biocypher 0.5.30__py3-none-any.whl → 0.5.31__py3-none-any.whl

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Files changed (8) hide show
  1. biocypher/_core.py +1 -1
  2. biocypher/_mapping.py +1 -1
  3. biocypher/_metadata.py +1 -1
  4. biocypher/_ontology.py +2 -2
  5. {biocypher-0.5.30.dist-info → biocypher-0.5.31.dist-info}/METADATA +1 -1
  6. {biocypher-0.5.30.dist-info → biocypher-0.5.31.dist-info}/RECORD +8 -8
  7. {biocypher-0.5.30.dist-info → biocypher-0.5.31.dist-info}/LICENSE +0 -0
  8. {biocypher-0.5.30.dist-info → biocypher-0.5.31.dist-info}/WHEEL +0 -0
biocypher/_core.py CHANGED
@@ -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/_mapping.py CHANGED
@@ -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/_metadata.py CHANGED
@@ -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/_ontology.py CHANGED
@@ -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.dist-info → biocypher-0.5.31.dist-info}/METADATA 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.dist-info → biocypher-0.5.31.dist-info}/RECORD RENAMED
@@ -6,19 +6,19 @@ biocypher/_config/test_schema_config.yaml,sha256=D1600WgEj3iTXrumVU9LIivJHJO36ia
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  biocypher/_config/test_schema_config_disconnected.yaml,sha256=Qm8FLxEn2spHcyj_5F859KjcDvKSxNhxDvi4b4LLkvQ,68
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  biocypher/_config/test_schema_config_extended.yaml,sha256=wn3A76142hhjnImhMF6RODbCFESTJ2TtPvcFdIFsAT0,3309
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  biocypher/_connect.py,sha256=0oSyO6CEIlKL8rHo-HHE7y0FzGfSi4vnEXSDy1TnIUE,12456
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- biocypher/_core.py,sha256=xDMIdpDXffUzUygC8B3GzXTGLvFH6dqTs39ele68VFE,22270
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+ biocypher/_core.py,sha256=2o3hhhM6kfaZI6TU3ZmzoBJc-RJgFFGWGe0MZW-oA3U,22301
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  biocypher/_create.py,sha256=vpUchUdEpWupZi1LgFLxAWMtqoBwnWbP7PwEDUCBS4A,10202
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  biocypher/_deduplicate.py,sha256=BBvfpXzu6L5YDY5FdtXxnf8YlsbJpbCE8RdUoKsm0n0,4949
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  biocypher/_get.py,sha256=HrJuBm_i9zfi_Mzzi1s5kp0OyPh_oKQk0wwyYsxg0qA,9189
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  biocypher/_logger.py,sha256=rEn_-ESh9cPxk6vdWZ1a25escCWHBWX4D1gtpNowyvI,3186
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- biocypher/_mapping.py,sha256=XJZjmXTPnXVkyub1ZU0h3EKXQ2YROaGaJOaGyPMqgy4,9338
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- biocypher/_metadata.py,sha256=uhKcqAgegfsACy-ebv23rGzCNVhgBfN7a5aKDhm1EU8,1658
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+ biocypher/_mapping.py,sha256=ERSNH2Bg19145KytxbFE4BInPaiP-LWW7osOBot29Eo,9304
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+ biocypher/_metadata.py,sha256=kpXUxF5Umh3tsT9xxcrntbPWxL38kATPLhgrqRNV1cs,1658
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  biocypher/_misc.py,sha256=wsjGVOqBDVM5hxbE_TEaZ69u1kJc8HXwRAtQHUgE8XQ,4545
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- biocypher/_ontology.py,sha256=zqHHwfy0BM1lhtNuG4ldy4Mpycss5DKPDH_5GsTs8Bk,22991
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+ biocypher/_ontology.py,sha256=lIEHtdUGPFVbj7jrojwHNmP2-KJlXSET8bqVLRam3vI,23010
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  biocypher/_pandas.py,sha256=GVCFM68J7yBjh40MpkNVgD8qT1RFMrrIjMOtD3iKsf4,3040
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  biocypher/_translate.py,sha256=nj4Y60F0U3JBH36N2dh5pFcC8Ot86rskJ2ChJwje9dI,16494
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  biocypher/_write.py,sha256=nvb75OwElu8fLUp0FjEBqQ1VNpx6iRrk-t7v_TOlDhg,68165
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- biocypher-0.5.30.dist-info/LICENSE,sha256=SjUaQkq671iQUZOxEUpC4jvJxXOlfSiHTTueyz9kXJM,1065
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- biocypher-0.5.30.dist-info/METADATA,sha256=2_eNgfnwrwxBN4S_SfTFxBdYSmBvX7opXE4DS9RVZT8,10274
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- biocypher-0.5.30.dist-info/WHEEL,sha256=Zb28QaM1gQi8f4VCBhsUklF61CTlNYfs9YAZn-TOGFk,88
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- biocypher-0.5.30.dist-info/RECORD,,
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+ biocypher-0.5.31.dist-info/LICENSE,sha256=SjUaQkq671iQUZOxEUpC4jvJxXOlfSiHTTueyz9kXJM,1065
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+ biocypher-0.5.31.dist-info/METADATA,sha256=Kzl2LeK_Y4Ul8bzzfPzYv7aXEjAohoQqfRJO_GdFhXs,10274
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+ biocypher-0.5.31.dist-info/WHEEL,sha256=Zb28QaM1gQi8f4VCBhsUklF61CTlNYfs9YAZn-TOGFk,88
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+ biocypher-0.5.31.dist-info/RECORD,,