From 4b00537735085a5583f50f11ca5561ec0f0d1265 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Tue, 19 Mar 2024 16:23:33 -0700 Subject: [PATCH 01/10] First draft --- docs/source/conf_extlinks.py | 2 ++ docs/source/extensions.rst | 48 ++++++++++++++++++++++++++++++++++++ docs/source/index.rst | 1 + 3 files changed, 51 insertions(+) create mode 100644 docs/source/extensions.rst diff --git a/docs/source/conf_extlinks.py b/docs/source/conf_extlinks.py index 279d953..7ebf702 100644 --- a/docs/source/conf_extlinks.py +++ b/docs/source/conf_extlinks.py @@ -55,6 +55,8 @@ 'ibl-website': ('https://www.internationalbrainlab.com/%s', '%s'), 'mindscope-program': ('https://alleninstitute.org/what-we-do/brain-science/research/mindscope-program/%s', '%s'), 'jupyter-book': ('https://jupyterbook.org/en/stable/%s', '%s'), + 'nep-review': ('https://github.com/nwb-extensions/nep-review/%s', '%s'), + 'nwb-tab': ('https://docs.google.com/document/d/e/2PACX-1vSynhRf8Zykfqnov81Ddi1tSo12RV4zYv3RRCEfLR2OqhpER_7PTmaoTNrRh5Coh8xg2LvwuriiHlsJ/pub/%s', '%s'), } # Use this for mapping for links to commonly used documentation diff --git a/docs/source/extensions.rst b/docs/source/extensions.rst new file mode 100644 index 0000000..77925a2 --- /dev/null +++ b/docs/source/extensions.rst @@ -0,0 +1,48 @@ +.. _extensions-catalog: + +******************************** +Extensions Catalog and Proposals +******************************** + +NWB Extensions (NDX) Catalog +============================ + +The :ndx-catalog:`NDX Catalog website <>` contains published +extensions created by the community to add support for a wide variety of data types. +Before creating your own extension, we recommend that you explore the Catalog to +make sure that someone has not already created an extension that suits your needs +or that you could build off of. + +Policies on Community-driven Development and Integration of New Neuroscience Technologies with NWB + +- `Sharing Guidelines: requirements and strategy for sharing format extensions for NWB `_ +- `Sharing Strategies: standard practices and strategies for sharing format extensions for NWB `_ +- `Versioning Guidelines: requirements and strategy for versioning namespaces for the NWB core schema and extensions `_ + +NWB Enhancement Proposals (NEPs) +================================ + +The NWB data standard is not static but evolves to adapt to changing needs from the neuroscience community, +clarify ambiguities, and fix bugs, among others. Users can propose smaller changes, such as improvements to +documentation or addition of a new optional field to an existing data type, on the +:nwb-schema-src:`NWB Schema GitHub repository <>`. Users can propose larger changes, such as addition of +several new data types to support a new data modality, or a major restructuring of existing data types, +through NWB Enhancement Proposals (NEPs). + +NEPs are often collaborative and led by members of the community to address a significant need by the +community. Here is a list of NEPs that have been started: + ++--------+----------------------------------------------------------+-----------------+----------------------------------------------------------------------------------------------------------------+ +| NEP | Title | Lead | URLs | ++========+==========================================================+=================+================================================================================================================+ +| NEP001 | Events and TTL Data | Ryan Ly | [google doc](https://docs.google.com/document/d/1qcsjyFVX9oI_746RdMoDdmQPu940s0YtDjb1en1Xtdw/edit?usp=sharing) | +| NEP002 | Probe devices and channel mapping in extracellular ephys | Alessio Buccino | [google doc](https://docs.google.com/document/d/1q-haFEEHEgZpRoCzzQsuSWCKN4QfMsTzLnlptLaf-yw/edit?usp=sharing) | ++--------+----------------------------------------------------------+-----------------+----------------------------------------------------------------------------------------------------------------+ + +Review of NEPs for acceptance to the NWB core data standard is led by the +:nwb-tab:`NWB Technical Advisory Board (TAB) <>` +and involves several phases. To submit a NEP for review and explore previous NEP reviews, see the +:nep-review:`NEP Review GitHub repo <>`. For more information on the NEP process, see the following links: + +- `Proposal Review Process: process by which extensions to the NWB core standard are proposed, evaluated, reviewed, and accepted `_ +- `Working Groups for Evaluating NEPs Policy: process for evaluation and review of NWB Extension Proposals (NEPs) by a review working group (RWG) to provide guidance and a formal framework for RWG members. `_ diff --git a/docs/source/index.rst b/docs/source/index.rst index cf1eaae..b8d2b73 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -34,6 +34,7 @@ for each of those tasks and point you to the best tools to use for your preferre :maxdepth: 1 community_gallery/community_gallery.rst + extensions faq .. toctree:: From f7cef1c86ae2501733f315aed1528f45d89dd21c Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Tue, 19 Mar 2024 16:33:15 -0700 Subject: [PATCH 02/10] Update docs/source/extensions.rst --- docs/source/extensions.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/source/extensions.rst b/docs/source/extensions.rst index 77925a2..d5c9727 100644 --- a/docs/source/extensions.rst +++ b/docs/source/extensions.rst @@ -39,6 +39,9 @@ community. Here is a list of NEPs that have been started: | NEP002 | Probe devices and channel mapping in extracellular ephys | Alessio Buccino | [google doc](https://docs.google.com/document/d/1q-haFEEHEgZpRoCzzQsuSWCKN4QfMsTzLnlptLaf-yw/edit?usp=sharing) | +--------+----------------------------------------------------------+-----------------+----------------------------------------------------------------------------------------------------------------+ +To add a new NEP to this list, please file an issue on the :nwb-overview-src:`NWB Overview GitHub repo <>` +or create a pull request that modifies the table. + Review of NEPs for acceptance to the NWB core data standard is led by the :nwb-tab:`NWB Technical Advisory Board (TAB) <>` and involves several phases. To submit a NEP for review and explore previous NEP reviews, see the From 3f66ccc7a798959989c78a3f93972ad43ad59ad6 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Tue, 19 Mar 2024 16:33:29 -0700 Subject: [PATCH 03/10] Update conf_extlinks.py --- docs/source/conf_extlinks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/conf_extlinks.py b/docs/source/conf_extlinks.py index 7ebf702..37549ea 100644 --- a/docs/source/conf_extlinks.py +++ b/docs/source/conf_extlinks.py @@ -56,7 +56,7 @@ 'mindscope-program': ('https://alleninstitute.org/what-we-do/brain-science/research/mindscope-program/%s', '%s'), 'jupyter-book': ('https://jupyterbook.org/en/stable/%s', '%s'), 'nep-review': ('https://github.com/nwb-extensions/nep-review/%s', '%s'), - 'nwb-tab': ('https://docs.google.com/document/d/e/2PACX-1vSynhRf8Zykfqnov81Ddi1tSo12RV4zYv3RRCEfLR2OqhpER_7PTmaoTNrRh5Coh8xg2LvwuriiHlsJ/pub/%s', '%s'), + 'nwb-tab': ('https://docs.google.com/document/d/e/2PACX-1vSynhRf8Zykfqnov81Ddi1tSo12RV4zYv3RRCEfLR2OqhpER_7PTmaoTNrRh5Coh8xg2LvwuriiHlsJ/pub%s', '%s'), } # Use this for mapping for links to commonly used documentation From 5d285ebf41ad8a96e86d0c8269cde2fd70a09db2 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Tue, 19 Mar 2024 16:36:40 -0700 Subject: [PATCH 04/10] Fix table? --- docs/source/extensions.rst | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/docs/source/extensions.rst b/docs/source/extensions.rst index d5c9727..11f33eb 100644 --- a/docs/source/extensions.rst +++ b/docs/source/extensions.rst @@ -32,12 +32,22 @@ through NWB Enhancement Proposals (NEPs). NEPs are often collaborative and led by members of the community to address a significant need by the community. Here is a list of NEPs that have been started: -+--------+----------------------------------------------------------+-----------------+----------------------------------------------------------------------------------------------------------------+ -| NEP | Title | Lead | URLs | -+========+==========================================================+=================+================================================================================================================+ -| NEP001 | Events and TTL Data | Ryan Ly | [google doc](https://docs.google.com/document/d/1qcsjyFVX9oI_746RdMoDdmQPu940s0YtDjb1en1Xtdw/edit?usp=sharing) | -| NEP002 | Probe devices and channel mapping in extracellular ephys | Alessio Buccino | [google