Test cleanup: fixtures, coverage, and stub removal

.gitignore

@@ -1,5 +1,13 @@
 # Folder for generating test Zarr files
-test_files/ 
+test_files/
+
+# Coverage artifacts produced by tools/run_coverage.m
+test/coverageReport/
+test/cobertura.xml
+test/coverage_results.mat
+
+# Leaked by tZarrRead/tooBigArray (runs outside a WorkingFolderFixture)
+test/bigData/
 
 # Windows default autosave extension
 *.asv
@@ -10,3 +18,8 @@ test_files/
 # Bytecode-compiled version of python code
 PythonModule/__pycache__
 *.pyc
+.venv-zarr/
+
+# Local Claude Code profile (per-developer, not shared)
+.claude/
+.claude-profiles

CLAUDE.md

@@ -0,0 +1,63 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Overview
+
+MATLAB interface for reading and writing Zarr v2 arrays and metadata, from both local storage and Amazon S3. The MATLAB layer delegates the actual Zarr I/O to Google's [tensorstore](https://github.com/google/tensorstore) Python library, which it calls through MATLAB's `py.` Python bridge.
+
+## Architecture
+
+The codebase is a three-language stack. Data and type information flow across all three layers, so a change to the data path usually touches each:
+
+1. **User-facing MATLAB functions** (`zarrread.m`, `zarrwrite.m`, `zarrcreate.m`, `zarrinfo.m`, `zarrwriteatt.m`) — thin wrappers that do `arguments`-block input validation and construct a `Zarr` object. These are the documented public API.
+
+2. **`Zarr.m`** — the central gateway class (`classdef Zarr < handle`). It owns the connection between MATLAB and Python: bootstrapping the Python module path (`pySetup`/`ZarrPy`), building the tensorstore KVStore schema (local `file` driver vs. S3 `s3` driver), resolving/creating paths and Zarr groups, validating partial-read parameters, and converting between MATLAB and numpy arrays. Most non-trivial logic lives here as static helper methods.
+
+3. **`PythonModule/ZarrPy.py`** — a small wrapper over tensorstore. Exposes `createKVStore`, `createZarr`, `writeZarr`, `readZarr`. This is the only code that talks to tensorstore directly. `Zarr.m` imports it via `py.importlib.import_module('ZarrPy')` after inserting `PythonModule/` onto `py.sys.path`.
+
+### Key cross-cutting concerns
+
+- **Datatype mapping** (`ZarrDatatype.m`): a single class holds three parallel arrays mapping MATLAB types ↔ tensorstore types ↔ Zarr dtype strings (e.g. `"double"` ↔ `"float64"` ↔ `"<f8"`). Construct via the static `fromMATLABType` / `fromTensorstoreType` / `fromZarrType` methods, never the private constructor. Any new supported datatype must be added to all three arrays in lockstep.
+
+- **Index convention conversion**: MATLAB is 1-based and uses *count*; tensorstore is 0-based and uses *end index* (exclusive). The translation happens in `Zarr.read` (`start = start - 1`, `endInds = start + stride.*count`). Partial-read validation (Start/Stride/Count bounds, scalar-into-vector indexing) is in `Zarr.processPartialReadParams`.
+
+- **Local vs. remote (S3)**: `obj.isRemote` is detected from an IRI prefix on the path. S3 URLs/URIs in six different formats are parsed into bucket + object path by `Zarr.extractS3BucketNameAndPath`. Some validity checks (e.g. `isZarrArray`) are skipped for `http`-style remote paths because they would fail even on valid arrays.
+
+- **Zarr metadata files**: `.zarray` marks an array, `.zgroup` marks a group, `.zattrs` holds user-defined attributes (all Zarr v2, read/written as JSON). `zarr.json` is the Zarr v3 metadata file — it is detected by `zarrinfo` but writing v3 is not supported. `zarrinfo.m` reads these JSON files directly in MATLAB (not via Python); creating group hierarchies writes `.zgroup` files directly too.
+
+## Commands
+
+There is no build step — it's interpreted MATLAB plus a Python module on the path.
+
+**Run the full test suite** (from the `test/` directory, since tests resolve data paths relative to `pwd`):
+```matlab
+cd test
+results = runtests('IncludeSubfolders', true)
+```
+
+**Run a single test class or method:**
+```matlab
+cd test
+runtests('tZarrRead')                       % one class
+runtests('tZarrRead/verifyPartialArrayData') % one method
+```
+
+CI (`.github/workflows/test_setup.yml`) runs `matlab-actions/run-tests` with `select-by-folder: 'test'` across Ubuntu/Windows/macOS and MATLAB R2024a + latest.
+
+## Setup requirements
+
+- MATLAB R2024a or newer. Add the repo root to the MATLAB path (`addpath`).
+- Python 3.10+ configured for MATLAB (`pyenv`), with `numpy` and `tensorstore` installed (see `PythonModule/requirements.txt`; CI pins `tensorstore==0.1.71`, the minimum supported version).
+
+When iterating on `ZarrPy.py`, MATLAB caches the imported module. Reload with `Zarr.pyReloadInProcess()` (after `clear classes`) for in-process Python, or `terminate(pyenv)` for out-of-process.
+
+## Tests
+
+xUnit-style classes (`matlab.unittest.TestCase`) named `t<Feature>.m` in `test/`. They inherit shared fixtures from `SharedZarrTestSetup.m`, which adds the parent source folder to the path and copies `test/dataFiles/` into a `WorkingFolderFixture` so write tests don't pollute the repo. Read-test fixtures live in `test/dataFiles/grp_v2` (and `grp_v3`); expected results are stored in `expZarrArrData.mat` / `expZarrArrInfo.mat`.
+
+## Conventions
+
+- All error messages use `error("MATLAB:<area>:<id>", ...)` identifiers — match the existing namespacing when adding new ones.
+- Function help text is the block comment directly under the signature; keep it current since the README points users to `help <function>`.
+- Spelling is checked in CI by codespell (`.codespellrc`); add false positives to `ignore-words-list`.

