orfdata 0.34.0__tar.gz → 0.34.1__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 (274) hide show
  1. {orfdata-0.34.0/orfdata.egg-info → orfdata-0.34.1}/PKG-INFO +3 -3
  2. {orfdata-0.34.0 → orfdata-0.34.1}/README.md +1 -1
  3. {orfdata-0.34.0 → orfdata-0.34.1}/docs/index.md +1 -1
  4. orfdata-0.34.1/orfdata/version.py +1 -0
  5. {orfdata-0.34.0 → orfdata-0.34.1/orfdata.egg-info}/PKG-INFO +3 -3
  6. {orfdata-0.34.0 → orfdata-0.34.1}/pyproject.toml +2 -2
  7. orfdata-0.34.0/orfdata/version.py +0 -1
  8. {orfdata-0.34.0 → orfdata-0.34.1}/LICENSE +0 -0
  9. {orfdata-0.34.0 → orfdata-0.34.1}/MANIFEST.in +0 -0
  10. {orfdata-0.34.0 → orfdata-0.34.1}/deploy.sh +0 -0
  11. {orfdata-0.34.0 → orfdata-0.34.1}/docs/catalogs.md +0 -0
  12. {orfdata-0.34.0 → orfdata-0.34.1}/docs/copy-yeast.md +0 -0
  13. {orfdata-0.34.0 → orfdata-0.34.1}/docs/coverage.md +0 -0
  14. {orfdata-0.34.0 → orfdata-0.34.1}/docs/dog-peptides.md +0 -0
  15. {orfdata-0.34.0 → orfdata-0.34.1}/docs/examples.md +0 -0
  16. {orfdata-0.34.0 → orfdata-0.34.1}/docs/human-tissue.md +0 -0
  17. {orfdata-0.34.0 → orfdata-0.34.1}/docs/ingolia-yeast.md +0 -0
  18. {orfdata-0.34.0 → orfdata-0.34.1}/docs/measurements.md +0 -0
  19. {orfdata-0.34.0 → orfdata-0.34.1}/docs/pairing.md +0 -0
  20. {orfdata-0.34.0 → orfdata-0.34.1}/docs/pfizer-protein.md +0 -0
  21. {orfdata-0.34.0 → orfdata-0.34.1}/docs/pfizer-rna.md +0 -0
  22. {orfdata-0.34.0 → orfdata-0.34.1}/docs/proteome.md +0 -0
  23. {orfdata-0.34.0 → orfdata-0.34.1}/docs/reference.md +0 -0
  24. {orfdata-0.34.0 → orfdata-0.34.1}/docs/search-references.md +0 -0
  25. {orfdata-0.34.0 → orfdata-0.34.1}/docs/source-references.md +0 -0
  26. {orfdata-0.34.0 → orfdata-0.34.1}/docs/species.md +0 -0
  27. {orfdata-0.34.0 → orfdata-0.34.1}/docs/storage.md +0 -0
  28. {orfdata-0.34.0 → orfdata-0.34.1}/docs/stylesheets/docs.css +0 -0
  29. {orfdata-0.34.0 → orfdata-0.34.1}/docs/viral.md +0 -0
  30. {orfdata-0.34.0 → orfdata-0.34.1}/docs.sh +0 -0
  31. {orfdata-0.34.0 → orfdata-0.34.1}/lint.sh +0 -0
  32. {orfdata-0.34.0 → orfdata-0.34.1}/mkdocs.yml +0 -0
  33. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/__init__.py +0 -0
  34. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/_pinned_genome.py +0 -0
  35. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/_structure.py +0 -0
  36. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/build.py +0 -0
  37. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/catalog.py +0 -0
  38. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/catalog_cli.py +0 -0
  39. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/catalog_manifest.py +0 -0
  40. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/catalogs.py +0 -0
  41. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/cli.py +0 -0
  42. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/catalogs.json +0 -0
  43. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/chains.json +0 -0
  44. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/datasets.json +0 -0
  45. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/genomes.json +0 -0
  46. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/ires/rfam-15.1-human-ires.json +0 -0
  47. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/orf-evidence/AUTHOR-LICENSE.txt +0 -0
  48. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/orf-evidence/NOTICE.txt +0 -0
  49. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/orf-evidence/catalog.json.gz +0 -0
  50. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/orf-evidence/manifest.json +0 -0
  51. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/uorf-evidence/AUTHOR-LICENSE.txt +0 -0
  52. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/uorf-evidence/NOTICE.txt +0 -0
  53. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/uorf-evidence/catalog.json.gz +0 -0
  54. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/uorf-evidence/manifest.json +0 -0
  55. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/viral/NOTICE.md +0 -0
  56. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/data/viral/hpv16-refseq-CDS.json.gz +0 -0
  57. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/dataset.py +0 -0
  58. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/dataset_cli.py +0 -0
  59. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/datasets.py +0 -0
  60. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/evidence.py +0 -0
  61. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/evidence_summary.py +0 -0
  62. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/genomes.py +0 -0
  63. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/genomes_cli.py +0 -0
  64. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/initiation_context.py +0 -0
  65. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/install.py +0 -0
  66. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/liftover.py +0 -0
  67. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/liftover_cli.py +0 -0
  68. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/measurements.py +0 -0
  69. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/model.py +0 -0
  70. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/pairing.py +0 -0
  71. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/proteome.py +0 -0
  72. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/proteome_cli.py +0 -0
  73. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/reference.py +0 -0
  74. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/reference_mapping.py +0 -0
  75. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/refseq.py +0 -0
  76. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/rna.py +0 -0
  77. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/search_reference.py +0 -0
  78. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/sequence.py +0 -0
