biocypher 0.10.0__py3-none-any.whl → 0.11.0__py3-none-any.whl

biocypher/output/in_memory/_airr.py

@@ -1,10 +1,15 @@
-from typing import Any, Optional
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, Any, Optional
 
 from biocypher._create import BioCypherEdge, BioCypherNode
 from biocypher._deduplicate import Deduplicator
 from biocypher._logger import logger
 from biocypher.output.in_memory._in_memory_kg import _InMemoryKG
 
+if TYPE_CHECKING:
+    from scirpy.io import AirrCell
+
 try:
     from scirpy.io import AirrCell
 
@@ -74,7 +79,7 @@ class AirrKG(_InMemoryKG):
         if not HAS_SCIRPY:
             msg = (
                 "AirrCell module from scirpy not detected. "
-                "Install it with 'poetry add biocypher[scirpy]' or 'poetry add scirpy'."
+                "Install it with 'uv add biocypher[scirpy]' or 'uv add scirpy'."
             )
             raise ImportError(msg)
 
@@ -354,6 +359,7 @@ class AirrKG(_InMemoryKG):
             list: List of generated AIRR cells
 
         """
+        self._check_dependencies()
         if not entities:
             msg = "No entities provided for conversion."
             raise ValueError(msg)
@@ -419,6 +425,7 @@ class AirrKG(_InMemoryKG):
         paired: bool,
         receptor_epitope_mapping: dict[str, set] | None = None,
     ) -> list[AirrCell]:
+        self._check_dependencies()
         cell = AirrCell(cell_id=cell_id)
 
         # Process both chains
@@ -464,6 +471,7 @@ class AirrKG(_InMemoryKG):
             List of cells with metadata added
 
         """
+        self._check_dependencies()
         cells = []
         if not metadata_nodes:
             cell["data_source"] = "BioCypher"

{biocypher-0.10.0.dist-info → biocypher-0.11.0.dist-info}/METADATA

@@ -1,12 +1,16 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: biocypher
-Version: 0.10.0
+Version: 0.11.0
 Summary: A unifying framework for biomedical research knowledge graphs
-Home-page: https://github.com/biocypher/biocypher
+Project-URL: Homepage, https://biocypher.org
+Project-URL: Documentation, https://biocypher.org
+Project-URL: Repository, https://github.com/biocypher/biocypher
+Project-URL: Issues, https://github.com/biocypher/biocypher/issues
+Project-URL: Bug Tracker, https://github.com/biocypher/biocypher/issues
+Author-email: Sebastian Lobentanzer <sebastian.lobentanzer@gmail.com>, Denes Turei <turei.denes@gmail.com>
 License: MIT
-Author: Sebastian Lobentanzer
-Author-email: sebastian.lobentanzer@gmail.com
-Requires-Python: >=3.10,<4.0
+License-File: LICENSE
+Keywords: bioinformatics,biomedical-data,graph-database,knowledge-graph
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
@@ -14,25 +18,20 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Provides-Extra: scirpy
-Requires-Dist: PyYAML (>=5.0)
+Requires-Python: >=3.10
 Requires-Dist: appdirs
-Requires-Dist: more_itertools
-Requires-Dist: neo4j-utils (==0.0.7)
-Requires-Dist: networkx (>=3.0,<4.0)
-Requires-Dist: pandas (>=2.0.1,<3.0.0)
-Requires-Dist: pooch (>=1.7.0,<2.0.0)
-Requires-Dist: rdflib (>=6.2.0,<7.0.0)
-Requires-Dist: scirpy (>=0.22.0,<0.23.0) ; extra == "scirpy"
-Requires-Dist: tqdm (>=4.65.0,<5.0.0)
-Requires-Dist: treelib (==1.6.4)
-Project-URL: Bug Tracker, https://github.com/biocypher/biocypher/issues
-Project-URL: Repository, https://github.com/biocypher/biocypher
+Requires-Dist: more-itertools
+Requires-Dist: neo4j-utils==0.0.7
+Requires-Dist: networkx>=3.0
+Requires-Dist: pandas>=2.0.1
+Requires-Dist: pooch>=1.7.0
+Requires-Dist: pyyaml>=5.0
+Requires-Dist: rdflib>=6.2.0
+Requires-Dist: tqdm>=4.65.0
+Requires-Dist: treelib==1.6.4
+Provides-Extra: scirpy
+Requires-Dist: scirpy>=0.22.0; extra == 'scirpy'
 Description-Content-Type: text/markdown
 
 # BioCypher
@@ -81,7 +80,7 @@ Board](https://github.com/orgs/biocypher/projects/3/views/2).
 
 Install the package from PyPI using `pip install biocypher`. More comprehensive
 installation and configuration instructions can be found
-[here](https://biocypher.org/installation.html).
+[here](https://biocypher.org/BioCypher/installation/).
 
