Update snakeyaml to 2.2

[scala-steward-projectglow[bot]]

About this PR

📦 Updates org.yaml:snakeyaml from 2.0 to 2.2

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🔍 Files still referring to the old version number

The following files still refer to the old version number (2.0). You might want to review and update them manually. ``` .circleci/config.yml .github/workflows/scala-steward.yml .scalafmt.conf CONTRIBUTING.md LICENSE.txt build.sbt conftest.py core/functions.scala.TEMPLATE core/src/main/java/org/projectglow/sql/Functions.java core/src/main/scala-2.13+/io/projectglow/transformers/util/StringUtils.scala core/src/main/scala-2.13-/io/projectglow/transformers/util/StringUtils.scala core/src/main/scala/htsjdk/variant/variantcontext/writer/VCFHeaderWriter.scala core/src/main/scala/htsjdk/variant/vcf/VCFEncoderUtils.scala core/src/main/scala/io/projectglow/Glow.scala core/src/main/scala/io/projectglow/SparkShimBase.scala core/src/main/scala/io/projectglow/bgen/BgenConverterUtils.scala core/src/main/scala/io/projectglow/bgen/BgenFileFormat.scala core/src/main/scala/io/projectglow/bgen/BgenFileIterator.scala core/src/main/scala/io/projectglow/bgen/BgenGenotypeReader.scala core/src/main/scala/io/projectglow/bgen/BgenHeaderWriter.scala core/src/main/scala/io/projectglow/bgen/BgenRecordWriter.scala core/src/main/scala/io/projectglow/bgen/BgenRowToInternalRowConverter.scala core/src/main/scala/io/projectglow/bgen/BgenSchemaInferrer.scala core/src/main/scala/io/projectglow/bgen/BigBgenDatasource.scala core/src/main/scala/io/projectglow/bgen/InternalRowToBgenRowConverter.scala core/src/main/scala/io/projectglow/common/ConverterUtils.scala core/src/main/scala/io/projectglow/common/GlowLogging.scala core/src/main/scala/io/projectglow/common/HailUtils.scala core/src/main/scala/io/projectglow/common/HasStringency.scala core/src/main/scala/io/projectglow/common/Named.scala core/src/main/scala/io/projectglow/common/PythonUtils.scala core/src/main/scala/io/projectglow/common/SimpleInterval.scala core/src/main/scala/io/projectglow/common/WithUtils.scala core/src/main/scala/io/projectglow/common/datasourceOptions.scala core/src/main/scala/io/projectglow/common/logging/HlsEventRecorder.scala core/src/main/scala/io/projectglow/common/logging/HlsUsageLogging.scala core/src/main/scala/io/projectglow/common/schemas.scala core/src/main/scala/io/projectglow/functions.scala core/src/main/scala/io/projectglow/gff/GffDataSource.scala core/src/main/scala/io/projectglow/plink/BedFileIterator.scala core/src/main/scala/io/projectglow/plink/PlinkFileFormat.scala core/src/main/scala/io/projectglow/plink/PlinkRowToInternalRowConverter.scala core/src/main/scala/io/projectglow/sql/BigFileDatasource.scala core/src/main/scala/io/projectglow/sql/GlowConf.scala core/src/main/scala/io/projectglow/sql/SqlExtensionProvider.scala core/src/main/scala/io/projectglow/sql/dsl/package.scala core/src/main/scala/io/projectglow/sql/expressions/CovariateQRContext.scala core/src/main/scala/io/projectglow/sql/expressions/ExpressionHelper.scala core/src/main/scala/io/projectglow/sql/expressions/FirthTest.scala core/src/main/scala/io/projectglow/sql/expressions/LiftOverCoordinatesExpr.scala core/src/main/scala/io/projectglow/sql/expressions/LikelihoodRatioTest.scala core/src/main/scala/io/projectglow/sql/expressions/LinearRegressionExpr.scala core/src/main/scala/io/projectglow/sql/expressions/LinearRegressionGwas.scala core/src/main/scala/io/projectglow/sql/expressions/LogisticRegressionExpr.scala core/src/main/scala/io/projectglow/sql/expressions/LogisticRegressionGwas.scala core/src/main/scala/io/projectglow/sql/expressions/MeanSubstitute.scala core/src/main/scala/io/projectglow/sql/expressions/MomentAggState.scala core/src/main/scala/io/projectglow/sql/expressions/NormalizeVariantExpr.scala core/src/main/scala/io/projectglow/sql/expressions/PerSampleSummaryStatistics.scala core/src/main/scala/io/projectglow/sql/expressions/SampleCallSummaryStats.scala core/src/main/scala/io/projectglow/sql/expressions/VariantQcExprs.scala