diff --git a/.github/workflows/test_external_links.yml b/.github/workflows/test_external_links.yml index f81811d..09eae99 100644 --- a/.github/workflows/test_external_links.yml +++ b/.github/workflows/test_external_links.yml @@ -1,5 +1,10 @@ name: Testing External Links -on: pull_request +on: + schedule: + - cron: '0 5 * * 0' # every Sunday at 05:00 UTC (midnight EST) + pull_request: + workflow_dispatch: + jobs: build-and-test: name: Testing External Links @@ -7,12 +12,12 @@ jobs: strategy: fail-fast: false steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - run: git fetch --prune --unshallow --tags - name: Setup Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: - python-version: 3.9 + python-version: 3.11 - name: Install sphinx Dependencies run: pip install -r requirements.txt - name: Test External Links diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 86fbfe1..6047ad6 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,9 +6,9 @@ version: 2 build: - os: ubuntu-20.04 + os: ubuntu-22.04 tools: - python: '3.8' + python: '3.11' # Build documentation in the docs/ directory with Sphinx sphinx: @@ -25,8 +25,3 @@ formats: all python: install: - requirements: requirements.txt - -# Optionally include all submodules -submodules: - include: all - recursive: true diff --git a/docs/source/community_gallery/community_gallery.rst b/docs/source/community_gallery/community_gallery.rst index 7ce7f35..c87f920 100644 --- a/docs/source/community_gallery/community_gallery.rst +++ b/docs/source/community_gallery/community_gallery.rst @@ -14,7 +14,7 @@ Data Conversion :class: align-left, no-scaled-link :width: 100 -:neuroconv-docs:`NeuroConv Catalog ` is a collection of real-world examples of labs using :neuroconv-docs:`NeuroConv <>` to convert their data to NWB files. Each project listed contains a description and a link to an open GitHub repository. Many of the projects listed use advanced customization features beyond what is demonstrated in the core :neuroconv-docs:`NeuroConv conversion gallery `. :bdg-link-primary:`NeuroConv Catalog ` +:neuroconv-docs:`NeuroConv Catalog ` is a collection of real-world examples of labs using :neuroconv-docs:`NeuroConv <>` to convert their data to NWB files. Each project listed contains a description and a link to an open GitHub repository. Many of the projects listed use advanced customization features beyond what is demonstrated in the core :neuroconv-docs:`NeuroConv conversion gallery `. :bdg-link-primary:`NeuroConv Catalog ` .. image:: figures/bristol_neuroscience_data_guide.png :class: align-left, no-scaled-link @@ -41,7 +41,7 @@ Data Analysis and Reuse .. raw:: html
- + In addition, the neuroscience community is creating examples demonstrating the reuse of NWB data published on DANDI. For example: * The `INCF working group on NWB `_ has created a `library of MATLAB examples `_ using DANDI datasets authored as MATLAB live scripts. :bdg-link-primary:`Source ` diff --git a/docs/source/conf_extlinks.py b/docs/source/conf_extlinks.py index 279d953..5ed80bf 100644 --- a/docs/source/conf_extlinks.py +++ b/docs/source/conf_extlinks.py @@ -48,7 +48,7 @@ 'nwb-helpdesk': ('https://github.com/dandi/helpdesk/discussions/%s', '%s'), 'nwb-mailing-list': ('https://mailchi.mp/fe2a9bc55a1a/nwb-signup/%s', '%s'), 'datajoint': ('https://www.datajoint.com/%s', '%s'), - 'datajoint-elements': ('https://www.datajoint.com/elements/%s', '%s'), + 'datajoint-elements': ('https://datajoint.com/docs/elements/%s', '%s'), 'openscope-databook': ('https://alleninstitute.github.io/openscope_databook/%s', '%s'), 'openscope-project': ('https://alleninstitute.org/what-we-do/brain-science/research/mindscope-program/openscope/%s', '%s'), diff --git a/docs/source/conversion_tutorial/02_format_conversions.md b/docs/source/conversion_tutorial/02_format_conversions.md index 96d61d1..1105f44 100644 --- a/docs/source/conversion_tutorial/02_format_conversions.md +++ b/docs/source/conversion_tutorial/02_format_conversions.md @@ -2,11 +2,11 @@ [NeuroConv](https://neuroconv.readthedocs.io/) is a library for automatic conversions from proprietary formats to NWB. A gallery of all supported formats can be found -[here](https://neuroconv.readthedocs.io/en/main/conversion_examples_gallery/conversion_example_gallery.html). +[here](https://neuroconv.readthedocs.io/en/main/conversion_examples_gallery/index.html). If NeuroConv supports your source data format, this is the recommended approach, because it is easiest to implement and automatically helps you adhere to best practices. For advanced usage of NeuroConv, including creating conversions of ensembles of multiple data streams, see the -[NeuroConv User Guide](https://neuroconv.readthedocs.io/en/main/user_guide/user_guide.html). +[NeuroConv User Guide](https://neuroconv.readthedocs.io/en/main/user_guide/index.html). Although NeuroConv supports many common formats, it may not support every type of source data you need. If your source format is likely to be a common need in the community, for example the output of an acquisition diff --git a/docs/source/tools/datajoint/datajoint.rst b/docs/source/tools/datajoint/datajoint.rst index 01769a3..8402a99 100644 --- a/docs/source/tools/datajoint/datajoint.rst +++ b/docs/source/tools/datajoint/datajoint.rst @@ -5,6 +5,6 @@ DataJoint .. short_description_start -:ref:`analysistools-datajoint` is an open-source project for defining and operating computational data pipelines—sequences of steps for data acquisition, processing, and transformation. Some `DataJoint Elements `_ support automatic conversion to NWB :bdg-link-primary:`Export element_array_ephys to NWB ` +:ref:`analysistools-datajoint` is an open-source project for defining and operating computational data pipelines—sequences of steps for data acquisition, processing, and transformation. Some :datajoint-elements:`DataJoint Elements <>` support automatic conversion to NWB :bdg-link-primary:`Export element_array_ephys to NWB ` .. short_description_end \ No newline at end of file diff --git a/docs/source/tools/extract/extract.rst b/docs/source/tools/extract/extract.rst index 2230db5..873ff62 100644 --- a/docs/source/tools/extract/extract.rst +++ b/docs/source/tools/extract/extract.rst @@ -10,7 +10,7 @@ which *extracts* the activities of cells as time series from both one-photon and EXTRACT makes minimal assumptions about the data, which is the main reason behind its high robustness and superior performance. :bdg-link-primary:`Source ` -:bdg-link-primary:`NWB tutorials ` +:bdg-link-primary:`NWB demos ` :bdg-link-primary:`Publication ` .. image:: https://img.shields.io/github/stars/schnitzer-lab/EXTRACT-public?style=social diff --git a/docs/source/tools/pynapple/pynapple.rst b/docs/source/tools/pynapple/pynapple.rst index d694ca4..2ae19d3 100644 --- a/docs/source/tools/pynapple/pynapple.rst +++ b/docs/source/tools/pynapple/pynapple.rst @@ -6,7 +6,7 @@ pynapple .. short_description_start :ref:`analysistools-pynapple` is a unified toolbox for integrated analysis of multiple data sources. Designed to be "plug & play", users define and import their own time-relevant variables. Supported data sources include, but are not limited to, electrophysiology, calcium imaging, and motion capture data. Pynapple contains integrated functions for common neuroscience analyses, including cross-correlograms, tuning curves, decoding and perievent time histogram. -:bdg-link-primary:`Docs ` :bdg-link-primary:`DANDI Demo ` :bdg-link-primary:`Source ` :bdg-link-primary:`Twitter ` +:bdg-link-primary:`Docs ` :bdg-link-primary:`DANDI Demo ` :bdg-link-primary:`Source ` :bdg-link-primary:`Twitter ` .. image:: https://img.shields.io/github/stars/pynapple-org/pynapple?style=social :alt: GitHub Repo stars for pynapple