From bfcf54f7670628dfcae8de5870fdd969b7e4b1ca Mon Sep 17 00:00:00 2001 From: mavaylon1 Date: Fri, 19 Jan 2024 08:39:38 -0800 Subject: [PATCH 01/15] Boundary for SpatialSeries --- core/nwb.behavior.yaml | 4 ++++ hdmf-common-schema | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/core/nwb.behavior.yaml b/core/nwb.behavior.yaml index 1a951b2f..f19a68ad 100644 --- a/core/nwb.behavior.yaml +++ b/core/nwb.behavior.yaml @@ -38,6 +38,10 @@ groups: is 'meters'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'. required: false + - name: bounds + dtype: numeric + doc: The boundary range for the data. The units are the same as te units for the data. + quantity: '?' - name: reference_frame dtype: text doc: Description defining what exactly 'straight-ahead' means. diff --git a/hdmf-common-schema b/hdmf-common-schema index 9b2580a2..62408d9c 160000 --- a/hdmf-common-schema +++ b/hdmf-common-schema @@ -1 +1 @@ -Subproject commit 9b2580a21647e06be54708fabf2d44cef73d32cb +Subproject commit 62408d9c9a61be7483e2e385850f91f9b42296c9 From f0baddfceca9549b91731cda7a262ef72518c627 Mon Sep 17 00:00:00 2001 From: mavaylon1 Date: Fri, 19 Jan 2024 08:42:08 -0800 Subject: [PATCH 02/15] float --- core/nwb.behavior.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/nwb.behavior.yaml b/core/nwb.behavior.yaml index f19a68ad..2520de0a 100644 --- a/core/nwb.behavior.yaml +++ b/core/nwb.behavior.yaml @@ -39,7 +39,7 @@ groups: To access the data in these units, multiply 'data' by 'conversion' and add 'offset'. required: false - name: bounds - dtype: numeric + dtype: float32 doc: The boundary range for the data. The units are the same as te units for the data. quantity: '?' - name: reference_frame From a2ce7ab76c795c4a74d6ab8a8e26cd5817712b93 Mon Sep 17 00:00:00 2001 From: mavaylon1 Date: Fri, 19 Jan 2024 08:43:10 -0800 Subject: [PATCH 03/15] learn to spell --- core/nwb.behavior.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/nwb.behavior.yaml b/core/nwb.behavior.yaml index 2520de0a..e5f28691 100644 --- a/core/nwb.behavior.yaml +++ b/core/nwb.behavior.yaml @@ -40,7 +40,7 @@ groups: required: false - name: bounds dtype: float32 - doc: The boundary range for the data. The units are the same as te units for the data. + doc: The boundary range for the data. The units are the same as the units for the data. quantity: '?' - name: reference_frame dtype: text From 3b2ec3aa8e3b63566d344f7200368b72b326e9dc Mon Sep 17 00:00:00 2001 From: mavaylon1 Date: Fri, 19 Jan 2024 08:45:48 -0800 Subject: [PATCH 04/15] required --- core/nwb.behavior.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/nwb.behavior.yaml b/core/nwb.behavior.yaml index e5f28691..e722971e 100644 --- a/core/nwb.behavior.yaml +++ b/core/nwb.behavior.yaml @@ -41,7 +41,7 @@ groups: - name: bounds dtype: float32 doc: The boundary range for the data. The units are the same as the units for the data. - quantity: '?' + required: false - name: reference_frame dtype: text doc: Description defining what exactly 'straight-ahead' means. From 27c7e6b4b3c27135037fae94e960ff3447557217 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Fri, 19 Jan 2024 08:48:08 -0800 Subject: [PATCH 05/15] Update PULL_REQUEST_TEMPLATE.md --- .github/PULL_REQUEST_TEMPLATE.md | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index bf154a9f..ad14caa5 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -6,6 +6,7 @@ For all schema changes: - [ ] Add release notes for the PR to `docs/format/source/format_release_notes.rst`. +- [ ] Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged. If this is the first schema change after a schema release (i.e., the version string in `core/nwb.namespace.yaml` does not end in "-alpha"), then: From dd5ca2a96b9b866dee2b573ee95ef42749e36177 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Fri, 19 Jan 2024 08:50:52 -0800 Subject: [PATCH 06/15] Update format_release_notes.rst --- docs/format/source/format_release_notes.