From c8c72f0c4b40804728484a13ba4dbe8c0721ff31 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Mon, 22 May 2023 17:29:17 -0500 Subject: [PATCH 1/8] Remove Google Analytics key --- .github/workflows/u24_element_release_call.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/u24_element_release_call.yaml b/.github/workflows/u24_element_release_call.yaml index fa8deba..4324cca 100644 --- a/.github/workflows/u24_element_release_call.yaml +++ b/.github/workflows/u24_element_release_call.yaml @@ -17,7 +17,6 @@ jobs: secrets: TWINE_USERNAME: ${{secrets.TWINE_TEST_USERNAME}} TWINE_PASSWORD: ${{secrets.TWINE_TEST_PASSWORD}} - GOOGLE_ANALYTICS_KEY: ${{secrets.GOOGLE_ANALYTICS_KEY}} call_u24_elements_release_alpine: if: >- github.event.workflow_run.conclusion == 'success' && github.repository_owner == 'datajoint' && !contains(github.event.workflow_run.head_branch, 'test') @@ -27,4 +26,3 @@ jobs: secrets: TWINE_USERNAME: ${{secrets.TWINE_USERNAME}} TWINE_PASSWORD: ${{secrets.TWINE_PASSWORD}} - GOOGLE_ANALYTICS_KEY: ${{secrets.GOOGLE_ANALYTICS_KEY}} From e6037e0ffb7991b34995a4ea011080138693c1db Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Mon, 22 May 2023 17:29:33 -0500 Subject: [PATCH 2/8] Remove Google Analytics key --- docs/docker-compose.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/docker-compose.yaml b/docs/docker-compose.yaml index 7b87029..1ca7eae 100644 --- a/docs/docker-compose.yaml +++ b/docs/docker-compose.yaml @@ -15,7 +15,6 @@ services: - PACKAGE - UPSTREAM_REPO - MODE - - GOOGLE_ANALYTICS_KEY - PATCH_VERSION - JUPYTER_PLATFORM_DIRS=1 volumes: From bde3edb829b2700b95bd06ea08991ff893b7ac68 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Mon, 22 May 2023 17:30:32 -0500 Subject: [PATCH 3/8] Update docs --- docs/.docker/pip_requirements.txt | 3 ++- docs/mkdocs.yaml | 21 +++++++-------------- 2 files changed, 9 insertions(+), 15 deletions(-) diff --git a/docs/.docker/pip_requirements.txt b/docs/.docker/pip_requirements.txt index 5b7b2f4..ae44fb5 100644 --- a/docs/.docker/pip_requirements.txt +++ b/docs/.docker/pip_requirements.txt @@ -8,4 +8,5 @@ mkdocs-gen-files mkdocs-literate-nav mkdocs-exclude-search mkdocs-markdownextradata-plugin -mkdocs-jupyter \ No newline at end of file +mkdocs-jupyter +mkdocs-section-index \ No newline at end of file diff --git a/docs/mkdocs.yaml b/docs/mkdocs.yaml index e26968c..a1533f8 100644 --- a/docs/mkdocs.yaml +++ b/docs/mkdocs.yaml @@ -51,17 +51,14 @@ nav: # UPSTREAM_REPO=https://github.com/datajoint/element-{ELEMENT}.git \ # HOST_UID=$(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: From 70e2e3e52975748f3d4edca7265831e359266d19 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Mon, 22 May 2023 17:35:13 -0500 Subject: [PATCH 4/8] Add DeepLabCut citation --- CHANGELOG.md | 5 +++++ docs/src/citation.md | 6 +++--- element_deeplabcut/version.py | 2 +- 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7858e69..7fdad57 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,10 @@ 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 citation + ## [0.2.5] - 2023-05-11 + Fix - `.ipynb` dark mode output for all notebooks. @@ -63,6 +67,7 @@ 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 diff --git a/docs/src/citation.md b/docs/src/citation.md index 9092911..3efa7fb 100644 --- a/docs/src/citation.md +++ b/docs/src/citation.md @@ -7,6 +7,6 @@ Resource Identifier (RRID). 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 }}) - \ No newline at end of file ++ DataJoint Element DeepLabCut - [RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894) - Version {{ PATCH_VERSION }} + +If your work uses DeepLabCut, please cite the respective [manuscripts](https://github.com/DeepLabCut/DeepLabCut#references). diff --git a/element_deeplabcut/version.py b/element_deeplabcut/version.py index 46b058e..21ce3f8 100644 --- a/element_deeplabcut/version.py +++ b/element_deeplabcut/version.py @@ -1,4 +1,4 @@ """ Package metadata """ -__version__ = "0.2.5" +__version__ = "0.2.6" From 26deff520ab727208ebc7eefd45345e0545a5194 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Mon, 22 May 2023 18:31:36 -0500 Subject: [PATCH 5/8] Update citation page --- docs/src/citation.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/docs/src/citation.md b/docs/src/citation.md index 3efa7fb..9c15373 100644 --- a/docs/src/citation.md +++ b/docs/src/citation.md @@ -1,12 +1,13 @@ # 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 + + 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 - [RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894) - Version {{ PATCH_VERSION }} + + DataJoint Element DeepLabCut - [RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894) - Version {{ PATCH_VERSION }} -If your work uses DeepLabCut, please cite the respective [manuscripts](https://github.com/DeepLabCut/DeepLabCut#references). ++ DeepLabCut + + [Manuscripts](https://github.com/DeepLabCut/DeepLabCut#references) From 4293562ca4a798755d1be02465de21a3cf706e0c Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Mon, 22 May 2023 18:32:31 -0500 Subject: [PATCH 6/8] Update citation page --- docs/src/citation.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/src/citation.md b/docs/src/citation.md index 9c15373..3403379 100644 --- a/docs/src/citation.md +++ b/docs/src/citation.md @@ -2,12 +2,12 @@ If your work uses the following resources, please cite the respective manuscript and/or Research Resource Identifier (RRID): -+ DataJoint Element DeepLabCut ++ 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 Element DeepLabCut - [RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894) - Version {{ PATCH_VERSION }} + + [RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894) + DeepLabCut + [Manuscripts](https://github.com/DeepLabCut/DeepLabCut#references) From e3d2bd998b14fcc31e1ddd85d4221178ff307a15 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Mon, 22 May 2023 18:36:23 -0500 Subject: [PATCH 7/8] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7fdad57..dbf14f9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and ## [0.2.6] - 2023-05-22 + Add - DeepLabCut citation ++ Update - mkdocs.yaml ## [0.2.5] - 2023-05-11 From 26922a4c7c26aa96f1c950352b11e8c554fec4c9 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Mon, 22 May 2023 19:05:10 -0500 Subject: [PATCH 8/8] Add NWB and DANDI citations --- CHANGELOG.md | 2 +- docs/src/citation.md | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dbf14f9..b264da9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and ## [0.2.6] - 2023-05-22 -+ Add - DeepLabCut citation ++ Add - DeepLabCut, NWB, and DANDI citations + Update - mkdocs.yaml ## [0.2.5] - 2023-05-11 diff --git a/docs/src/citation.md b/docs/src/citation.md index 3403379..7b28f20 100644 --- a/docs/src/citation.md +++ b/docs/src/citation.md @@ -11,3 +11,9 @@ If your work uses the following resources, please cite the respective manuscript + 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)