Skip to content

Commit

Permalink
Merge branch 'main' into z/pr-029/add/codemeta.json
Browse files Browse the repository at this point in the history
  • Loading branch information
@ehennestad
ehennestad authored Dec 13, 2024
2 parents 9f35980 + e929735 commit b432b14
Show file tree
Hide file tree
Showing 3,154 changed files with 40,915 additions and 13,844 deletions.
The diff you're trying to view is too large. We only load the first 3000 changed files.
2 changes: 1 addition & 1 deletion .github/badges/code_issues.svg
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2 changes: 1 addition & 1 deletion .github/badges/tests.svg
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2 changes: 1 addition & 1 deletion README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@

# openMINDS Metadata Models for MATLAB
[![Version Number](https://img.shields.io/github/v/release/openMetadataInitiative/openMINDS_MATLAB?label=version)](https://github.com/openMetadataInitiative/openMINDS_MATLAB/releases/latest)
[![Open in MATLAB Online](https://github.com/openMetadataInitiative/openMINDS_MATLAB/blob/gh-badges/.github/badges/open-in-matlab-online.svg)](https://matlab.mathworks.com/open/github/v1?repo=openMetadataInitiative/openMINDS_MATLAB&file=code/gettingStarted.mlx)
[![Open in MATLAB Online](https://github.com/openMetadataInitiative/openMINDS_MATLAB/blob/gh-badges/.github/badges/open-in-matlab-online.svg)](https://matlab.mathworks.com/open/fileexchange/v1?id=134212)
[![View openMINDS_MATLAB on File Exchange](https://github.com/openMetadataInitiative/openMINDS_MATLAB/blob/gh-badges/.github/badges/matlab-file-exchange.svg)](https://se.mathworks.com/matlabcentral/fileexchange/134212-openminds_matlab)
[![MATLAB Tests](.github/badges/tests.svg)](https://github.com/openMetadataInitiative/openMINDS_MATLAB/actions/workflows/update.yml)
[![codecov](https://codecov.io/gh/openMetadataInitiative/openMINDS_MATLAB/graph/badge.svg?token=FTD5FHZSFA)](https://codecov.io/gh/openMetadataInitiative/openMINDS_MATLAB)
Expand Down
9 changes: 4 additions & 5 deletions code/+openminds/@Collection/Collection.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -272,7 +272,7 @@ function updateLinks(obj)
obj openminds.Collection
savePath (1,1) string
options.SaveToSingleFile (1,1) logical = true
%options.IncludeEmptyProperties (1,1) logical = false
% options.IncludeEmptyProperties (1,1) logical = false
end

% Update links before saving
Expand Down Expand Up @@ -336,12 +336,11 @@ function load(obj, filePath)%, options)
outputPaths = saveInstances(instance, filePath, options)

instances = loadInstances(filePath)

end

methods (Access = protected)

%Add an instance to the Node container.
% Add an instance to the Node container.
function addNode(obj, instance, options)

arguments
Expand All @@ -362,7 +361,7 @@ function addNode(obj, instance, options)

if isConfigured(obj.Nodes)
if isKey(obj.Nodes, instance.id)
%warning('Node with id %s already exists in collection', instance.id)
% warning('Node with id %s already exists in collection', instance.id)
if options.AbortIfNodeExists
return
end
Expand All @@ -389,7 +388,7 @@ function addNode(obj, instance, options)
obj.addSubNodes(instance)
end

%Add sub node instances (linked types) to the Node container.
% Add sub node instances (linked types) to the Node container.
function addSubNodes(obj, instance)
% Add links.
linkedTypes = instance.getLinkedTypes();
Expand Down
4 changes: 2 additions & 2 deletions code/+openminds/@Collection/loadInstances.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

arguments
filePath (1,:) string = ""
%options.RecursionDepth = 1
% options.RecursionDepth = 1
end

import openminds.internal.serializer.JsonLdSerializer
Expand Down Expand Up @@ -39,7 +39,7 @@

if ~isfield(thisInstance, 'at_type')
continue % Todo: Why skip?
%instances{i} = struct('id', thisInstance.at_id);
% instances{i} = struct('id', thisInstance.at_id);
else
openMindsType = thisInstance.at_type;
className = openminds.internal.utility.string.type2class(openMindsType);
Expand Down
2 changes: 1 addition & 1 deletion code/Contents.m
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
% openMINDS Metadata Models
% Version 0.9.3 (R2022b+) 01-Oct-2024
% Version 0.9.4 (R2022b+) 15-Nov-2024
%
% Copyright (c) 2024, openMetadataInitiative
% ------------------------------------------
6 changes: 3 additions & 3 deletions code/enumerations/latest/+openminds/+enum/Models.m
View file
Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
classdef Models
enumeration
SANDS
chemicals
computation
publications
controlledTerms
chemicals
SANDS
core
ephys
publications
specimenPrep
stimulation
end
Expand Down
2 changes: 0 additions & 2 deletions code/enumerations/latest/+openminds/+enum/Types.m
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
classdef Types < openminds.abstract.TypesEnumeration

enumeration
None('None')
AtlasAnnotation("openminds.sands.atlas.AtlasAnnotation")
Expand Down Expand Up @@ -221,5 +220,4 @@
StimulationActivity("openminds.stimulation.activity.StimulationActivity")
EphysStimulus("openminds.stimulation.stimulus.EphysStimulus")
end

end
2 changes: 0 additions & 2 deletions code/enumerations/v1.0/+openminds/+enum/Types.m
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
classdef Types < openminds.abstract.TypesEnumeration

enumeration
None('None')
AnatomicalEntity("openminds.sands.AnatomicalEntity")
Expand Down Expand Up @@ -88,5 +87,4 @@
TissueSampleCollectionState("openminds.core.research.TissueSampleCollectionState")
TissueSampleState("openminds.core.research.TissueSampleState")
end

end
2 changes: 0 additions & 2 deletions code/enumerations/v2.0/+openminds/+enum/Types.m
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
classdef Types < openminds.abstract.TypesEnumeration

enumeration
None('None')
AtlasAnnotation("openminds.sands.atlas.AtlasAnnotation")
Expand Down Expand Up @@ -102,5 +101,4 @@
TissueSampleCollectionState("openminds.core.research.TissueSampleCollectionState")
TissueSampleState("openminds.core.research.TissueSampleState")
end

end
6 changes: 3 additions & 3 deletions code/enumerations/v3.0/+openminds/+enum/Models.m
View file
Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
classdef Models
enumeration
SANDS
chemicals
computation
publications
controlledTerms
chemicals
SANDS
core
ephys
publications
specimenPrep
stimulation
end
Expand Down
2 changes: 0 additions & 2 deletions code/enumerations/v3.0/+openminds/+enum/Types.m
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
classdef Types < openminds.abstract.TypesEnumeration

enumeration
None('None')
AtlasAnnotation("openminds.sands.atlas.AtlasAnnotation")
Expand Down Expand Up @@ -219,5 +218,4 @@
StimulationActivity("openminds.stimulation.activity.StimulationActivity")
EphysStimulus("openminds.stimulation.stimulus.EphysStimulus")
end

end
13 changes: 13 additions & 0 deletions code/enumerations/v4.0/+openminds/+enum/Models.m
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
classdef Models
enumeration
SANDS
chemicals
computation
controlledTerms
core
ephys
publications
specimenPrep
stimulation
end
end
Loading

0 comments on commit b432b14

Please sign in to comment.