[PUSHPAK-JAISWAL]

Description

Closes #38 (Tracking: #46)

Why this change was needed

The required statisticsTest CI gate runs 59 tests across 26 classes, of which 8 were previously annotated with bare @Ignore annotations:

1. Four of those tests (CenteredIBSTest.testCenteredIBSTest, NormalizedIBSTest.testNormalizedIBSTest, DominanceNormalizedIBSTest.testDominanceNormalizedIBSTest, and PrinCompTest.test) pass on develop, except that PrinCompTest (and SolveByOrtholgonalizingTest) would fail if DoubleMatrixTest.testBlas ran earlier and left the global DoubleMatrixFactory.DEFAULT set to FactoryType.blas.
2. DoubleMatrixTest mutated DoubleMatrixFactory.DEFAULT via DoubleMatrixFactory.setDefault(...) in each test without restoring the previous factory type afterward.
3. DoubleMatrixTest.testBlas was unconditionally @Ignored instead of checking at runtime whether the optional native TasselBlas JNI library (Retire or test: the native BLAS path (TasselBlas JNI) #45) is available.
4. The remaining three failing tests (MLMTest.testCompressionP3D, AdditiveSiteTest.testGenotypeAdditiveSite, and StepwiseAdditiveModelFitterTest.test) had bare @Ignore annotations with no reason or issue link (Require a reason and an issue link on every @Ignore #35).

What changed

• Re-enabled 4 passing tests: Removed @Ignore (and unused org.junit.Ignore imports) from CenteredIBSTest, NormalizedIBSTest, DominanceNormalizedIBSTest, and PrinCompTest.
• Isolated DoubleMatrixFactory.DEFAULT state in DoubleMatrixTest: Added @Before saveFactory() and @After restoreFactory() hooks to save DoubleMatrixFactory.DEFAULT.getType() before each test and restore it via DoubleMatrixFactory.setDefault(savedType) afterward.
• Converted DoubleMatrixTest.testBlas to a runtime assumption: Replaced @Ignore with Assume.assumeTrue(canLoadTasselBlas()) around System.loadLibrary("TasselBlas") so the test self-skips when TasselBlas is absent and runs when present (Retire or test: the native BLAS path (TasselBlas JNI) #45).
• Documented remaining @Ignore annotations (Require a reason and an issue link on every @Ignore #35): Added issue links and reasons to MLMTest.testCompressionP3D (MLMTest.testCompressionP3D: compression table has 125 rows, expected 131 #39), AdditiveSiteTest.testGenotypeAdditiveSite (Stepwise model fitter tests fail: AdditiveSiteTest and StepwiseAdditiveModelFitterTest #40), and StepwiseAdditiveModelFitterTest.test (Stepwise model fitter tests fail: AdditiveSiteTest and StepwiseAdditiveModelFitterTest #40).

Effects & Verification

• ./gradlew statisticsTest now runs all 59 tests with 55 passing, 0 failures, and 4 skipped (DoubleMatrixTest.testBlas via Assume plus the 3 @Ignored tests tracked in MLMTest.testCompressionP3D: compression table has 125 rows, expected 131 #39 and Stepwise model fitter tests fail: AdditiveSiteTest and StepwiseAdditiveModelFitterTest #40).
• DoubleMatrixTest no longer leaks DoubleMatrixFactory.DEFAULT mutations to subsequent tests (PrinCompTest and SolveByOrtholgonalizingTest pass reliably when run after DoubleMatrixTest).
• No bare @Ignore annotations remain in the statisticsTest gate.

• Re-enable CenteredIBSTest, NormalizedIBSTest, DominanceNormalizedIBSTest, and PrinCompTest in the statisticsTest gate (Statistics gate: re-enable 4 of the 8 skipped tests #38)
• Save and restore DoubleMatrixFactory.DEFAULT around each test in DoubleMatrixTest and guard testBlas with Assume.assumeTrue on TasselBlas availability (Statistics gate: re-enable 4 of the 8 skipped tests #38, Retire or test: the native BLAS path (TasselBlas JNI) #45)
• Add issue references and reasons to the remaining @Ignore annotations in MLMTest, AdditiveSiteTest, and StepwiseAdditiveModelFitterTest (Require a reason and an issue link on every @Ignore #35, MLMTest.testCompressionP3D: compression table has 125 rows, expected 131 #39, Stepwise model fitter tests fail: AdditiveSiteTest and StepwiseAdditiveModelFitterTest #40)

Type of change

What type of changes does your code introduce? Put an x in boxes that apply.

• CHANGE (fix or feature that would cause existing functionality to not work as expected)
• FEATURE (non-breaking change which adds functionality)
• BUGFIX (non-breaking change which fixes an issue)
• ENHANCEMENT (non-breaking change which improves existing functionality)
• NONE (if none of the other choices apply. Example, tooling, build system, CI, docs, etc.)

Checklist:

• The base branch of this PR is develop (use the hotfix template if this targets main)
• I have updated the version variable in build.gradle.kts
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have updated relevant documentation

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 25.38%. Comparing base (b5d5066) to head (b239c98).

Additional details and impacted files

@@              Coverage Diff              @@
##             develop      #47      +/-   ##
=============================================
+ Coverage      25.09%   25.38%   +0.28%     
- Complexity      4872     4918      +46     
=============================================
  Files            610      610              
  Lines          73053    73053              
  Branches       12590    12590              
=============================================
+ Hits           18336    18546     +210     
+ Misses         52842    52628     -214     
- Partials        1875     1879       +4     

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