Merge branch 'datajoint:main' into main

kushalbakshi · Apr 18, 2024 · 41e4d6d · 41e4d6d
2 parents fd5e9fa + 9299142
commit 41e4d6d
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diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -4,14 +4,6 @@ on:
 jobs:
   make_github_release:
     uses: datajoint/.github/.github/workflows/make_github_release.yaml@main
-  pypi_release:
-    needs: make_github_release
-    uses: datajoint/.github/.github/workflows/pypi_release.yaml@main
-    secrets:
-      TWINE_USERNAME: ${{secrets.TWINE_USERNAME}}
-      TWINE_PASSWORD: ${{secrets.TWINE_PASSWORD}}
-    with:
-      UPLOAD_URL: ${{needs.make_github_release.outputs.release_upload_url}}
   mkdocs_release:
     uses: datajoint/.github/.github/workflows/mkdocs_release.yaml@main
     permissions: 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,24 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
  [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.3.4] - 2024-03-22
+
++ Add - pytest
++ Update - Ephys schema changed from `ephys_acute` to `ephys_no_curation` in `tutorial.ipynb`
+
+
+## [0.3.3] - 2024-01-24
++ Update - remove PyPi release from `release.yml` since it will fail after the new `setup.py`
+
+## [0.3.2] - 2024-01-12
++ Fix - `probe_geometry` bugfix for incorrect handling of probes with staggered electrode positions
+
+## [0.3.1] - 2023-11-28
++ Update - Flowchart borders for consistency with other DataJoint Elements
++ Fix - `dj.config()` setup moved to `tutorial_pipeline.py` instead of `__init__.py`
++ Update - Elements installed directly from GitHub instead of PyPI 
++ Update - Structure of the tutorial notebook
+
 ## [0.3.0] - 2023-10-25
 
 + Add - DevContainer for codespaces

diff --git a/docs/src/.overrides/assets/stylesheets/extra.css b/docs/src/.overrides/assets/stylesheets/extra.css
@@ -92,21 +92,6 @@ html a[title="YouTube"].md-social__link svg {
     /* --md-footer-fg-color: var(--dj-white); */
 }
 
-table {
-    border-collapse: collapse;
-}
-
-tr {
-    border-left: 1px solid var(--dj-black);
-    border-right: 1px solid var(--dj-black);
-}
-
-td, th {
-    border-top: 1px solid var(--dj-black);
-    border-bottom: 1px solid var(--dj-black);
-}
-
-[data-md-color-scheme="slate"] td, th {
-    background-color: var(--dj-white);
+[data-md-color-scheme="slate"] .jupyter-wrapper .Table Td {
     color: var(--dj-black);
 }
diff --git a/element_array_ephys/ephys_acute.py b/element_array_ephys/ephys_acute.py
@@ -1049,9 +1049,11 @@ def make(self, key):
         spike_time_key = (
             "spike_times_sec_adj"
             if "spike_times_sec_adj" in kilosort_dataset.data
-            else "spike_times_sec"
-            if "spike_times_sec" in kilosort_dataset.data
-            else "spike_times"
+            else (
+                "spike_times_sec"
+                if "spike_times_sec" in kilosort_dataset.data
+                else "spike_times"
+            )
         )
         spike_times = kilosort_dataset.data[spike_time_key]
         kilosort_dataset.extract_spike_depths()
@@ -1086,11 +1088,13 @@ def make(self, key):
                         "spike_sites": spike_sites[
                             kilosort_dataset.data["spike_clusters"] == unit
                         ],
-                        "spike_depths": spike_depths[
-                            kilosort_dataset.data["spike_clusters"] == unit
-                        ]
-                        if spike_depths is not None
-                        else None,
+                        "spike_depths": (
+                            spike_depths[
+                                kilosort_dataset.data["spike_clusters"] == unit
+                            ]
+                            if spike_depths is not None
+                            else None
+                        ),
                     }
                 )
 