 Exemplary usage of BioCypher to build a graph database is shown in our tutorial
 and the various pipelines we have created. You can find these on the [Components
@@ -114,4 +113,3 @@ as a preprint at https://arxiv.org/abs/2212.13543.
 This project has received funding from the European Union’s Horizon 2020
 research and innovation programme under grant agreement No 965193 for DECIDER
 and No 116030 for TransQST.
-

{biocypher-0.10.0.dist-info → biocypher-0.11.0.dist-info}/RECORD

@@ -1,26 +1,28 @@
-biocypher/__init__.py,sha256=-iq15Q3LhB8WBQjnD15ghszEdaqJ1XvQIF5IaF88KNQ,783
-biocypher/_config/__init__.py,sha256=ku86JZaRrzW5NEz5EXsCRktFwxS0Yo2dwX4UuazdfA4,3416
-biocypher/_config/biocypher_config.yaml,sha256=nrlwSW7YP8qTZYm-HvWdTCZy81jnd2FkIGWH8Se2MzI,3651
-biocypher/_config/test_config.yaml,sha256=Np8jeS5_EP6HHOvMKb7B_Tkyqd5YaYlYz_DVsXypt-A,119
-biocypher/_config/test_schema_config.yaml,sha256=D1600WgEj3iTXrumVU9LIivJHJO36iaxfkOgyam9zVU,3129
-biocypher/_config/test_schema_config_disconnected.yaml,sha256=Qm8FLxEn2spHcyj_5F859KjcDvKSxNhxDvi4b4LLkvQ,68
-biocypher/_config/test_schema_config_extended.yaml,sha256=wn3A76142hhjnImhMF6RODbCFESTJ2TtPvcFdIFsAT0,3309
+biocypher/__init__.py,sha256=MsH0rhfqWSPY0ZJN_-fptOFYN4LeG14Fp17XoqxeOJU,992
 biocypher/_core.py,sha256=lP5CC35oXPtfiFY3C-UxZev8p1nMg9E2E4qN5BD9BTg,27437
 biocypher/_create.py,sha256=QsvXrwEQ8k0uNXvCG06UKejvw-QsJwzSaumrBjx9n1k,9884
 biocypher/_deduplicate.py,sha256=rtglcaLRaVzNjLtaPwTGP8VvCM4PHYQ5CZ-cm32CrKQ,4840
 biocypher/_get.py,sha256=_wUjhRjH2J6Qhq0Ndy3kdfaWhHDTT-dxyCvtuH36My4,14868
+biocypher/_graph.py,sha256=YVC8N4SJqKL12Tkv6lmWqED2jp-dr9B9QCXGd5N-Umc,26650
 biocypher/_logger.py,sha256=y9dh3SPJOCWXnkFSYSK7aj_-pB7zlAkNCf43Dp1lt74,2941
 biocypher/_mapping.py,sha256=ntspG2C_NaQODhWTBFk0CDvolkOCjtqlQ9E-NkJAuTg,9030
-biocypher/_metadata.py,sha256=m8xeGsUl8MT9Tdlh_KKcPCa8Pf8Tn84yUlsWkJoxi2M,1416
+biocypher/_metadata.py,sha256=AqFD2kPyn8_KRZTlBGer2Ue6tsd0u3VtOhQMC96Z3-k,2047
 biocypher/_misc.py,sha256=YzlY7zwa0mim9QFg9HwXErkJFIH3cvLrbgjF8tKOIT8,6353
 biocypher/_ontology.py,sha256=lipZxU3aj6zrTbBrJZmCW6IRCuz-KQG3AfbYCVq6aFE,33133
 biocypher/_translate.py,sha256=NKSM9lxNjNNbgQrK_24eWYh3B41TS7kjnSwjySnK3s0,16851
+biocypher/_workflow.py,sha256=av22D_gj9osOczGYP86-wrrjmjG6PvWC0df_920Ff5s,27603
+biocypher/_config/__init__.py,sha256=ku86JZaRrzW5NEz5EXsCRktFwxS0Yo2dwX4UuazdfA4,3416
+biocypher/_config/biocypher_config.yaml,sha256=nrlwSW7YP8qTZYm-HvWdTCZy81jnd2FkIGWH8Se2MzI,3651
+biocypher/_config/test_config.yaml,sha256=Np8jeS5_EP6HHOvMKb7B_Tkyqd5YaYlYz_DVsXypt-A,119
+biocypher/_config/test_schema_config.yaml,sha256=D1600WgEj3iTXrumVU9LIivJHJO36iaxfkOgyam9zVU,3129
+biocypher/_config/test_schema_config_disconnected.yaml,sha256=Qm8FLxEn2spHcyj_5F859KjcDvKSxNhxDvi4b4LLkvQ,68
+biocypher/_config/test_schema_config_extended.yaml,sha256=wn3A76142hhjnImhMF6RODbCFESTJ2TtPvcFdIFsAT0,3309
 biocypher/output/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biocypher/output/connect/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biocypher/output/connect/_get_connector.py,sha256=Qimv3kTkXYkhJZRT6nq8mwIM2wORCnyqqHqF2IByuuc,1152
 biocypher/output/connect/_neo4j_driver.py,sha256=kXjOXW12wZFfEp7plAuo40bPSvOfd-i9m4YaXoMq-p0,12357
 biocypher/output/in_memory/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biocypher/output/in_memory/_airr.py,sha256=tOYww8eHaH4EOElRKFxwShlVW83tXx4xbv7ZfrInphg,20461
+biocypher/output/in_memory/_airr.py,sha256=nd_muSyo3aC9rY90_SWZmjuQQuKxga-FllM7XwJe0JY,20663
 biocypher/output/in_memory/_get_in_memory_kg.py,sha256=NQ-AT8jgAvb-aTK7zsYrItvlDEow_Mfni5tKEJjwjx0,1256
 biocypher/output/in_memory/_in_memory_kg.py,sha256=BTBtqb2ZC_zxXdOJ59BQKUoGXZSpiaRG6VecjZGWCm0,3526
 biocypher/output/in_memory/_networkx.py,sha256=cSOSAreP7S3oeGT6noZ1kAIvSnkVnU3NUp1OY4yqzn0,1515
@@ -40,7 +42,7 @@ biocypher/output/write/relational/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeR
 biocypher/output/write/relational/_csv.py,sha256=m0BSQXts88Qu5AEvoIgnwRz54ia38g4VN3PaA3LCYM8,2807
 biocypher/output/write/relational/_postgresql.py,sha256=75iJvv-0ewSsQXhVeoYoGnmYQnKY_B4iItZV7DpEBto,12190
 biocypher/output/write/relational/_sqlite.py,sha256=BuGWOeeNA83lbUvjpkzqcR9_baWLsbfmLXBKe4O1EPE,2105
-biocypher-0.10.0.dist-info/LICENSE,sha256=oejgxuxyjSnyPw3YPloz6-dCBB_nYizJ4jDQnr-xZUU,1082
-biocypher-0.10.0.dist-info/METADATA,sha256=TAd1YjHL94Sdp0_aW0ag7Qkbr5cJOCm7zvc6DqvG_ko,10706
-biocypher-0.10.0.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-biocypher-0.10.0.dist-info/RECORD,,
+biocypher-0.11.0.dist-info/METADATA,sha256=_zMd2fQMKTEZsePK-Y-AkApV43-ebtJ5Xx30XbNAKEo,10673
+biocypher-0.11.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+biocypher-0.11.0.dist-info/licenses/LICENSE,sha256=oejgxuxyjSnyPw3YPloz6-dCBB_nYizJ4jDQnr-xZUU,1082
+biocypher-0.11.0.dist-info/RECORD,,

{biocypher-0.10.0.dist-info → biocypher-0.11.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.8.1
+Generator: hatchling 1.27.0
 Root-Is-Purelib: true
 Tag: py3-none-any