polars-bio 0.13.0__tar.gz → 0.13.1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (162) hide show
  1. {polars_bio-0.13.0 → polars_bio-0.13.1}/Cargo.lock +1 -1
  2. {polars_bio-0.13.0 → polars_bio-0.13.1}/Cargo.toml +1 -1
  3. {polars_bio-0.13.0 → polars_bio-0.13.1}/PKG-INFO +1 -1
  4. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/__init__.py +2 -2
  5. {polars_bio-0.13.0 → polars_bio-0.13.1}/pyproject.toml +1 -1
  6. {polars_bio-0.13.0 → polars_bio-0.13.1}/.github/workflows/publish_documentation.yml +0 -0
  7. {polars_bio-0.13.0 → polars_bio-0.13.1}/.github/workflows/publish_to_pypi.yml +0 -0
  8. {polars_bio-0.13.0 → polars_bio-0.13.1}/.github/workflows/release.yml +0 -0
  9. {polars_bio-0.13.0 → polars_bio-0.13.1}/.gitignore +0 -0
  10. {polars_bio-0.13.0 → polars_bio-0.13.1}/.pre-commit-config.yaml +0 -0
  11. {polars_bio-0.13.0 → polars_bio-0.13.1}/.readthedocs.yaml +0 -0
  12. {polars_bio-0.13.0 → polars_bio-0.13.1}/LICENSE +0 -0
  13. {polars_bio-0.13.0 → polars_bio-0.13.1}/Makefile +0 -0
  14. {polars_bio-0.13.0 → polars_bio-0.13.1}/README.md +0 -0
  15. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/api.md +0 -0
  16. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/count-overlaps-parallel.png +0 -0
  17. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/count-overlaps-single.png +0 -0
  18. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/coverage-parallel.png +0 -0
  19. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/coverage-single.png +0 -0
  20. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/logo-large.png +0 -0
  21. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/logo.png +0 -0
  22. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/memory/bioframe.png +0 -0
  23. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/memory/bioframe_sink.png +0 -0
  24. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/memory/dataframes/polars-bio-overlap-mem.png +0 -0
  25. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/memory/dataframes/polars-bio-overlap-pd-mem.png +0 -0
  26. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/memory/dataframes/polars-bio-overlap-pl-mem.png +0 -0
  27. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/memory/polars-bio.png +0 -0
  28. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/memory/polars-bio_sink.png +0 -0
  29. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/memory/polars-bio_stream_sink.png +0 -0
  30. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/memory/pyranges0.png +0 -0
  31. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/memory/pyranges0_sink.png +0 -0
  32. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/memory/pyranges1.png +0 -0
  33. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/memory/pyranges1_sink.png +0 -0
  34. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/nearest-parallel.png +0 -0
  35. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/nearest-single.png +0 -0
  36. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/overlap-parallel.png +0 -0
  37. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/overlap-single.png +0 -0
  38. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/results-nearest-0.1.1.png +0 -0
  39. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/assets/results-overlap-0.1.1.png +0 -0
  40. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/contact.md +0 -0
  41. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/faq.md +0 -0
  42. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/features.md +0 -0
  43. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/index.md +0 -0
  44. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/example.bam +0 -0
  45. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/example.bed.bgz +0 -0
  46. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/example.fastq.gz +0 -0
  47. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/example.gff3.bgz +0 -0
  48. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/example.vcf +0 -0
  49. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/exons/.part-00000-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet.crc +0 -0
  50. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/exons/.part-00001-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet.crc +0 -0
  51. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/exons/_SUCCESS +0 -0
  52. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/exons/part-00000-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet +0 -0
  53. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/exons/part-00001-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet +0 -0
  54. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/fBrain-DS14718/.part-00000-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet.crc +0 -0
  55. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/fBrain-DS14718/.part-00001-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet.crc +0 -0
  56. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/fBrain-DS14718/_SUCCESS +0 -0
  57. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/fBrain-DS14718/part-00000-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet +0 -0
  58. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/data/fBrain-DS14718/part-00001-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet +0 -0
  59. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/notebooks/tutorial.ipynb +0 -0
  60. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/performance.md +0 -0
  61. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/quickstart.md +0 -0
  62. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/requirements.txt +0 -0
  63. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/supplement.md +0 -0
  64. {polars_bio-0.13.0 → polars_bio-0.13.1}/docs/versions.json +0 -0
