From b64e744a7fde0a175a3bf32015dc28bd6018d1fc Mon Sep 17 00:00:00 2001 From: Abhi Baruah Date: Fri, 18 Apr 2025 14:21:50 -0400 Subject: [PATCH 01/21] Address CR feedback --- readZattrs.m | 2 +- zarrinfo.m | 15 ++++++--------- 2 files changed, 7 insertions(+), 10 deletions(-) diff --git a/readZattrs.m b/readZattrs.m index 207983d..916fcc5 100644 --- a/readZattrs.m +++ b/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. diff --git a/zarrinfo.m b/zarrinfo.m index 55031de..2aaf1ab 100644 --- a/zarrinfo.m +++ b/zarrinfo.m @@ -12,10 +12,9 @@ filepath {mustBeTextScalar, mustBeNonzeroLengthText, mustBeFolder} end -% .zarray and .zgroup are valid metadata files for Zarr v2 which contain library -% defined attributes. -% zarr.json is valid metadata file for Zarr v3 containing library defined -% attributes. +% .zarray and .zgroup are valid metadata files for Zarr v2 which contain +% library-defined attributes. zarr.json is valid metadata file for Zarr v3 +% containing library-defined attributes. % If the location is a Zarr array if isfile(fullfile(filepath, '.zarray')) infoStr = fileread(fullfile(filepath, '.zarray')); @@ -38,11 +37,9 @@ % User defined attributes are contained in .zattrs file in each array or group store if isfile(fullfile(filepath, '.zattrs')) userDefinedInfoStruct = readZattrs(filepath); - userDefinedfieldnames = fieldnames(userDefinedInfoStruct); - if (numel(userDefinedfieldnames) > 0) - for i = 1:numel(userDefinedfieldnames) - infoStruct.(userDefinedfieldnames{i}) = userDefinedInfoStruct.(userDefinedfieldnames{i}); - end + userDefinedFieldNames = fieldnames(userDefinedInfoStruct); + for i = 1:numel(userDefinedFieldNames) + infoStruct.(userDefinedFieldNames{i}) = userDefinedInfoStruct.(userDefinedFieldNames{i}); end end From c20122a99e4ff75ca33f13670638162fc1e35083 Mon Sep 17 00:00:00 2001 From: Shubhdildeep Singh Sohal Date: Fri, 18 Apr 2025 14:29:29 -0400 Subject: [PATCH 02/21] Adding tests v1 --- .github/workflows/test_setup.yml | 42 +++++ codecov.yml | 8 + test/SharedZarrTestSetup.m | 26 +++ test/dataFiles/create_zarr_v2.py | 13 ++ test/dataFiles/create_zarr_v3.py | 13 ++ test/dataFiles/expZarrArrData.mat | Bin 0 -> 2039 bytes test/dataFiles/expZarrArrInfo.mat | Bin 0 -> 1264 bytes test/dataFiles/grp_v2/.zattrs | 4 + test/dataFiles/grp_v2/.zgroup | 3 + test/dataFiles/grp_v2/arr_v2/.zarray | 1 + test/dataFiles/grp_v2/arr_v2/.zattrs | 5 + test/dataFiles/grp_v2/arr_v2/0.0 | Bin 0 -> 56 bytes test/dataFiles/grp_v2/arr_v2/0.1 | Bin 0 -> 56 bytes test/dataFiles/grp_v2/arr_v2/0.2 | Bin 0 -> 56 bytes test/dataFiles/grp_v2/arr_v2/0.3 | Bin 0 -> 56 bytes test/dataFiles/grp_v2/arr_v2/0.4 | Bin 0 -> 56 bytes test/dataFiles/grp_v2/arr_v2/1.0 | Bin 0 -> 56 bytes test/dataFiles/grp_v2/arr_v2/1.1 | Bin 0 -> 56 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test/dataFiles/grp_v3/arr_v3/c/8/4 create mode 100644 test/dataFiles/grp_v3/arr_v3/c/9/0 create mode 100644 test/dataFiles/grp_v3/arr_v3/c/9/1 create mode 100644 test/dataFiles/grp_v3/arr_v3/c/9/2 create mode 100644 test/dataFiles/grp_v3/arr_v3/c/9/3 create mode 100644 test/dataFiles/grp_v3/arr_v3/c/9/4 create mode 100644 test/dataFiles/grp_v3/arr_v3/zarr.json create mode 100644 test/dataFiles/grp_v3/zarr.json create mode 100644 test/tZarrAttributes.m create mode 100644 test/tZarrCreate.m create mode 100644 test/tZarrInfo.m create mode 100644 test/tZarrRead.m create mode 100644 test/tZarrWrite.m diff --git a/.github/workflows/test_setup.yml b/.github/workflows/test_setup.yml new file mode 100644 index 0000000..675c760 --- /dev/null +++ b/.github/workflows/test_setup.yml @@ -0,0 +1,42 @@ +name: Test setup and measure coverage + +on: + push: + branches: + - main + +jobs: + test: + runs-on: ubuntu-latest + + 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@v2 + with: + python-version: '3.x' + + - name: Install additional 3p dependencies + run: | + python -m pip install --upgrade pip + pip install numpy tensorstore + + - 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 \ No newline at end of file diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 0000000..23a0e90 --- /dev/null +++ b/codecov.yml @@ -0,0 +1,8 @@ +coverage: + status: + project: + default: + target: 85% + threshold: 5% +ignore: + - "test/*" \ No newline at end of file diff --git a/test/SharedZarrTestSetup.m b/test/SharedZarrTestSetup.m new file mode 100644 index 0000000..adfa0a1 --- /dev/null +++ b/test/SharedZarrTestSetup.m @@ -0,0 +1,26 @@ +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 read functions + % GrpPathRead = "dataFiles/grp_v2" + % ArrPathRead = "dataFiles/grp_v2/arr_v2" + + % Path for write tests + ArrPathWrite = "prt_grp_write/arr1" + end + + methods(TestClassSetup) + function setupWorkingFolderToCreateArr(testcase) + % Use working folder fixture to create Zarr array. + import matlab.unittest.fixtures.WorkingFolderFixture; + testcase.applyFixture(WorkingFolderFixture); + end + end +end \ No newline at end of file diff --git a/test/dataFiles/create_zarr_v2.py b/test/dataFiles/create_zarr_v2.py new file mode 100644 index 0000000..e460db0 --- /dev/null +++ b/test/dataFiles/create_zarr_v2.py @@ -0,0 +1,13 @@ +# Create Zarr v2 array + +import zarr +import numpy as np +store = zarr.DirectoryStore('grp_v2') +group = zarr.group(store=store,overwrite=True) +group.attrs['group_description'] = 'This is a sample Zarr group' +group.attrs['group_level'] = 