Merge branch 'main' of https://github.com/datajoint/element-calcium-i…

…maging into per-plane-processing
datajoint · Feb 1, 2024 · f32dd8d · f32dd8d
2 parents bc63a6e + 2480906
commit f32dd8d
Show file tree

Hide file tree

Showing 9 changed files with 1,308 additions and 14,052 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -4,9 +4,9 @@
     "editor.rulers": [
         88
     ],
-    "python.formatting.provider": "black",
+    "python.formatting.provider": "none",
     "[python]": {
-        "editor.defaultFormatter": null
+        "editor.defaultFormatter": "ms-python.black-formatter"
     },
     "[markdown]": {
         "editor.defaultFormatter": "disable"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,21 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.9.3] - 2024-01-29
+
++ Update - DataJoint Elements to install from GitHub instead of PyPI
++ Fix - `element-interface` required during package installation
++ Fix - apply formatting with `black` across the repository
+
+## [0.9.2] - 2024-01-10
+
++ Fix - Imports and attribute values in notebooks to resolve DataJoint errors
+
+## [0.9.1] - 2023-12-19
+
++ Update - Tutorial notebook
++ Fix - minor fixes in `setup.py` and `README`
+
 ## [0.9.0] - 2023-10-13
 
 + Add - Export to NWB and upload to DANDI
@@ -181,6 +196,10 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - `scan` and `imaging` modules
 + Add - Readers for `ScanImage`, `ScanBox`, `Suite2p`, `CaImAn`
 
+[0.9.3]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.9.3
+[0.9.2]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.9.2
+[0.9.1]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.9.1
+[0.9.0]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.9.0
 [0.8.1]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.8.1
 [0.8.0]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.8.0
 [0.7.9]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.7.9

diff --git a/README.md b/README.md
@@ -35,7 +35,7 @@ documentation page.
 + Clone the repository to your computer
 
   ```bash
-  git clone https://github.com/<enter_github_username>/element-calcium-imaging
+  git clone https://github.com/<enter_github_username>/element-calcium-imaging.git
   ```
 
 + Install with `pip`

diff --git a/docs/src/.overrides/assets/stylesheets/extra.css b/docs/src/.overrides/assets/stylesheets/extra.css
@@ -96,7 +96,6 @@ html a[title="YouTube"].md-social__link svg {
     /* --md-footer-fg-color: var(--dj-white); */
 }
 
-[data-md-color-scheme="slate"] td,
-th {
+[data-md-color-scheme="slate"] .jupyter-wrapper .Table Td {
     color: var(--dj-black)
 }
diff --git a/element_calcium_imaging/version.py b/element_calcium_imaging/version.py
@@ -1,3 +1,3 @@
 """Package metadata."""
 
-__version__ = "0.9.2"
+__version__ = "0.9.3"
diff --git a/notebooks/demo.ipynb b/notebooks/demo.ipynb
diff --git a/notebooks/quality_metrics.ipynb b/notebooks/quality_metrics.ipynb
diff --git a/notebooks/tutorial.ipynb b/notebooks/tutorial.ipynb
diff --git a/setup.py b/setup.py
@@ -38,16 +38,17 @@
         "ipykernel>=6.0.1",
         "ipywidgets",
         "plotly",
+        "element-interface @ git+https://github.com/datajoint/element-interface.git",
     ],
     extras_require={
         "caiman_requirements": [caiman_requirements],
         "caiman": ["caiman @ git+https://github.com/datajoint/CaImAn.git"],
         "elements": [
-            "element-animal>=0.1.8",
-            "element-event>=0.2.3",
             "element-interface @ git+https://github.com/datajoint/element-interface.git@staging",
-            "element-lab>=0.3.0",
-            "element-session>=0.1.5",
+            "element-animal @ git+https://github.com/datajoint/element-animal.git",
+            "element-event @ git+https://github.com/datajoint/element-event.git",
+            "element-lab @ git+https://github.com/datajoint/element-lab.git",
+            "element-session @ git+https://github.com/datajoint/element-session.git",
         ],
         "extract": ["matlabengine", "scipy"],
         "nd2": ["nd2"],