codecov.yml

@@ -5,4 +5,5 @@ coverage:
         target: 85%
         threshold: 5%
 ignore:
-  - "test/*"
+  - "test/*"
+  - "tools/*"

test/tZarr.m

@@ -35,6 +35,104 @@ function verifyReload(testcase)
 
         end
 
-
+        function verifyIsZarrArrayAndGroup(testcase)
+            % Verify that isZarrArray and isZarrGroup correctly identify a
+            % Zarr array (has .zarray) versus a Zarr group (has .zgroup).
+            % SharedZarrTestSetup copies the *contents* of dataFiles into
+            % the working folder, so fixtures live at grp_v2/... directly.
+            arrPath = "grp_v2/arr_v2";
+            grpPath = "grp_v2";
+
+            testcase.verifyTrue(Zarr.isZarrArray(arrPath),...
+                "Expected an array path to be a Zarr array.");
+            testcase.verifyFalse(Zarr.isZarrArray(grpPath),...
+                "Did not expect a group path to be a Zarr array.");
+
+            testcase.verifyTrue(Zarr.isZarrGroup(grpPath),...
+                "Expected a group path to be a Zarr group.");
+            testcase.verifyFalse(Zarr.isZarrGroup(arrPath),...
+                "Did not expect an array path to be a Zarr group.");
+        end
+
+        function verifyDatatypeRoundTrip(testcase)
+            % Verify that ZarrDatatype maps consistently across MATLAB,
+            % Tensorstore, and Zarr type names, regardless of which static
+            % constructor is used to create it.
+            mlType = "double";
+            tsType = "float64";
+            zType  = "<f8";
+
+            fromML = ZarrDatatype.fromMATLABType(mlType);
+            fromTS = ZarrDatatype.fromTensorstoreType(tsType);
+            fromZarr = ZarrDatatype.fromZarrType(zType);
+
+            for dt = [fromML, fromTS, fromZarr]
+                testcase.verifyEqual(dt.MATLABType, mlType);
+                testcase.verifyEqual(dt.TensorstoreType, tsType);
+                testcase.verifyEqual(dt.ZarrType, zType);
+            end
+        end
+
+        function verifyInvalidTensorstoreType(testcase)
+            % Verify error when an unsupported Tensorstore type name is used.
+            testcase.verifyError(...
+                @()ZarrDatatype.fromTensorstoreType("not_a_type"),...
+                "MATLAB:validators:mustBeMember");
+        end
+
+        function verifyCreateGroupMakesFolder(testcase)
+            % Verify that createGroup creates the directory when it does not
+            % already exist, and writes a valid .zgroup file into it.
+            groupPath = fullfile(pwd, "brandNewGroup");
+            testcase.verifyFalse(isfolder(groupPath),...
+                "Group folder should not exist before createGroup.");
+
+            Zarr.createGroup(groupPath);
+
+            testcase.verifyTrue(isfolder(groupPath),...
+                "createGroup should have created the folder.");
+            testcase.verifyTrue(isfile(fullfile(groupPath, ".zgroup")),...
+                "createGroup should have written a .zgroup file.");
+            testcase.verifyEqual(zarrinfo(groupPath).node_type, 'group',...
+                "createGroup should produce a valid Zarr group.");
+        end
+
+        function verifyCreateGroupOpenFailure(testcase)
+            % Verify error when the .zgroup file cannot be opened for
+            % writing. Everything lives inside an isolated temporary folder
+            % fixture, so no real data is modified.
+            %
+            % We make the existing .zgroup *file* read-only rather than its
+            % folder: a read-only folder does not prevent file creation on
+            % Windows (the directory read-only attribute is ignored there),
+            % whereas a read-only file is honored on both Windows and Unix.
+            import matlab.unittest.fixtures.TemporaryFolderFixture
+            tempFixture = testcase.applyFixture(TemporaryFolderFixture);
+
+            groupPath = fullfile(tempFixture.Folder, "readOnlyGroup");
+            Zarr.createGroup(groupPath);            % writes .zgroup
+            zgroupFile = fullfile(groupPath, ".zgroup");
+
+            fileattrib(zgroupFile, '-w');
+            % Restore write permission before the fixture is torn down so its
+            % contents can be removed (runs before the fixture's rmdir).
+            testcase.addTeardown(@()fileattrib(zgroupFile, '+w'));
+
+            testcase.verifyError(@()Zarr.createGroup(groupPath),...
+                "MATLAB:Zarr:fileOpenFailure");
+        end
+
+        function verifyWriteScalarShapedArray(testcase)
+            % Verify writing to an array whose stored shape is a true scalar
+            % (shape [1]). This exercises the isscalar(info.shape) branch of
+            % Zarr.write, which zarrcreate cannot produce on its own because
+            % it expands scalar sizes to [1 N].
+            scalarPath = "grp_v2/scalarData";
+
+            zarrwrite(scalarPath, 42);
+            testcase.verifyEqual(zarrread(scalarPath), 42,...
+                "Failed to write/read a scalar-shaped Zarr array.");
+        end
+
     end
 end