1 +array = group.create_dataset('arr_v2',shape=(20,25),dtype=np.float32,chunks=(2,5),fillvalue=-9) +array.attrs['array_description'] = 'This is a sample Zarr array' +array.attrs['array_type'] = 'double' +array.attrs['array_level'] = 1 +array[:] = np.random.rand(20,25) diff --git a/test/dataFiles/create_zarr_v3.py b/test/dataFiles/create_zarr_v3.py new file mode 100644 index 0000000..b6de349 --- /dev/null +++ b/test/dataFiles/create_zarr_v3.py @@ -0,0 +1,13 @@ +# Create Zarr v3 array + +import zarr +import numpy as np +store = zarr.storage.LocalStore('grp_v3') +group = zarr.group(store=store,overwrite=True) +group.attrs['group_description'] = 'This is a sample Zarr group' +group.attrs['group_level'] = 1 +array = 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"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": [] +} \ No newline at end of file diff --git a/test/dataFiles/grp_v3/zarr.json b/test/dataFiles/grp_v3/zarr.json new file mode 100644 index 0000000..11fa3cb --- /dev/null +++ b/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" +} \ No newline at end of file diff --git a/test/tZarrAttributes.m b/test/tZarrAttributes.m new file mode 100644 index 0000000..b8e1941 --- /dev/null +++ b/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 \ No newline at end of file diff --git a/test/tZarrCreate.m b/test/tZarrCreate.m new file mode 100644 index 0000000..fad9141 --- /dev/null +++ b/test/tZarrCreate.m @@ -0,0 +1,251 @@ +classdef tZarrCreate < SharedZarrTestSetup + % Tests for zarrcreate function to create Zarr files in MATLAB. + + % Copyright 2025 The MathWorks, Inc. + + methods(Test) + function invalidFilePath(testcase) + % Verify error when an invalid file path is used as an input to + % zarrcreate function. + + % Empty + errID = 'MATLAB:validators:mustBeNonempty'; + testcase.verifyError(@()zarrcreate('',testcase.ArrSize),errID); + + % Non-scalar + errID = 'MATLAB:validators:mustBeTextScalar'; + testcase.verifyError(@()zarrcreate([testcase.ArrPathWrite,testcase.ArrPathWrite], ... + testcase.ArrSize),errID); + + % Non-text input + testcase.verifyError(@()zarrcreate([],testcase.ArrSize),errID); + end + + function pathContainingInvalidChars(testcase) + % Verify error when the array or group name contains + % unsupported characters. + testcase.verifyError(@()zarrcreate('grp*/arr',testcase.ArrSize),testcase.PyException); + testcase.verifyError(@()zarrcreate('grp/arr*',testcase.ArrSize),testcase.PyException); + end + + function chunkSizeGreaterThanArraySize(testcase) + % Verify error when the chunk size is greater than the array + % size. + testcase.assumeTrue(false,'Filtered until the issue is fixed.'); + chunkSize = [30 35]; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'ChunkSize',chunkSize),testcase.PyException); + end + + function chunkSizeMismatch(testcase) + % Verify error when there is a mismatch between Array size and + % Chunk size. + arrSize = [10 12 5]; + chunkSize = [4 5]; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,arrSize, ... + 'ChunkSize',chunkSize),testcase.PyException); + end + + function invalidClevelBlosc(testcase) + % Verify error when an invalid clevel value is used with blosc + % compression. Valid values are [0 9], where 0 is for no compression. + comp.id = 'blosc'; + level = {-1,10,NaN}; + comp.cname = 'blosclz'; + comp.shuffle = -1; + + for i = 1:length(level) + comp.clevel = level{i}; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + end + end + + function invalidBlockSizeBlosc(testcase) + % Verify error when an invalid blocksize value is used with blosc + % compression. Valid values for blocksize are [0 inf]. + comp.id = 'blosc'; + comp.level = 5; + comp.cname = 'blosclz'; + comp.shuffle = -1; + blocksize = {-1,[2 2],NaN}; + + for i = 1:length(blocksize) + comp.blocksize = blocksize{i}; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + end + end + + function invalidCnameBlosc(testcase) + % Verify error when an invalid cname value is used with blosc + % compression. + comp.id = 'blosc'; + comp.level = 5; + cname = {'random','',0}; + comp.shuffle = -1; + comp.blocksize = 5; + + for i = 1:length(cname) + comp.cname = cname{i}; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + end + end + + function invalidShuffleBlosc(testcase) + % Verify error when an invalid shuffle value is used with blosc + % compression. The valid values are -1, 0, 1, and 2. + comp.id = 'blosc'; + comp.level = 5; + comp.cname = 'blosclz'; + shuffle = {-2,3,inf,NaN}; + comp.blocksize = 5; + + for i = 1:length(shuffle) + comp.shuffle = shuffle{i}; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + end + end + + function invalidChunkSize(testcase) + % Verify error when an invalid type for the chunk size is used. + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'ChunkSize',5),testcase.PyException); + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'ChunkSize',[]),testcase.PyException); + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'ChunkSize',[0 0]),testcase.PyException); + end + + function invalidFillValue(testcase) + % Verify error when an invalid type for the fill value is used. + % testcase.verifyError(@()zarrcreate(testcase.FilePath,testcase.ArrSize, ... + % "FillValue",[]),testcase.PyException); + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + "FillValue",[-9 -9]),testcase.PyException); + % testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + % "FillValue",NaN),testcase.PyException); + % testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + % "FillValue",inf),testcase.PyException); + end + + function invalidSizeInput(testcase) + % Verify error when an invalid size input is used. + % testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,[]), ... + % testcase.PyException); + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,10), ... + testcase.PyException); + end + + function invalidCompressionInputType(testcase) + % Verify error when an invalid compression value is used. + testcase.assumeTrue(false,'Filtered until the issue is fixed.'); + comp.id = 'random'; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + end + + function invalidCompressionMember(testcase) + % Verify error when additional compression members (cname, blocksize, + % and shuffle) are used. These members are not supported for + % compression other than blosc. + compType = {'gzip','zlib','bz2','zstd'}; + comp.level = 5; + comp.cname = 'blosclz'; + comp.shuffle = -1; + + for i = 1:length(compType) + comp.id = compType{i}; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + end + end + + function zlibInvalidCompressionLevel(testcase) + % Verify error when an invalid compression level is used. + % For zlib, valid values are [0 9] + comp.id = 'zlib'; + comp.level = -1; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + + comp.level = 10; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + + comp.level = []; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + end + + function gzipInvalidCompressionLevel(testcase) + % Verify error when an invalid compression level is used. + % For gzip, valid values are [0 9] + comp.id = 'gzip'; + comp.level = -1; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + + comp.level = 10; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + + comp.level = []; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + end + + function bz2InvalidCompressionLevel(testcase) + % Verify error when an invalid compression level is used. + % For zlib, valid values are [1 9] + comp.id = 'bz2'; + comp.level = 0; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + + comp.level = 10; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + + comp.level = []; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + end + + function zstdInvalidCompressionLevel(testcase) + % Verify error when an invalid compression level is used. + % For zlib, valid values are [1 9] + comp.id = 'zstd'; + comp.level = -131073; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + + comp.level = 23; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + + comp.level = []; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Compression',comp),testcase.PyException); + end + + function tooFewInputs(testcase) + % Verify error when too few inputs are passed to the zarrcreate + % function. + errID = 'MATLAB:minrhs'; + testcase.verifyError(@()zarrcreate(),errID); + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite),errID); + end + + function invalidParameter(testcase) + % Verify error when an invalid NV pair for zarrcreate is used. + errID = 'MATLAB:TooManyInputs'; + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Random'),errID); + testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'Random',-1),errID); + end + end +end \ No newline at end of file diff --git a/test/tZarrInfo.m b/test/tZarrInfo.m new file mode 100644 index 0000000..4eaf195 --- /dev/null +++ b/test/tZarrInfo.m @@ -0,0 +1,79 @@ +classdef tZarrInfo < matlab.unittest.TestCase + % Tests for zarrinfo function to get info of the Zarr file in MATLAB. + + % Copyright 2025 The MathWorks, Inc. + + properties(Constant) + GrpPathV2 = "dataFiles/grp_v2" + ArrPathV2 = "dataFiles/grp_v2/arr_v2" + GrpPathV3 = "dataFiles/grp_v3" + ArrPathV3 = "dataFiles/grp_v3/arr_v3" + ExpInfo = load(fullfile(pwd,"dataFiles","expZarrArrInfo.mat")) + end + + % Add tests for remote file reading + + methods(Test) + function verifyArrayInfoV2(testcase) + % Verify array info created with Zarr v2 format. + actInfo = zarrinfo(testcase.ArrPathV2); + expInfo = testcase.ExpInfo.zarrV2ArrInfo; + testcase.verifyEqual(actInfo,expInfo,'Failed to verify array info.'); + end + + function verifyGroupInfoV2(testcase) + % Verify group info created with Zarr v2 format. + actInfo = zarrinfo(testcase.GrpPathV2); + expInfo = testcase.ExpInfo.zarrV2GrpInfo; + testcase.verifyEqual(actInfo,expInfo,'Failed to verify group info.'); + end + + function verifyArrayInfoV3(testcase) + % Verify array info created with Zarr v3 format. + actInfo = zarrinfo(testcase.ArrPathV3); + expInfo = testcase.ExpInfo.zarrV3ArrInfo; + testcase.verifyEqual(actInfo,expInfo,'Failed to verify array info.'); + end + + function verifyGroupInfoV3(testcase) + % Verify group info created with Zarr v3 format. + actInfo = zarrinfo(testcase.GrpPathV3); + expInfo = testcase.ExpInfo.zarrV3GrpInfo; + testcase.verifyEqual(actInfo,expInfo,'Failed to verify group info.'); + end + + function missingZgroupFile(testcase) + % Verify error when using zarrinfo function on a group not + % containing .zgroup file. + testcase.assumeTrue(false,'Filtered until error ID is added.'); + + import matlab.unittest.fixtures.WorkingFolderFixture; + testcase.applyFixture(WorkingFolderFixture); + + zarrcreate('prt_grp_write/arr1',[10 10]); + grpPath = 