  65. {polars_bio-0.13.0 → polars_bio-0.13.1}/it/README.md +0 -0
  66. {polars_bio-0.13.0 → polars_bio-0.13.1}/it/bin/.env +0 -0
  67. {polars_bio-0.13.0 → polars_bio-0.13.1}/it/bin/start.sh +0 -0
  68. {polars_bio-0.13.0 → polars_bio-0.13.1}/it/bin/stop.sh +0 -0
  69. {polars_bio-0.13.0 → polars_bio-0.13.1}/it/data/policy-anonymous.json +0 -0
  70. {polars_bio-0.13.0 → polars_bio-0.13.1}/it/data/policy-priv.json +0 -0
  71. {polars_bio-0.13.0 → polars_bio-0.13.1}/it/data/test.fasta +0 -0
  72. {polars_bio-0.13.0 → polars_bio-0.13.1}/it/data/vep.vcf +0 -0
  73. {polars_bio-0.13.0 → polars_bio-0.13.1}/it/data/vep.vcf.bgz +0 -0
  74. {polars_bio-0.13.0 → polars_bio-0.13.1}/it/docker-compose.yml +0 -0
  75. {polars_bio-0.13.0 → polars_bio-0.13.1}/it/it_ensembl_vcf_bgz.py +0 -0
  76. {polars_bio-0.13.0 → polars_bio-0.13.1}/it/it_object_storage_io.py +0 -0
  77. {polars_bio-0.13.0 → polars_bio-0.13.1}/mkdocs.yml +0 -0
  78. {polars_bio-0.13.0 → polars_bio-0.13.1}/poetry.lock +0 -0
  79. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars-bio.iml +0 -0
  80. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/constants.py +0 -0
  81. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/context.py +0 -0
  82. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/interval_op_helpers.py +0 -0
  83. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/io.py +0 -0
  84. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/logging.py +0 -0
  85. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/operations.py +0 -0
  86. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/polars_ext.py +0 -0
  87. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/range_op.py +0 -0
  88. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/range_op_helpers.py +0 -0
  89. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/range_op_io.py +0 -0
  90. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/range_utils.py +0 -0
  91. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/sql.py +0 -0
  92. {polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/utils.py +0 -0
  93. {polars_bio-0.13.0 → polars_bio-0.13.1}/requirements.txt +0 -0
  94. {polars_bio-0.13.0 → polars_bio-0.13.1}/rust-toolchain.toml +0 -0
  95. {polars_bio-0.13.0 → polars_bio-0.13.1}/rustfmt.toml +0 -0
  96. {polars_bio-0.13.0 → polars_bio-0.13.1}/src/context.rs +0 -0
  97. {polars_bio-0.13.0 → polars_bio-0.13.1}/src/lib.rs +0 -0
  98. {polars_bio-0.13.0 → polars_bio-0.13.1}/src/operation.rs +0 -0
  99. {polars_bio-0.13.0 → polars_bio-0.13.1}/src/option.rs +0 -0
  100. {polars_bio-0.13.0 → polars_bio-0.13.1}/src/query.rs +0 -0
  101. {polars_bio-0.13.0 → polars_bio-0.13.1}/src/scan.rs +0 -0
  102. {polars_bio-0.13.0 → polars_bio-0.13.1}/src/streaming.rs +0 -0
  103. {polars_bio-0.13.0 → polars_bio-0.13.1}/src/udtf.rs +0 -0
  104. {polars_bio-0.13.0 → polars_bio-0.13.1}/src/utils.rs +0 -0
  105. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/_expected.py +0 -0
  106. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/count_overlaps/reads.csv +0 -0
  107. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/count_overlaps/targets.csv +0 -0
  108. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/coverage/reads.csv +0 -0
  109. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/coverage/targets.csv +0 -0
  110. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/exons/.part-00000-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet.crc +0 -0
  111. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/exons/.part-00001-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet.crc +0 -0
  112. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/exons/_SUCCESS +0 -0
  113. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/exons/part-00000-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet +0 -0
  114. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/exons/part-00001-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet +0 -0
  115. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/fBrain-DS14718/.part-00000-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet.crc +0 -0
  116. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/fBrain-DS14718/.part-00001-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet.crc +0 -0
  117. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/fBrain-DS14718/_SUCCESS +0 -0
  118. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/fBrain-DS14718/part-00000-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet +0 -0
  119. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/fBrain-DS14718/part-00001-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet +0 -0
  120. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/bam/test.bam +0 -0
  121. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/bam/test.bam.bai +0 -0
  122. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/bed/ENCFF001XKR.bed.gz +0 -0
  123. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/bed/chr16_fragile_site.bed +0 -0
  124. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/bed/chr16_fragile_site.bed.bgz +0 -0
  125. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/bed/test.bed +0 -0
  126. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/fasta/test.fasta +0 -0
  127. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/fastq/example.fastq +0 -0
  128. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/fastq/example.fastq.bgz +0 -0
  129. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/fastq/example.fastq.bgz.gzi +0 -0
  130. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/fastq/example.fastq.gz +0 -0
  131. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/fastq/sample_parallel.fastq.bgz +0 -0
  132. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/fastq/sample_parallel.fastq.bgz.gzi +0 -0
  133. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/fastq/test.fastq +0 -0
