biocypher 0.10.1__py3-none-any.whl → 0.11.0__py3-none-any.whl

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Files changed (9) hide show
  1. biocypher/__init__.py +8 -0
  2. biocypher/_graph.py +819 -0
  3. biocypher/_metadata.py +21 -8
  4. biocypher/_workflow.py +798 -0
  5. biocypher/output/in_memory/_airr.py +1 -1
  6. {biocypher-0.10.1.dist-info → biocypher-0.11.0.dist-info}/METADATA +22 -24
  7. {biocypher-0.10.1.dist-info → biocypher-0.11.0.dist-info}/RECORD +15 -13
  8. {biocypher-0.10.1.dist-info → biocypher-0.11.0.dist-info}/WHEEL +1 -1
  9. {biocypher-0.10.1.dist-info → biocypher-0.11.0.dist-info/licenses}/LICENSE +0 -0
biocypher/output/in_memory/_airr.py CHANGED
@@ -79,7 +79,7 @@ class AirrKG(_InMemoryKG):
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  if not HAS_SCIRPY:
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  msg = (
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  "AirrCell module from scirpy not detected. "
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- "Install it with 'poetry add biocypher[scirpy]' or 'poetry add scirpy'."
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+ "Install it with 'uv add biocypher[scirpy]' or 'uv add scirpy'."
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  )
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  raise ImportError(msg)
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{biocypher-0.10.1.dist-info → biocypher-0.11.0.dist-info}/METADATA RENAMED
@@ -1,12 +1,16 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.4
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  Name: biocypher
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- Version: 0.10.1
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+ Version: 0.11.0
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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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+ Project-URL: Homepage, https://biocypher.org
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+ Project-URL: Documentation, https://biocypher.org
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+ Project-URL: Repository, https://github.com/biocypher/biocypher
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+ Project-URL: Issues, https://github.com/biocypher/biocypher/issues
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+ Project-URL: Bug Tracker, https://github.com/biocypher/biocypher/issues
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+ Author-email: Sebastian Lobentanzer <sebastian.lobentanzer@gmail.com>, Denes Turei <turei.denes@gmail.com>
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  License: MIT
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- Author: Sebastian Lobentanzer
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- Author-email: sebastian.lobentanzer@gmail.com
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- Requires-Python: >=3.10,<4.0
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+ License-File: LICENSE
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+ Keywords: bioinformatics,biomedical-data,graph-database,knowledge-graph
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  Classifier: Development Status :: 3 - Alpha
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  Classifier: Intended Audience :: Developers
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  Classifier: Intended Audience :: Science/Research
@@ -14,25 +18,20 @@ Classifier: License :: OSI Approved :: MIT License
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  Classifier: Natural Language :: English
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  Classifier: Operating System :: OS Independent
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  Classifier: Programming Language :: Python
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- Classifier: Programming Language :: Python :: 3
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- Classifier: Programming Language :: Python :: 3.10
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- Classifier: Programming Language :: Python :: 3.11
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- Classifier: Programming Language :: Python :: 3.12
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  Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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- Provides-Extra: scirpy
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- Requires-Dist: PyYAML (>=5.0)
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+ Requires-Python: >=3.10
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  Requires-Dist: appdirs
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- Requires-Dist: more_itertools
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- Requires-Dist: neo4j-utils (==0.0.7)
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- Requires-Dist: networkx (>=3.0,<4.0)
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- Requires-Dist: pandas (>=2.0.1,<3.0.0)
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- Requires-Dist: pooch (>=1.7.0,<2.0.0)
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- Requires-Dist: rdflib (>=6.2.0,<7.0.0)
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- Requires-Dist: scirpy (>=0.22.0,<0.23.0) ; extra == "scirpy"
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- Requires-Dist: tqdm (>=4.65.0,<5.0.0)
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- Requires-Dist: treelib (==1.6.4)
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- Project-URL: Bug Tracker, https://github.com/biocypher/biocypher/issues
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- Project-URL: Repository, https://github.com/biocypher/biocypher
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+ Requires-Dist: more-itertools
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+ Requires-Dist: neo4j-utils==0.0.7
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+ Requires-Dist: networkx>=3.0
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+ Requires-Dist: pandas>=2.0.1
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+ Requires-Dist: pooch>=1.7.0
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+ Requires-Dist: pyyaml>=5.0
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+ Requires-Dist: rdflib>=6.2.0
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+ Requires-Dist: tqdm>=4.65.0
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+ Requires-Dist: treelib==1.6.4
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+ Provides-Extra: scirpy
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+ Requires-Dist: scirpy>=0.22.0; extra == 'scirpy'
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  Description-Content-Type: text/markdown
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  # BioCypher
@@ -114,4 +113,3 @@ as a preprint at https://arxiv.org/abs/2212.13543.
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  This project has received funding from the European Union’s Horizon 2020
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  research and innovation programme under grant agreement No 965193 for DECIDER
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  and No 116030 for TransQST.
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-
{biocypher-0.10.1.dist-info → biocypher-0.11.0.dist-info}/RECORD RENAMED
@@ -1,26 +1,28 @@
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- biocypher/__init__.py,sha256=-iq15Q3LhB8WBQjnD15ghszEdaqJ1XvQIF5IaF88KNQ,783
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- biocypher/_config/__init__.py,sha256=ku86JZaRrzW5NEz5EXsCRktFwxS0Yo2dwX4UuazdfA4,3416
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- biocypher/_config/biocypher_config.yaml,sha256=nrlwSW7YP8qTZYm-HvWdTCZy81jnd2FkIGWH8Se2MzI,3651
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- biocypher/_config/test_config.yaml,sha256=Np8jeS5_EP6HHOvMKb7B_Tkyqd5YaYlYz_DVsXypt-A,119
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- biocypher/_config/test_schema_config.yaml,sha256=D1600WgEj3iTXrumVU9LIivJHJO36iaxfkOgyam9zVU,3129
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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/__init__.py,sha256=MsH0rhfqWSPY0ZJN_-fptOFYN4LeG14Fp17XoqxeOJU,992
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  biocypher/_core.py,sha256=lP5CC35oXPtfiFY3C-UxZev8p1nMg9E2E4qN5BD9BTg,27437
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  biocypher/_create.py,sha256=QsvXrwEQ8k0uNXvCG06UKejvw-QsJwzSaumrBjx9n1k,9884
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  biocypher/_deduplicate.py,sha256=rtglcaLRaVzNjLtaPwTGP8VvCM4PHYQ5CZ-cm32CrKQ,4840
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  biocypher/_get.py,sha256=_wUjhRjH2J6Qhq0Ndy3kdfaWhHDTT-dxyCvtuH36My4,14868
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+ biocypher/_graph.py,sha256=YVC8N4SJqKL12Tkv6lmWqED2jp-dr9B9QCXGd5N-Umc,26650
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  biocypher/_logger.py,sha256=y9dh3SPJOCWXnkFSYSK7aj_-pB7zlAkNCf43Dp1lt74,2941
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  biocypher/_mapping.py,sha256=ntspG2C_NaQODhWTBFk0CDvolkOCjtqlQ9E-NkJAuTg,9030
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- biocypher/_metadata.py,sha256=dz_VeWCq0wx6Cr1hCzscvEVPLSRY1F8Tecu2saeAhkg,1416
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+ biocypher/_metadata.py,sha256=AqFD2kPyn8_KRZTlBGer2Ue6tsd0u3VtOhQMC96Z3-k,2047
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  biocypher/_misc.py,sha256=YzlY7zwa0mim9QFg9HwXErkJFIH3cvLrbgjF8tKOIT8,6353
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  biocypher/_ontology.py,sha256=lipZxU3aj6zrTbBrJZmCW6IRCuz-KQG3AfbYCVq6aFE,33133
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  biocypher/_translate.py,sha256=NKSM9lxNjNNbgQrK_24eWYh3B41TS7kjnSwjySnK3s0,16851
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+ biocypher/_workflow.py,sha256=av22D_gj9osOczGYP86-wrrjmjG6PvWC0df_920Ff5s,27603
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+ biocypher/_config/__init__.py,sha256=ku86JZaRrzW5NEz5EXsCRktFwxS0Yo2dwX4UuazdfA4,3416
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+ biocypher/_config/biocypher_config.yaml,sha256=nrlwSW7YP8qTZYm-HvWdTCZy81jnd2FkIGWH8Se2MzI,3651
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+ biocypher/_config/test_config.yaml,sha256=Np8jeS5_EP6HHOvMKb7B_Tkyqd5YaYlYz_DVsXypt-A,119
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+ biocypher/_config/test_schema_config.yaml,sha256=D1600WgEj3iTXrumVU9LIivJHJO36iaxfkOgyam9zVU,3129
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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/output/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  biocypher/output/connect/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  biocypher/output/connect/_get_connector.py,sha256=Qimv3kTkXYkhJZRT6nq8mwIM2wORCnyqqHqF2IByuuc,1152
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  biocypher/output/connect/_neo4j_driver.py,sha256=kXjOXW12wZFfEp7plAuo40bPSvOfd-i9m4YaXoMq-p0,12357
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  biocypher/output/in_memory/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- biocypher/output/in_memory/_airr.py,sha256=wOYg2x1WCs7DTImtdxNyyoCmjDUVg1Ovh29kzMOQ688,20671
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+ biocypher/output/in_memory/_airr.py,sha256=nd_muSyo3aC9rY90_SWZmjuQQuKxga-FllM7XwJe0JY,20663
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  biocypher/output/in_memory/_get_in_memory_kg.py,sha256=NQ-AT8jgAvb-aTK7zsYrItvlDEow_Mfni5tKEJjwjx0,1256
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  biocypher/output/in_memory/_in_memory_kg.py,sha256=BTBtqb2ZC_zxXdOJ59BQKUoGXZSpiaRG6VecjZGWCm0,3526
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  biocypher/output/in_memory/_networkx.py,sha256=cSOSAreP7S3oeGT6noZ1kAIvSnkVnU3NUp1OY4yqzn0,1515
@@ -40,7 +42,7 @@ biocypher/output/write/relational/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeR
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  biocypher/output/write/relational/_csv.py,sha256=m0BSQXts88Qu5AEvoIgnwRz54ia38g4VN3PaA3LCYM8,2807
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  biocypher/output/write/relational/_postgresql.py,sha256=75iJvv-0ewSsQXhVeoYoGnmYQnKY_B4iItZV7DpEBto,12190
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  biocypher/output/write/relational/_sqlite.py,sha256=BuGWOeeNA83lbUvjpkzqcR9_baWLsbfmLXBKe4O1EPE,2105
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- biocypher-0.10.1.dist-info/LICENSE,sha256=oejgxuxyjSnyPw3YPloz6-dCBB_nYizJ4jDQnr-xZUU,1082
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- biocypher-0.10.1.dist-info/METADATA,sha256=Pxq7NgLmZcVn5zrge_QpB0xozDZWrtghWm2RMuOWZGU,10712
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- biocypher-0.10.1.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
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- biocypher-0.10.1.dist-info/RECORD,,
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+ biocypher-0.11.0.dist-info/METADATA,sha256=_zMd2fQMKTEZsePK-Y-AkApV43-ebtJ5Xx30XbNAKEo,10673
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+ biocypher-0.11.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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+ biocypher-0.11.0.dist-info/licenses/LICENSE,sha256=oejgxuxyjSnyPw3YPloz6-dCBB_nYizJ4jDQnr-xZUU,1082
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+ biocypher-0.11.0.dist-info/RECORD,,
{biocypher-0.10.1.dist-info → biocypher-0.11.0.dist-info}/WHEEL RENAMED
@@ -1,4 +1,4 @@
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  Wheel-Version: 1.0
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- Generator: poetry-core 1.8.1
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+ Generator: hatchling 1.27.0
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  Root-Is-Purelib: true
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  Tag: py3-none-any