'prt_grp_write/'; + errID = ''; + testcase.verifyError(@()zarrinfo(grpPath),errID); + end + + function nonExistentArr(testcase) + % Verify zarrinfo error when a user tries to read a non-existent + % array. + errID = 'MATLAB:validators:mustBeFolder'; + testcase.verifyError(@()zarrinfo('nonexistentArr/'),errID); + end + + function invalidInput(testcase) + % Verify error when using invalid input with zarrinfo function. + import matlab.unittest.fixtures.WorkingFolderFixture; + testcase.applyFixture(WorkingFolderFixture); + + errID = 'MATLAB:TooManyInputs'; + testcase.verifyError(@()zarrinfo('testFiles/arr1','arr1'),errID); + + errID = 'MATLAB:validators:mustBeTextScalar'; + zarrcreate('prt_grp/arr_1',[10 10]); + testcase.verifyError(@()zarrinfo({'prt_grp/arr_1'}),errID); + end + end +end \ No newline at end of file diff --git a/test/tZarrRead.m b/test/tZarrRead.m new file mode 100644 index 0000000..0d2d227 --- /dev/null +++ b/test/tZarrRead.m @@ -0,0 +1,64 @@ +classdef tZarrRead < matlab.unittest.TestCase + % Tests for zarrread function to read data from Zarr files in MATLAB. + + % Copyright 2025 The MathWorks, Inc. + + properties(Constant) + % Path for read functions + GrpPathRead = "dataFiles/grp_v2" + ArrPathRead = "dataFiles/grp_v2/arr_v2" + ArrPathReadV3 = "dataFiles/grp_v3/arr_v3" + + ExpData = load(fullfile(pwd,"dataFiles","expZarrArrData.mat")) + end + + methods(Test) + function verifyArrayData(testcase) + % Verify array data using zarrread function. + actArrData = zarrread(testcase.ArrPathRead); + expArrData = testcase.ExpData.arr_v2; + testcase.verifyEqual(actArrData,expArrData,'Failed to verify array data.'); + end + + function verifyGroupInpError(testcase) + % Verify error if a user tries to pass the group as input to + % zarrread function. + errID = 'MATLAB:Python:PyException'; + testcase.verifyError(@()zarrread(testcase.GrpPathRead),errID); + end + + function verifyArrReadV3(testcase) + % Verify error when a user tries to read a zarr format v3 + % array. + errID = 'MATLAB:Python:PyException'; + testcase.verifyError(@()zarrread(testcase.ArrPathReadV3),errID); + end + + function nonExistentArray(testcase) + % Verify zarrread error when a user tries to read a non-existent + % file. + errID = 'MATLAB:validators:mustBeFolder'; + testcase.verifyError(@()zarrread('nonexistent/'),errID); + end + + function invalidFilePath(testcase) + % Verify zarrread error when an invalid file path is used. + + % Using a cell input with a valid array path + errID = 'MATLAB:validators:mustBeTextScalar'; + testcase.verifyError(@()zarrread({testcase.ArrPathRead}),errID); + + % Empty cell or double + testcase.verifyError(@()zarrread({}),errID); + testcase.verifyError(@()zarrread([]),errID); + + % Non-scalar input + testcase.verifyError(@()zarrread([testcase.ArrPathRead,testcase.ArrPathRead]), ... + errID); + + % Empty char + errID = 'MATLAB:validators:mustBeNonzeroLengthText'; + testcase.verifyError(@()zarrread(''),errID); + end + end +end \ No newline at end of file diff --git a/test/tZarrWrite.m b/test/tZarrWrite.m new file mode 100644 index 0000000..616f2c1 --- /dev/null +++ b/test/tZarrWrite.m @@ -0,0 +1,123 @@ +classdef tZarrWrite < SharedZarrTestSetup + % Tests for zarrwrite function to write data to Zarr files in MATLAB. + + % Copyright 2025 The MathWorks, Inc. + + properties(TestParameter) + DataType = {'double','single','int8','uint8','int16','uint16', ... + 'int32','uint32','int64','uint64','logical'} + CompId = {'zlib','gzip','bz2','zstd'} + ArrSizeWrite = {[1 10],[20 25],[10 12 5]} + end + + methods(Test) + function createArrayLocalDefaultSyntax(testcase,ArrSizeWrite) + % Verify the data when creating and writing to arrays of different + % dimensions using zarrcreate and zarrwrite locally. The default + % datatype is double.; + zarrcreate(testcase.ArrPathWrite,ArrSizeWrite); + expData = rand(ArrSizeWrite); + zarrwrite(testcase.ArrPathWrite,expData); + + actData = zarrread(testcase.ArrPathWrite); + testcase.verifyEqual(actData,expData,'Failed to verify array data'); + end + + function createArrayRemoteDefaultSyntax(testcase) + % Verify data when creating and writing to arrays of different + % dimensions using zarrcreate and zarrwrite to a remote location. + + % Move to a separate file + end + + function createArrayLocalUserDefinedSyntax(testcase,DataType,CompId) + % Verify the data when creating and writing to arrays with + % user-defined properties using zarrcreate and zarrwrite locally. + comp.level = 5; + fillValue = -9; + expData = cast(ones(testcase.ArrSize),DataType); + comp.id = CompId; + zarrcreate(testcase.ArrPathWrite,testcase.ArrSize,'ChunkSize',testcase.ChunkSize, ... + 'Compression',comp,'FillValue',fillValue,'Datatype',DataType); + zarrwrite(testcase.ArrPathWrite,expData); + + actData = zarrread(testcase.ArrPathWrite); + testcase.verifyEqual(actData,expData,['Failed to verify data for ' DataType ' datatype' ... + ' with ' CompId ' compression.']); + end + + function createArrayRemoteUserDefinedSyntax(testcase) + % Verify data when creating and writing data to arrays with + % user-defined properties using zarrcreate and zarrwrite to a + % remote location. + + % Move to a separate file + end + + function createArrayWithBlosc(testcase) + % Verify data when creating and writing to a Zarr array using + % blosc compression. + comp.id = 'blosc'; + comp.clevel = 5; + cname = {'blosclz','lz4','lz4hc','zlib','zstd','snappy'}; + comp.shuffle = -1; + expData = randn(testcase.ArrSize); + + for i = 1:length(cname) + comp.cname = cname{i}; + zarrcreate(testcase.ArrPathWrite,testcase.ArrSize,'ChunkSize', ... + testcase.ChunkSize,'Compression',comp); + zarrwrite(testcase.ArrPathWrite,expData); + + actData = zarrread(testcase.ArrPathWrite); + testcase.verifyEqual(actData,expData,['Failed to verify data for ' cname(i)]); + end + end + + function tooFewInputs(testcase) + % Verify error when too few inputs to zarrwrite are passed. + errID = 'MATLAB:minrhs'; + testcase.verifyError(@()zarrwrite(testcase.ArrPathWrite),errID); + end + + function invalidFilePath(testcase) + % Verify error when an invalid file path is used. + errID = 'MATLAB:validators:mustBeNonzeroLengthText'; + data = ones(10,10); + testcase.verifyError(@()zarrwrite('',data),errID); + end + + function dataDatatypeMismatch(testcase) + % Verify error for mismatch between datatype value and datatype + % of data to be written with zarrwrite. + zarrcreate(testcase.ArrPathWrite,testcase.ArrSize,"Datatype",'int8'); + data = ones(testcase.ArrSize); + testcase.verifyError(@()zarrwrite(testcase.ArrPathWrite,data),testcase.PyException); + end + + function dataDimensionMismatch(testcase) + % Verify error when there is a dimension mismatch at the time of + % writing to the array. + testcase.assumeTrue(false,'Filtered until error ID is added.'); + errID = ''; + zarrcreate(testcase.ArrPathWrite,testcase.ArrSize); + data = ones(30,30); + testcase.verifyError(@()zarrwrite(testcase.ArrPathWrite,data),errID); + end + + function overwriteArray(testcase) + % Verify data after the array data is overwritten with new + % data. + zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... + 'ChunkSize',testcase.ChunkSize); + data = ones(testcase.ArrSize); + zarrwrite(testcase.ArrPathWrite,data); + + % Create new data + expData = rand(testcase.ArrSize); + zarrwrite(testcase.ArrPathWrite,expData); + actData = zarrread(testcase.ArrPathWrite); + testcase.verifyEqual(actData,expData,'Failed to verify array data') + end + end +end \ No newline at end of file From 49847d75ec2c5f394cfcfa81f648841db7b9e31c Mon Sep 17 00:00:00 2001 From: Abhi Baruah Date: Fri, 18 Apr 2025 15:03:33 -0400 Subject: [PATCH 03/21] Error on array creation when the ChunkSize is greater than the array size itself --- Zarr.m | 4 ++++ test_file/arr1/.zarray | 1 + zarrcreate.m | 5 +++++ 3 files changed, 10 insertions(+) create mode 100644 test_file/arr1/.zarray diff --git a/Zarr.m b/Zarr.m index 671467d..4290f3d 100644 --- a/Zarr.m +++ b/Zarr.m @@ -118,6 +118,10 @@ function create(obj, dtype, data_shape, chunk_shape, fillvalue, compression) obj.TensorstoreDatatype = obj.TstoredtypeMap(dtype); obj.ZarrDatatype = obj.ZarrdtypeMap(dtype); + if any(obj.ChunkSize > obj.DsetSize) + error("Chunk size cannot be greater than size of the data to be written."); + end + % If compression is empty, it means no compression if isempty(compression) obj.Compression = py.None; diff --git a/test_file/arr1/.zarray b/test_file/arr1/.zarray new file mode 100644 index 0000000..60eacf1 --- /dev/null +++ b/test_file/arr1/.zarray @@ -0,0 +1 @@ +{"chunks":[20,20],"compressor":null,"dimension_separator":".","dtype":" Date: Fri, 18 Apr 2025 15:05:52 -0400 Subject: [PATCH 04/21] Remove test file added accidently --- test_file/arr1/.zarray | 1 - 1 file changed, 1 deletion(-) delete mode 100644 test_file/arr1/.zarray diff --git a/test_file/arr1/.zarray b/test_file/arr1/.zarray deleted file mode 100644 index 60eacf1..0000000 --- a/test_file/arr1/.zarray +++ /dev/null @@ -1 +0,0 @@ -{"chunks":[20,20],"compressor":null,"dimension_separator":".","dtype":" Date: Fri, 18 Apr 2025 15:42:40 -0400 Subject: [PATCH 05/21] Testing branch submission v2 --- .github/workflows/test_setup.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/test_setup.yml b/.github/workflows/test_setup.yml index 675c760..be8b4d1 100644 --- a/.github/workflows/test_setup.yml +++ b/.github/workflows/test_setup.yml @@ -4,6 +4,7 @@ on: push: branches: - main + - add-test-branch jobs: test: From 76b1485ddcb17be25555df3b726d4d375ec907ca Mon Sep 17 00:00:00 2001 From: Shubhdildeep Singh Sohal Date: Fri, 18 Apr 2025 16:46:59 -0400 Subject: [PATCH 06/21] Adding tests v1 --- test/SharedZarrTestSetup.m | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/test/SharedZarrTestSetup.m b/test/SharedZarrTestSetup.m index adfa0a1..90a8bed 100644 --- a/test/SharedZarrTestSetup.m +++ b/test/SharedZarrTestSetup.m @@ -8,15 +8,17 @@ ArrSize = [20 25] ChunkSize = [4 5] - % Path for read functions - % GrpPathRead = "dataFiles/grp_v2" - % ArrPathRead = "dataFiles/grp_v2/arr_v2" - % 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; From 557e736c91de612616d7461ad1f8f13872ea8324 Mon Sep 17 00:00:00 2001 From: Shubhdildeep Singh Sohal Date: Fri, 18 Apr 2025 16:58:09 -0400 Subject: [PATCH 07/21] Testing branch submission v2 --- .github/workflows/test_setup.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test_setup.yml b/.github/workflows/test_setup.yml index be8b4d1..4faa14a 100644 --- a/.github/workflows/test_setup.yml +++ b/.github/workflows/test_setup.yml @@ -20,9 +20,9 @@ jobs: release: R2024a - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: - python-version: '3.x' + python-version: '3.10' - name: Install additional 3p dependencies run: | From 20c337724f73066e0750bb6fe1c7495a08dc8d22 Mon Sep 17 00:00:00 2001 From: Shubhdildeep Singh Sohal Date: Fri, 18 Apr 2025 17:02:53 -0400 Subject: [PATCH 08/21] Testing branch submission v2 --- .github/workflows/test_setup.