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Fix matnwb doc links
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rly authored Dec 23, 2024
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2 changes: 1 addition & 1 deletion docs/source/conf_extlinks.py
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Expand Up @@ -14,7 +14,7 @@
'hdmf-src': ('https://github.com/hdmf-dev/hdmf/%s', '%s'),
'hdmf-specification-language': ('https://hdmf-schema-language.readthedocs.io/en/latest/%s', '%s'),
'matnwb-src': ('https://github.com/NeurodataWithoutBorders/matnwb/%s', '%s'),
'matnwb-docs': ('https://neurodatawithoutborders.github.io/matnwb/%s', '%s'),
'matnwb-docs': ('https://matnwb.readthedocs.io/en/latest/%s', '%s'),
'neuroconv-docs': ('https://neuroconv.readthedocs.io/en/main/%s', '%s'),
'neuroconv-src': ('https://github.com/catalystneuro/neuroconv/%s', '%s'),
'nwbinspector-docs': ('https://nwbinspector.readthedocs.io/en/dev/%s', '%s'),
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8 changes: 4 additions & 4 deletions docs/source/conversion_tutorial/03_nwb_apis.rst
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Expand Up @@ -29,24 +29,24 @@ modality:

`23 min video <https://www.youtube.com/watch?v=rlywed3ar-s&ab_channel=NeurodataWithoutBorders>`__

- `tutorial <https://neurodatawithoutborders.github.io/matnwb/tutorials/html/ecephys.html>`__
- `tutorial <https://matnwb.readthedocs.io/en/latest/pages/tutorials/ecephys.html>`__

`46 min video <https://www.youtube.com/watch?v=W8t4_quIl1k&ab_channel=NeurodataWithoutBorders>`__
* - Writing intracellular electrophysiology
- `tutorial <https://pynwb.readthedocs.io/en/stable/tutorials/domain/plot_icephys.html#sphx-glr-tutorials-domain-plot-icephys-py>`__
- `tutorial <https://neurodatawithoutborders.github.io/matnwb/tutorials/html/icephys.html>`__
- `tutorial <https://matnwb.readthedocs.io/en/latest/pages/tutorials/icephys.html>`__
* - Writing calcium imaging
- `tutorial <https://pynwb.readthedocs.io/en/stable/tutorials/domain/ophys.html#sphx-glr-tutorials-domain-ophys-py>`__

`31 min video <https://www.youtube.com/watch?v=HPjSxBjdFpM&ab_channel=NeurodataWithoutBorders>`__
- `tutorial <https://neurodatawithoutborders.github.io/matnwb/tutorials/html/ophys.html>`__
- `tutorial <https://matnwb.readthedocs.io/en/latest/pages/tutorials/ophys.html>`__

`39 min video <https://www.youtube.com/watch?v=OBidHdocnTc&ab_channel=NeurodataWithoutBorders>`__
* - Advanced I/O
- `tutorials <https://pynwb.readthedocs.io/en/stable/tutorials/index.html#advanced-i-o>`__

`26 min video <https://www.youtube.com/watch?v=wduZHfNOaNg&ab_channel=NeurodataWithoutBorders>`__
- `tutorial <https://neurodatawithoutborders.github.io/matnwb/tutorials/html/dataPipe.html>`__
- `tutorial <https://matnwb.readthedocs.io/en/latest/pages/tutorials/dataPipe.html>`__

`16 min video <https://www.youtube.com/watch?v=PIE_F4iVv98&ab_channel=NeurodataWithoutBorders>`__

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2 changes: 1 addition & 1 deletion docs/source/core_tools/core_tools_home.rst
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Expand Up @@ -31,7 +31,7 @@ The NWB reference APIs provide full support for reading and writing all componen
:class: align-left, no-scaled-link
:width: 100

:matnwb-docs:`MatNWB <>` is a MATLAB library for reading and writing NWB files. :bdg-link-primary:`Docs <https://neurodatawithoutborders.github.io/matnwb/>` :bdg-link-primary:`Tutorials <https://neurodatawithoutborders.github.io/matnwb/#tutorials>` :bdg-link-primary:`Source <https://github.com/NeurodataWithoutBorders/matnwb/>`
:matnwb-docs:`MatNWB <>` is a MATLAB library for reading and writing NWB files. :bdg-link-primary:`Docs <https://matnwb.readthedocs.io/>` :bdg-link-primary:`Tutorials <https://matnwb.readthedocs.io/en/latest/pages/tutorials>` :bdg-link-primary:`Source <https://github.com/NeurodataWithoutBorders/matnwb/>`