core/src/main/scala/io/projectglow/sql/expressions/VariantUtilExprs.scala core/src/main/scala/io/projectglow/sql/expressions/glueExpressions.scala core/src/main/scala/io/projectglow/sql/optimizer/hlsOptimizerRules.scala core/src/main/scala/io/projectglow/sql/util/BGZFCodec.scala core/src/main/scala/io/projectglow/sql/util/ComDatabricksDataSource.scala core/src/main/scala/io/projectglow/sql/util/ExpectsGenotypeFields.scala core/src/main/scala/io/projectglow/sql/util/HadoopLineIterator.scala core/src/main/scala/io/projectglow/sql/util/LeveneHaldane.scala core/src/main/scala/io/projectglow/sql/util/RowConverter.scala core/src/main/scala/io/projectglow/sql/util/SerializableConfiguration.scala core/src/main/scala/io/projectglow/transformers/LiftOverVariantsTransformer.scala core/src/main/scala/io/projectglow/transformers/blockvariantsandsamples/BlockVariantsAndSamplesTransformer.scala core/src/main/scala/io/projectglow/transformers/blockvariantsandsamples/VariantSampleBlockMaker.scala core/src/main/scala/io/projectglow/transformers/normalizevariants/NormalizeVariantsTransformer.scala core/src/main/scala/io/projectglow/transformers/normalizevariants/VariantNormalizer.scala core/src/main/scala/io/projectglow/transformers/pipe/CleanupPipeTransformer.scala core/src/main/scala/io/projectglow/transformers/pipe/PipeTransformer.scala core/src/main/scala/io/projectglow/transformers/pipe/Piper.scala core/src/main/scala/io/projectglow/transformers/pipe/UTF8TextInputFormatter.scala core/src/main/scala/io/projectglow/transformers/pipe/UTF8TextOutputFormatter.scala core/src/main/scala/io/projectglow/transformers/splitmultiallelics/SplitMultiallelicsTransformer.scala core/src/main/scala/io/projectglow/transformers/splitmultiallelics/VariantSplitter.scala core/src/main/scala/io/projectglow/vcf/AnnotationUtils.scala core/src/main/scala/io/projectglow/vcf/BigVCFDatasource.scala core/src/main/scala/io/projectglow/vcf/InternalRowToVariantContextConverter.scala core/src/main/scala/io/projectglow/vcf/LineIteratorImpl.scala core/src/main/scala/io/projectglow/vcf/TabixIndexHelper.scala core/src/main/scala/io/projectglow/vcf/VCFFileFormat.scala core/src/main/scala/io/projectglow/vcf/VCFFileWriter.scala core/src/main/scala/io/projectglow/vcf/VCFHeaderUtils.scala core/src/main/scala/io/projectglow/vcf/VCFInputFormatter.scala core/src/main/scala/io/projectglow/vcf/VCFLineToInternalRowConverter.scala core/src/main/scala/io/projectglow/vcf/VCFMetadataLoader.scala core/src/main/scala/io/projectglow/vcf/VCFOutputFormatter.scala core/src/main/scala/io/projectglow/vcf/VCFRowHeaderLines.scala core/src/main/scala/io/projectglow/vcf/VCFSchemaInferrer.scala core/src/main/scala/io/projectglow/vcf/VCFStreamWriter.scala core/src/main/scala/io/projectglow/vcf/VCFWriterUtils.scala core/src/main/scala/io/projectglow/vcf/VariantContextToInternalRowConverter.scala core/src/main/scala/org/apache/spark/sql/SQLUtils.scala core/src/main/scala/org/apache/spark/sql/catalyst/expressions/QuinaryExpression.scala core/src/main/scala/org/apache/spark/sql/catalyst/expressions/SenaryExpression.scala core/src/main/scala/org/hadoop_bam/util/GlowBGZFOutputStream.scala core/src/main/shim/3.4/SparkShim.scala core/src/main/shim/3.5/SparkShim.scala core/src/main/shim/4.0/SparkShim.scala core/src/test/scala/io/projectglow/GlowSuite.scala core/src/test/scala/io/projectglow/SparkSuite.scala core/src/test/scala/io/projectglow/SparkTestShimBase.scala core/src/test/scala/io/projectglow/bgen/BgenConverterBaseTest.scala core/src/test/scala/io/projectglow/bgen/BgenReaderSuite.scala core/src/test/scala/io/projectglow/bgen/BgenRowConverterSuite.scala core/src/test/scala/io/projectglow/bgen/BgenWriterSuite.scala core/src/test/scala/io/projectglow/common/SimpleIntervalSuite.scala core/src/test/scala/io/projectglow/common/TestUtils.scala core/src/test/scala/io/projectglow/common/WithUtilsSuite.scala core/src/test/scala/io/projectglow/gff/GffReaderSuite.scala core/src/test/scala/io/projectglow/plink/PlinkReaderSuite.scala core/src/test/scala/io/projectglow/sql/BigFileDatasourceSuite.scala