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/format/source/format_release_notes.rst b/docs/format/source/format_release_notes.rst index 99d96d42..90af2f61 100644 --- a/docs/format/source/format_release_notes.rst +++ b/docs/format/source/format_release_notes.rst @@ -12,6 +12,7 @@ Minor changes - Deprecated `ImagingRetinotopy` neurodata type. (#565) - Modified `OptogeneticSeries` to allow 2D data, primarily in extensions of `OptogeneticSeries`. (#564) - Added optional ``stimulus_template`` column to ``IntracellularStimuliTable`` as part of the ``IntracellularRecordingsTable``. (#545) +- Added optional `bounds` attribute to `SpatialSeries.data`. (#567) 2.6.0 (January 17, 2023) ----------------------- From bf842181565a8f95d84a492df0661960ab2c008f Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Tue, 30 Jan 2024 15:02:47 -0800 Subject: [PATCH 07/15] Update format_release_notes.rst --- docs/format/source/format_release_notes.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/format/source/format_release_notes.rst b/docs/format/source/format_release_notes.rst index 90af2f61..0ba968a4 100644 --- a/docs/format/source/format_release_notes.rst +++ b/docs/format/source/format_release_notes.rst @@ -9,10 +9,10 @@ Release Notes Minor changes ^^^^^^^^^^^^^ - Fixed typos in docstrings. (#560) -- Deprecated `ImagingRetinotopy` neurodata type. (#565) -- Modified `OptogeneticSeries` to allow 2D data, primarily in extensions of `OptogeneticSeries`. (#564) +- Deprecated ``ImagingRetinotopy`` neurodata type. (#565) +- Modified ``OptogeneticSeries`` to allow 2D data, primarily in extensions of ``OptogeneticSeries``. (#564) - Added optional ``stimulus_template`` column to ``IntracellularStimuliTable`` as part of the ``IntracellularRecordingsTable``. (#545) -- Added optional `bounds` attribute to `SpatialSeries.data`. (#567) +- Added optional ``bounds`` attribute to ``SpatialSeries.data``. (#567) 2.6.0 (January 17, 2023) ----------------------- From 8b33524bb61a982a639e5a25c11029d5221df11e Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Tue, 5 Mar 2024 08:31:29 -0800 Subject: [PATCH 08/15] Update core/nwb.behavior.yaml Co-authored-by: Ryan Ly --- core/nwb.behavior.yaml | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/core/nwb.behavior.yaml b/core/nwb.behavior.yaml index e722971e..29805737 100644 --- a/core/nwb.behavior.yaml +++ b/core/nwb.behavior.yaml @@ -40,7 +40,21 @@ groups: required: false - name: bounds dtype: float32 - doc: The boundary range for the data. The units are the same as the units for the data. + doc: The boundary range (min, max) for each dimension of `data`. The units are the same as the units for the data. + shape: + - - 1 + - 2 + - - 2 + - 2 + - - 3 + - 2 + dims: + - - x + - min,max + - - x,y + - min,max + - - x,y,z + - min,max required: false - name: reference_frame dtype: text From baa1f77cf967560d91b4c9c6e7e5adfbb5e2d35b Mon Sep 17 00:00:00 2001 From: mavaylon1 Date: Tue, 5 Mar 2024 11:12:09 -0800 Subject: [PATCH 09/15] common --- hdmf-common-schema | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hdmf-common-schema b/hdmf-common-schema index 9b2580a2..4d2ddd63 160000 --- a/hdmf-common-schema +++ b/hdmf-common-schema @@ -1 +1 @@ -Subproject commit 9b2580a21647e06be54708fabf2d44cef73d32cb +Subproject commit 4d2ddd6387c4e36f21f41964fe8873c083680b15 From 1e46530323a054b4aceac348ad96bec0a8760565 Mon Sep 17 00:00:00 2001 From: mavaylon1 Date: Tue, 5 Mar 2024 11:14:00 -0800 Subject: [PATCH 10/15] doc --- docs/format/source/format_release_notes.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/format/source/format_release_notes.rst b/docs/format/source/format_release_notes.rst index 3092227a..2d9805ff 100644 --- a/docs/format/source/format_release_notes.rst +++ b/docs/format/source/format_release_notes.rst @@ -3,6 +3,12 @@ Release Notes ============= +2.8.0 (Upcoming) +------------------------ +Minor changes +^^^^^^^^^^^^^ +- Added support to set boundary metadata for ``SpatialSeries``. (#524) + 2.7.0 (February 7, 2024) ------------------------ From 3b6f13144e856eb6ef001b97594d4540819ec6db Mon Sep 17 00:00:00 2001 From: mavaylon1 Date: Tue, 5 Mar 2024 11:20:34 -0800 Subject: [PATCH 11/15] update version --- core/nwb.namespace.yaml | 2 +- docs/format/source/conf.