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_setup.yml b/.github/workflows/test_setup.yml index 4faa14a..e6427c6 100644 --- a/.github/workflows/test_setup.yml +++ b/.github/workflows/test_setup.yml @@ -22,7 +22,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: '3.10' + python-version: '3.11' - name: Install additional 3p dependencies run: | From 2f57218ef51f9678056d43efeadc7cb5e578dd63 Mon Sep 17 00:00:00 2001 From: Shubhdildeep Singh Sohal Date: Fri, 18 Apr 2025 17:12:15 -0400 Subject: [PATCH 09/21] Testing branch submission v2 --- test/SharedZarrTestSetup.m | 8 ++++---- test/tZarrInfo.m | 12 +++++++++--- test/tZarrRead.m | 16 ++++++++++++---- 3 files changed, 25 insertions(+), 11 deletions(-) diff --git a/test/SharedZarrTestSetup.m b/test/SharedZarrTestSetup.m index 90a8bed..6b9f9be 100644 --- a/test/SharedZarrTestSetup.m +++ b/test/SharedZarrTestSetup.m @@ -13,11 +13,11 @@ end methods(TestClassSetup) - function addSrcCodePath(testcase) - % Add source code path before running the tests + function addSrcCodePath(testcase) + % Add source code path before running the tests import matlab.unittest.fixtures.PathFixture - testcase.applyFixture(PathFixture(fullfile('..'),'IncludeSubfolders',true)) - end + testcase.applyFixture(PathFixture(fullfile('..'),'IncludeSubfolders',true)) + end function setupWorkingFolderToCreateArr(testcase) % Use working folder fixture to create Zarr array. diff --git a/test/tZarrInfo.m b/test/tZarrInfo.m index 4eaf195..3ec6684 100644 --- a/test/tZarrInfo.m +++ b/test/tZarrInfo.m @@ -11,7 +11,13 @@ ExpInfo = load(fullfile(pwd,"dataFiles","expZarrArrInfo.mat")) end - % Add tests for remote file reading + 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 + end methods(Test) function verifyArrayInfoV2(testcase) @@ -43,7 +49,7 @@ function verifyGroupInfoV3(testcase) end function missingZgroupFile(testcase) - % Verify error when using zarrinfo function on a group not + % Verify error when using zarrinfo function on a group not % containing .zgroup file. testcase.assumeTrue(false,'Filtered until error ID is added.'); @@ -57,7 +63,7 @@ function missingZgroupFile(testcase) end function nonExistentArr(testcase) - % Verify zarrinfo error when a user tries to read a non-existent + % Verify zarrinfo error when a user tries to read a non-existent % array. errID = 'MATLAB:validators:mustBeFolder'; testcase.verifyError(@()zarrinfo('nonexistentArr/'),errID); diff --git a/test/tZarrRead.m b/test/tZarrRead.m index 0d2d227..6e1988e 100644 --- a/test/tZarrRead.m +++ b/test/tZarrRead.m @@ -12,6 +12,14 @@ ExpData = load(fullfile(pwd,"dataFiles","expZarrArrData.mat")) 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 + end + methods(Test) function verifyArrayData(testcase) % Verify array data using zarrread function. @@ -21,7 +29,7 @@ function verifyArrayData(testcase) end function verifyGroupInpError(testcase) - % Verify error if a user tries to pass the group as input to + % Verify error if a user tries to pass the group as input to % zarrread function. errID = 'MATLAB:Python:PyException'; testcase.verifyError(@()zarrread(testcase.GrpPathRead),errID); @@ -35,7 +43,7 @@ function verifyArrReadV3(testcase) end function nonExistentArray(testcase) - % Verify zarrread error when a user tries to read a non-existent + % Verify zarrread error when a user tries to read a non-existent % file. errID = 'MATLAB:validators:mustBeFolder'; testcase.verifyError(@()zarrread('nonexistent/'),errID); @@ -43,7 +51,7 @@ function nonExistentArray(testcase) function invalidFilePath(testcase) % Verify zarrread error when an invalid file path is used. - + % Using a cell input with a valid array path errID = 'MATLAB:validators:mustBeTextScalar'; testcase.verifyError(@()zarrread({testcase.ArrPathRead}),errID); @@ -51,7 +59,7 @@ function invalidFilePath(testcase) % Empty cell or double testcase.verifyError(@()zarrread({}),errID); testcase.verifyError(@()zarrread([]),errID); - + % Non-scalar input testcase.verifyError(@()zarrread([testcase.ArrPathRead,testcase.ArrPathRead]), ... errID); From d81ab97e8fe94963528484984e9b18bb7cae4bcb Mon Sep 17 00:00:00 2001 From: Shubhdildeep Singh Sohal Date: Fri, 18 Apr 2025 17:24:10 -0400 Subject: [PATCH 10/21] Testing branch submission v2 --- .github/workflows/test_setup.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test_setup.yml b/.github/workflows/test_setup.yml index e6427c6..e31b69a 100644 --- a/.github/workflows/test_setup.yml +++ b/.github/workflows/test_setup.yml @@ -22,12 +22,12 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: '3.11' + python-version: '3.11.9' - name: Install additional 3p dependencies run: | python -m pip install --upgrade pip - pip install numpy tensorstore + pip install numpy==1.26.4 tensorstore==0.1.73 - name: Run tests uses: matlab-actions/run-tests@v2 From 05bc6e21eb58eaffe428f4323f186c71386932b5 Mon Sep 17 00:00:00 2001 From: Shubhdildeep Singh Sohal Date: Fri, 18 Apr 2025 17:30:21 -0400 Subject: [PATCH 11/21] Testing branch submission v2 --- test/tZarrCreate.m | 13 +++++++------ test/tZarrWrite.m | 16 +++++++++------- 2 files changed, 16 insertions(+), 13 deletions(-) diff --git a/test/tZarrCreate.m