core/src/test/scala/io/projectglow/sql/ComDatabricksDataSourceSuite.scala core/src/test/scala/io/projectglow/sql/GlowBaseTest.scala core/src/test/scala/io/projectglow/sql/GlowTestData.scala core/src/test/scala/io/projectglow/sql/SingleFileWriterSuite.scala core/src/test/scala/io/projectglow/sql/SqlExtensionProviderSuite.scala core/src/test/scala/io/projectglow/sql/util/ExpectsGenotypeFieldsSuite.scala core/src/test/scala/io/projectglow/tertiary/LiftOverCoordinatesExprSuite.scala core/src/test/scala/io/projectglow/tertiary/LinearRegressionSuite.scala core/src/test/scala/io/projectglow/tertiary/LogisticRegressionSuite.scala core/src/test/scala/io/projectglow/tertiary/MomentAggStateSuite.scala core/src/test/scala/io/projectglow/tertiary/NewtonIterationsStateSuite.scala core/src/test/scala/io/projectglow/tertiary/RegressionTestUtils.scala core/src/test/scala/io/projectglow/tertiary/SampleQcExprsSuite.scala core/src/test/scala/io/projectglow/tertiary/VariantQcExprsSuite.scala core/src/test/scala/io/projectglow/tertiary/VariantUtilExprsSuite.scala core/src/test/scala/io/projectglow/transformers/LiftOverVariantsTransformerSuite.scala core/src/test/scala/io/projectglow/transformers/blockvariantsandsamples/BlockVariantsAndSamplesTransformerSuite.scala core/src/test/scala/io/projectglow/transformers/normalizevariants/NormalizeVariantsTransformerSuite.scala core/src/test/scala/io/projectglow/transformers/normalizevariants/VariantNormalizerSuite.scala core/src/test/scala/io/projectglow/transformers/pipe/PipeTransformerSuite.scala core/src/test/scala/io/projectglow/transformers/pipe/TextPiperSuite.scala core/src/test/scala/io/projectglow/transformers/splitmultiallelics/SplitMultiallelicsTransformerSuite.scala core/src/test/scala/io/projectglow/transformers/splitmultiallelics/VariantSplitterSuite.scala core/src/test/scala/io/projectglow/transformers/util/StringUtilsSuite.scala core/src/test/scala/io/projectglow/vcf/InternalRowToVariantContextConverterSuite.scala core/src/test/scala/io/projectglow/vcf/TabixHelperSuite.scala core/src/test/scala/io/projectglow/vcf/VCFConverterBaseTest.scala core/src/test/scala/io/projectglow/vcf/VCFDatasourceSuite.scala core/src/test/scala/io/projectglow/vcf/VCFFileWriterSuite.scala core/src/test/scala/io/projectglow/vcf/VCFHeaderUtilsSuite.scala core/src/test/scala/io/projectglow/vcf/VCFPiperSuite.scala core/src/test/scala/io/projectglow/vcf/VCFSchemaInferrerSuite.scala core/src/test/scala/io/projectglow/vcf/VCFStreamWriterSuite.scala core/src/test/scala/io/projectglow/vcf/VariantContextToInternalRowConverterSuite.scala core/src/test/scala/org/apache/spark/sql/catalyst/expressions/QuinaryExpressionSuite.scala core/src/test/shim/3.4/SparkTestShim.scala core/src/test/shim/3.5/SparkTestShim.scala core/src/test/shim/4.0/SparkTestShim.scala docs/extensions/notebook.py docs/source/_static/notebooks/0_setup_constants_glow.html docs/source/_static/notebooks/2_setup_metadata.html docs/source/_static/notebooks/etl/10_liftOver.html docs/source/_static/notebooks/etl/1_simulate_covariates_phenotypes_offset.html docs/source/_static/notebooks/etl/2_simulate_delta_pvcf.html docs/source/_static/notebooks/etl/3_delta_to_vcf.html docs/source/_static/notebooks/etl/6_explode_variant_dataframe.html docs/source/_static/notebooks/etl/7_etl_gff_annotations.html docs/source/_static/notebooks/etl/8_create_database_for_querying.html docs/source/_static/notebooks/etl/9_query_variant_db.html docs/source/_static/notebooks/etl/data/download_1000G.html docs/source/_static/notebooks/etl/merge-vcf.html docs/source/_static/notebooks/etl/normalizevariants.html docs/source/_static/notebooks/etl/python/functions.html docs/source/_static/notebooks/etl/sample-qc-demo.html docs/source/_static/notebooks/etl/splitmultiallelics-transformer.html docs/source/_static/notebooks/etl/variant-data.html docs/source/_static/notebooks/etl/variant-qc-demo.html docs/source/_static/notebooks/etl/vcf2delta.html docs/source/_static/notebooks/tertiary/0_ingest_vcf2delta.html