Merging doc-branch with main

.github/workflows/test_setup.yml

@@ -0,0 +1,45 @@
+name: Run Tests
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ${{matrix.os}}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-14]
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Set up MATLAB R2024a
+      uses: matlab-actions/setup-matlab@v2
+      with:
+        release: R2024a
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11.9'
+
+    - name: Install additional 3p dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install numpy==1.26.4 tensorstore==0.1.73
+
+    - name: Run tests
+      uses: matlab-actions/run-tests@v2
+      with:
+        select-by-folder: 'test'
+        code-coverage-cobertura: cobertura.xml
+
+    - name: Upload codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{secrets.CODECOV_TOKEN}}
+        files: ./target/site/cobertura/coverage.xml
+        name: codecov-umbrella.xml

README.md

@@ -1,3 +1,5 @@
+[![codecov](https://codecov.io/gh/mathworks/MATLAB-support-for-Zarr-files/graph/badge.svg?token=ZBLNDOLQyA)](https://codecov.io/gh/mathworks/MATLAB-support-for-Zarr-files)
+
 # MATLAB Support for Zarr files
 
 [Zarr®](https://zarr-specs.readthedocs.io/en/latest/specs.html) is a chunked, compressed, _N_-dimensional array storage format optimized for performance and scalability. It is widely used in scientific computing for handling large arrays efficiently.
@@ -77,7 +79,7 @@ filepath   = "myZarrfiles\singleDset";
 data_shape = [10,10];              % shape of the Zarr array to be written
 data       = 5*ones(10,10);        % Data to be written
 
-zarrcreate (filepath, data_shape)  % Create the Zarr array with default attributes
+zarrcreate(filepath, data_shape)  % Create the Zarr array with default attributes
 zarrwrite(filepath, data)          % Write data to the Zarr array
 ```
 
@@ -127,4 +129,4 @@ The license is available in the `License.txt` file in this GitHub repository.
 ## Community Support
 [MATLAB Central](https://www.mathworks.com/matlabcentral)
 
-Copyright 2025 The MathWorks, Inc.
+Copyright 2025 The MathWorks, Inc.

codecov.yml

@@ -0,0 +1,8 @@
+coverage:
+  status:
+    project:
+      default:
+        target: 85%
+        threshold: 5%
+ignore:
+  - "test/*"

readZattrs.m

@@ -1,6 +1,6 @@
 function zattrsStruct = readZattrs(filepath)
 %READZATTRS Helper function to read the JSON file .zattrs which contains
-%user defined attributes for a Zarr array or group.
+%user-defined attributes for a Zarr array or group.
 
 %   Copyright 2025 The MathWorks, Inc.
 

test/SharedZarrTestSetup.m

@@ -0,0 +1,28 @@
+classdef SharedZarrTestSetup < matlab.unittest.TestCase
+    % Shared test set up for Zarr tests.
+
+    % Copyright 2025 The MathWorks, Inc.
+
+    properties
+        PyException = "MATLAB:Python:PyException"
+        ArrSize = [20 25]
+        ChunkSize = [4 5]
+
+        % Path for write tests
+        ArrPathWrite = "prt_grp_write/arr1"
+    end
+
+    methods(TestClassSetup)
+    	function addSrcCodePath(testcase)
+    	    % Add source code path before running the tests
+            import matlab.unittest.fixtures.PathFixture
+    	    testcase.applyFixture(PathFixture(fullfile('..'),'IncludeSubfolders',true))
+    	end
+
+        function setupWorkingFolderToCreateArr(testcase)
+            % Use working folder fixture to create Zarr array.
+            import matlab.unittest.fixtures.WorkingFolderFixture;
+            testcase.applyFixture(WorkingFolderFixture);
+        end
+    end
+end

test/dataFiles/grp_v2/.zattrs

@@ -0,0 +1,4 @@
+{
+    "group_description": "This is a sample Zarr group",
+    "group_level": 1
+}

test/dataFiles/grp_v2/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

test/dataFiles/grp_v2/arr_v2/.zarray

@@ -0,0 +1 @@
+{"chunks":[2,5],"compressor":{"blocksize":0,"clevel":5,"cname":"lz4","id":"blosc","shuffle":1},"dtype":"<f4","fill_value":-9,"filters":[],"order":"C","shape":[20,25],"zarr_format":2,"Attr1":"var"}

test/dataFiles/grp_v2/arr_v2/.zattrs

@@ -0,0 +1,5 @@
+{
+    "array_description": "This is a sample Zarr array",
+    "array_level": 1,
+    "array_type": "double"
+}

test/dataFiles/grp_v3/arr_v3/zarr.json

@@ -0,0 +1,46 @@
+{
+  "shape": [
+    20,
+    25
+  ],
+  "data_type": "float32",
+  "chunk_grid": {
+    "name": "regular",
+    "configuration": {
+      "chunk_shape": [
+        2,
+        5
+      ]
+    }
+  },
+  "chunk_key_encoding": {
+    "name": "default",
+    "configuration": {
+      "separator": "/"
+    }
+  },
+  "fill_value": -9.0,
+  "codecs": [
+    {
+      "name": "bytes",
+      "configuration": {
+        "endian": "little"
+      }
+    },
+    {
+      "name": "zstd",
+      "configuration": {
+        "level": 0,
+        "checksum": false
+      }
+    }
+  ],
+  "attributes": {
+    "array_description": "This is a sample Zarr array",
+    "array_type": "double",
+    "array_level": 1
+  },
+  "zarr_format": 3,
+  "node_type": "array",
+  "storage_transformers": []
+}

test/dataFiles/grp_v3/zarr.json

@@ -0,0 +1,9 @@
+{
+  "attributes": {
+    "group_description": "This is a sample Zarr group",
+    "group_level": 1
+  },
+  "zarr_format": 3,
+  "consolidated_metadata": null,
+  "node_type": "group"
+}

test/tZarrAttributes.m

@@ -0,0 +1,108 @@
+classdef tZarrAttributes < SharedZarrTestSetup
+    % Tests for zarrwriteatt function to get attribute info of the Zarr file in MATLAB.
+
+    % Copyright 2025 The MathWorks, Inc.
+
+    methods(TestClassSetup)
+        function createZarrArrayWithAttrs(testcase)
+            % Create Zarr array and add some attributes.
+            zarrcreate(testcase.ArrPathWrite,testcase.ArrSize);
+            zarrwriteatt(testcase.ArrPathWrite,'attr1','This is an array attribute.');
+            zarrwriteatt(testcase.ArrPathWrite,'attr2',{1,2,3});
+            attr3.numVal = 10;
+            attr3.strArr = ["array","attribute"];
+            zarrwriteatt(testcase.ArrPathWrite,'attr3',attr3);
+        end
+    end
+
+    methods(Test)
+        function verifyArrayAttributeInfo(testcase)
+            % Write attribute info using zarrwriteatt function to an array.
+
+            arrInfo = zarrinfo(testcase.ArrPathWrite);
+            actAttr.attr1 = arrInfo.attr1;
+
+            % TODO: Enable code once Issue-34 is fixed.
+            %actAttr.attr2 = arrInfo.attr2;
+            %actAttr.attr3 = arrInfo.attr3;
+
+            expAttr.attr1 = 'This is an array attribute.';
+            %expAttr.attr2 = {1,2,3};
+            %expAttr.attr3.numVal = 10;
+            %expAttr.attr4.strArr = ["array","attribute"];
+
+            testcase.verifyEqual(actAttr,expAttr,'Failed to verify attribute info.');
+        end
+
+        function verifyAttrOverwrite(testcase)
+            % Verify attribute value after overwrite.
+            %testcase.assumeTrue(false,'Filtered until the attributes display is fixed.');
+            expAttrStr = ["new","attribute","value"];
+            zarrwriteatt(testcase.ArrPathWrite,'attr1',expAttrStr);
+            expAttrDbl = 10;
+            zarrwriteatt(testcase.ArrPathWrite,'attr2',expAttrDbl);
+
+            arrInfo = zarrinfo(testcase.ArrPathWrite);
+
+            % TODO: Enable code once Issue-34 is fixed.
+            %actAttrStr = arrInfo.attr1;
+            actAttrDbl = arrInfo.attr2;
+
+            %testcase.verifyEqual(actAttrStr,expAttrStr,'Failed to verify string attribute info');
+            testcase.verifyEqual(actAttrDbl,expAttrDbl,'Failed to verify double attribute info');
+        end
+
+        function verifyGroupAttributeInfo(testcase)
+            % Write attribute info using zarrwriteatt function to a group.
+            testcase.assumeTrue(false,'Filtered until Issue-35 is fixed.');
+
+            % Unable to read attribute data from a group/array created
+            % using Python.
+        end
+
+        function verifyZarrV3WriteError(testcase)
+            % Verify error when a user tries to write attribute to zarr v3
+            % file.
+            testcase.assumeTrue(false,'Filtered until the right error message is thrown.');
+            filePath = 'dataFiles/grp_v3/arr_v3';
+            testcase.verifyError(@()zarrwriteatt(filePath,'myAttr','attrVal'), ...
+                testcase.PyException);
+        end
+
+        function nonExistentFile(testcase)
+            % Verify error when using a non-existent file with zarrwriteatt 
+            % function.
+            testcase.verifyError(@()zarrwriteatt('testFile/nonExistentArr','myAttr','attrVal'), ...
+                'MATLAB:validators:mustBeFolder');
+        end
+
+        function tooManyInputs(testcase)
+            % Verify error when too many inputs are used with zarrwrite
+            % function.
+            testcase.verifyError(@()zarrwriteatt(testcase.ArrPathWrite,'myAttr','attrVal','extra'), ...
+                'MATLAB:TooManyInputs');
+        end
+
+        function tooFewInputs(testcase)
+            % Verify error when too few inputs with zarrwriteatt function 
+            % are used.
+            testcase.verifyError(@()zarrwriteatt(testcase.ArrPathWrite,'myAttr'), ...
+                'MATLAB:minrhs');
+        end
+
+        function invalidInput(testcase)
+            % Verify error when invalid input is used for zarrwriteatt
+            % function.
+            errID =  'MATLAB:validators:mustBeFolder';
+
+            % Invalid file path type
+            testcase.verifyError(@()zarrwriteatt('nonexistent','myAttr',10),errID);
+
+            % Invalid attribute name
+            errID = 'MATLAB:validators:mustBeNonzeroLengthText';
+            testcase.verifyError(@()zarrwriteatt(testcase.ArrPathWrite,'',10),errID);
+            errID = 'MATLAB:validators:mustBeTextScalar';
+            testcase.verifyError(@()zarrwriteatt(testcase.ArrPathWrite,10,10),errID);
+        end
+    end
+end