.. raw:: html

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2 changes: 1 addition & 1 deletion docs/source/file_read/file_read.rst
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Expand Up @@ -3,7 +3,7 @@
Reading NWB Files
==================

This section provides an introduction on how to read NWB files in Python using PyNWB and Matlab using MatNWB. If you are interested in converting your data to NWB, then please see the :neuroconv-docs:`NeuroConv User Guide <user_guide>` as well as for more in-depth tutorials visit the :pynwb-docs:`PyNWB <tutorials>` and :matnwb-docs:`MatNWB <#tutorials>` tutorials and documentation.
This section provides an introduction on how to read NWB files in Python using PyNWB and Matlab using MatNWB. If you are interested in converting your data to NWB, then please see the :neuroconv-docs:`NeuroConv User Guide <user_guide>` as well as for more in-depth tutorials visit the :pynwb-docs:`PyNWB <tutorials>` and :matnwb-docs:`MatNWB <pages/tutorials>` tutorials and documentation.

Reading With PyNWB
~~~~~~~~~~~~~~~~~~
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2 changes: 1 addition & 1 deletion docs/source/file_read/matnwb/dynamictable.rst
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Expand Up @@ -34,4 +34,4 @@ Finally, if you prefer to select using your custom ``id`` column, you can specif
tableData = dynamicTable.getRow(<idValue>, 'useId', true);
For more information regarding Dynamic Tables in MatNWB as well as information regarding writing data to them, please see the `MatNWB DynamicTables Tutorial <https://neurodatawithoutborders.github.io/matnwb/tutorials/html/dynamic_tables.html>`_.
For more information regarding Dynamic Tables in MatNWB as well as information regarding writing data to them, please see the `MatNWB DynamicTables Tutorial <https://matnwb.readthedocs.io/en/latest/pages/tutorials/dynamic_tables.html>`_.
2 changes: 1 addition & 1 deletion docs/source/file_read/matnwb/untyped.rst
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Expand Up @@ -35,7 +35,7 @@ DataStubs and DataPipes

.. image:: /img/matnwb_datastub.png

**DataPipes** are similar to DataStubs in that they allow you to load data from disk; however, they also provide a wide array of features that allow the user to write data to disk, either by streaming parts of data in at a time or by compressing the data before writing. The DataPipe is an advanced type and users looking to leverage DataPipe's capabilities to stream/iteratively write or compress data should read the `Advanced Data Write Tutorial <https://neurodatawithoutborders.github.io/matnwb/tutorials/html/dataPipe.html>`_.
**DataPipes** are similar to DataStubs in that they allow you to load data from disk; however, they also provide a wide array of features that allow the user to write data to disk, either by streaming parts of data in at a time or by compressing the data before writing. The DataPipe is an advanced type and users looking to leverage DataPipe's capabilities to stream/iteratively write or compress data should read the `Advanced Data Write Tutorial <https://matnwb.readthedocs.io/en/latest/pages/tutorials/dataPipe.html>`_.

.. _matnwb-read-untyped-links-views:

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2 changes: 1 addition & 1 deletion docs/source/intro_to_nwb/4_apis.rst
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Expand Up @@ -45,7 +45,7 @@ researchers and developers interested in using NWB and in learning more about th

A growing collection of :ref:`analysistools-home` (gray) developed by the neurophysiology community along with a
broad range of :ref:`core tools <core-tools-home>` (red) help users with conversion, extension, validation and use of
NWB data files. Commonly, these tools build on the :pynwb-docs:`PyNWB (Python) <>` and :matnwb-docs:`MatNWB (Matlab) <>`
NWB data files. Commonly, these tools build on the :pynwb-docs:`PyNWB (Python) <>` and :matnwb-docs:`MatNWB (MATLAB) <>`
reference APIs (lilac) to read and write NWB files. Each of the APIs and tools provides their own in-depth
tutorials and documentation to help guide users in adopting and using the software.

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