test/tZarrAttributes.m

@@ -110,14 +110,31 @@ function notZarrObject(testcase)
         end
 
         function noWritePermissions(testcase)
-            % Verify error if there are no write permissions to the Zarr array.
-
-            % Make the folder read-only.
-            fileattrib(testcase.ArrPathWrite,'-w','','s');
-            testcase.addTeardown(@()fileattrib(testcase.ArrPathWrite,'+w','','s'));
+            % Verify error if the .zattrs file cannot be opened for writing.
+            % Everything lives inside an isolated temporary folder fixture so
+            % no shared fixture data is modified.
+            %
+            % We make the existing .zattrs *file* read-only rather than its
+            % folder: a read-only folder does not prevent file creation on
+            % Windows (the directory read-only attribute is ignored there),
+            % whereas a read-only file is honored on both Windows and Unix.
+            import matlab.unittest.fixtures.TemporaryFolderFixture
+            tempFixture = testcase.applyFixture(TemporaryFolderFixture);
+
+            arrPath = fullfile(tempFixture.Folder, "roArr");
+            zarrcreate(arrPath, testcase.ArrSize);
+            % Write one attribute so the .zattrs file exists, then make it
+            % read-only so the next write cannot open it.
+            zarrwriteatt(arrPath, 'existingAttr', 1);
+            zattrsFile = fullfile(arrPath, '.zattrs');
+
+            fileattrib(zattrsFile, '-w');
+            % Restore write permission before the fixture is torn down so its
+            % contents can be removed (runs before the fixture's rmdir).
+            testcase.addTeardown(@()fileattrib(zattrsFile, '+w'));
 
             errID = 'MATLAB:zarrwriteatt:fileOpenFailure';
-            testcase.verifyError(@()zarrwriteatt(testcase.ArrPathWrite,'myAttr','attrVal'), ...
+            testcase.verifyError(@()zarrwriteatt(arrPath,'myAttr','attrVal'), ...
                 errID);
         end
 

test/tZarrCreate.m

@@ -48,13 +48,11 @@ function createIntermediateZgroups(testcase)
 
         function createArrayRelativePath(testcase)
             % Verify that the array is successfully created if a relative
-            % path is used.
-            newDir = 'myFolder';
-            currDir = pwd;
-            mkdir(newDir);
-            testcase.addTeardown(@()cd(currDir));
+            % path is used. Work from a fresh temporary folder (which the
+            % fixture enters and cleans up) so the "../" path resolves.
+            import matlab.unittest.fixtures.WorkingFolderFixture
+            testcase.applyFixture(WorkingFolderFixture);
 