docs/source/_static/notebooks/tertiary/1_quality_control.html docs/source/_static/notebooks/tertiary/2_quantitative_glowgr.html docs/source/_static/notebooks/tertiary/3_linear_gwas_glow.html docs/source/_static/notebooks/tertiary/4_binary_glowgr.html docs/source/_static/notebooks/tertiary/5_logistic_gwas_glow.html docs/source/_static/notebooks/tertiary/8_pipeline_runs_comparison.html docs/source/_static/notebooks/tertiary/binaryglowgr.html docs/source/_static/notebooks/tertiary/glowgr.html docs/source/_static/notebooks/tertiary/gwas-binary.html docs/source/_static/notebooks/tertiary/gwas-quantitative.html docs/source/_static/notebooks/tertiary/pandas-lmm.html docs/source/_static/notebooks/tertiary/parallel_bcftools_filter.html docs/source/_static/notebooks/tertiary/pipe-transformer-plink.html docs/source/_static/notebooks/tertiary/pipe-transformer-vep.html docs/source/_static/notebooks/tertiary/pipe-transformer.html docs/source/_static/zzz_GENERATED_NOTEBOOK_SOURCE/tertiary/1_quality_control.py docs/source/conf.py docs/source/conftest.py docs/source/environment.yml docs/source/etl/utility-functions.rst functions.yml levels_ridge_regression_tutorial.ipynb project/plugins.sbt pyspark-setup.py python/LICENSE.txt python/environment.yml python/glow/__init__.py python/glow/conftest.py python/glow/conversions.py python/glow/functions.py python/glow/functions.py.TEMPLATE python/glow/glow.py python/glow/gwas/tests/functions.py python/glow/tests/test_conversions.py python/glow/tests/test_register.py python/glow/tests/test_transform.py python/glow/wgr/__init__.py python/glow/wgr/logistic_ridge_regression.py python/glow/wgr/logistic_udfs.py python/glow/wgr/model_functions.py python/glow/wgr/ridge_reduction.py python/glow/wgr/ridge_regression.py python/glow/wgr/ridge_udfs.py python/glow/wgr/tests/test_block_variants_and_samples.py python/glow/wgr/tests/test_estimate_loco_offsets.py python/glow/wgr/tests/test_functions.py python/glow/wgr/tests/test_logistic_ridge_regression.py python/glow/wgr/tests/test_ridge_regression.py python/glow/wgr/tests/test_sample_id_extraction.py python/glow/wgr/wgr_functions.py python/render_template.py python/setup.py python/spark-4-environment.yml python/test_render_template.py python/version.py sonatype.sbt test-data/1000G.phase3.broad.withGenotypes.chr20.10100000.vcf test-data/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.vcf test-data/biallelic.CEUTrio.HiSeq.WGS.b37.NA12878.20.21.vcf test-data/plink/five-samples-five-variants/map-ped/test.map test-data/regenie/covariates.txt test-data/regenie/example_3chr.sample test-data/regenie/fit_bin_out_2.loco test-data/regenie/phenotype.txt test-data/regenie/test_bin_out_firth_Y1.regenie test-data/regenie/test_bin_out_firth_Y2.regenie test-data/regenie/test_bin_out_half_firth_Y1.regenie test-data/regenie/test_bin_out_half_firth_Y2.regenie test-data/regenie/test_bin_out_missing_firth_Y1.regenie test-data/regenie/test_bin_out_missing_firth_Y2.regenie test-data/regenie/test_lin_out_3chr_Y1.regenie test-data/regenie/test_lin_out_3chr_Y2.regenie test-data/regenie/test_lin_out_Y1.regenie test-data/regenie/test_lin_out_Y2.regenie test-data/regenie/test_lin_out_missing_Y1.regenie test-data/regenie/test_lin_out_missing_Y2.regenie test-data/vcf/scripts/gwas-region.py test-data/wgr/logistic-regression/cov.csv test-data/wgr/logistic-regression/test_map_irls_eqn.json test-data/wgr/logistic-regression/test_reduce_irls_eqn.json test-data/wgr/ridge-regression/X0.csv test-data/wgr/ridge-regression/X1.csv test-data/wgr/ridge-regression/X2.csv test-data/wgr/ridge-regression/pts.csv version.sbt ```

⚙ Adjust future updates

Add this to your `.scala-steward.conf` file to ignore future updates of this dependency: ``` updates.ignore = [ { groupId = "org.yaml", artifactId = "snakeyaml" } ] ``` Or, add this to slow down future updates of this dependency: ``` dependencyOverrides = [{ pullRequests = { frequency = "30 days" }, dependency = { groupId = "org.yaml", artifactId = "snakeyaml" } }] ```

^{labels: library-update, old-version-remains, commit-count:1}