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/core/nwb.namespace.yaml b/core/nwb.namespace.yaml index 4f8da78a..aabf4534 100644 --- a/core/nwb.namespace.yaml +++ b/core/nwb.namespace.yaml @@ -57,4 +57,4 @@ namespaces: - doc: This source module contains neurodata_type for retinotopy data. source: nwb.retinotopy.yaml title: Retinotopy - version: "2.7.0" + version: "2.8.0-alpha" diff --git a/docs/format/source/conf.py b/docs/format/source/conf.py index fb644ebd..8b0919b6 100644 --- a/docs/format/source/conf.py +++ b/docs/format/source/conf.py @@ -83,9 +83,9 @@ def setup(app): # built documents. # # The short X.Y version. -version = '2.7.0' +version = '2.8.0-alpha' # The full version, including alpha/beta/rc tags. -release = '2.7.0' +release = '2.8.0-alpha' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. From 4020fb88660acefd6fa626a942f3dc9e17ae075d Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 6 Mar 2024 13:14:01 -0800 Subject: [PATCH 12/15] Update core/nwb.behavior.yaml Co-authored-by: Ryan Ly --- core/nwb.behavior.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/nwb.behavior.yaml b/core/nwb.behavior.yaml index 29805737..4636e759 100644 --- a/core/nwb.behavior.yaml +++ b/core/nwb.behavior.yaml @@ -39,7 +39,7 @@ groups: To access the data in these units, multiply 'data' by 'conversion' and add 'offset'. required: false - name: bounds - dtype: float32 + dtype: numeric doc: The boundary range (min, max) for each dimension of `data`. The units are the same as the units for the data. shape: - - 1 From 7ad35febfdc35d525f53dbd9e9749523d9479323 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 6 Mar 2024 13:22:49 -0800 Subject: [PATCH 13/15] Update PULL_REQUEST_TEMPLATE.md --- .github/PULL_REQUEST_TEMPLATE.md | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index ad14caa5..1079aa1e 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -7,6 +7,7 @@ For all schema changes: - [ ] Add release notes for the PR to `docs/format/source/format_release_notes.rst`. - [ ] Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged. +- [ ] `hdmf-common-schema` needs to point to the latest release and not the latest of the `main ` branch. If this is the first schema change after a schema release (i.e., the version string in `core/nwb.namespace.yaml` does not end in "-alpha"), then: From 03396ad9cda88547404b729f8256512248fa7702 Mon Sep 17 00:00:00 2001 From: mavaylon1 Date: Wed, 6 Mar 2024 13:24:02 -0800 Subject: [PATCH 14/15] common --- hdmf-common-schema | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hdmf-common-schema b/hdmf-common-schema index 4d2ddd63..5b4cbb31 160000 --- a/hdmf-common-schema +++ b/hdmf-common-schema @@ -1 +1 @@ -Subproject commit 4d2ddd6387c4e36f21f41964fe8873c083680b15 +Subproject commit 5b4cbb31dbafcff51ca70bf218f464b186568151 From 5f8fe99123cd497fed90e9b433360852ab7b0339 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Fri, 8 Mar 2024 14:50:41 -0800 Subject: [PATCH 15/15] Update .github/PULL_REQUEST_TEMPLATE.md --- .github/PULL_REQUEST_TEMPLATE.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 1079aa1e..238d911a 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -7,7 +7,7 @@ For all schema changes: - [ ] Add release notes for the PR to `docs/format/source/format_release_notes.rst`. - [ ] Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged. -- [ ] `hdmf-common-schema` needs to point to the latest release and not the latest of the `main ` branch. +- [ ] Make sure that `hdmf-common-schema` points to the latest release and not the latest commit on the `main` branch. If this is the first schema change after a schema release (i.e., the version string in `core/nwb.namespace.yaml` does not end in "-alpha"), then: