biocypher 0.5.30__tar.gz → 0.5.31__tar.gz

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  1. {biocypher-0.5.30 → biocypher-0.5.31}/PKG-INFO +1 -1
  2. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_core.py +1 -1
  3. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_mapping.py +1 -1
  4. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_metadata.py +1 -1
  5. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_ontology.py +2 -2
  6. {biocypher-0.5.30 → biocypher-0.5.31}/pyproject.toml +1 -1
  7. {biocypher-0.5.30 → biocypher-0.5.31}/LICENSE +0 -0
  8. {biocypher-0.5.30 → biocypher-0.5.31}/README.md +0 -0
  9. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/__init__.py +0 -0
  10. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_config/__init__.py +0 -0
  11. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_config/biocypher_config.yaml +0 -0
  12. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_config/test_config.yaml +0 -0
  13. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_config/test_schema_config.yaml +0 -0
  14. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_config/test_schema_config_disconnected.yaml +0 -0
  15. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_config/test_schema_config_extended.yaml +0 -0
  16. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_connect.py +0 -0
  17. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_create.py +0 -0
  18. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_deduplicate.py +0 -0
  19. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_get.py +0 -0
  20. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_logger.py +0 -0
  21. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_misc.py +0 -0
  22. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_pandas.py +0 -0
  23. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_translate.py +0 -0
  24. {biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_write.py +0 -0
{biocypher-0.5.30 → biocypher-0.5.31}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: biocypher
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- Version: 0.5.30
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+ Version: 0.5.31
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  Summary: A unifying framework for biomedical research knowledge graphs
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  Home-page: https://github.com/biocypher/biocypher
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  License: MIT
{biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_core.py RENAMED
@@ -181,7 +181,7 @@ class BioCypher:
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  """
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  if not self._schema_config_path:
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- return None
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+ self._ontology_mapping = OntologyMapping()
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  if not self._ontology_mapping:
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  self._ontology_mapping = OntologyMapping(
{biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_mapping.py RENAMED
@@ -40,7 +40,7 @@ class OntologyMapping:
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  Read the configuration file and store the ontology mapping and extensions.
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  """
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  if config_file is None:
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- schema_config = _config.module_data("schema_config")
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+ schema_config = {}
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  # load yaml file from web
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  elif config_file.startswith("http"):
{biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_metadata.py RENAMED
@@ -19,7 +19,7 @@ import importlib.metadata
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  import toml
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- _VERSION = "0.5.30"
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+ _VERSION = "0.5.31"
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  def get_metadata():
{biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_ontology.py RENAMED
@@ -571,7 +571,7 @@ class Ontology:
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  else:
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  msg = f"Showing ontology structure based on {len(self._tail_ontology_meta)+1} ontologies: "
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- print(msg)
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+ logger.info(msg)
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  if not full:
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  # set of leaves and their intermediate parents up to the root
@@ -600,7 +600,7 @@ class Ontology:
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  f"{self.mapping.extended_schema[node].get('synonym_for')}"
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  )
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- tree.show()
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+ logger.info(f"\n{tree}")
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  return tree
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{biocypher-0.5.30 → biocypher-0.5.31}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "biocypher"
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- version = "0.5.30"
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+ version = "0.5.31"
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  description = "A unifying framework for biomedical research knowledge graphs"
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  authors = [
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  "Sebastian Lobentanzer <sebastian.lobentanzer@gmail.com>",
{biocypher-0.5.30 → biocypher-0.5.31}/LICENSE RENAMED
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{biocypher-0.5.30 → biocypher-0.5.31}/README.md RENAMED
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{biocypher-0.5.30 → biocypher-0.5.31}/biocypher/_get.py RENAMED
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