
192192
x_coords = x_coords + row_offset
193193

194194
shank_cols = np.tile(range(col_count_per_shank), row_count)

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