  79. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/sources/__init__.py +0 -0
  80. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/sources/copy.py +0 -0
  81. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/sources/ingolia.py +0 -0
  82. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/sources/kaabinejadian.py +0 -0
  83. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/sources/ncorf_mammals.py +0 -0
  84. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/sources/openprot.py +0 -0
  85. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/sources/peptideatlas.py +0 -0
  86. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/sources/pfizer.py +0 -0
  87. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/sources/pfizer_rna.py +0 -0
  88. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/sources/riborf.py +0 -0
  89. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/sources/wang.py +0 -0
  90. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata/viral.py +0 -0
  91. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata.egg-info/SOURCES.txt +0 -0
  92. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata.egg-info/dependency_links.txt +0 -0
  93. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata.egg-info/entry_points.txt +0 -0
  94. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata.egg-info/requires.txt +0 -0
  95. {orfdata-0.34.0 → orfdata-0.34.1}/orfdata.egg-info/top_level.txt +0 -0
  96. {orfdata-0.34.0 → orfdata-0.34.1}/setup.cfg +0 -0
  97. {orfdata-0.34.0 → orfdata-0.34.1}/test.sh +0 -0
  98. {orfdata-0.34.0 → orfdata-0.34.1}/tests/conftest.py +0 -0
  99. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/aggregate_evidence.json +0 -0
  100. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/GSM1905474.soft +0 -0
  101. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/GSM1905474_KL9_fpkm.txt.gz +0 -0
  102. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/GSM1905476.soft +0 -0
  103. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/GSM1905476_KL10_fpkm.txt.gz +0 -0
  104. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/GSM1905478.soft +0 -0
  105. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/GSM1905478_KL11_fpkm.txt.gz +0 -0
  106. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/GSM1905479.soft +0 -0
  107. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/GSM1905479_KL12_fpkm.txt.gz +0 -0
  108. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/NOTICE.md +0 -0
  109. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/expected.json +0 -0
  110. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/geo-series.soft +0 -0
  111. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/manifest.json +0 -0
  112. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/methods.pdf +0 -0
  113. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/paper.xml +0 -0
  114. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/pmc-metadata.json +0 -0
  115. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/qconcat.fasta +0 -0
  116. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/copy/workbook.xlsx +0 -0
  117. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346111.metadata.txt +0 -0
  118. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346111.quant.txt.gz +0 -0
  119. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346114.metadata.txt +0 -0
  120. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346114.quant.txt.gz +0 -0
  121. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346115.metadata.txt +0 -0
  122. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346115.quant.txt.gz +0 -0
  123. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346116.metadata.txt +0 -0
  124. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346116.quant.txt.gz +0 -0
  125. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346117.metadata.txt +0 -0
  126. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346117.quant.txt.gz +0 -0
  127. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346118.metadata.txt +0 -0
  128. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346118.quant.txt.gz +0 -0
  129. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346120.metadata.txt +0 -0
  130. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346120.quant.txt.gz +0 -0
  131. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346122.metadata.txt +0 -0
  132. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/GSM346122.quant.txt.gz +0 -0
  133. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/NOTICE.md +0 -0
  134. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/expected.json +0 -0
  135. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/manifest.json +0 -0
  136. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ingolia/readMe.txt.gz +0 -0
  137. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/kaabinejadian/README.md +0 -0
  138. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/kaabinejadian/Results.zip +0 -0
  139. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/kaabinejadian/manifest.json +0 -0
  140. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/kaabinejadian/sdrf.tsv +0 -0
  141. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ncorf_mammals/README.md +0 -0
  142. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ncorf_mammals/S3.xlsx +0 -0
  143. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ncorf_mammals/ensembl107.cdna.fa.gz +0 -0
  144. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ncorf_mammals/ensembl107.gtf.gz +0 -0
  145. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ncorf_mammals/human-ensembl107.gtf.gz +0 -0
  146. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ncorf_mammals/human.bed +0 -0
  147. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ncorf_mammals/human.pep.fa +0 -0
