Merge pull request #252 from NeurodataWithoutBorders/remove-submodules

Remove submodules

Author: lawrence-mbf

+misc/getNamespaceDir.m

@@ -1,4 +1,4 @@
-function [namespaceDir] = getNamespaceDir(varargin)
+function namespaceDir = getNamespaceDir(varargin)
     % Get the location of the namespaces directory regardless of current MATLAB working directory.
     % started: 2020.07.02 [11:20:30]
     % inputs
@@ -8,51 +8,18 @@
 
     % changelog
         % 2020.07.02 [11:24:10] - Function created and added warning if namespaces directory could not be found. - Biafra Ahanonu.
+        % 2020.12.29 [13:40:00] - Function simplified to use local namespace directory first.
     % TODO
         %
-
-    try
-       % Get the actual location of the matnwb directory.
-       fnDir = misc.getMatnwbDir();
-
-       % Get full path name to namespaces directory and list of files
-       namespaceDir = fullfile(fnDir, 'namespaces');
-
-       % Check directory exists else throw a warning letting the user know.
-       dirExists = subfxnDirCheck(namespaceDir,1);
-       if dirExists==0
-            namespaceDir = subfxnDefaultNamespaces();
-        elseif dirExists==1
-            % Do nothing.
-        end
-    catch err
-        % Attempt to load namespaces directory using prior methods.
-        namespaceDir = subfxnDefaultNamespaces();
-        disp(repmat('@',1,7))
-        disp(getReport(err,'extended','hyperlinks','on'));
-        disp(repmat('@',1,7))
-    end
-end
-function dirExists = subfxnDirCheck(namespaceDir,dispWarning)
-   if exist(namespaceDir,'dir')==7
-        dirExists = 1;
-   else
-        dirExists = 0;
-        if dispWarning==1
-            warning('Directory "namespaces" not found at %s. Using defaults.',namespaceDir)
-        end
-   end
-end
-function namespaceDir = subfxnDefaultNamespaces()
-    try
-        namespaceDir = fullfile(misc.getWorkspace(), 'namespaces');
-        dirExists = subfxnDirCheck(namespaceDir,0);
-        if dirExists==0
-            namespaceDir = 'namespaces';
-            subfxnDirCheck(namespaceDir,0);
-        end
-    catch
-        namespaceDir = 'namespaces';
-        subfxnDirCheck(namespaceDir,0);
+        
+    localNamespace = fullfile(misc.getWorkspace(), 'namespaces');
+    rootNamespace = fullfile(misc.getMatnwbDir(), 'namespaces');
+    if 7 == exist(localNamespace, 'dir')
+        namespaceDir = localNamespace;
+    elseif 7 == exist(rootNamespace, 'dir')
+        namespaceDir = rootNamespace;
+    else
+        warning('Directory "namespaces" not found.');
+        namespaceDir = '';
     end
 end

+tests/+system/smokeTest.m

@@ -5,14 +5,10 @@
 function setupOnce(testCase)
 rootPath = fullfile(fileparts(mfilename('fullpath')), '..', '..');
 testCase.applyFixture(matlab.unittest.fixtures.PathFixture(rootPath));
-% corePath = fullfile(rootPath, 'schema', 'core', 'nwb.namespace.yaml');
-% testCase.TestData.registry = generateCore(corePath);
+generateCore();
 end
 
 function teardownOnce(testCase)
-% classes = fieldnames(testCase.TestData.registry);
-% files = strcat(fullfile('+types', classes), '.m');
-% delete(files{:});
 end
 
 function setup(testCase)

+tests/+unit/multipleShapesTest.m

@@ -3,19 +3,17 @@
 end
 
 function setupOnce(testCase)
-fileLoc = fileparts(mfilename('fullpath'));
-rootPath = fullfile(fileLoc, '..', '..');
-schemaPath = fullfile(fileLoc, 'multipleShapesSchema', 'mss.namespace.yaml');
+schemaPath = fullfile(misc.getMatnwbDir(),...
+    '+tests', '+unit', 'multipleShapesSchema', 'mss.namespace.yaml');
 generateExtension(schemaPath);
-testCase.applyFixture(matlab.unittest.fixtures.PathFixture(rootPath));
 end
 
 function setup(testCase)
 testCase.applyFixture(matlab.unittest.fixtures.WorkingFolderFixture);
 end
 
 function teardownOnce(~)
-rmdir(fullfile('+types', '+mss'), 's'); 
+% rmdir(fullfile('+types', '+mss'), 's');
 end
 
 function testMultipleShapesDataset(testCase)