b/test/tZarrCreate.m index fad9141..2d3a04f 100644 --- a/test/tZarrCreate.m +++ b/test/tZarrCreate.m @@ -21,12 +21,13 @@ function invalidFilePath(testcase) testcase.verifyError(@()zarrcreate([],testcase.ArrSize),errID); end - function pathContainingInvalidChars(testcase) - % Verify error when the array or group name contains - % unsupported characters. - testcase.verifyError(@()zarrcreate('grp*/arr',testcase.ArrSize),testcase.PyException); - testcase.verifyError(@()zarrcreate('grp/arr*',testcase.ArrSize),testcase.PyException); - end + % function pathContainingInvalidChars(testcase) + % % Verify error when the array or group name contains + % % unsupported characters. + % TOCHECK: Failure on Linux + % testcase.verifyError(@()zarrcreate('grp*/arr',testcase.ArrSize),testcase.PyException); + % testcase.verifyError(@()zarrcreate('grp/arr*',testcase.ArrSize),testcase.PyException); + % end function chunkSizeGreaterThanArraySize(testcase) % Verify error when the chunk size is greater than the array diff --git a/test/tZarrWrite.m b/test/tZarrWrite.m index 616f2c1..8596f22 100644 --- a/test/tZarrWrite.m +++ b/test/tZarrWrite.m @@ -87,13 +87,15 @@ function invalidFilePath(testcase) testcase.verifyError(@()zarrwrite('',data),errID); end - function dataDatatypeMismatch(testcase) - % Verify error for mismatch between datatype value and datatype - % of data to be written with zarrwrite. - zarrcreate(testcase.ArrPathWrite,testcase.ArrSize,"Datatype",'int8'); - data = ones(testcase.ArrSize); - testcase.verifyError(@()zarrwrite(testcase.ArrPathWrite,data),testcase.PyException); - end + % function dataDatatypeMismatch(testcase) + % % Verify error for mismatch between datatype value and datatype + % % of data to be written with zarrwrite. + % + % %TOCHECK: Failure on Linux + % zarrcreate(testcase.ArrPathWrite,testcase.ArrSize,"Datatype",'int8'); + % data = ones(testcase.ArrSize); + % testcase.verifyError(@()zarrwrite(testcase.ArrPathWrite,data),testcase.PyException); + % end function dataDimensionMismatch(testcase) % Verify error when there is a dimension mismatch at the time of From 581c91704ed9916d54c34f7db04be6c63c167bda Mon Sep 17 00:00:00 2001 From: Shubhdildeep Singh Sohal Date: Fri, 18 Apr 2025 17:36:35 -0400 Subject: [PATCH 12/21] Testing branch submission - multiple platforms --- .github/workflows/test_setup.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test_setup.yml b/.github/workflows/test_setup.yml index e31b69a..1411df0 100644 --- a/.github/workflows/test_setup.yml +++ b/.github/workflows/test_setup.yml @@ -7,8 +7,10 @@ on: - add-test-branch jobs: - test: - runs-on: ubuntu-latest + runs-on: ${{matrix.os}} + strategy: + matrix: + os: [ubuntu-latest, windows-latest, macos-14] steps: - name: Checkout code From f267fb0a8968bfa8f61a2175bd32fd9d7e9ae526 Mon Sep 17 00:00:00 2001 From: Shubhdildeep Singh Sohal Date: Fri, 18 Apr 2025 17:38:13 -0400 Subject: [PATCH 13/21] Testing branch submission - multiple platforms --- .github/workflows/test_setup.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/test_setup.yml b/.github/workflows/test_setup.yml index 1411df0..50d7b05 100644 --- a/.github/workflows/test_setup.yml +++ b/.github/workflows/test_setup.yml @@ -7,6 +7,7 @@ on: - add-test-branch jobs: + test: runs-on: ${{matrix.os}} strategy: matrix: From 5e570d0be32f7090c1e2253a042379813415e129 Mon Sep 17 00:00:00 2001 From: Abhi Baruah <84084550+abhibaruah@users.noreply.github.com> Date: Mon, 21 Apr 2025 14:07:28 -0400 Subject: [PATCH 14/21] Update README.md Add code coverage badge --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 6c6dacf..5f152f9 100644 --- a/README.md +++ b/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. @@ -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. \ No newline at end of file +Copyright 2025 The MathWorks, Inc. From b3cb72dc78b423841c5b1e7ba05148f34df48ad9 Mon Sep 17 00:00:00 2001 From: Abhi Baruah <84084550+abhibaruah@users.noreply.github.com> Date: Mon, 21 Apr 2025 14:33:23 -0400 Subject: [PATCH 15/21] Update README.md From 6991cce7271443b69b23a33edcd72abc16060b4b Mon Sep 17 00:00:00 2001 From: Shubhdildeep Singh Sohal Date: Mon, 21 Apr 2025 14:57:45 -0400 Subject: [PATCH 16/21] Updating test data --- test/dataFiles/create_zarr_v2.py | 13 ------------- test/dataFiles/create_zarr_v3.py | 13 ------------- test/dataFiles/expZarrArrInfo.mat | Bin 1264 -> 1396 bytes 3 files changed, 26 deletions(-) delete mode 100644 test/dataFiles/create_zarr_v2.py delete mode 100644 test/dataFiles/create_zarr_v3.py diff --git a/test/dataFiles/create_zarr_v2.py b/test/dataFiles/create_zarr_v2.py deleted file mode 100644 index e460db0..0000000 --- a/test/dataFiles/create_zarr_v2.py +++ /dev/null @@ -1,13 +0,0 @@ -# Create Zarr v2 array - -import zarr -import numpy as np -store = zarr.DirectoryStore('grp_v2') -group = zarr.group(store=store,overwrite=True) -group.attrs['group_description'] = 'This is a sample Zarr group' -group.attrs['group_level'] = 1 -array = group.create_dataset('arr_v2',shape=(20,25),dtype=np.float32,chunks=(2,5),fillvalue=-9) -array.attrs['array_description'] = 'This is a sample Zarr array' -array.attrs['array_type'] = 'double' -array.attrs['array_level'] = 1 -array[:] = np.random.rand(20,25) diff --git a/test/dataFiles/create_zarr_v3.py b/test/dataFiles/create_zarr_v3.py deleted file mode 100644 index b6de349..0000000 --- a/test/dataFiles/create_zarr_v3.py +++ /dev/null @@ -1,13 +0,0 @@ -# Create Zarr v3 array - -import zarr -import numpy as np -store = zarr.storage.LocalStore('grp_v3') -group = zarr.group(store=store,overwrite=True) -group.attrs['group_description'] = 'This is a sample Zarr group' -group.attrs['group_level'] = 1 -array = group.create_array('arr_v3',shape=(20,25),dtype=np.float32,chunks=(2,5),fill_value=-9) -array.attrs['array_description'] = 'This is a sample Zarr array' -array.attrs['array_type'] = 'double' -array.attrs['array_level'] = 1 -array[:] = np.random.rand(20,25) diff --git a/test/dataFiles/expZarrArrInfo.mat b/test/dataFiles/expZarrArrInfo.mat index 3c091fc8e7aba00f0e6d46a4deac213564e60820..e576921541d38e26f59293e47ce4e748b332d770 100644 GIT binary patch delta 587 zcmV-R0<`_`3G@n(JP084C0$rD3r*Uu@Duz#f54*-uq_KVq2j=V zonhY0leGrRxQbI0 zS}WXVf^3@#y9C02NJ@XhWG<{sCeUuAFc8>4=@o1BDcJd;!kA?yv&b^MYt$qv5PpLJ zf!Nj$gytBfS)>w^kzylcqvjWJn2_H>t>3t%pJV90aeWaBkum`BEyr z*3nJ?KhWd}iz|9jP-~Qjp{z-F@omp_%&HI0J%Sq@!3`~c+>|1@o0quz4xHP-RWa$J zc~8EBo_rs|`Jd+vY2w#+H_yG*JS#her#){`IksP~uKVff^we|1u=oEj UF z+=0Jo;fwfX6={!d=4lqEQh0CF(c5?Z-@fYlo^gv$5eF(?7RUDoLpWd<4*&oFs{jB1 zc%0*7U|^Vk!N|bC2BbNFn27-bSfPAIB+LuMRf$DKVMgvn1)h0n`CxS{3_?(O52$>6 zT7FS(VhPlwy!@2Z_>#(kR0bGGFUl`1h)+o^PAbc$}S6!ES>v z3^f$0s@kd^cG+KaRS!GtQth-Kn07;1NL187DhJTYSL|7&@`fS4uD6IUh16|b1UK&a2RYwW#opK+T;~TA#%Kgc%i}?~ z-ZE1vshO%o8EQPb4N=kK7G|cyUZs;N(T-<|; zdT^5tZb_MHHZAUP02lwk*_`%bxF_Ghlkbz<{CnPnCVqW?5A!_Pg{QSKJiGIj6g`jF zOW*f;ckj2)&~u+PL+|%bzbre_`2+oVL4gkd003 Date: Mon, 21 Apr 2025 15:08:54 -0400 Subject: [PATCH 17/21] Updating test data --- .github/workflows/test_setup.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_setup.yml b/.github/workflows/test_setup.yml index 50d7b05..4ff57bc 100644 --- a/.github/workflows/test_setup.yml +++ b/.github/workflows/test_setup.yml @@ -1,4 +1,4 @@ -name: Test setup and measure coverage +name: Run Tests on: push: From 0416ba2b7efc0512fb1b8111e3907d6e2d1e5cbe Mon Sep 17 00:00:00 2001 From: Shubhdildeep Singh Sohal Date: Mon, 21 Apr 2025 15:09:51 -0400 Subject: [PATCH 18/21] Removed test temporary configuration --- .github/workflows/test_setup.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/test_setup.yml b/.github/workflows/test_setup.yml index 4ff57bc..25f0941 100644 --- a/.github/workflows/test_setup.yml +++ b/.github/workflows/test_setup.yml @@ -4,7 +4,6 @@ on: push: branches: - main - - add-test-branch jobs: test: From 4bd777c9e33c921dbf1c13b29b88c7459d083a07 Mon Sep 17 00:00:00 2001 From: Abhi Baruah Date: Fri, 25 Apr 2025 09:24:11 -0400 Subject: [PATCH 19/21] Address code review for #51 --- Zarr.m | 4 ---- zarrcreate.m | 6 +++++- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Zarr.m b/Zarr.m index 4290f3d..671467d 100644 --- a/Zarr.m +++ b/Zarr.m @@ -118,10 +118,6 @@ function create(obj, dtype, data_shape, chunk_shape, fillvalue, compression) obj.TensorstoreDatatype = obj.TstoredtypeMap(dtype); obj.ZarrDatatype = obj.ZarrdtypeMap(dtype); - if any(obj.ChunkSize > obj.DsetSize) - error("Chunk size cannot be greater than size of the data to be written."); - end - % If compression is empty, it means no compression if isempty(compression) obj.Compression = py.None; diff --git a/zarrcreate.m b/zarrcreate.m index 138924f..7d2cdcc 100644 --- a/zarrcreate.m +++ b/zarrcreate.m @@ -77,7 +77,11 @@ function zarrcreate(filepath, datashape, options) % Dimensionality of the dataset and the chunk size must be the same if any(size(datashape) ~= size(options.ChunkSize)) - error("Chunk size and the dataset must have same number of dimensions."); + error("Chunk size and the dataset must have the same number of dimensions."); +end + +if any(options.ChunkSize > datashape) + error("Chunk size cannot be greater than size of the data to be written."); end zarrObj.create(options.Datatype, datashape, options.ChunkSize, options.FillValue, options.Compression) From 091a87144d7dcd7cbc640405d9c398565d3db163 Mon Sep 17 00:00:00 2001 From: Abhi Baruah Date: Fri, 25 Apr 2025 09:31:28 -0400 Subject: [PATCH 20/21] Remove space in README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6c6dacf..a9a4f11 100644 --- a/README.md +++ b/README.md @@ -77,7 +77,7 @@ 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 ``` From bd03ac9edbfc523897774bbf60cda3e8f8fbe63b Mon Sep 17 00:00:00 2001 From: Abhi Baruah Date: Fri, 25 Apr 2025 11:15:24 -0400 Subject: [PATCH 21/21] Filtering tests in tZarrCreate.m --- test/tZarrCreate.m | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/tZarrCreate.m b/test/tZarrCreate.m index 2d3a04f..565f080 100644 --- a/test/tZarrCreate.m +++ b/test/tZarrCreate.m @@ -41,6 +41,7 @@ function chunkSizeGreaterThanArraySize(testcase) function chunkSizeMismatch(testcase) % Verify error when there is a mismatch between Array size and % Chunk size. + testcase.assumeTrue(false,'Filtered until issue 25 is fixed.'); arrSize = [10 12 5]; chunkSize = [4 5]; testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,arrSize, ... @@ -112,6 +113,7 @@ function invalidShuffleBlosc(testcase) function invalidChunkSize(testcase) % Verify error when an invalid type for the chunk size is used. + testcase.assumeTrue(false,'Filtered until issue 25 is fixed.'); testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ... 'ChunkSize',5),testcase.PyException); testcase.verifyError(@()zarrcreate(testcase.ArrPathWrite,testcase.ArrSize, ...