-            cd(newDir);
             inpPath = fullfile('..','myGrp','myArr');
             zarrcreate(inpPath,[10 10]);
             arrInfo = zarrinfo(inpPath);

test/tZarrInfo.m

@@ -1,22 +1,18 @@
-classdef tZarrInfo < matlab.unittest.TestCase
+classdef tZarrInfo < SharedZarrTestSetup
     % 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
+        % SharedZarrTestSetup copies the contents of dataFiles/ into the
+        % working folder, so fixtures are at the working folder root.
+        GrpPathV2 = "grp_v2"
+        ArrPathV2 = "grp_v2/arr_v2"
+        GrpPathV3 = "grp_v3"
+        ArrPathV3 = "grp_v3/arr_v3"
 
-    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
+        % Loaded at class-load time, while pwd is still the test folder.
+        ExpInfo = load(fullfile(pwd,"dataFiles","expZarrArrInfo.mat"))
     end
 
     methods(Test)
@@ -35,9 +31,12 @@ function verifyGroupInfoV2(testcase)
         end
 
         function getArrayInfoRelativePath(testcase)
-            % Verify array info if the input is using relative path to the
-            % array.
-            inpPath = fullfile('..','test',testcase.ArrPathV2);
+            % Verify array info if the input is using a relative path to the
+            % array. Read from a subfolder using a "../" prefixed path.
+            import matlab.unittest.fixtures.CurrentFolderFixture
+            testcase.applyFixture(CurrentFolderFixture("grp_v2"));
+
+            inpPath = fullfile('..', testcase.ArrPathV2);
             actInfo = zarrinfo(inpPath);
             expInfo = testcase.ExpInfo.zarrV2ArrInfo;
             testcase.verifyEqual(actInfo, expInfo, ['Failed to verify array info ' ...

test/tZarrRead.m

@@ -1,28 +1,23 @@
-classdef tZarrRead < matlab.unittest.TestCase
+classdef tZarrRead < SharedZarrTestSetup
     % 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"
-        ArrPathReadSmall = "dataFiles/grp_v2/smallArr"
-        ArrPathReadVector = "dataFiles/grp_v2/vectorData"
-        ArrPathReadScalar = "dataFiles/grp_v2/scalarData"
-        ArrPathReadV3 = "dataFiles/grp_v3/arr_v3"
-
+        % Paths for read functions. SharedZarrTestSetup copies the contents
+        % of dataFiles/ into the working folder, so fixtures are at the
+        % working folder root (grp_v2/..., grp_v3/...).
+        GrpPathRead = "grp_v2"
+        ArrPathRead = "grp_v2/arr_v2"
+        ArrPathReadSmall = "grp_v2/smallArr"
+        ArrPathReadVector = "grp_v2/vectorData"
+        ArrPathReadScalar = "grp_v2/scalarData"
+        ArrPathReadV3 = "grp_v3/arr_v3"
+
+        % Loaded at class-load time, while pwd is still the test folder.
         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.
@@ -88,9 +83,12 @@ function verifyReadScalarData(testcase)
         end
 
         function verifyArrayDataRelativePath(testcase)
-            % Verify array data if the input is using relative path to the
-            % array.
-            inpPath = fullfile('..','test',testcase.ArrPathRead);
+            % Verify array data if the input is using a relative path to the
+            % array. Read from a subfolder using a "../" prefixed path.
+            import matlab.unittest.fixtures.CurrentFolderFixture
+            testcase.applyFixture(CurrentFolderFixture("grp_v2"));
+
+            inpPath = fullfile('..', testcase.ArrPathRead);
             actArrData = zarrread(inpPath);
             expArrData = testcase.ExpData.arr_v2;
             testcase.verifyEqual(actArrData,expArrData,['Failed to verify array ' ...

test/tZarrWrite.m

@@ -28,13 +28,6 @@ function createArrayLocalDefaultSyntax(testcase,ArrSizeWrite)
             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.
@@ -51,14 +44,6 @@ function createArrayLocalUserDefinedSyntax(testcase,DataType,CompId)
                 ' 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 createArrayWithDefaultBloscConfig(testcase)
             % Verify data when creating and writing to a Zarr array using 
             % a default blosc compression configuration.