.gitmodules

@@ -42,10 +42,13 @@ function export(obj, filename)
             try
                 output_file_id = H5F.create(filename);
             catch ME % if file exists, open and edit
-                isLibraryError = strcmp(ME.identifier,...
-                    'MATLAB:imagesci:hdf5lib:libraryError');
-                isFileExistsError = isLibraryError &&...
-                    contains(ME.message, '''File exists''');
+                if verLessThan('matlab', '9.9') % < 2020b
+                    isFileExistsError = strcmp(ME.identifier, 'MATLAB:imagesci:hdf5lib:libraryError')...
+                        && contains(ME.message, '''File exists''');
+                else
+                    isFileExistsError = strcmp(ME.identifier, 'MATLAB:imagesci:hdf5io:resourceAlreadyExists');
+                end
+                
                 if isFileExistsError
                     output_file_id = H5F.open(filename, 'H5F_ACC_RDWR', 'H5P_DEFAULT');
                 else

NwbFile.m

@@ -5,13 +5,11 @@ pool:
   vmImage: 'ubuntu-latest'
 
 steps:
-  - checkout: self
-    submodules: recursive
-
   - task: InstallMATLAB@0
     # default to latest version of Matlab installed
     #inputs:
     #  release: R2020a
+  - checkout: self
 
   - task: UsePythonVersion@0
     inputs:
@@ -25,5 +23,5 @@ steps:
 
   - task: RunMATLABCommand@0
     inputs:
-      command: "try, addpath(genpath(pwd)); generateCore(); results = nwbtest; if isempty(results), exit(1); end; catch err, disp(err.message); exit(1); end"
+      command: "try, addpath(genpath(pwd)); results = nwbtest; if isempty(results), exit(1); end; catch err, disp(err.message); exit(1); end"
 