  148. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ncorf_mammals/mouse.bed +0 -0
  149. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/ncorf_mammals/mouse.pep.fa +0 -0
  150. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/openprot/README.md +0 -0
  151. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/openprot/ensembl106.cdna.fa.gz +0 -0
  152. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/openprot/ensembl106.gtf.gz +0 -0
  153. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/openprot/mouse-openprot-2_2-altprots+isoforms-min_2_pep-GRCm39.106.bed.zip +0 -0
  154. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/openprot/mouse-openprot-2_2-altprots+isoforms-min_2_pep-GRCm39.106.fasta.zip +0 -0
  155. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/openprot/mouse-openprot-2_2-altprots+isoforms-min_2_pep-GRCm39.106.tsv.zip +0 -0
  156. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/peptideatlas/README.md +0 -0
  157. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/peptideatlas/atlas_build.tsv.zip +0 -0
  158. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/peptideatlas/ensembl.pep.fa.gz +0 -0
  159. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/peptideatlas/manifest.json +0 -0
  160. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/NOTICE.md +0 -0
  161. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/dog/expected.json +0 -0
  162. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/dog/manifest.json +0 -0
  163. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/dog/protein.tsv +0 -0
  164. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/dog/search.fasta +0 -0
  165. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/human/expected.json +0 -0
  166. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/human/manifest.json +0 -0
  167. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/human/protein.tsv +0 -0
  168. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/human/search.fasta +0 -0
  169. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/mouse/expected.json +0 -0
  170. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/mouse/manifest.json +0 -0
  171. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/mouse/protein.tsv +0 -0
  172. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer/mouse/search.fasta +0 -0
  173. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer_rna/GSE325522_family.soft.gz +0 -0
  174. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer_rna/GSE325523_family.soft.gz +0 -0
  175. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer_rna/GSE325525_family.soft.gz +0 -0
  176. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer_rna/NOTICE.md +0 -0
  177. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer_rna/counts.csv.gz +0 -0
  178. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer_rna/dog-annotation.gtf.gz +0 -0
  179. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer_rna/dog-expected.json +0 -0
  180. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer_rna/dog-manifest.json +0 -0
  181. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer_rna/mouse-annotation.gtf.gz +0 -0
  182. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer_rna/mouse-expected.json +0 -0
  183. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer_rna/mouse-manifest.json +0 -0
  184. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/pfizer_rna/samples.xlsx +0 -0
  185. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/references/README.md +0 -0
  186. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/references/canis_lupus_familiaris.json +0 -0
  187. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/references/context-keys-v0.4.json +0 -0
  188. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/references/ensembl115.json +0 -0
  189. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/references/homo_sapiens.json +0 -0
  190. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/references/mitochondrial.json +0 -0
  191. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/references/mus_musculus.json +0 -0
  192. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/references/saccharomyces_cerevisiae.json +0 -0
  193. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/references/uniprot_literature.json +0 -0
  194. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/regions/NOTICE.md +0 -0
  195. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/regions/ingolia.json +0 -0
  196. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/README.md +0 -0
  197. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/SD3.xlsx +0 -0
  198. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/ensembl107.cdna.fa.gz +0 -0
  199. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/ensembl107.gtf.gz +0 -0
  200. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/ensembl107.ncrna.fa.gz +0 -0
  201. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/human-ensembl105.cdna.fa.gz +0 -0
  202. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/human-ensembl105.gtf.gz +0 -0
  203. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/human-ensembl105.ncrna.fa.gz +0 -0
  204. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/worm-ensembl105.cdna.fa.gz +0 -0
  205. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/worm-ensembl105.gtf.gz +0 -0
  206. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/worm-ensembl105.ncrna.fa.gz +0 -0
  207. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/yeast-ensembl115.cdna.fa.gz +0 -0
  208. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/yeast-ensembl115.dna.fa.gz +0 -0
  209. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/yeast-ensembl115.gtf.gz +0 -0
  210. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/zebrafish-ensembl115.cdna.fa.gz +0 -0