  134. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/fastq/wrong_extension.fastq.gz +0 -0
  135. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/gff/gencode.v38.annotation.gff3 +0 -0
  136. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/gff/gencode.v38.annotation.gff3.bgz +0 -0
  137. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/gff/gencode.v38.annotation.gff3.gz +0 -0
  138. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/gff/wrong_extension.gff3.gz +0 -0
  139. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/vcf/ensembl-2.vcf +0 -0
  140. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/vcf/ensembl.vcf +0 -0
  141. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/vcf/vep.vcf +0 -0
  142. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/vcf/vep.vcf.bgz +0 -0
  143. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/vcf/vep.vcf.gz +0 -0
  144. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/vcf/wrong_extension.vcf.bgz +0 -0
  145. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/io/vcf/wrong_extension.vcf.gz +0 -0
  146. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/merge/input.csv +0 -0
  147. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/nearest/reads.csv +0 -0
  148. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/nearest/targets.csv +0 -0
  149. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/overlap/reads.csv +0 -0
  150. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/data/overlap/targets.csv +0 -0
  151. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/test_bioframe.py +0 -0
  152. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/test_ensembl_parsing.py +0 -0
  153. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/test_ensembl_vcf_parsing.py +0 -0
  154. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/test_io.py +0 -0
  155. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/test_native.py +0 -0
  156. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/test_overlap_algorithms.py +0 -0
  157. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/test_pandas.py +0 -0
  158. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/test_parallel_io.py +0 -0
  159. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/test_polars.py +0 -0
  160. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/test_polars_ext.py +0 -0
  161. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/test_streaming.py +0 -0
  162. {polars_bio-0.13.0 → polars_bio-0.13.1}/tests/test_warnings.py +0 -0
{polars_bio-0.13.0 → polars_bio-0.13.1}/Cargo.lock RENAMED
@@ -5203,7 +5203,7 @@ dependencies = [
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  [[package]]
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  name = "polars_bio"
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- version = "0.13.0"
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+ version = "0.13.1"
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  dependencies = [
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  "arrow",
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  "arrow-array",
{polars_bio-0.13.0 → polars_bio-0.13.1}/Cargo.toml RENAMED
@@ -1,6 +1,6 @@
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  [package]
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  name = "polars_bio"
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- version = "0.13.0"
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+ version = "0.13.1"
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  edition = "2021"
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  readme = "README.md"
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{polars_bio-0.13.0 → polars_bio-0.13.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: polars-bio
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- Version: 0.13.0
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+ Version: 0.13.1
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  Classifier: Programming Language :: Rust
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  Classifier: Programming Language :: Python :: Implementation :: CPython
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  Classifier: Programming Language :: Python :: Implementation :: PyPy
{polars_bio-0.13.0 → polars_bio-0.13.1}/polars_bio/__init__.py RENAMED
@@ -2,7 +2,7 @@ import os
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  # Set POLARS_FORCE_NEW_STREAMING to "1" by default if not already set
4
4
  if "POLARS_FORCE_NEW_STREAMING" not in os.environ:
5
- os.environ["POLARS_FORCE_NEW_STREAMING"] = "1"
5
+ os.environ["POLARS_FORCE_NEW_STREAMING"] = "0"
6
6
 
7
7
  from polars_bio.polars_bio import GffReadOptions, InputFormat
8
8
  from polars_bio.polars_bio import PyObjectStorageOptions as ObjectStorageOptions
@@ -73,7 +73,7 @@ except ImportError:
73
73
  POLARS_BIO_MAX_THREADS = "datafusion.execution.target_partitions"
74
74
 
75
75
 
76
- __version__ = "0.13.0"
76
+ __version__ = "0.13.1"
77
77
  __all__ = [
78
78
  "ctx",
79
79
  "FilterOp",
{polars_bio-0.13.0 → polars_bio-0.13.1}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "maturin"
4
4
 
5
5
  [project]
6
6
  name = "polars-bio"
7
- version = "0.13.0"
7
+ version = "0.13.1"
8
8
  description = "Blazing fast genomic operations on large Python dataframes"
9
9
  authors = []
10
10
  requires-python = ">=3.9"
{polars_bio-0.13.0 → polars_bio-0.13.1}/.gitignore RENAMED
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{polars_bio-0.13.0 → polars_bio-0.13.1}/LICENSE RENAMED
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{polars_bio-0.13.0 → polars_bio-0.13.1}/src/context.rs RENAMED
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{polars_bio-0.13.0 → polars_bio-0.13.1}/src/query.rs RENAMED
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