diff --git a/element_array_ephys/ephys_chronic.py b/element_array_ephys/ephys_chronic.py
@@ -973,9 +973,11 @@ def make(self, key):
         spike_time_key = (
             "spike_times_sec_adj"
             if "spike_times_sec_adj" in kilosort_dataset.data
-            else "spike_times_sec"
-            if "spike_times_sec" in kilosort_dataset.data
-            else "spike_times"
+            else (
+                "spike_times_sec"
+                if "spike_times_sec" in kilosort_dataset.data
+                else "spike_times"
+            )
         )
         spike_times = kilosort_dataset.data[spike_time_key]
         kilosort_dataset.extract_spike_depths()
@@ -1010,11 +1012,13 @@ def make(self, key):
                         "spike_sites": spike_sites[
                             kilosort_dataset.data["spike_clusters"] == unit
                         ],
-                        "spike_depths": spike_depths[
-                            kilosort_dataset.data["spike_clusters"] == unit
-                        ]
-                        if spike_depths is not None
-                        else None,
+                        "spike_depths": (
+                            spike_depths[
+                                kilosort_dataset.data["spike_clusters"] == unit
+                            ]
+                            if spike_depths is not None
+                            else None
+                        ),
                     }
                 )
 

diff --git a/element_array_ephys/ephys_no_curation.py b/element_array_ephys/ephys_no_curation.py
@@ -988,9 +988,11 @@ def make(self, key):
         spike_time_key = (
             "spike_times_sec_adj"
             if "spike_times_sec_adj" in kilosort_dataset.data
-            else "spike_times_sec"
-            if "spike_times_sec" in kilosort_dataset.data
-            else "spike_times"
+            else (
+                "spike_times_sec"
+                if "spike_times_sec" in kilosort_dataset.data
+                else "spike_times"
+            )
         )
         spike_times = kilosort_dataset.data[spike_time_key]
         kilosort_dataset.extract_spike_depths()

diff --git a/element_array_ephys/ephys_precluster.py b/element_array_ephys/ephys_precluster.py
@@ -962,9 +962,11 @@ def make(self, key):
         spike_time_key = (
             "spike_times_sec_adj"
             if "spike_times_sec_adj" in kilosort_dataset.data
-            else "spike_times_sec"
-            if "spike_times_sec" in kilosort_dataset.data
-            else "spike_times"
+            else (
+                "spike_times_sec"
+                if "spike_times_sec" in kilosort_dataset.data
+                else "spike_times"
+            )
         )
         spike_times = kilosort_dataset.data[spike_time_key]
         kilosort_dataset.extract_spike_depths()
@@ -999,11 +1001,13 @@ def make(self, key):
                         "spike_sites": spike_sites[
                             kilosort_dataset.data["spike_clusters"] == unit
                         ],
-                        "spike_depths": spike_depths[
-                            kilosort_dataset.data["spike_clusters"] == unit
-                        ]
-                        if spike_depths is not None
-                        else None,
+                        "spike_depths": (
+                            spike_depths[
+                                kilosort_dataset.data["spike_clusters"] == unit
+                            ]
+                            if spike_depths is not None
+                            else None
+                        ),
                     }
                 )
 

diff --git a/element_array_ephys/ephys_report.py b/element_array_ephys/ephys_report.py
@@ -75,9 +75,11 @@ def make(self, key):
             fig_prefix = (
                 "-".join(
                     [
-                        v.strftime("%Y%m%d%H%M%S")
-                        if isinstance(v, datetime.datetime)
-                        else str(v)
+                        (
+                            v.strftime("%Y%m%d%H%M%S")
+                            if isinstance(v, datetime.datetime)
+                            else str(v)
+                        )
                         for v in key.values()
                     ]
                 )

diff --git a/element_array_ephys/probe.py b/element_array_ephys/probe.py
@@ -1,6 +1,7 @@
 """
 Neuropixels Probes
 """
+
 import datajoint as dj
 
 from .readers import probe_geometry

diff --git a/element_array_ephys/readers/probe_geometry.py b/element_array_ephys/readers/probe_geometry.py
@@ -188,7 +188,7 @@ def build_electrode_layouts(
         row_offset = np.zeros_like(x_coords)
     else:
         assert len(row_offset) == row_count
-        row_offset = np.tile(row_offset, col_count_per_shank)
+        row_offset = np.repeat(row_offset, col_count_per_shank)
     x_coords = x_coords + row_offset
 
     shank_cols = np.tile(range(col_count_per_shank), row_count)

diff --git a/element_array_ephys/version.py b/element_array_ephys/version.py
@@ -1,2 +1,3 @@
 """Package metadata."""
-__version__ = "0.3.0"
+
+__version__ = "0.3.4"