Merge pull request #80 from kabilar/main

Add DeepLabCut, NWB, and DANDI citations

Author: dimitri-yatsenko

CHANGELOG.md

@@ -3,6 +3,11 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and 
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.2.6] - 2023-05-22
+
++ Add - DeepLabCut, NWB, and DANDI citations
++ Update - mkdocs.yaml
+
 ## [0.2.5] - 2023-05-11
 
 + Fix - `.ipynb` dark mode output for all notebooks.
@@ -63,6 +68,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
   graciously provided by the Mathis Lab.
 + Add - Support for 2d single-animal models
 
+[0.2.6]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.6
 [0.2.5]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.5
 [0.2.4]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.4
 [0.2.3]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.3

docs/.docker/pip_requirements.txt

@@ -8,4 +8,5 @@ mkdocs-gen-files
 mkdocs-literate-nav
 mkdocs-exclude-search
 mkdocs-markdownextradata-plugin
-mkdocs-jupyter
+mkdocs-jupyter
+mkdocs-section-index

docs/docker-compose.yaml

@@ -15,7 +15,6 @@ services:
       - PACKAGE
       - UPSTREAM_REPO
       - MODE
-      - GOOGLE_ANALYTICS_KEY 
       - PATCH_VERSION
       - JUPYTER_PLATFORM_DIRS=1
     volumes:

docs/mkdocs.yaml

@@ -51,17 +51,14 @@ nav:
 #     UPSTREAM_REPO=https://github.com/datajoint/element-{ELEMENT}.git \
 #     HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build
 #     ```
-# 02. Site analytics depend on a local environment variable GOOGLE_ANALYTICS_KEY
-#     You can find this in LastPass or declare with any string to suprress errors
-# 03. The API section will pull docstrings.
+# 02. The API section will pull docstrings.
 #     A. Follow google styleguide e.g., 
 #        https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html
 #        With typing suggestions: https://docs.python.org/3/library/typing.html
 #     B. To pull a specific workflow fork, change ./docs/src/api/make_pages.py#L19
-# 04. To see your fork of the workflow-{element} in this render, change the
+# 03. To see your fork of the workflow-{element} in this render, change the
 #     URL in ./docs/src/api/make_pages.py#L19 to your fork.
-# 05. For redirecting options For redirect options, see 'redirects' below.
-# 06. To deploy this site on your fork, 
+# 04. To deploy this site on your fork, 
 #     A. declare a branch called gh-pages
 #     B. go to the your fork > settings > pages 
 #     C. direct pages to render from the gh-pages branch at root
@@ -97,9 +94,6 @@ theme:
 plugins:
   - markdownextradata: {}
   - search
-  # - redirects: # OPTIONAL REDIRECTS
-  #     redirect_maps:
-  #       "index.md": "getting_started.md"
   - mkdocstrings:
       default_handler: python
       handlers:
@@ -119,7 +113,7 @@ plugins:
   - mkdocs-jupyter:
       ignore_h1_titles: True
       ignore: ["*make_pages.py"]
-
+  - section-index
 markdown_extensions:
   - attr_list
   - toc:
@@ -140,13 +134,12 @@ markdown_extensions:
       linenums: true
   - pymdownx.inlinehilite
   - pymdownx.snippets
-  
+  - pymdownx.magiclink # Displays bare URLs as links
+  - pymdownx.tasklist: # Renders check boxes in tasks lists
+      custom_checkbox: true
 extra:
   PATCH_VERSION: !ENV PATCH_VERSION
   generator: false # Disable watermark
-  analytics:
-    provider: google
-    property: !ENV GOOGLE_ANALYTICS_KEY
   version:
     provider: mike
   social:

docs/src/citation.md

@@ -1,12 +1,19 @@
 # Citation
 
-If your work uses this Element, please cite the following manuscript and Research
-Resource Identifier (RRID).
+If your work uses the following resources, please cite the respective manuscript and/or Research Resource Identifier (RRID):
 
-+ Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D,
-  Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for
-  Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358
++ DataJoint Element DeepLabCut - Version {{ PATCH_VERSION }}
+     + Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D,
+     Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for
+     Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358
 
-+ DataJoint Elements ([RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894)) -
-  Element DeepLabCut (version {{ PATCH_VERSION }})
-  
+     + [RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894)
+ 
++ DeepLabCut 
+     + [Manuscripts](https://github.com/DeepLabCut/DeepLabCut#references)
+
++ NWB
+  + [Manuscript](https://www.nwb.org/publications/)
+
++ DANDI
+  + [Citation options](https://www.dandiarchive.org/handbook/10_using_dandi/#citing-dandi)

element_deeplabcut/version.py

@@ -1,4 +1,4 @@
 """
 Package metadata
 """
-__version__ = "0.2.5"
+__version__ = "0.2.6"