  211. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/zebrafish-ensembl115.gtf.gz +0 -0
  212. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/riborf/zebrafish-ensembl115.ncrna.fa.gz +0 -0
  213. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/search_reference/NOTICE.md +0 -0
  214. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/search_reference/dog.fasta +0 -0
  215. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/search_reference/ensembl83-expected.json +0 -0
  216. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/search_reference/ensembl83-human.fasta.gz +0 -0
  217. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/search_reference/expected.json +0 -0
  218. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/storage/README.md +0 -0
  219. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/storage/generate.py +0 -0
  220. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/storage/v1.json +0 -0
  221. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/storage/v1.sqlite +0 -0
  222. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/storage/v2.json +0 -0
  223. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/storage/v2.sqlite +0 -0
  224. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/storage/v3.json +0 -0
  225. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/storage/v3.sqlite +0 -0
  226. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/storage/v4.json +0 -0
  227. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/storage/v4.sqlite +0 -0
  228. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/viral/NC_001526.4.gb.gz +0 -0
  229. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/wang/NOTICE.md +0 -0
  230. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/wang/annotation.gtf.gz +0 -0
  231. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/wang/copies.zip +0 -0
  232. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/wang/expected.json +0 -0
  233. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/wang/manifest.json +0 -0
  234. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/wang/protein.zip +0 -0
  235. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/wang/rna.zip +0 -0
  236. {orfdata-0.34.0 → orfdata-0.34.1}/tests/data/wang/search.fasta.gz +0 -0
  237. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_catalog_registry.py +0 -0
  238. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_copy.py +0 -0
  239. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_cross_reference_pairing.py +0 -0
  240. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_dog_peptides.py +0 -0
  241. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_ensembl_search_reference.py +0 -0
  242. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_evidence_rules.py +0 -0
  243. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_evidence_summary.py +0 -0
  244. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_genetic_codes.py +0 -0
  245. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_genomes.py +0 -0
  246. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_ingolia.py +0 -0
  247. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_initiation_context.py +0 -0
  248. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_liftover.py +0 -0
  249. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_local_build_queries.py +0 -0
  250. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_measurements.py +0 -0
  251. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_merge_catalogs.py +0 -0
  252. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_more_species.py +0 -0
  253. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_ncorf_mammals.py +0 -0
  254. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_openprot.py +0 -0
  255. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_orf_cases.py +0 -0
  256. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_paired_selectors.py +0 -0
  257. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_pairing.py +0 -0
  258. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_pfizer.py +0 -0
  259. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_pfizer_rna.py +0 -0
  260. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_proteome.py +0 -0
  261. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_reference_context.py +0 -0
  262. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_reference_mapping.py +0 -0
  263. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_reference_orf.py +0 -0
  264. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_refseq.py +0 -0
  265. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_region_targets.py +0 -0
  266. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_riborf.py +0 -0
  267. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_search_reference.py +0 -0
  268. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_selectors.py +0 -0
  269. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_storage.py +0 -0
  270. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_uorf_catalog.py +0 -0
  271. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_viral.py +0 -0
  272. {orfdata-0.34.0 → orfdata-0.34.1}/tests/test_wang.py +0 -0
  273. {orfdata-0.34.0 → orfdata-0.34.1}/tools/__init__.py +0 -0
  274. {orfdata-0.34.0 → orfdata-0.34.1}/tools/build_hpv16_cds.py +0 -0
@@ -1,10 +1,10 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: orfdata
3
- Version: 0.34.0
3
+ Version: 0.34.1
4
4
  Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
5
5
  Author: OpenVax
6
6
  License-Expression: Apache-2.0
7
- Requires-Python: >=3.9
7
+ Requires-Python: >=3.11
8
8
  Description-Content-Type: text/markdown
9
9
  License-File: LICENSE
10
10
  Provides-Extra: pyensembl
@@ -45,7 +45,7 @@ evidence.
45
45
 