doc](https://docs.google.com/document/d/1q-haFEEHEgZpRoCzzQsuSWCKN4QfMsTzLnlptLaf-yw/edit?usp=sharing) | -+--------+----------------------------------------------------------+-----------------+----------------------------------------------------------------------------------------------------------------+ +.. list-table:: NEPs + :widths: 15 45 25 15 + :header-rows: 1 + + * - NEP + - Title + - Lead + - URLs + * - NEP001 + - Events and TTL Data + - Ryan Ly + - `Google Doc `_ + * - NEP002 + - Probe devices and channel mapping in extracellular ephys + - Alessio Buccino + - `Google Doc `_ To add a new NEP to this list, please file an issue on the :nwb-overview-src:`NWB Overview GitHub repo <>` or create a pull request that modifies the table. From 07c1ff1191f824a374abbdca8eac810215c30696 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Wed, 20 Mar 2024 10:45:51 -0700 Subject: [PATCH 05/10] Add subsubheader --- docs/source/extensions.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/extensions.rst b/docs/source/extensions.rst index 11f33eb..6e8ef3a 100644 --- a/docs/source/extensions.rst +++ b/docs/source/extensions.rst @@ -14,6 +14,7 @@ make sure that someone has not already created an extension that suits your need or that you could build off of. Policies on Community-driven Development and Integration of New Neuroscience Technologies with NWB +-------------------------------------------------------------------------------------------------- - `Sharing Guidelines: requirements and strategy for sharing format extensions for NWB `_ - `Sharing Strategies: standard practices and strategies for sharing format extensions for NWB `_ From e50ca9cb133bb932835f9dced588929db2767f1c Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 26 Aug 2024 23:16:26 -0700 Subject: [PATCH 06/10] Update conf_extlinks.py --- docs/source/conf_extlinks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/conf_extlinks.py b/docs/source/conf_extlinks.py index 5e17271..a304517 100644 --- a/docs/source/conf_extlinks.py +++ b/docs/source/conf_extlinks.py @@ -54,7 +54,7 @@ 'ibl-website': ('https://www.internationalbrainlab.com/%s', '%s'), 'mindscope-program': ('https://alleninstitute.org/what-we-do/brain-science/research/mindscope-program/%s', '%s'), 'jupyter-book': ('https://jupyterbook.org/en/stable/%s', '%s'), - 'nep-review': ('https://github.com/nwb-extensions/nep-review/%s', '%s'), + 'nwbep-review': ('https://github.com/nwb-extensions/nwbep-review/%s', '%s'), 'nwb-tab': ('https://docs.google.com/document/d/e/2PACX-1vSynhRf8Zykfqnov81Ddi1tSo12RV4zYv3RRCEfLR2OqhpER_7PTmaoTNrRh5Coh8xg2LvwuriiHlsJ/pub%s', '%s'), 'lindi-src': ('https://github.com/NeurodataWithoutBorders/lindi/%s', '%s'), } From 68aeafed3a900c3649804d4a7a2a1f1f0290f1f3 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 26 Aug 2024 23:17:41 -0700 Subject: [PATCH 07/10] Rename NEP to NWBEP --- docs/source/extensions.rst | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/docs/source/extensions.rst b/docs/source/extensions.rst index 6e8ef3a..74a1097 100644 --- a/docs/source/extensions.rst +++ b/docs/source/extensions.rst @@ -20,7 +20,7 @@ Policies on Community-driven Development and Integration of New Neuroscience Tec - `Sharing Strategies: standard practices and strategies for sharing format extensions for NWB `_ - `Versioning Guidelines: requirements and strategy for versioning namespaces for the NWB core schema and extensions `_ -NWB Enhancement Proposals (NEPs) +NWB Enhancement Proposals (NWBEPs) ================================ The NWB data standard is not static but evolves to adapt to changing needs from the neuroscience community, @@ -28,35 +28,35 @@ clarify ambiguities, and fix bugs, among others. Users can propose smaller chang documentation or addition of a new optional field to an existing data type, on the :nwb-schema-src:`NWB Schema GitHub repository <>`. Users can propose larger changes, such as addition of several new data types to support a new data modality, or a major restructuring of existing data types, -through NWB Enhancement Proposals (NEPs). +through NWB Enhancement Proposals (NWBEPs). -NEPs are often collaborative and led by members of the community to address a significant need by the -community. Here is a list of NEPs that have been started: +NWBEPs are often collaborative and led by members of the community to address a significant need by the +community. Here is a list of NWBEPs that have been