azure-pipelines.yml

@@ -0,0 +1,206 @@
+datasets:
+- neurodata_type_def: NWBData
+  neurodata_type_inc: Data
+  doc: An abstract data type for a dataset.
+
+- neurodata_type_def: Image
+  neurodata_type_inc: NWBData
+  dtype: numeric
+  dims:
+  - - x
+    - y
+  - - x
+    - y
+    - r, g, b
+  - - x
+    - y
+    - r, g, b, a
+  shape:
+  - - null
+    - null
+  - - null
+    - null
+    - 3
+  - - null
+    - null
+    - 4
+  doc: An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the
+    third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or
+    (x, y, (r, g, b, a)).
+  attributes:
+  - name: resolution
+    dtype: float32
+    doc: Pixel resolution of the image, in pixels per centimeter.
+    required: false
+  - name: description
+    dtype: text
+    doc: Description of the image.
+    required: false
+
+groups:
+- neurodata_type_def: NWBContainer
+  neurodata_type_inc: Container
+  doc: An abstract data type for a generic container storing collections of data and
+    metadata. Base type for all data and metadata containers.
+
+- neurodata_type_def: NWBDataInterface
+  neurodata_type_inc: NWBContainer
+  doc: An abstract data type for a generic container storing collections of data,
+    as opposed to metadata.
+
+- neurodata_type_def: TimeSeries
+  neurodata_type_inc: NWBDataInterface
+  doc: General purpose time series.
+  attributes:
+  - name: description
+    dtype: text
+    default_value: no description
+    doc: Description of the time series.
+    required: false
+  - name: comments
+    dtype: text
+    default_value: no comments
+    doc: Human-readable comments about the TimeSeries. This second descriptive field
+      can be used to store additional information, or descriptive information if the
+      primary description field is populated with a computer-readable string.
+    required: false
+  datasets:
+  - name: data
+    dims:
+    - - num_times
+    - - num_times
+      - num_DIM2
+    - - num_times
+      - num_DIM2
+      - num_DIM3
+    - - num_times
+      - num_DIM2
+      - num_DIM3
+      - num_DIM4
+    shape:
+    - - null
+    - - null
+      - null
+    - - null
+      - null
+      - null
+    - - null
+      - null
+      - null
+      - null
+    doc: Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension
+      should always represent time. This can also be used to store binary data
+      (e.g., image frames). This can also be a link to data stored in an external file.
+    attributes:
+    - name: conversion
+      dtype: float32
+      default_value: 1.0
+      doc: Scalar to multiply each element in data to convert it to the specified 'unit'.
+        If the data are stored in acquisition system units or other units
+        that require a conversion to be interpretable, multiply the data by 'conversion'
+        to convert the data to the specified 'unit'. e.g. if the data acquisition system
+        stores values in this object as signed 16-bit integers (int16 range
+        -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data
+        acquisition system gain is 8000X, then the 'conversion' multiplier to get from
+        raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.
+      required: false
+    - name: resolution
+      dtype: float32
+      default_value: -1.0
+      doc: Smallest meaningful difference between values in data, stored in the specified
+        by unit, e.g., the change in value of the least significant bit, or a larger
+        number if signal noise is known to be present. If unknown, use -1.0.
+      required: false
+    - name: unit
+      dtype: text
+      doc: Base unit of measurement for working with the data. Actual stored values are
+        not necessarily stored in these units. To access the data in these units,
+        multiply 'data' by 'conversion'.
+  - name: starting_time
+    dtype: float64
+    doc: Timestamp of the first sample in seconds. When timestamps are uniformly
+      spaced, the timestamp of the first sample can be specified and all subsequent
+      ones calculated from the sampling rate attribute.
+    quantity: '?'
+    attributes:
+    - name: rate
+      dtype: float32
+      doc: Sampling rate, in Hz.
+    - name: unit
+      dtype: text
+      value: seconds
+      doc: Unit of measurement for time, which is fixed to 'seconds'.
+  - name: timestamps
+    dtype: float64
+    dims:
+    - num_times
+    shape:
+    - null
+    doc: Timestamps for samples stored in data, in seconds, relative to the
+      common experiment master-clock stored in NWBFile.timestamps_reference_time.
+    quantity: '?'
+    attributes:
+    - name: interval
+      dtype: int32
+      value: 1
+      doc: Value is '1'
+    - name: unit
+      dtype: text
+      value: seconds
+      doc: Unit of measurement for timestamps, which is fixed to 'seconds'.
+  - name: control
+    dtype: uint8
+    dims:
+    - num_times
+    shape:
+    - null
+    doc: Numerical labels that apply to each time point in data for the purpose of
+      querying and slicing data by these values. If present, the length of this
+      array should be the same size as the first dimension of data.
+    quantity: '?'
+  - name: control_description
+    dtype: text
+    dims:
+    - num_control_values
+    shape:
+    - null
+    doc: Description of each control value. Must be present if control is present.
+      If present, control_description[0] should describe time points where control == 0.
+    quantity: '?'
+  groups:
+  - name: sync
+    doc: Lab-specific time and sync information as provided directly from hardware
+      devices and that is necessary for aligning all acquired time information to
+      a common timebase. The timestamp array stores time in the common timebase.
+      This group will usually only be populated in TimeSeries that are
+      stored external to the NWB file, in files storing raw data. Once timestamp
+      data is calculated, the contents of 'sync' are mostly for archival purposes.
+    quantity: '?'
+
+- neurodata_type_def: ProcessingModule
+  neurodata_type_inc: NWBContainer
+  doc: A collection of processed data.
+  attributes:
+  - name: description
+    dtype: text
+    doc: Description of this collection of processed data.
+  groups:
+  - neurodata_type_inc: NWBDataInterface
+    doc: Data objects stored in this collection.
+    quantity: '*'
+  - neurodata_type_inc: DynamicTable
+    doc: Tables stored in this collection.
+    quantity: '*'
+
+- neurodata_type_def: Images
+  neurodata_type_inc: NWBDataInterface
+  default_name: Images
+  doc: A collection of images.
+  attributes:
+  - name: description
+    dtype: text
+    doc: Description of this collection of images.
+  datasets:
+  - neurodata_type_inc: Image
+    doc: Images stored in this collection.
+    quantity: '+'