afquery 0.2.0__tar.gz → 0.2.1__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 (119) hide show
  1. afquery-0.2.1/Dockerfile +16 -0
  2. {afquery-0.2.0 → afquery-0.2.1}/PKG-INFO +1 -1
  3. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/_version.py +2 -2
  4. afquery-0.2.0/Dockerfile +0 -6
  5. {afquery-0.2.0 → afquery-0.2.1}/.dockerignore +0 -0
  6. {afquery-0.2.0 → afquery-0.2.1}/.github/workflows/ci.yml +0 -0
  7. {afquery-0.2.0 → afquery-0.2.1}/.github/workflows/docs.yml +0 -0
  8. {afquery-0.2.0 → afquery-0.2.1}/.github/workflows/release.yml +0 -0
  9. {afquery-0.2.0 → afquery-0.2.1}/.gitignore +0 -0
  10. {afquery-0.2.0 → afquery-0.2.1}/LICENSE +0 -0
  11. {afquery-0.2.0 → afquery-0.2.1}/README.md +0 -0
  12. {afquery-0.2.0 → afquery-0.2.1}/docs/advanced/benchmarking.md +0 -0
  13. {afquery-0.2.0 → afquery-0.2.1}/docs/advanced/debugging-results.md +0 -0
  14. {afquery-0.2.0 → afquery-0.2.1}/docs/advanced/filter-pass-tracking.md +0 -0
  15. {afquery-0.2.0 → afquery-0.2.1}/docs/advanced/multi-cohort-strategies.md +0 -0
  16. {afquery-0.2.0 → afquery-0.2.1}/docs/advanced/performance.md +0 -0
  17. {afquery-0.2.0 → afquery-0.2.1}/docs/advanced/pipeline-integration.md +0 -0
  18. {afquery-0.2.0 → afquery-0.2.1}/docs/advanced/ploidy-and-sex-chroms.md +0 -0
  19. {afquery-0.2.0 → afquery-0.2.1}/docs/faq.md +0 -0
  20. {afquery-0.2.0 → afquery-0.2.1}/docs/getting-started/concepts.md +0 -0
  21. {afquery-0.2.0 → afquery-0.2.1}/docs/getting-started/installation.md +0 -0
  22. {afquery-0.2.0 → afquery-0.2.1}/docs/getting-started/motivation.md +0 -0
  23. {afquery-0.2.0 → afquery-0.2.1}/docs/getting-started/preprocessing.md +0 -0
  24. {afquery-0.2.0 → afquery-0.2.1}/docs/getting-started/quickstart.md +0 -0
  25. {afquery-0.2.0 → afquery-0.2.1}/docs/getting-started/understanding-output.md +0 -0
  26. {afquery-0.2.0 → afquery-0.2.1}/docs/guides/annotate-vcf.md +0 -0
  27. {afquery-0.2.0 → afquery-0.2.1}/docs/guides/create-database.md +0 -0
  28. {afquery-0.2.0 → afquery-0.2.1}/docs/guides/dump-export.md +0 -0
  29. {afquery-0.2.0 → afquery-0.2.1}/docs/guides/manifest-format.md +0 -0
  30. {afquery-0.2.0 → afquery-0.2.1}/docs/guides/query.md +0 -0
  31. {afquery-0.2.0 → afquery-0.2.1}/docs/guides/sample-filtering.md +0 -0
  32. {afquery-0.2.0 → afquery-0.2.1}/docs/guides/update-database.md +0 -0
  33. {afquery-0.2.0 → afquery-0.2.1}/docs/index.md +0 -0
  34. {afquery-0.2.0 → afquery-0.2.1}/docs/reference/cli.md +0 -0
  35. {afquery-0.2.0 → afquery-0.2.1}/docs/reference/data-model.md +0 -0
  36. {afquery-0.2.0 → afquery-0.2.1}/docs/reference/glossary.md +0 -0
  37. {afquery-0.2.0 → afquery-0.2.1}/docs/reference/python-api.md +0 -0
  38. {afquery-0.2.0 → afquery-0.2.1}/docs/troubleshooting.md +0 -0
  39. {afquery-0.2.0 → afquery-0.2.1}/docs/use-cases/acmg-use-cases.md +0 -0
  40. {afquery-0.2.0 → afquery-0.2.1}/docs/use-cases/clinical-prioritization.md +0 -0
  41. {afquery-0.2.0 → afquery-0.2.1}/docs/use-cases/cohort-stratification.md +0 -0
  42. {afquery-0.2.0 → afquery-0.2.1}/docs/use-cases/population-specific-af.md +0 -0
  43. {afquery-0.2.0 → afquery-0.2.1}/docs/use-cases/pseudo-controls.md +0 -0
  44. {afquery-0.2.0 → afquery-0.2.1}/docs/use-cases/sex-specific-af.md +0 -0
  45. {afquery-0.2.0 → afquery-0.2.1}/docs/use-cases/technology-integration.md +0 -0
  46. {afquery-0.2.0 → afquery-0.2.1}/mkdocs.yml +0 -0
  47. {afquery-0.2.0 → afquery-0.2.1}/plans/issue-01-remove-publication-section.md +0 -0
  48. {afquery-0.2.0 → afquery-0.2.1}/plans/issue-02-drop-schema-v1.md +0 -0
  49. {afquery-0.2.0 → afquery-0.2.1}/plans/issue-03-query-syntax-chrom-pos.md +0 -0
  50. {afquery-0.2.0 → afquery-0.2.1}/plans/issue-04-wes-bed-validation.md +0 -0
  51. {afquery-0.2.0 → afquery-0.2.1}/plans/issue-05-update-sample-metadata.md +0 -0
  52. {afquery-0.2.0 → afquery-0.2.1}/plans/issue-06-multi-chromosome-query.md +0 -0
  53. {afquery-0.2.0 → afquery-0.2.1}/plans/issue-07-doc-formatting-fixes.md +0 -0
  54. {afquery-0.2.0 → afquery-0.2.1}/plans/issue-08-index-feature-list.md +0 -0
  55. {afquery-0.2.0 → afquery-0.2.1}/plans/issue-09-doc-content-improvements.md +0 -0
  56. {afquery-0.2.0 → afquery-0.2.1}/pyproject.toml +0 -0
  57. {afquery-0.2.0 → afquery-0.2.1}/recipes/afquery/meta.yaml +0 -0
  58. {afquery-0.2.0 → afquery-0.2.1}/resources/normalize_vcf.sh +0 -0
  59. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/__init__.py +0 -0
  60. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/annotate.py +0 -0
  61. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/benchmark.py +0 -0
  62. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/bitmaps.py +0 -0
  63. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/capture.py +0 -0
  64. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/cli.py +0 -0
  65. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/cli.pyr +0 -0
  66. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/constants.py +0 -0
  67. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/database.py +0 -0
  68. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/dump.py +0 -0
  69. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/models.py +0 -0
  70. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/ploidy.py +0 -0
  71. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/preprocess/__init__.py +0 -0
  72. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/preprocess/build.py +0 -0
  73. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/preprocess/compact.py +0 -0
  74. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/preprocess/ingest.py +0 -0
  75. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/preprocess/manifest.py +0 -0
  76. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/preprocess/regions.py +0 -0
  77. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/preprocess/synth.py +0 -0
  78. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/preprocess/update.py +0 -0
  79. {afquery-0.2.0 → afquery-0.2.1}/src/afquery/query.py +0 -0
  80. {afquery-0.2.0 → afquery-0.2.1}/tests/conftest.py +0 -0
  81. {afquery-0.2.0 → afquery-0.2.1}/tests/data/annotate_input.vcf +0 -0
  82. {afquery-0.2.0 → afquery-0.2.1}/tests/data/annotate_multi_bucket.vcf +0 -0
  83. {afquery-0.2.0 → afquery-0.2.1}/tests/data/annotate_multi_chrom.vcf +0 -0
  84. {afquery-0.2.0 → afquery-0.2.1}/tests/data/beds/wes_kit_a.bed +0 -0
  85. {afquery-0.2.0 → afquery-0.2.1}/tests/data/beds/wes_kit_b.bed +0 -0
  86. {afquery-0.2.0 → afquery-0.2.1}/tests/data/expected_results.json +0 -0
  87. {afquery-0.2.0 → afquery-0.2.1}/tests/data/manifest.tsv +0 -0
  88. {afquery-0.2.0 → afquery-0.2.1}/tests/data/vcfs/S00.vcf +0 -0
  89. {afquery-0.2.0 → afquery-0.2.1}/tests/data/vcfs/S01.vcf +0 -0
  90. {afquery-0.2.0 → afquery-0.2.1}/tests/data/vcfs/S02.vcf +0 -0
  91. {afquery-0.2.0 → afquery-0.2.1}/tests/data/vcfs/S03.vcf +0 -0
  92. {afquery-0.2.0 → afquery-0.2.1}/tests/data/vcfs/S04.vcf +0 -0
  93. {afquery-0.2.0 → afquery-0.2.1}/tests/data/vcfs/S05.vcf +0 -0
  94. {afquery-0.2.0 → afquery-0.2.1}/tests/data/vcfs/S06.vcf +0 -0
  95. {afquery-0.2.0 → afquery-0.2.1}/tests/data/vcfs/S07.vcf +0 -0
  96. {afquery-0.2.0 → afquery-0.2.1}/tests/data/vcfs/S08.vcf +0 -0
  97. {afquery-0.2.0 → afquery-0.2.1}/tests/data/vcfs/S09.vcf +0 -0
  98. {afquery-0.2.0 → afquery-0.2.1}/tests/test_annotate.py +0 -0
  99. {afquery-0.2.0 → afquery-0.2.1}/tests/test_batch.py +0 -0
  100. {afquery-0.2.0 → afquery-0.2.1}/tests/test_benchmark.py +0 -0
  101. {afquery-0.2.0 → afquery-0.2.1}/tests/test_bitmaps.py +0 -0
  102. {afquery-0.2.0 → afquery-0.2.1}/tests/test_capture.py +0 -0
  103. {afquery-0.2.0 → afquery-0.2.1}/tests/test_cli.py +0 -0
  104. {afquery-0.2.0 → afquery-0.2.1}/tests/test_cli_docs_consistency.py +0 -0
  105. {afquery-0.2.0 → afquery-0.2.1}/tests/test_compact.py +0 -0
  106. {afquery-0.2.0 → afquery-0.2.1}/tests/test_constants.py +0 -0
  107. {afquery-0.2.0 → afquery-0.2.1}/tests/test_dump.py +0 -0
  108. {afquery-0.2.0 → afquery-0.2.1}/tests/test_haploid_stats.py +0 -0
  109. {afquery-0.2.0 → afquery-0.2.1}/tests/test_info.py +0 -0
  110. {afquery-0.2.0 → afquery-0.2.1}/tests/test_pass_filter.py +0 -0
  111. {afquery-0.2.0 → afquery-0.2.1}/tests/test_ploidy.py +0 -0
  112. {afquery-0.2.0 → afquery-0.2.1}/tests/test_preprocess.py +0 -0
  113. {afquery-0.2.0 → afquery-0.2.1}/tests/test_query.py +0 -0
  114. {afquery-0.2.0 → afquery-0.2.1}/tests/test_sample_filter.py +0 -0
  115. {afquery-0.2.0 → afquery-0.2.1}/tests/test_synth.py +0 -0
  116. {afquery-0.2.0 → afquery-0.2.1}/tests/test_synthetic_stats.py +0 -0
  117. {afquery-0.2.0 → afquery-0.2.1}/tests/test_update.py +0 -0
  118. {afquery-0.2.0 → afquery-0.2.1}/tests/test_update_metadata.py +0 -0
  119. {afquery-0.2.0 → afquery-0.2.1}/tests/test_warnings.py +0 -0
@@ -0,0 +1,16 @@
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+ FROM python:3.11-slim AS builder
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+
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+ RUN apt-get update && \
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+ apt-get install -y --no-install-recommends build-essential && \
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+ rm -rf /var/lib/apt/lists/*
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+
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+ ARG VERSION
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+ RUN pip install --no-cache-dir afquery==${VERSION}
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+
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+
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+ FROM python:3.11-slim
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+
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+ COPY --from=builder /usr/local/lib/python3.11/site-packages /usr/local/lib/python3.11/site-packages
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+ COPY --from=builder /usr/local/bin/afquery /usr/local/bin/afquery
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+
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+ ENTRYPOINT ["afquery"]
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: afquery
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- Version: 0.2.0
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+ Version: 0.2.1
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  Summary: Genomic allele frequency query engine with bitmap-encoded genotypes
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  License: MIT
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  License-File: LICENSE
@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
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  commit_id: COMMIT_ID
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  __commit_id__: COMMIT_ID
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- __version__ = version = '0.2.0'
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- __version_tuple__ = version_tuple = (0, 2, 0)
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+ __version__ = version = '0.2.1'
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+ __version_tuple__ = version_tuple = (0, 2, 1)
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  __commit_id__ = commit_id = None
afquery-0.2.0/Dockerfile DELETED
@@ -1,6 +0,0 @@
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- FROM python:3.11-slim
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-
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- ARG VERSION
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- RUN pip install --no-cache-dir afquery==${VERSION}
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-
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- ENTRYPOINT ["afquery"]
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