started: -.. list-table:: NEPs +.. list-table:: NWBEPs :widths: 15 45 25 15 :header-rows: 1 - * - NEP + * - NBWEP - Title - Lead - URLs - * - NEP001 + * - NWBEP001 - Events and TTL Data - Ryan Ly - `Google Doc `_ - * - NEP002 + * - NWBEP002 - Probe devices and channel mapping in extracellular ephys - Alessio Buccino - `Google Doc `_ -To add a new NEP to this list, please file an issue on the :nwb-overview-src:`NWB Overview GitHub repo <>` +To add a new NWBEP to this list, please file an issue on the :nwb-overview-src:`NWB Overview GitHub repo <>` or create a pull request that modifies the table. -Review of NEPs for acceptance to the NWB core data standard is led by the +Review of NWBEPs for acceptance to the NWB core data standard is led by the :nwb-tab:`NWB Technical Advisory Board (TAB) <>` -and involves several phases. To submit a NEP for review and explore previous NEP reviews, see the -:nep-review:`NEP Review GitHub repo <>`. For more information on the NEP process, see the following links: +and involves several phases. To submit a NWBEP for review and explore previous NWBEP reviews, see the +:nwbep-review:`NWBEP Review GitHub repo <>`. For more information on the NWBEP process, see the following links: - `Proposal Review Process: process by which extensions to the NWB core standard are proposed, evaluated, reviewed, and accepted `_ -- `Working Groups for Evaluating NEPs Policy: process for evaluation and review of NWB Extension Proposals (NEPs) by a review working group (RWG) to provide guidance and a formal framework for RWG members. `_ +- `Working Groups for Evaluating NWBEPs Policy: process for evaluation and review of NWB Extension Proposals (NWBEPs) by a review working group (RWG) to provide guidance and a formal framework for RWG members. `_ From a3cbe4a22ed0ef62b8dac8d8aabcedfff14992c1 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 26 Aug 2024 23:18:52 -0700 Subject: [PATCH 08/10] Add NWBEP003 --- docs/source/extensions.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/source/extensions.rst b/docs/source/extensions.rst index 74a1097..176528b 100644 --- a/docs/source/extensions.rst +++ b/docs/source/extensions.rst @@ -49,6 +49,11 @@ community. Here is a list of NWBEPs that have been started: - Probe devices and channel mapping in extracellular ephys - Alessio Buccino - `Google Doc `_ + * - NWBEP003 + - Multichannel volumetric imaging + - Daniel Sprague + - `Google Doc `_ + To add a new NWBEP to this list, please file an issue on the :nwb-overview-src:`NWB Overview GitHub repo <>` or create a pull request that modifies the table. From d506376f77c716c902f3995612e2c45d04933f79 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 26 Aug 2024 23:20:22 -0700 Subject: [PATCH 09/10] Add evaluation form --- docs/source/extensions.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/extensions.rst b/docs/source/extensions.rst index 176528b..feeccdd 100644 --- a/docs/source/extensions.rst +++ b/docs/source/extensions.rst @@ -65,3 +65,4 @@ and involves several phases. To submit a NWBEP for review and explore previous N - `Proposal Review Process: process by which extensions to the NWB core standard are proposed, evaluated, reviewed, and accepted `_ - `Working Groups for Evaluating NWBEPs Policy: process for evaluation and review of NWB Extension Proposals (NWBEPs) by a review working group (RWG) to provide guidance and a formal framework for RWG members. `_ +- `NWBEP Evaluation Form `_ From cf0040c865998a14c7682a60a1054b6486608b2f Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Tue, 27 Aug 2024 00:05:40 -0700 Subject: [PATCH 10/10] Update docs/source/extensions.rst --- docs/source/extensions.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/extensions.rst b/docs/source/extensions.rst index feeccdd..b377bfa 100644 --- a/docs/source/extensions.rst +++ b/docs/source/extensions.rst @@ -65,4 +65,4 @@ and involves several phases. To submit a NWBEP for review and explore previous N - `Proposal Review Process: process by which extensions to the NWB core standard are proposed, evaluated, reviewed, and accepted `_ - `Working Groups for Evaluating NWBEPs Policy: process for evaluation and review of NWB Extension Proposals (NWBEPs) by a review working group (RWG) to provide guidance and a formal framework for RWG members. `_ -- `NWBEP Evaluation Form `_ +- `NWBEP Evaluation Form `_