biocypher 0.9.3__tar.gz → 0.9.4__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 biocypher might be problematic. Click here for more details.

Files changed (44) hide show
  1. {biocypher-0.9.3 → biocypher-0.9.4}/PKG-INFO +1 -1
  2. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_core.py +4 -4
  3. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_metadata.py +1 -1
  4. {biocypher-0.9.3 → biocypher-0.9.4}/pyproject.toml +2 -2
  5. {biocypher-0.9.3 → biocypher-0.9.4}/LICENSE +0 -0
  6. {biocypher-0.9.3 → biocypher-0.9.4}/README.md +0 -0
  7. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/__init__.py +0 -0
  8. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_config/__init__.py +0 -0
  9. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_config/biocypher_config.yaml +0 -0
  10. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_config/test_config.yaml +0 -0
  11. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_config/test_schema_config.yaml +0 -0
  12. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_config/test_schema_config_disconnected.yaml +0 -0
  13. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_config/test_schema_config_extended.yaml +0 -0
  14. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_create.py +0 -0
  15. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_deduplicate.py +0 -0
  16. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_get.py +0 -0
  17. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_logger.py +0 -0
  18. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_mapping.py +0 -0
  19. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_misc.py +0 -0
  20. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_ontology.py +0 -0
  21. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_translate.py +0 -0
  22. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/__init__.py +0 -0
  23. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/connect/__init__.py +0 -0
  24. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/connect/_get_connector.py +0 -0
  25. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/connect/_neo4j_driver.py +0 -0
  26. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/in_memory/__init__.py +0 -0
  27. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/in_memory/_get_in_memory_kg.py +0 -0
  28. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/in_memory/_in_memory_kg.py +0 -0
  29. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/in_memory/_networkx.py +0 -0
  30. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/in_memory/_pandas.py +0 -0
  31. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/__init__.py +0 -0
  32. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/_batch_writer.py +0 -0
  33. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/_get_writer.py +0 -0
  34. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/_writer.py +0 -0
  35. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/graph/__init__.py +0 -0
  36. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/graph/_arangodb.py +0 -0
  37. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/graph/_neo4j.py +0 -0
  38. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/graph/_networkx.py +0 -0
  39. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/graph/_owl.py +0 -0
  40. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/graph/_rdf.py +0 -0
  41. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/relational/__init__.py +0 -0
  42. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/relational/_csv.py +0 -0
  43. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/relational/_postgresql.py +0 -0
  44. {biocypher-0.9.3 → biocypher-0.9.4}/biocypher/output/write/relational/_sqlite.py +0 -0
{biocypher-0.9.3 → biocypher-0.9.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: biocypher
3
- Version: 0.9.3
3
+ Version: 0.9.4
4
4
  Summary: A unifying framework for biomedical research knowledge graphs
5
5
  Home-page: https://github.com/biocypher/biocypher
6
6
  License: MIT
{biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_core.py RENAMED
@@ -301,7 +301,7 @@ class BioCypher:
301
301
 
302
302
  return self._translator
303
303
 
304
- def _get_writer(self):
304
+ def _initialize_writer(self) -> None:
305
305
  """Create writer if not online.
306
306
 
307
307
  Set as instance variable `self._writer`.
@@ -328,8 +328,6 @@ class BioCypher:
328
328
  msg = "Cannot get writer in online mode."
329
329
  raise NotImplementedError(msg)
330
330
 
331
- return self._writer
332
-
333
331
  def _get_driver(self):
334
332
  """Create driver if not exists.
335
333
 
@@ -385,7 +383,9 @@ class BioCypher:
385
383
  translated_nodes = self._translator.translate_entities(nodes)
386
384
 
387
385
  if self._offline:
388
- passed = self._get_writer().write_nodes(
386
+ if not self._writer:
387
+ self._initialize_writer()
388
+ passed = self._writer.write_nodes(
389
389
  translated_nodes,
390
390
  batch_size=batch_size,
391
391
  force=force,
{biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_metadata.py RENAMED
@@ -10,7 +10,7 @@ import pathlib
10
10
 
11
11
  import toml
12
12
 
13
- _VERSION = "0.9.3"
13
+ _VERSION = "0.9.4"
14
14
 
15
15
 
16
16
  def get_metadata():
{biocypher-0.9.3 → biocypher-0.9.4}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [tool.poetry]
2
2
  name = "biocypher"
3
- version = "0.9.3"
3
+ version = "0.9.4"
4
4
  description = "A unifying framework for biomedical research knowledge graphs"
5
5
  authors = [
6
6
  "Sebastian Lobentanzer <sebastian.lobentanzer@gmail.com>",
@@ -62,7 +62,7 @@ ipython = "^8.7.0"
62
62
  ipykernel = "^6.23.1"
63
63
  sphinxext-opengraph = "^0.8.2"
64
64
  coverage-badge = "^1.1.0"
65
- nbsphinx = "^0.9.3"
65
+ nbsphinx = "^0.9.4"
66
66
  ruff = "^0.2.0"
67
67
 
68
68
  [build-system]
{biocypher-0.9.3 → biocypher-0.9.4}/LICENSE RENAMED
File without changes
{biocypher-0.9.3 → biocypher-0.9.4}/README.md RENAMED
File without changes
{biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_get.py RENAMED
File without changes
{biocypher-0.9.3 → biocypher-0.9.4}/biocypher/_misc.py RENAMED
File without changes