pheval 0.6.1__tar.gz → 0.6.2__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.

Potentially problematic release.

This version of pheval might be problematic. Click here for more details.

Files changed (56) hide show
  1. {pheval-0.6.1 → pheval-0.6.2}/PKG-INFO +1 -1
  2. {pheval-0.6.1 → pheval-0.6.2}/pyproject.toml +1 -1
  3. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/post_processing/phenopacket_truth_set.py +3 -1
  4. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/post_processing/post_processing.py +4 -1
  5. {pheval-0.6.1 → pheval-0.6.2}/LICENSE +0 -0
  6. {pheval-0.6.1 → pheval-0.6.2}/README.md +0 -0
  7. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/__init__.py +0 -0
  8. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/analyse/__init__.py +0 -0
  9. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/analyse/benchmark.py +0 -0
  10. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/analyse/benchmark_db_manager.py +0 -0
  11. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/analyse/benchmark_output_type.py +0 -0
  12. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/analyse/binary_classification_curves.py +0 -0
  13. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/analyse/binary_classification_stats.py +0 -0
  14. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/analyse/generate_plots.py +0 -0
  15. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/analyse/generate_rank_comparisons.py +0 -0
  16. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/analyse/rank_stats.py +0 -0
  17. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/analyse/run_data_parser.py +0 -0
  18. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/cli.py +0 -0
  19. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/cli_pheval.py +0 -0
  20. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/cli_pheval_utils.py +0 -0
  21. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/config_parser.py +0 -0
  22. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/implementations/__init__.py +0 -0
  23. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/implementations/pheval_class_resolver.py +0 -0
  24. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/infra/__init__.py +0 -0
  25. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/infra/exomiserdb.py +0 -0
  26. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/post_processing/__init__.py +0 -0
  27. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/post_processing/mondo_mapping.py +0 -0
  28. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/post_processing/validate_result_format.py +0 -0
  29. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/prepare/__init__.py +0 -0
  30. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/prepare/create_noisy_phenopackets.py +0 -0
  31. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/prepare/create_spiked_vcf.py +0 -0
  32. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/prepare/custom_exceptions.py +0 -0
  33. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/prepare/prepare_corpus.py +0 -0
  34. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/prepare/update_phenopacket.py +0 -0
  35. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/resources/alternate_ouputs/CADA_results.txt +0 -0
  36. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/resources/alternate_ouputs/DeepPVP_results.txt +0 -0
  37. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/resources/alternate_ouputs/OVA_results.txt +0 -0
  38. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/resources/alternate_ouputs/Phen2Gene_results.json +0 -0
  39. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/resources/alternate_ouputs/Phenolyzer_results.txt +0 -0
  40. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/resources/alternate_ouputs/lirical_results.tsv +0 -0
  41. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/resources/alternate_ouputs/svanna_results.tsv +0 -0
  42. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/resources/hgnc_complete_set.txt +0 -0
  43. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/resources/metadata.json +0 -0
  44. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/resources/mondo.sssom.tsv +0 -0
  45. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/run_metadata.py +0 -0
  46. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/runners/__init__.py +0 -0
  47. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/runners/runner.py +0 -0
  48. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/utils/__init__.py +0 -0
  49. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/utils/docs_gen.py +0 -0
  50. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/utils/docs_gen.sh +0 -0
  51. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/utils/exomiser.py +0 -0
  52. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/utils/file_utils.py +0 -0
  53. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/utils/logger.py +0 -0
  54. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/utils/phenopacket_utils.py +0 -0
  55. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/utils/semsim_utils.py +0 -0
  56. {pheval-0.6.1 → pheval-0.6.2}/src/pheval/utils/utils.py +0 -0
{pheval-0.6.1 → pheval-0.6.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.3
2
2
  Name: pheval
3
- Version: 0.6.1
3
+ Version: 0.6.2
4
4
  Summary:
5
5
  Author: Yasemin Bridges
6
6
  Author-email: y.bridges@qmul.ac.uk
{pheval-0.6.1 → pheval-0.6.2}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [tool.poetry]
2
2
  name = "pheval"
3
- version = "0.6.1"
3
+ version = "0.6.2"
4
4
  description = ""
5
5
  authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>",
6
6
  "Julius Jacobsen <j.jacobsen@qmul.ac.uk>",
{pheval-0.6.1 → pheval-0.6.2}/src/pheval/post_processing/phenopacket_truth_set.py RENAMED
@@ -225,7 +225,9 @@ class PhenopacketTruthSet:
225
225
  pl.lit(0).cast(pl.Int64).alias("rank"),
226
226
  pl.lit(True).alias("true_positive"),
227
227
  pl.col("disease_identifier")
228
- .map_elements(lambda x: map_disease_id(x, mondo_mapping_table))
228
+ .map_elements(
229
+ lambda x: map_disease_id(x, mondo_mapping_table), return_dtype=pl.Utf8
230
+ )
229
231
  .alias("mondo_identifier"),
230
232
  ]
231
233
  )
{pheval-0.6.1 → pheval-0.6.2}/src/pheval/post_processing/post_processing.py RENAMED
@@ -150,7 +150,10 @@ def _get_result_type(
150
150
  case ResultType.VARIANT:
151
151
  return phenopacket_truth_set.classified_variant, _write_variant_result
152
152
  case ResultType.DISEASE:
153
- return phenopacket_truth_set.classified_disease, _write_disease_result
153
+ return (
154
+ lambda id_: phenopacket_truth_set.classified_disease(id_, mondo_mapping_table),
155
+ _write_disease_result,
156
+ )
154
157
 
155
158
 
156
159
  def create_empty_pheval_result(
{pheval-0.6.1 → pheval-0.6.2}/LICENSE RENAMED
File without changes
{pheval-0.6.1 → pheval-0.6.2}/README.md RENAMED
File without changes
{pheval-0.6.1 → pheval-0.6.2}/src/pheval/__init__.py RENAMED
File without changes
{pheval-0.6.1 → pheval-0.6.2}/src/pheval/cli.py RENAMED
File without changes
{pheval-0.6.1 → pheval-0.6.2}/src/pheval/cli_pheval.py RENAMED
File without changes
{pheval-0.6.1 → pheval-0.6.2}/src/pheval/utils/utils.py RENAMED
File without changes