46
46
  ## Installation
47
47
 
48
- Use Python 3.9 or later. Install orfdata and one PyEnsembl annotation:
48
+ Use Python 3.11 or later. Install orfdata and one PyEnsembl annotation:
49
49
 
50
50
  ```sh
51
51
  python -m pip install 'orfdata[pyensembl]'
@@ -13,7 +13,7 @@ evidence.
13
13
 
14
14
  ## Installation
15
15
 
16
- Use Python 3.9 or later. Install orfdata and one PyEnsembl annotation:
16
+ Use Python 3.11 or later. Install orfdata and one PyEnsembl annotation:
17
17
 
18
18
  ```sh
19
19
  python -m pip install 'orfdata[pyensembl]'
@@ -9,7 +9,7 @@ is a recorded host of the virus.
9
9
 
10
10
  ## Install
11
11
 
12
- Use Python 3.9 or later. Install orfdata and one PyEnsembl annotation:
12
+ Use Python 3.11 or later. Install orfdata and one PyEnsembl annotation:
13
13
 
14
14
  ```sh
15
15
  python -m pip install 'orfdata[pyensembl]'
@@ -0,0 +1 @@
1
+ __version__ = "0.34.1"
@@ -1,10 +1,10 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: orfdata
3
- Version: 0.34.0
3
+ Version: 0.34.1
4
4
  Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
5
5
  Author: OpenVax
6
6
  License-Expression: Apache-2.0
7
- Requires-Python: >=3.9
7
+ Requires-Python: >=3.11
8
8
  Description-Content-Type: text/markdown
9
9
  License-File: LICENSE
10
10
  Provides-Extra: pyensembl
@@ -45,7 +45,7 @@ evidence.
45
45
 
46
46
  ## Installation
47
47
 
48
- Use Python 3.9 or later. Install orfdata and one PyEnsembl annotation:
48
+ Use Python 3.11 or later. Install orfdata and one PyEnsembl annotation:
49
49
 
50
50
  ```sh
51
51
  python -m pip install 'orfdata[pyensembl]'
@@ -8,7 +8,7 @@ dynamic = ["version"]
8
8
  description = "Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes"
9
9
  readme = "README.md"
10
10
  license = "Apache-2.0"
11
- requires-python = ">=3.9"
11
+ requires-python = ">=3.11"
12
12
  authors = [{name = "OpenVax"}]
13
13
  dependencies = []
14
14
 
@@ -33,7 +33,7 @@ include = ["orfdata*"]
33
33
  orfdata = ["data/uorf-evidence/*", "data/orf-evidence/*", "data/ires/*", "data/viral/*", "data/datasets.json", "data/catalogs.json", "data/chains.json", "data/genomes.json"]
34
34
 
35
35
  [tool.ruff]
36
- target-version = "py39"
36
+ target-version = "py311"
37
37
  line-length = 100
38
38
 
39
39
  [tool.ruff.lint]
@@ -1 +0,0 @@
1
- __version__ = "0.34.0"
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes