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03/33] Address semsimian being optional dependency --- src/oaklib/implementations/__init__.py | 57 ++++++++++++------- .../semsimian/semsimian_implementation.py | 6 +- 2 files changed, 40 insertions(+), 23 deletions(-) diff --git a/src/oaklib/implementations/__init__.py b/src/oaklib/implementations/__init__.py index 0e972c1a6..5786a8430 100644 --- a/src/oaklib/implementations/__init__.py +++ b/src/oaklib/implementations/__init__.py @@ -41,9 +41,6 @@ OntoPortalImplementationBase, ) from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation -from oaklib.implementations.semsimian.semsimian_implementation import ( - SemSimianImplementation, -) from oaklib.implementations.simpleobo.simple_obo_implementation import ( SimpleOboImplementation, ) @@ -65,6 +62,16 @@ ) from oaklib.interfaces import OntologyInterface +SEMSIMIAN_AVAILABLE = False +try: + from oaklib.implementations.semsimian.semsimian_implementation import ( + SemSimianImplementation, + ) + SEMSIMIAN_AVAILABLE = True +except ImportError: + pass + + __all__ = [ "get_implementation_resolver", # Concrete classes @@ -96,8 +103,7 @@ "UniprotImplementation", "TranslatorImplementation", "OakMetaModelImplementation", - "SemSimianImplementation", -] +] + (["SemSimianImplementation"] if SEMSIMIAN_AVAILABLE else []) @cache @@ -122,30 +128,37 @@ def get_implementation_resolver() -> ClassResolver[OntologyInterface]: :return: A ClassResolver capable of resolving an OntologyInterface implementation """ + skip_classes = { + OntoPortalImplementationBase, + BaseOlsImplementation, + } + + resolver_synonyms = { + "obolibrary": ProntoImplementation, + "prontolib": ProntoImplementation, + "simpleobo": SimpleOboImplementation, + "sqlite": SqlImplementation, + "rdflib": SparqlImplementation, + "oak": OakMetaModelImplementation, + "cx": CXImplementation, + "ndexbio": CXImplementation, + } + + if not SEMSIMIAN_AVAILABLE: + skip_classes.add('SemSimianImplementation') + resolver_synonyms['semsimian'] = SemSimianImplementation + implementation_resolver: ClassResolver[OntologyInterface] = ClassResolver.from_subclasses( OntologyInterface, suffix="Implementation", - skip={ - OntoPortalImplementationBase, - BaseOlsImplementation, - }, + skip=skip_classes, ) # if an implementation uses a shorthand name that is # different from the class name (minus Implementation), then # it should be added here - implementation_resolver.synonyms.update( - { - "obolibrary": ProntoImplementation, - "prontolib": ProntoImplementation, - "simpleobo": SimpleOboImplementation, - "sqlite": SqlImplementation, - "rdflib": SparqlImplementation, - "oak": OakMetaModelImplementation, - "cx": CXImplementation, - "ndexbio": CXImplementation, - "semsimian": SemSimianImplementation, - } - ) + + + implementation_resolver.synonyms.update(resolver_synonyms) # Plugins which want to register an implementation should use # the entrypoint group "oaklib.plugins". The name of the entry diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 9b17c8a01..0cb6cc439 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -6,7 +6,11 @@ from dataclasses import dataclass, field from typing import ClassVar, Dict, Iterable, Iterator, List, Optional, Tuple, Union -from semsimian import Semsimian +try: + from semsimian import Semsimian +except ImportError: + raise ImportError("The 'semsimian' package is not installed. Please install it to continue.") + from oaklib.datamodels.similarity import ( BestMatch, From 40b75449a27a6a02a237b5b8c91dc02a53712bbe Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 6 Mar 2024 17:28:54 -0600 Subject: [PATCH 04/33] formatted --- src/oaklib/implementations/__init__.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/oaklib/implementations/__init__.py b/src/oaklib/implementations/__init__.py index 5786a8430..de172d88c 100644 --- a/src/oaklib/implementations/__init__.py +++ b/src/oaklib/implementations/__init__.py @@ -67,9 +67,10 @@ from oaklib.implementations.semsimian.semsimian_implementation import ( SemSimianImplementation, ) + SEMSIMIAN_AVAILABLE = True except ImportError: - pass + pass __all__ = [ @@ -145,8 +146,8 @@ def get_implementation_resolver() -> ClassResolver[OntologyInterface]: } if not SEMSIMIAN_AVAILABLE: - skip_classes.add('SemSimianImplementation') - resolver_synonyms['semsimian'] = SemSimianImplementation + skip_classes.add("SemSimianImplementation") + resolver_synonyms["semsimian"] = SemSimianImplementation implementation_resolver: ClassResolver[OntologyInterface] = ClassResolver.from_subclasses( OntologyInterface, @@ -156,7 +157,6 @@ def get_implementation_resolver() -> ClassResolver[OntologyInterface]: # if an implementation uses a shorthand name that is # different from the class name (minus Implementation), then # it should be added here - implementation_resolver.synonyms.update(resolver_synonyms) From fe2f06bf283b406766b7f189eb2df13505c23de7 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 6 Mar 2024 17:30:31 -0600 Subject: [PATCH 05/33] updated message --- .../implementations/semsimian/semsimian_implementation.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 0cb6cc439..aaeccef6a 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -9,7 +9,9 @@ try: from semsimian import Semsimian except ImportError: - raise ImportError("The 'semsimian' package is not installed. Please install it to continue.") + raise ImportError( + "The 'semsimian' package (optional) is not installed. Please install it to continue." + ) from oaklib.datamodels.similarity import ( From 0d2138547d3c3742c7e19854203aa7553a1d11ef Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 6 Mar 2024 17:34:26 -0600 Subject: [PATCH 06/33] formatted --- src/oaklib/implementations/__init__.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/oaklib/implementations/__init__.py b/src/oaklib/implementations/__init__.py index de172d88c..b741445ab 100644 --- a/src/oaklib/implementations/__init__.py +++ b/src/oaklib/implementations/__init__.py @@ -104,7 +104,9 @@ "UniprotImplementation", "TranslatorImplementation", "OakMetaModelImplementation", -] + (["SemSimianImplementation"] if SEMSIMIAN_AVAILABLE else []) +] +if SEMSIMIAN_AVAILABLE: + __all__.append("SemSimianImplementation") @cache From 6857a11b4e88a6af0991fde50787327cbf9274a8 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 08:35:23 -0600 Subject: [PATCH 07/33] Use TYPE_CHECKING --- .../implementations/semsimian/semsimian_implementation.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index aaeccef6a..448db0f98 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -4,14 +4,10 @@ import logging import math from dataclasses import dataclass, field -from typing import ClassVar, Dict, Iterable, Iterator, List, Optional, Tuple, Union +from typing import TYPE_CHECKING, ClassVar, Dict, Iterable, Iterator, List, Optional, Tuple, Union -try: +if TYPE_CHECKING: from semsimian import Semsimian -except ImportError: - raise ImportError( - "The 'semsimian' package (optional) is not installed. Please install it to continue." - ) from oaklib.datamodels.similarity import ( From 5752f41bdab7710f9f1d628d8ef4b526a6070682 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 09:58:01 -0600 Subject: [PATCH 08/33] roll back init --- src/oaklib/implementations/__init__.py | 57 ++++++++++---------------- 1 file changed, 21 insertions(+), 36 deletions(-) diff --git a/src/oaklib/implementations/__init__.py b/src/oaklib/implementations/__init__.py index b741445ab..0e972c1a6 100644 --- a/src/oaklib/implementations/__init__.py +++ b/src/oaklib/implementations/__init__.py @@ -41,6 +41,9 @@ OntoPortalImplementationBase, ) from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation +from oaklib.implementations.semsimian.semsimian_implementation import ( + SemSimianImplementation, +) from oaklib.implementations.simpleobo.simple_obo_implementation import ( SimpleOboImplementation, ) @@ -62,17 +65,6 @@ ) from oaklib.interfaces import OntologyInterface -SEMSIMIAN_AVAILABLE = False -try: - from oaklib.implementations.semsimian.semsimian_implementation import ( - SemSimianImplementation, - ) - - SEMSIMIAN_AVAILABLE = True -except ImportError: - pass - - __all__ = [ "get_implementation_resolver", # Concrete classes @@ -104,9 +96,8 @@ "UniprotImplementation", "TranslatorImplementation", "OakMetaModelImplementation", + "SemSimianImplementation", ] -if SEMSIMIAN_AVAILABLE: - __all__.append("SemSimianImplementation") @cache @@ -131,36 +122,30 @@ def get_implementation_resolver() -> ClassResolver[OntologyInterface]: :return: A ClassResolver capable of resolving an OntologyInterface implementation """ - skip_classes = { - OntoPortalImplementationBase, - BaseOlsImplementation, - } - - resolver_synonyms = { - "obolibrary": ProntoImplementation, - "prontolib": ProntoImplementation, - "simpleobo": SimpleOboImplementation, - "sqlite": SqlImplementation, - "rdflib": SparqlImplementation, - "oak": OakMetaModelImplementation, - "cx": CXImplementation, - "ndexbio": CXImplementation, - } - - if not SEMSIMIAN_AVAILABLE: - skip_classes.add("SemSimianImplementation") - resolver_synonyms["semsimian"] = SemSimianImplementation - implementation_resolver: ClassResolver[OntologyInterface] = ClassResolver.from_subclasses( OntologyInterface, suffix="Implementation", - skip=skip_classes, + skip={ + OntoPortalImplementationBase, + BaseOlsImplementation, + }, ) # if an implementation uses a shorthand name that is # different from the class name (minus Implementation), then # it should be added here - - implementation_resolver.synonyms.update(resolver_synonyms) + implementation_resolver.synonyms.update( + { + "obolibrary": ProntoImplementation, + "prontolib": ProntoImplementation, + "simpleobo": SimpleOboImplementation, + "sqlite": SqlImplementation, + "rdflib": SparqlImplementation, + "oak": OakMetaModelImplementation, + "cx": CXImplementation, + "ndexbio": CXImplementation, + "semsimian": SemSimianImplementation, + } + ) # Plugins which want to register an implementation should use # the entrypoint group "oaklib.plugins". The name of the entry From cf1959edf02ccd069c520dc77927b31087207261 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 09:59:12 -0600 Subject: [PATCH 09/33] formatted --- .../semsimian/semsimian_implementation.py | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 448db0f98..5ac35a3da 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -4,12 +4,21 @@ import logging import math from dataclasses import dataclass, field -from typing import TYPE_CHECKING, ClassVar, Dict, Iterable, Iterator, List, Optional, Tuple, Union +from typing import ( + TYPE_CHECKING, + ClassVar, + Dict, + Iterable, + Iterator, + List, + Optional, + Tuple, + Union, +) if TYPE_CHECKING: from semsimian import Semsimian - from oaklib.datamodels.similarity import ( BestMatch, TermInfo, From 18c2e44df096fa67bd9cb29f7f71171d5211e931 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 10:27:11 -0600 Subject: [PATCH 10/33] add sesmimian as dependency in tox --- tox.ini | 1 + 1 file changed, 1 insertion(+) diff --git a/tox.ini b/tox.ini index 066214e7b..4b7ce2dc0 100644 --- a/tox.ini +++ b/tox.ini @@ -27,6 +27,7 @@ deps = semsimian gilda linkml + semsimian [testenv:lock] skip_install = true From b91038d09655c01936fec8203a3c012e453242dc Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 10:27:34 -0600 Subject: [PATCH 11/33] duplicate --- tox.ini | 1 - 1 file changed, 1 deletion(-) diff --git a/tox.ini b/tox.ini index 4b7ce2dc0..066214e7b 100644 --- a/tox.ini +++ b/tox.ini @@ -27,7 +27,6 @@ deps = semsimian gilda linkml - semsimian [testenv:lock] skip_install = true From 2cfa6b5036337783c86bcadb40c9899446a90d2c Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 10:30:33 -0600 Subject: [PATCH 12/33] add semsimian install --- .github/workflows/main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 0e1d8f676..4b0bd9ddf 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -88,7 +88,7 @@ jobs: # install your root project, if required #---------------------------------------------- - name: Install library - run: poetry install --no-interaction --extras "gilda" + run: poetry install --no-interaction --extras "gilda semsimian" - name: Get Gilda resources run: | From d4cb659210061f896345b898b374ebd0c966352c Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 10:38:23 -0600 Subject: [PATCH 13/33] add semsimian install --- .github/workflows/main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 4b0bd9ddf..b0a3c2a03 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -100,7 +100,7 @@ jobs: #---------------------------------------------- - name: Generate coverage results run: | - poetry run pip install -U pytest + poetry run pip install -U pytest semsimian poetry run coverage run -p -m pytest tests/ poetry run coverage combine poetry run coverage xml From b7db86ae7c543eb772ad6d1d5f44ac1058028443 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 10:38:48 -0600 Subject: [PATCH 14/33] edit semsimian install --- .github/workflows/main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index b0a3c2a03..53ff1c056 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -88,7 +88,7 @@ jobs: # install your root project, if required #---------------------------------------------- - name: Install library - run: poetry install --no-interaction --extras "gilda semsimian" + run: poetry install --no-interaction --extras "gilda" - name: Get Gilda resources run: | From 89e736f314fdb6e3c7b596661277551f5e31689d Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 11:55:04 -0600 Subject: [PATCH 15/33] undo semsimian install --- .github/workflows/main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 53ff1c056..0e1d8f676 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -100,7 +100,7 @@ jobs: #---------------------------------------------- - name: Generate coverage results run: | - poetry run pip install -U pytest semsimian + poetry run pip install -U pytest poetry run coverage run -p -m pytest tests/ poetry run coverage combine poetry run coverage xml From 3c2214d9c67174dd0e52c15f366e6625205a8891 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 11:57:58 -0600 Subject: [PATCH 16/33] fixed semsimian mystery --- .github/workflows/main.yaml | 2 +- poetry.lock | 3 ++- pyproject.toml | 1 + 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 0e1d8f676..4b0bd9ddf 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -88,7 +88,7 @@ jobs: # install your root project, if required #---------------------------------------------- - name: Install library - run: poetry install --no-interaction --extras "gilda" + run: poetry install --no-interaction --extras "gilda semsimian" - name: Get Gilda resources run: | diff --git a/poetry.lock b/poetry.lock index dc5cdf17a..1aaae4472 100644 --- a/poetry.lock +++ b/poetry.lock @@ -6500,8 +6500,9 @@ docs = [] gilda = ["gilda", "urllib3"] llm = ["llm"] seaborn = [] +semsimian = [] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0.0" -content-hash = "92a86269b9d388365b0c594a84d6d4b1d483265f133bcb0007f6978779177c08" +content-hash = "b4ed410508a38afde0e6ed636db83feae0bfec82133cf62bc26cbfc652ec5118" diff --git a/pyproject.toml b/pyproject.toml index d4653f0b9..aaca7bea1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -72,6 +72,7 @@ docs = ["Sphinx", "sphinx-rtd-theme", "sphinxcontrib-mermaid", "sphinx-copybutto gilda = ["scipy", "gilda", "urllib3"] llm = ["llm"] seaborn = ["seaborn"] +semsimian = ["semsimian"] [tool.black] line-length = 100 From 05ee23b5ea9ab1ed8c04d47c63a102f6ae7a3b21 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 13:04:54 -0600 Subject: [PATCH 17/33] semsimian as a group not an extra --- .github/workflows/main.yaml | 2 +- poetry.lock | 3 +-- pyproject.toml | 1 - 3 files changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 4b0bd9ddf..4da9615a5 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -88,7 +88,7 @@ jobs: # install your root project, if required #---------------------------------------------- - name: Install library - run: poetry install --no-interaction --extras "gilda semsimian" + run: poetry install --no-interaction --extras "gilda" --with semsimian - name: Get Gilda resources run: | diff --git a/poetry.lock b/poetry.lock index 1aaae4472..dc5cdf17a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -6500,9 +6500,8 @@ docs = [] gilda = ["gilda", "urllib3"] llm = ["llm"] seaborn = [] -semsimian = [] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0.0" -content-hash = "b4ed410508a38afde0e6ed636db83feae0bfec82133cf62bc26cbfc652ec5118" +content-hash = "92a86269b9d388365b0c594a84d6d4b1d483265f133bcb0007f6978779177c08" diff --git a/pyproject.toml b/pyproject.toml index aaca7bea1..d4653f0b9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -72,7 +72,6 @@ docs = ["Sphinx", "sphinx-rtd-theme", "sphinxcontrib-mermaid", "sphinx-copybutto gilda = ["scipy", "gilda", "urllib3"] llm = ["llm"] seaborn = ["seaborn"] -semsimian = ["semsimian"] [tool.black] line-length = 100 From 90a70c921949a23105a8173482c31ff8199498d2 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 15:17:49 -0600 Subject: [PATCH 18/33] optional semsimian possible solution --- src/oaklib/implementations/semsimian/semsimian_implementation.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 5ac35a3da..06f090a34 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -16,6 +16,7 @@ Union, ) +Semsimian: Optional["Semsimian"] = None if TYPE_CHECKING: from semsimian import Semsimian From b1f9b2c8bd7541a908a00d65833af6e91e7a88fe Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 15:21:02 -0600 Subject: [PATCH 19/33] formatted --- .../implementations/semsimian/semsimian_implementation.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 06f090a34..d30b576c4 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -16,10 +16,6 @@ Union, ) -Semsimian: Optional["Semsimian"] = None -if TYPE_CHECKING: - from semsimian import Semsimian - from oaklib.datamodels.similarity import ( BestMatch, TermInfo, @@ -34,6 +30,10 @@ from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface from oaklib.types import CURIE, PRED_CURIE +Semsimian: Optional["Semsimian"] = None +if TYPE_CHECKING: + from semsimian import Semsimian + wrapped_adapter: BasicOntologyInterface = None __all__ = [ From 290fb488fb0df6732c9aaad81c941b9f40c1f3f2 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 15:21:31 -0600 Subject: [PATCH 20/33] formatted --- .../implementations/semsimian/semsimian_implementation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index d30b576c4..e86374468 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -63,7 +63,7 @@ class SemSimianImplementation(SearchInterface, SemanticSimilarityInterface, OboG SemanticSimilarityInterface.information_content_scores, ] - semsimian_object_cache: Dict[Tuple[PRED_CURIE], Semsimian] = field(default_factory=dict) + semsimian_object_cache: Dict[Tuple[PRED_CURIE], Semsimian] = field(default_factory=dict) # type: ignore def __post_init__(self): slug = self.resource.slug From f5ddd46b40e33b3c67edc3739df4eff0b3f86611 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 15:23:37 -0600 Subject: [PATCH 21/33] formatted --- .../implementations/semsimian/semsimian_implementation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index e86374468..d6d6ad73f 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -63,7 +63,7 @@ class SemSimianImplementation(SearchInterface, SemanticSimilarityInterface, OboG SemanticSimilarityInterface.information_content_scores, ] - semsimian_object_cache: Dict[Tuple[PRED_CURIE], Semsimian] = field(default_factory=dict) # type: ignore + semsimian_object_cache: Dict[Tuple[PRED_CURIE], Semsimian] = field(default_factory=dict) # type: ignore def __post_init__(self): slug = self.resource.slug From 194280a6205fde83939af8c91b48e953941b19ec Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 15:31:00 -0600 Subject: [PATCH 22/33] updated gitignore --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index 64221ac0d..4157a66b2 100644 --- a/.gitignore +++ b/.gitignore @@ -30,3 +30,5 @@ tests/input/fhirjson_conf.json oak_hp.profile oak_semsimian_hp.profile notebooks/demo.tsv +tests/input/obo_conf.yaml +tests/input/obojson_conf.yaml From 2b6194621ef9a9a55215e9cc87b0940867e3a9b0 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 8 Mar 2024 15:50:34 -0600 Subject: [PATCH 23/33] corrected branch diff madness --- .../implementations/semsimian/semsimian_implementation.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 28523c199..8d187aa17 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -5,6 +5,7 @@ import math from dataclasses import dataclass, field from typing import ( + TYPE_CHECKING, ClassVar, Dict, Iterable, @@ -15,7 +16,6 @@ Union, ) - from oaklib.datamodels.similarity import ( BestMatch, TermInfo, @@ -30,7 +30,7 @@ from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface from oaklib.types import CURIE, PRED_CURIE -Semsimian: Optional["Semsimian"] = None +Semsimian: Optional["Semsimian"] = None # type: ignore if TYPE_CHECKING: from semsimian import Semsimian From d9e2d2f8b08cca4be3edd61b95a9a235584badbd Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 11 Mar 2024 10:06:04 -0500 Subject: [PATCH 24/33] don't initialize it to be None --- .../implementations/semsimian/semsimian_implementation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 125781b2a..bc2f1f774 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -64,7 +64,7 @@ class SemSimianImplementation(SearchInterface, SemanticSimilarityInterface, OboG SemanticSimilarityInterface.information_content_scores, ] - semsimian_object_cache: Dict[Tuple[PRED_CURIE], Semsimian] = field(default_factory=dict) # type: ignore + semsimian_object_cache: Dict[Tuple[PRED_CURIE], Optional[Semsimian]] = field(default_factory=dict) # type: ignore def __post_init__(self): slug = self.resource.slug From 40dc23024196c8101f62f7a63a25665937fac47d Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 11 Mar 2024 10:18:18 -0500 Subject: [PATCH 25/33] formatted --- src/oaklib/implementations/semsimian/semsimian_implementation.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index bc2f1f774..6b962cf7b 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -4,7 +4,6 @@ import logging import math from dataclasses import dataclass, field - from typing import ( TYPE_CHECKING, ClassVar, From 5b8758da6b992b01f2fd6d240b05f52caf473cfd Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 11 Mar 2024 11:15:58 -0500 Subject: [PATCH 26/33] Should fix the gh action error thanks @justaddcoffee --- poetry.lock | 307 +----------------- pyproject.toml | 6 +- .../semsimian/semsimian_implementation.py | 5 +- 3 files changed, 19 insertions(+), 299 deletions(-) diff --git a/poetry.lock b/poetry.lock index b0162a29f..900402fda 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "adeft" version = "0.11.2" description = "Acromine based Disambiguation of Entities From Text" -category = "main" optional = true python-versions = "*" files = [ @@ -25,7 +24,6 @@ test = ["pytest", "pytest-cov"] name = "aiohttp" version = "3.9.3" description = "Async http client/server framework (asyncio)" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -122,7 +120,6 @@ speedups = ["Brotli", "aiodns", "brotlicffi"] name = "aiosignal" version = "1.3.1" description = "aiosignal: a list of registered asynchronous callbacks" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -137,7 +134,6 @@ frozenlist = ">=1.1.0" name = "airium" version = "0.2.6" description = "Easy and quick html builder with natural syntax correspondence (python->html). No templates needed. Serves pure pythonic library with no dependencies." -category = "main" optional = false python-versions = "*" files = [ @@ -153,7 +149,6 @@ parse = ["beautifulsoup4 (>=4.10.0,<5.0)", "requests (>=2.12.0,<3)"] name = "alabaster" version = "0.7.16" description = "A light, configurable Sphinx theme" -category = "dev" optional = false python-versions = ">=3.9" files = [ @@ -165,7 +160,6 @@ files = [ name = "aniso8601" version = "9.0.1" description = "A library for parsing ISO 8601 strings." -category = "main" optional = true python-versions = "*" files = [ @@ -180,7 +174,6 @@ dev = ["black", "coverage", "isort", "pre-commit", "pyenchant", "pylint"] name = "annotated-types" version = "0.6.0" description = "Reusable constraint types to use with typing.Annotated" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -192,7 +185,6 @@ files = [ name = "antlr4-python3-runtime" version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" -category = "main" optional = false python-versions = "*" files = [ @@ -203,7 +195,6 @@ files = [ name = "anyio" version = "4.3.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -226,7 +217,6 @@ trio = ["trio (>=0.23)"] name = "appdirs" version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "main" optional = false python-versions = "*" files = [ @@ -238,7 +228,6 @@ files = [ name = "appnope" version = "0.1.4" description = "Disable App Nap on macOS >= 10.9" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -250,7 +239,6 @@ files = [ name = "argon2-cffi" version = "23.1.0" description = "Argon2 for Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -271,7 +259,6 @@ typing = ["mypy"] name = "argon2-cffi-bindings" version = "21.2.0" description = "Low-level CFFI bindings for Argon2" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -309,7 +296,6 @@ tests = ["pytest"] name = "arrow" version = "1.3.0" description = "Better dates & times for Python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -323,13 +309,12 @@ types-python-dateutil = ">=2.8.10" [package.extras] doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] -test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] +test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] [[package]] name = "asttokens" version = "2.4.1" description = "Annotate AST trees with source code positions" -category = "dev" optional = false python-versions = "*" files = [ @@ -348,7 +333,6 @@ test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"] name = "async-lru" version = "2.0.4" description = "Simple LRU cache for asyncio" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -363,7 +347,6 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} name = "async-timeout" version = "4.0.3" description = "Timeout context manager for asyncio programs" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -375,7 +358,6 @@ files = [ name = "attrs" version = "23.2.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -395,7 +377,6 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p name = "babel" version = "2.14.0" description = "Internationalization utilities" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -410,7 +391,6 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] name = "bcp47" version = "0.0.4" description = "Language tags made easy" -category = "main" optional = false python-versions = "*" files = [ @@ -422,7 +402,6 @@ files = [ name = "beautifulsoup4" version = "4.12.3" description = "Screen-scraping library" -category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -444,7 +423,6 @@ lxml = ["lxml"] name = "bleach" version = "6.1.0" description = "An easy safelist-based HTML-sanitizing tool." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -463,7 +441,6 @@ css = ["tinycss2 (>=1.1.0,<1.3)"] name = "blinker" version = "1.7.0" description = "Fast, simple object-to-object and broadcast signaling" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -475,7 +452,6 @@ files = [ name = "boto3" version = "1.34.58" description = "The AWS SDK for Python" -category = "main" optional = true python-versions = ">= 3.8" files = [ @@ -495,7 +471,6 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] name = "botocore" version = "1.34.58" description = "Low-level, data-driven core of boto 3." -category = "main" optional = true python-versions = ">= 3.8" files = [ @@ -518,7 +493,6 @@ crt = ["awscrt (==0.19.19)"] name = "cachetools" version = "5.3.3" description = "Extensible memoizing collections and decorators" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -530,7 +504,6 @@ files = [ name = "cattrs" version = "23.2.3" description = "Composable complex class support for attrs and dataclasses." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -556,7 +529,6 @@ ujson = ["ujson (>=5.7.0)"] name = "certifi" version = "2024.2.2" description = "Python package for providing Mozilla's CA Bundle." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -568,7 +540,6 @@ files = [ name = "cffi" version = "1.16.0" description = "Foreign Function Interface for Python calling C code." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -633,7 +604,6 @@ pycparser = "*" name = "cfgraph" version = "0.2.1" description = "rdflib collections flattening graph" -category = "dev" optional = false python-versions = "*" files = [ @@ -647,7 +617,6 @@ rdflib = ">=0.4.2" name = "chardet" version = "5.2.0" description = "Universal encoding detector for Python 3" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -659,7 +628,6 @@ files = [ name = "charset-normalizer" version = "3.3.2" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -759,7 +727,6 @@ files = [ name = "class-resolver" version = "0.4.3" description = "Lookup and instantiate classes with style." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -786,7 +753,6 @@ torch-geometric = ["torch", "torch-geometric", "torch-sparse"] name = "click" version = "8.1.7" description = "Composable command line interface toolkit" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -801,7 +767,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "click-default-group" version = "1.2.4" description = "click_default_group" -category = "main" optional = true python-versions = ">=2.7" files = [ @@ -819,7 +784,6 @@ test = ["pytest"] name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -831,7 +795,6 @@ files = [ name = "comm" version = "0.2.1" description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -849,7 +812,6 @@ test = ["pytest"] name = "contourpy" version = "1.2.0" description = "Python library for calculating contours of 2D quadrilateral grids" -category = "dev" optional = false python-versions = ">=3.9" files = [ @@ -913,7 +875,6 @@ test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"] name = "coverage" version = "6.5.0" description = "Code coverage measurement for Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -976,7 +937,6 @@ toml = ["tomli"] name = "curies" version = "0.7.7" description = "Idiomatic conversion between URIs and compact URIs (CURIEs)." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1001,7 +961,6 @@ tests = ["coverage", "pytest"] name = "cycler" version = "0.12.1" description = "Composable style cycles" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1017,7 +976,6 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"] name = "debugpy" version = "1.8.1" description = "An implementation of the Debug Adapter Protocol for Python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1049,7 +1007,6 @@ files = [ name = "decorator" version = "5.1.1" description = "Decorators for Humans" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -1061,7 +1018,6 @@ files = [ name = "defusedxml" version = "0.7.1" description = "XML bomb protection for Python stdlib modules" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -1073,7 +1029,6 @@ files = [ name = "deprecated" version = "1.2.14" description = "Python @deprecated decorator to deprecate old python classes, functions or methods." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1091,7 +1046,6 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"] name = "deprecation" version = "2.1.0" description = "A library to handle automated deprecations" -category = "main" optional = false python-versions = "*" files = [ @@ -1106,7 +1060,6 @@ packaging = "*" name = "distlib" version = "0.3.8" description = "Distribution utilities" -category = "dev" optional = false python-versions = "*" files = [ @@ -1118,7 +1071,6 @@ files = [ name = "distro" version = "1.9.0" description = "Distro - an OS platform information API" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -1130,7 +1082,6 @@ files = [ name = "docutils" version = "0.18.1" description = "Docutils -- Python Documentation Utilities" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -1142,7 +1093,6 @@ files = [ name = "editorconfig" version = "0.12.4" description = "EditorConfig File Locator and Interpreter for Python" -category = "main" optional = false python-versions = "*" files = [ @@ -1153,7 +1103,6 @@ files = [ name = "et-xmlfile" version = "1.1.0" description = "An implementation of lxml.xmlfile for the standard library" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1165,7 +1114,6 @@ files = [ name = "eutils" version = "0.6.0" description = "\"Python interface to NCBI's eutilities API\"" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1185,7 +1133,6 @@ dev = ["flake8", "ipython", "mock", "pytest", "pytest-cov", "restview", "setupto name = "exceptiongroup" version = "1.2.0" description = "Backport of PEP 654 (exception groups)" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1200,7 +1147,6 @@ test = ["pytest (>=6)"] name = "executing" version = "2.0.1" description = "Get the currently executing AST node of a frame, and other information" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -1215,7 +1161,6 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth name = "fastjsonschema" version = "2.19.1" description = "Fastest Python implementation of JSON schema" -category = "dev" optional = false python-versions = "*" files = [ @@ -1230,7 +1175,6 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc name = "fastobo" version = "0.12.3" description = "Faultless AST for Open Biomedical Ontologies in Python." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1286,7 +1230,6 @@ files = [ name = "filelock" version = "3.13.1" description = "A platform independent file lock." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1303,7 +1246,6 @@ typing = ["typing-extensions (>=4.8)"] name = "flask" version = "3.0.2" description = "A simple framework for building complex web applications." -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -1327,7 +1269,6 @@ dotenv = ["python-dotenv"] name = "flask-restx" version = "1.3.0" description = "Fully featured framework for fast, easy and documented API development with Flask" -category = "main" optional = true python-versions = "*" files = [ @@ -1352,7 +1293,6 @@ test = ["Faker (==2.0.0)", "blinker", "invoke (==2.2.0)", "mock (==3.0.5)", "pyt name = "fonttools" version = "4.49.0" description = "Tools to manipulate font files" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1418,7 +1358,6 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] name = "fqdn" version = "1.5.1" description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers" -category = "dev" optional = false python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" files = [ @@ -1430,7 +1369,6 @@ files = [ name = "frozenlist" version = "1.4.1" description = "A list-like structure which implements collections.abc.MutableSequence" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -1517,7 +1455,6 @@ files = [ name = "funowl" version = "0.2.3" description = "Python rendering of the OWL Functional syntax" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1537,7 +1474,6 @@ rfc3987 = "*" name = "ghp-import" version = "2.1.0" description = "Copy your docs directly to the gh-pages branch." -category = "main" optional = false python-versions = "*" files = [ @@ -1555,7 +1491,6 @@ dev = ["flake8", "markdown", "twine", "wheel"] name = "gilda" version = "1.1.0" description = "Grounding for biomedical entities with contextual disambiguation" -category = "main" optional = true python-versions = "*" files = [ @@ -1584,7 +1519,6 @@ ui = ["flask-bootstrap", "flask-wtf"] name = "graphviz" version = "0.20.1" description = "Simple Python interface for Graphviz" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1601,7 +1535,6 @@ test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>= name = "greenlet" version = "3.0.3" description = "Lightweight in-process concurrent programming" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1673,7 +1606,6 @@ test = ["objgraph", "psutil"] name = "h11" version = "0.14.0" description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1685,7 +1617,6 @@ files = [ name = "hbreader" version = "0.9.1" description = "Honey Badger reader - a generic file/url/string open and read tool" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1697,7 +1628,6 @@ files = [ name = "httpcore" version = "1.0.4" description = "A minimal low-level HTTP client." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1712,14 +1642,13 @@ h11 = ">=0.13,<0.15" [package.extras] asyncio = ["anyio (>=4.0,<5.0)"] http2 = ["h2 (>=3,<5)"] -socks = ["socksio (>=1.0.0,<2.0.0)"] +socks = ["socksio (==1.*)"] trio = ["trio (>=0.22.0,<0.25.0)"] [[package]] name = "httpx" version = "0.27.0" description = "The next generation HTTP client." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1730,21 +1659,20 @@ files = [ [package.dependencies] anyio = "*" certifi = "*" -httpcore = ">=1.0.0,<2.0.0" +httpcore = "==1.*" idna = "*" sniffio = "*" [package.extras] brotli = ["brotli", "brotlicffi"] -cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<14)"] +cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"] http2 = ["h2 (>=3,<5)"] -socks = ["socksio (>=1.0.0,<2.0.0)"] +socks = ["socksio (==1.*)"] [[package]] name = "idna" version = "3.6" description = "Internationalized Domain Names in Applications (IDNA)" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -1756,7 +1684,6 @@ files = [ name = "ijson" version = "3.2.3" description = "Iterative JSON parser with standard Python iterator interfaces" -category = "main" optional = false python-versions = "*" files = [ @@ -1855,7 +1782,6 @@ files = [ name = "imagesize" version = "1.4.1" description = "Getting image size from png/jpeg/jpeg2000/gif file" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1867,7 +1793,6 @@ files = [ name = "importlib-metadata" version = "7.0.2" description = "Read metadata from Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1887,7 +1812,6 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs name = "importlib-resources" version = "6.1.3" description = "Read resources from Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1906,7 +1830,6 @@ testing = ["jaraco.collections", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "py name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1918,7 +1841,6 @@ files = [ name = "ipykernel" version = "6.29.3" description = "IPython Kernel for Jupyter" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1932,7 +1854,7 @@ comm = ">=0.1.1" debugpy = ">=1.6.5" ipython = ">=7.23.1" jupyter-client = ">=6.1.12" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" matplotlib-inline = ">=0.1" nest-asyncio = "*" packaging = "*" @@ -1952,7 +1874,6 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio name = "ipython" version = "8.18.1" description = "IPython: Productive Interactive Computing" -category = "dev" optional = false python-versions = ">=3.9" files = [ @@ -1990,7 +1911,6 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pa name = "ipywidgets" version = "8.1.2" description = "Jupyter interactive widgets" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2012,7 +1932,6 @@ test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"] name = "isodate" version = "0.6.1" description = "An ISO 8601 date/time/duration parser and formatter" -category = "main" optional = false python-versions = "*" files = [ @@ -2027,7 +1946,6 @@ six = "*" name = "isoduration" version = "20.11.0" description = "Operations with ISO 8601 durations" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2042,7 +1960,6 @@ arrow = ">=0.15.0" name = "itsdangerous" version = "2.1.2" description = "Safely pass data to untrusted environments and back." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -2054,7 +1971,6 @@ files = [ name = "jedi" version = "0.19.1" description = "An autocompletion tool for Python that can be used for text editors." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2074,7 +1990,6 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] name = "jinja2" version = "3.1.3" description = "A very fast and expressive template engine." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2092,7 +2007,6 @@ i18n = ["Babel (>=2.7)"] name = "jmespath" version = "1.0.1" description = "JSON Matching Expressions" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -2104,7 +2018,6 @@ files = [ name = "joblib" version = "1.3.2" description = "Lightweight pipelining with Python functions" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -2116,7 +2029,6 @@ files = [ name = "jsbeautifier" version = "1.15.1" description = "JavaScript unobfuscator and beautifier." -category = "main" optional = false python-versions = "*" files = [ @@ -2131,7 +2043,6 @@ six = ">=1.13.0" name = "json-flattener" version = "0.1.9" description = "Python library for denormalizing nested dicts or json objects to tables and back" -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -2147,7 +2058,6 @@ pyyaml = "*" name = "json5" version = "0.9.22" description = "A Python implementation of the JSON5 data format." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2162,7 +2072,6 @@ dev = ["hypothesis"] name = "jsonasobj" version = "1.3.1" description = "JSON as python objects" -category = "main" optional = false python-versions = "*" files = [ @@ -2174,7 +2083,6 @@ files = [ name = "jsonasobj2" version = "1.0.4" description = "JSON as python objects - version 2" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2189,7 +2097,6 @@ hbreader = "*" name = "jsonlines" version = "4.0.0" description = "Library with helpers for the jsonlines file format" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2204,7 +2111,6 @@ attrs = ">=19.2.0" name = "jsonpatch" version = "1.33" description = "Apply JSON-Patches (RFC 6902)" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ @@ -2219,7 +2125,6 @@ jsonpointer = ">=1.9" name = "jsonpath-ng" version = "1.6.1" description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming." -category = "dev" optional = false python-versions = "*" files = [ @@ -2234,7 +2139,6 @@ ply = "*" name = "jsonpointer" version = "2.4" description = "Identify specific nodes in a JSON document (RFC 6901)" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ @@ -2246,7 +2150,6 @@ files = [ name = "jsonschema" version = "4.21.1" description = "An implementation of JSON Schema validation for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2277,7 +2180,6 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jsonschema-specifications" version = "2023.12.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2292,7 +2194,6 @@ referencing = ">=0.31.0" name = "jupyter" version = "1.0.0" description = "Jupyter metapackage. Install all the Jupyter components in one go." -category = "dev" optional = false python-versions = "*" files = [ @@ -2313,7 +2214,6 @@ qtconsole = "*" name = "jupyter-client" version = "8.6.0" description = "Jupyter protocol implementation and client libraries" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2323,7 +2223,7 @@ files = [ [package.dependencies] importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""} -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" python-dateutil = ">=2.8.2" pyzmq = ">=23.0" tornado = ">=6.2" @@ -2337,7 +2237,6 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt name = "jupyter-console" version = "6.6.3" description = "Jupyter terminal console" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2349,7 +2248,7 @@ files = [ ipykernel = ">=6.14" ipython = "*" jupyter-client = ">=7.0.0" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" prompt-toolkit = ">=3.0.30" pygments = "*" pyzmq = ">=17" @@ -2362,7 +2261,6 @@ test = ["flaky", "pexpect", "pytest"] name = "jupyter-core" version = "5.7.1" description = "Jupyter core package. A base package on which Jupyter projects rely." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2383,7 +2281,6 @@ test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] name = "jupyter-events" version = "0.9.0" description = "Jupyter Event System library" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2409,7 +2306,6 @@ test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "p name = "jupyter-lsp" version = "2.2.4" description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2425,7 +2321,6 @@ jupyter-server = ">=1.1.2" name = "jupyter-server" version = "2.13.0" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2438,7 +2333,7 @@ anyio = ">=3.1.0" argon2-cffi = "*" jinja2 = "*" jupyter-client = ">=7.4.4" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" jupyter-events = ">=0.9.0" jupyter-server-terminals = "*" nbconvert = ">=6.4.4" @@ -2462,7 +2357,6 @@ test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-sc name = "jupyter-server-terminals" version = "0.5.2" description = "A Jupyter Server Extension Providing Terminals." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2482,7 +2376,6 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (> name = "jupyterlab" version = "4.1.4" description = "JupyterLab computational environment" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2516,7 +2409,6 @@ test = ["coverage", "pytest (>=7.0)", "pytest-check-links (>=0.7)", "pytest-cons name = "jupyterlab-pygments" version = "0.3.0" description = "Pygments theme using JupyterLab CSS variables" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2528,7 +2420,6 @@ files = [ name = "jupyterlab-server" version = "2.25.3" description = "A set of server components for JupyterLab and JupyterLab like applications." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2555,7 +2446,6 @@ test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-v name = "jupyterlab-widgets" version = "3.0.10" description = "Jupyter interactive widgets for JupyterLab" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2567,7 +2457,6 @@ files = [ name = "kgcl-rdflib" version = "0.5.0" description = "Schema for the KGCL project." -category = "main" optional = false python-versions = ">=3.8,<4.0" files = [ @@ -2583,7 +2472,6 @@ linkml-runtime = ">=1.1.24" name = "kgcl-schema" version = "0.6.5" description = "Schema for the KGCL project." -category = "main" optional = false python-versions = ">=3.9,<4.0" files = [ @@ -2601,7 +2489,6 @@ prefixmaps = ">=0.2.0,<0.3.0" name = "kiwisolver" version = "1.4.5" description = "A fast implementation of the Cassowary constraint solver" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2715,7 +2602,6 @@ files = [ name = "lark" version = "1.1.9" description = "a modern parsing library" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2733,7 +2619,6 @@ regex = ["regex"] name = "linkml" version = "1.7.5" description = "Linked Open Data Modeling Language" -category = "dev" optional = false python-versions = ">=3.8.1,<4.0.0" files = [ @@ -2771,7 +2656,6 @@ watchdog = ">=0.9.0" name = "linkml-dataops" version = "0.1.0" description = "LinkML Data Operations API" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2790,7 +2674,6 @@ linkml-runtime = ">=1.1.6" name = "linkml-renderer" version = "0.3.0" description = "linkml-renderer" -category = "main" optional = false python-versions = ">=3.8,<4.0" files = [ @@ -2808,7 +2691,6 @@ pydantic = "*" name = "linkml-runtime" version = "1.7.2" description = "Runtime environment for LinkML, the Linked open data modeling language" -category = "main" optional = false python-versions = ">=3.8,<4.0" files = [ @@ -2835,7 +2717,6 @@ requests = "*" name = "llm" version = "0.13.1" description = "A CLI utility and Python library for interacting with Large Language Models, including OpenAI, PaLM and local models installed on your own machine." -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -2864,7 +2745,6 @@ test = ["black (>=24.1.0)", "cogapp", "mypy", "numpy", "pytest", "pytest-httpx", name = "lxml" version = "5.1.0" description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2958,7 +2838,6 @@ source = ["Cython (>=3.0.7)"] name = "markdown" version = "3.5.2" description = "Python implementation of John Gruber's Markdown." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2977,7 +2856,6 @@ testing = ["coverage", "pyyaml"] name = "markdown-it-py" version = "3.0.0" description = "Python port of markdown-it. Markdown parsing, done right!" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3002,7 +2880,6 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] name = "markupsafe" version = "2.1.5" description = "Safely add untrusted strings to HTML/XML markup." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3072,7 +2949,6 @@ files = [ name = "matplotlib" version = "3.8.3" description = "Python plotting package" -category = "dev" optional = false python-versions = ">=3.9" files = [ @@ -3122,7 +2998,6 @@ python-dateutil = ">=2.7" name = "matplotlib-inline" version = "0.1.6" description = "Inline Matplotlib backend for Jupyter" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -3137,7 +3012,6 @@ traitlets = "*" name = "mdit-py-plugins" version = "0.4.0" description = "Collection of plugins for markdown-it-py" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3157,7 +3031,6 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] name = "mdurl" version = "0.1.2" description = "Markdown URL utilities" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3169,7 +3042,6 @@ files = [ name = "mergedeep" version = "1.3.4" description = "A deep merge function for 🐍." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3181,7 +3053,6 @@ files = [ name = "mistune" version = "3.0.2" description = "A sane and fast Markdown parser with useful plugins and renderers" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3193,7 +3064,6 @@ files = [ name = "mkdocs" version = "1.5.3" description = "Project documentation with Markdown." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3225,7 +3095,6 @@ min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-imp name = "mkdocs-material" version = "9.5.13" description = "Documentation that simply works" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3255,7 +3124,6 @@ recommended = ["mkdocs-minify-plugin (>=0.7,<1.0)", "mkdocs-redirects (>=1.2,<2. name = "mkdocs-material-extensions" version = "1.3.1" description = "Extension pack for Python Markdown and MkDocs Material." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3267,7 +3135,6 @@ files = [ name = "mkdocs-mermaid2-plugin" version = "0.6.0" description = "A MkDocs plugin for including mermaid graphs in markdown sources" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -3289,7 +3156,6 @@ setuptools = ">=18.5" name = "more-click" version = "0.1.2" description = "More click." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3307,7 +3173,6 @@ tests = ["coverage", "pytest"] name = "multidict" version = "6.0.5" description = "multidict implementation" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -3407,7 +3272,6 @@ files = [ name = "myst-parser" version = "2.0.0" description = "An extended [CommonMark](https://spec.commonmark.org/) compliant parser," -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3434,7 +3298,6 @@ testing-docutils = ["pygments", "pytest (>=7,<8)", "pytest-param-files (>=0.3.4, name = "nbclient" version = "0.9.0" description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." -category = "dev" optional = false python-versions = ">=3.8.0" files = [ @@ -3444,7 +3307,7 @@ files = [ [package.dependencies] jupyter-client = ">=6.1.12" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" nbformat = ">=5.1" traitlets = ">=5.4" @@ -3457,7 +3320,6 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>= name = "nbconvert" version = "7.16.2" description = "Converting Jupyter Notebooks (.ipynb files) to other formats. Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script. nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3496,7 +3358,6 @@ webpdf = ["playwright"] name = "nbformat" version = "5.9.2" description = "The Jupyter Notebook format" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3518,7 +3379,6 @@ test = ["pep440", "pre-commit", "pytest", "testpath"] name = "ndex2" version = "3.8.0" description = "Nice CX Python includes a client and a data model." -category = "main" optional = false python-versions = "*" files = [ @@ -3540,7 +3400,6 @@ urllib3 = ">=1.16" name = "nest-asyncio" version = "1.6.0" description = "Patch asyncio to allow nested event loops" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -3552,7 +3411,6 @@ files = [ name = "networkx" version = "3.2.1" description = "Python package for creating and manipulating graphs and networks" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3571,7 +3429,6 @@ test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"] name = "nltk" version = "3.8.1" description = "Natural Language Toolkit" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -3597,7 +3454,6 @@ twitter = ["twython"] name = "notebook" version = "7.1.1" description = "Jupyter Notebook - A web-based notebook environment for interactive computing" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3621,7 +3477,6 @@ test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4 name = "notebook-shim" version = "0.2.4" description = "A shim layer for notebook traits and config" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3639,7 +3494,6 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync" name = "numpy" version = "1.26.4" description = "Fundamental package for array computing in Python" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3685,7 +3539,6 @@ files = [ name = "ols-client" version = "0.1.4" description = "A client to the EBI Ontology Lookup Service" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3708,7 +3561,6 @@ tests = ["coverage", "pytest"] name = "ontoportal-client" version = "0.0.4" description = "A client to BioPortal and other OntoPortal instances." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3728,7 +3580,6 @@ tests = ["coverage", "pytest", "unittest-templates"] name = "openai" version = "1.13.3" description = "The official Python library for the openai API" -category = "main" optional = true python-versions = ">=3.7.1" files = [ @@ -3752,7 +3603,6 @@ datalib = ["numpy (>=1)", "pandas (>=1.2.3)", "pandas-stubs (>=1.1.0.11)"] name = "openpyxl" version = "3.1.2" description = "A Python library to read/write Excel 2010 xlsx/xlsm files" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3767,7 +3617,6 @@ et-xmlfile = "*" name = "overrides" version = "7.7.0" description = "A decorator to automatically detect mismatch when overriding a method." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3779,7 +3628,6 @@ files = [ name = "packaging" version = "23.2" description = "Core utilities for Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3791,7 +3639,6 @@ files = [ name = "paginate" version = "0.5.6" description = "Divides large result sets into pages for easier browsing" -category = "main" optional = false python-versions = "*" files = [ @@ -3802,7 +3649,6 @@ files = [ name = "pandas" version = "2.2.1" description = "Powerful data structures for data analysis, time series, and statistics" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3876,7 +3722,6 @@ xml = ["lxml (>=4.9.2)"] name = "pandocfilters" version = "1.5.1" description = "Utilities for writing pandoc filters in python" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -3888,7 +3733,6 @@ files = [ name = "pansql" version = "0.0.1" description = "sqldf for pandas" -category = "main" optional = false python-versions = "*" files = [ @@ -3905,7 +3749,6 @@ sqlalchemy = "*" name = "parse" version = "1.20.1" description = "parse() is the opposite of format()" -category = "dev" optional = false python-versions = "*" files = [ @@ -3917,7 +3760,6 @@ files = [ name = "parso" version = "0.8.3" description = "A Python Parser" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3933,7 +3775,6 @@ testing = ["docopt", "pytest (<6.0.0)"] name = "pathspec" version = "0.12.1" description = "Utility library for gitignore style pattern matching of file paths." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3945,7 +3786,6 @@ files = [ name = "pexpect" version = "4.9.0" description = "Pexpect allows easy control of interactive console applications." -category = "dev" optional = false python-versions = "*" files = [ @@ -3960,7 +3800,6 @@ ptyprocess = ">=0.5" name = "pillow" version = "10.2.0" description = "Python Imaging Library (Fork)" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -4046,7 +3885,6 @@ xmp = ["defusedxml"] name = "pip" version = "24.0" description = "The PyPA recommended tool for installing Python packages." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -4058,7 +3896,6 @@ files = [ name = "platformdirs" version = "4.2.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4074,7 +3911,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest- name = "pluggy" version = "1.4.0" description = "plugin and hook calling mechanisms for python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4090,7 +3926,6 @@ testing = ["pytest", "pytest-benchmark"] name = "ply" version = "3.11" description = "Python Lex & Yacc" -category = "dev" optional = false python-versions = "*" files = [ @@ -4102,7 +3937,6 @@ files = [ name = "prefixcommons" version = "0.1.12" description = "A python API for working with ID prefixes" -category = "main" optional = false python-versions = ">=3.7,<4.0" files = [ @@ -4120,7 +3954,6 @@ requests = ">=2.28.1,<3.0.0" name = "prefixmaps" version = "0.2.2" description = "A python library for retrieving semantic prefix maps" -category = "main" optional = false python-versions = ">=3.8,<4.0" files = [ @@ -4136,7 +3969,6 @@ pyyaml = ">=5.3.1" name = "prometheus-client" version = "0.20.0" description = "Python client for the Prometheus monitoring system." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -4151,7 +3983,6 @@ twisted = ["twisted"] name = "prompt-toolkit" version = "3.0.43" description = "Library for building powerful interactive command lines in Python" -category = "dev" optional = false python-versions = ">=3.7.0" files = [ @@ -4166,7 +3997,6 @@ wcwidth = "*" name = "pronto" version = "2.5.6" description = "Python frontend to ontologies." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4184,7 +4014,6 @@ python-dateutil = ">=2.8,<3.0" name = "psutil" version = "5.9.8" description = "Cross-platform lib for process and system monitoring in Python." -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -4213,7 +4042,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] name = "ptyprocess" version = "0.7.0" description = "Run a subprocess in a pseudo terminal" -category = "dev" optional = false python-versions = "*" files = [ @@ -4225,7 +4053,6 @@ files = [ name = "pure-eval" version = "0.2.2" description = "Safely evaluate AST nodes without side effects" -category = "dev" optional = false python-versions = "*" files = [ @@ -4240,7 +4067,6 @@ tests = ["pytest"] name = "pycparser" version = "2.21" description = "C parser in Python" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -4252,7 +4078,6 @@ files = [ name = "pydantic" version = "2.6.3" description = "Data validation using Python type hints" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4272,7 +4097,6 @@ email = ["email-validator (>=2.0.0)"] name = "pydantic-core" version = "2.16.3" description = "" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4364,7 +4188,6 @@ typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0" name = "pygments" version = "2.17.2" description = "Pygments is a syntax highlighting package written in Python." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4380,7 +4203,6 @@ windows-terminal = ["colorama (>=0.4.6)"] name = "pyjsg" version = "0.11.10" description = "Python JSON Schema Grammar interpreter" -category = "main" optional = false python-versions = "*" files = [ @@ -4396,7 +4218,6 @@ jsonasobj = ">=1.2.1" name = "pymdown-extensions" version = "10.7.1" description = "Extension pack for Python Markdown." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4415,7 +4236,6 @@ extra = ["pygments (>=2.12)"] name = "pyparsing" version = "3.1.2" description = "pyparsing module - Classes and methods to define and execute parsing grammars" -category = "main" optional = false python-versions = ">=3.6.8" files = [ @@ -4430,7 +4250,6 @@ diagrams = ["jinja2", "railroad-diagrams"] name = "pyproject-api" version = "1.6.1" description = "API to interact with the python pyproject.toml based projects" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -4450,7 +4269,6 @@ testing = ["covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytes name = "pyreadline3" version = "3.4.1" description = "A python implementation of GNU readline." -category = "main" optional = true python-versions = "*" files = [ @@ -4462,7 +4280,6 @@ files = [ name = "pyshex" version = "0.8.1" description = "Python ShEx Implementation" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4485,7 +4302,6 @@ urllib3 = "*" name = "pyshexc" version = "0.9.1" description = "PyShExC - Python ShEx compiler" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4505,7 +4321,6 @@ shexjsg = ">=0.8.1" name = "pysolr" version = "3.9.0" description = "Lightweight Python client for Apache Solr" -category = "main" optional = false python-versions = "*" files = [ @@ -4522,7 +4337,6 @@ solrcloud = ["kazoo (>=2.5.0)"] name = "pystow" version = "0.5.3" description = "Easily pick a place to store data for your python package." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4547,7 +4361,6 @@ xml = ["lxml"] name = "pytest" version = "7.4.4" description = "pytest: simple powerful testing with Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4570,7 +4383,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "pytest-logging" version = "2015.11.4" description = "Configures logging and allows tweaking the log level with a py.test flag" -category = "main" optional = false python-versions = "*" files = [ @@ -4584,7 +4396,6 @@ pytest = ">=2.8.1" name = "python-dateutil" version = "2.9.0.post0" description = "Extensions to the standard Python datetime module" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -4599,7 +4410,6 @@ six = ">=1.5" name = "python-json-logger" version = "2.0.7" description = "A python library adding a json log formatter" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4611,7 +4421,6 @@ files = [ name = "python-ulid" version = "2.2.0" description = "Universally unique lexicographically sortable identifier" -category = "main" optional = true python-versions = ">=3.9" files = [ @@ -4623,7 +4432,6 @@ files = [ name = "pytrie" version = "0.4.0" description = "A pure Python implementation of the trie data structure." -category = "main" optional = false python-versions = "*" files = [ @@ -4637,7 +4445,6 @@ sortedcontainers = "*" name = "pytz" version = "2024.1" description = "World timezone definitions, modern and historical" -category = "main" optional = false python-versions = "*" files = [ @@ -4649,7 +4456,6 @@ files = [ name = "pywin32" version = "306" description = "Python for Window Extensions" -category = "dev" optional = false python-versions = "*" files = [ @@ -4673,7 +4479,6 @@ files = [ name = "pywinpty" version = "2.0.13" description = "Pseudo terminal support for Windows from Python." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -4689,7 +4494,6 @@ files = [ name = "pyyaml" version = "6.0.1" description = "YAML parser and emitter for Python" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -4750,7 +4554,6 @@ files = [ name = "pyyaml-env-tag" version = "0.1" description = "A custom YAML tag for referencing environment variables in YAML files. " -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -4765,7 +4568,6 @@ pyyaml = "*" name = "pyzmq" version = "25.1.2" description = "Python bindings for 0MQ" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4871,7 +4673,6 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""} name = "qtconsole" version = "5.5.1" description = "Jupyter Qt console" -category = "dev" optional = false python-versions = ">= 3.8" files = [ @@ -4897,7 +4698,6 @@ test = ["flaky", "pytest", "pytest-qt"] name = "qtpy" version = "2.4.1" description = "Provides an abstraction layer on top of the various Qt bindings (PyQt5/6 and PySide2/6)." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4915,7 +4715,6 @@ test = ["pytest (>=6,!=7.0.0,!=7.0.1)", "pytest-cov (>=3.0.0)", "pytest-qt"] name = "ratelimit" version = "2.2.1" description = "API rate limit decorator" -category = "main" optional = false python-versions = "*" files = [ @@ -4926,7 +4725,6 @@ files = [ name = "rdflib" version = "7.0.0" description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information." -category = "main" optional = false python-versions = ">=3.8.1,<4.0.0" files = [ @@ -4948,7 +4746,6 @@ networkx = ["networkx (>=2.0.0,<3.0.0)"] name = "rdflib-jsonld" version = "0.6.1" description = "rdflib extension adding JSON-LD parser and serializer" -category = "main" optional = false python-versions = "*" files = [ @@ -4963,7 +4760,6 @@ rdflib = ">=5.0.0" name = "rdflib-shim" version = "1.0.3" description = "Shim for rdflib 5 and 6 incompatibilities" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4979,7 +4775,6 @@ rdflib-jsonld = "0.6.1" name = "referencing" version = "0.33.0" description = "JSON Referencing + Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4995,7 +4790,6 @@ rpds-py = ">=0.7.0" name = "regex" version = "2023.12.25" description = "Alternative regular expression module, to replace re." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5098,7 +4892,6 @@ files = [ name = "requests" version = "2.31.0" description = "Python HTTP for Humans." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5120,7 +4913,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "requests-cache" version = "1.2.0" description = "A persistent cache for python requests" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5151,7 +4943,6 @@ yaml = ["pyyaml (>=6.0.1)"] name = "requests-toolbelt" version = "1.0.0" description = "A utility belt for advanced users of python-requests" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -5166,7 +4957,6 @@ requests = ">=2.0.1,<3.0.0" name = "rfc3339-validator" version = "0.1.4" description = "A pure python RFC3339 validator" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -5181,7 +4971,6 @@ six = "*" name = "rfc3986-validator" version = "0.1.1" description = "Pure python rfc3986 validator" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -5193,7 +4982,6 @@ files = [ name = "rfc3987" version = "1.3.8" description = "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)" -category = "main" optional = false python-versions = "*" files = [ @@ -5205,7 +4993,6 @@ files = [ name = "rpds-py" version = "0.18.0" description = "Python bindings to Rust's persistent data structures (rpds)" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5314,7 +5101,6 @@ files = [ name = "ruamel-yaml" version = "0.18.6" description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -5333,7 +5119,6 @@ jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"] name = "ruamel-yaml-clib" version = "0.2.8" description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -5393,7 +5178,6 @@ files = [ name = "s3transfer" version = "0.10.0" description = "An Amazon S3 Transfer Manager" -category = "main" optional = true python-versions = ">= 3.8" files = [ @@ -5411,7 +5195,6 @@ crt = ["botocore[crt] (>=1.33.2,<2.0a.0)"] name = "scikit-learn" version = "1.4.1.post1" description = "A set of python modules for machine learning and data mining" -category = "main" optional = true python-versions = ">=3.9" files = [ @@ -5454,7 +5237,6 @@ tests = ["black (>=23.3.0)", "matplotlib (>=3.3.4)", "mypy (>=1.3)", "numpydoc ( name = "scipy" version = "1.12.0" description = "Fundamental algorithms for scientific computing in Python" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -5497,7 +5279,6 @@ test = ["asv", "gmpy2", "hypothesis", "mpmath", "pooch", "pytest", "pytest-cov", name = "seaborn" version = "0.12.2" description = "Statistical data visualization" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -5519,8 +5300,7 @@ stats = ["scipy (>=1.3)", "statsmodels (>=0.10)"] name = "semsimian" version = "0.2.13" description = "Sematic similarity calculations for ontologies implemented in Rust." -category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "semsimian-0.2.13-cp310-cp310-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl", hash = "sha256:0cae647709461a8b32dbe4b8fdf3d0c3af4f159a508fd2761f6f359dbb8a5047"}, @@ -5564,7 +5344,6 @@ files = [ name = "semsql" version = "0.3.3" description = "" -category = "main" optional = false python-versions = ">=3.8,<4.0" files = [ @@ -5581,7 +5360,6 @@ SQLAlchemy-Utils = ">=0.38.2,<0.39.0" name = "send2trash" version = "1.8.2" description = "Send file to trash natively under Mac OS X, Windows and Linux" -category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" files = [ @@ -5598,7 +5376,6 @@ win32 = ["pywin32"] name = "setuptools" version = "69.1.1" description = "Easily download, build, install, upgrade, and uninstall Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5615,7 +5392,6 @@ testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jar name = "shexjsg" version = "0.8.2" description = "ShExJSG - Astract Syntax Tree for the ShEx 2.0 language" -category = "dev" optional = false python-versions = "*" files = [ @@ -5630,7 +5406,6 @@ pyjsg = ">=0.11.10" name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -5642,7 +5417,6 @@ files = [ name = "sniffio" version = "1.3.1" description = "Sniff out which async library your code is running under" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5654,7 +5428,6 @@ files = [ name = "snowballstemmer" version = "2.2.0" description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms." -category = "dev" optional = false python-versions = "*" files = [ @@ -5666,7 +5439,6 @@ files = [ name = "sortedcontainers" version = "2.4.0" description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set" -category = "main" optional = false python-versions = "*" files = [ @@ -5678,7 +5450,6 @@ files = [ name = "soupsieve" version = "2.5" description = "A modern CSS selector implementation for Beautiful Soup." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5690,7 +5461,6 @@ files = [ name = "sparqlslurper" version = "0.5.1" description = "SPARQL Slurper for rdflib" -category = "dev" optional = false python-versions = ">=3.7.4" files = [ @@ -5707,7 +5477,6 @@ sparqlwrapper = ">=1.8.2" name = "sparqlwrapper" version = "2.0.0" description = "SPARQL Endpoint interface to Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5728,7 +5497,6 @@ pandas = ["pandas (>=1.3.5)"] name = "sphinx" version = "7.2.6" description = "Python documentation generator" -category = "dev" optional = false python-versions = ">=3.9" files = [ @@ -5764,7 +5532,6 @@ test = ["cython (>=3.0)", "filelock", "html5lib", "pytest (>=4.6)", "setuptools name = "sphinx-click" version = "5.1.0" description = "Sphinx extension that automatically documents click applications" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -5781,7 +5548,6 @@ sphinx = ">=2.0" name = "sphinx-copybutton" version = "0.5.1" description = "Add a copy button to each of your code cells." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -5800,7 +5566,6 @@ rtd = ["ipython", "myst-nb", "sphinx", "sphinx-book-theme", "sphinx-examples"] name = "sphinx-rtd-theme" version = "1.3.0" description = "Read the Docs theme for Sphinx" -category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -5820,7 +5585,6 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"] name = "sphinxcontrib-applehelp" version = "1.0.8" description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" -category = "dev" optional = false python-versions = ">=3.9" files = [ @@ -5837,7 +5601,6 @@ test = ["pytest"] name = "sphinxcontrib-devhelp" version = "1.0.6" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents" -category = "dev" optional = false python-versions = ">=3.9" files = [ @@ -5854,7 +5617,6 @@ test = ["pytest"] name = "sphinxcontrib-htmlhelp" version = "2.0.5" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" -category = "dev" optional = false python-versions = ">=3.9" files = [ @@ -5871,7 +5633,6 @@ test = ["html5lib", "pytest"] name = "sphinxcontrib-jquery" version = "4.1" description = "Extension to include jQuery on newer Sphinx releases" -category = "dev" optional = false python-versions = ">=2.7" files = [ @@ -5886,7 +5647,6 @@ Sphinx = ">=1.8" name = "sphinxcontrib-jsmath" version = "1.0.1" description = "A sphinx extension which renders display math in HTML via JavaScript" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -5901,7 +5661,6 @@ test = ["flake8", "mypy", "pytest"] name = "sphinxcontrib-mermaid" version = "0.8.1" description = "Mermaid diagrams in yours Sphinx powered docs" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -5913,7 +5672,6 @@ files = [ name = "sphinxcontrib-qthelp" version = "1.0.7" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents" -category = "dev" optional = false python-versions = ">=3.9" files = [ @@ -5930,7 +5688,6 @@ test = ["pytest"] name = "sphinxcontrib-serializinghtml" version = "1.1.10" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)" -category = "dev" optional = false python-versions = ">=3.9" files = [ @@ -5947,7 +5704,6 @@ test = ["pytest"] name = "sqlalchemy" version = "2.0.28" description = "Database Abstraction Library" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -6035,7 +5791,6 @@ sqlcipher = ["sqlcipher3_binary"] name = "sqlalchemy-utils" version = "0.38.3" description = "Various utility functions for SQLAlchemy." -category = "main" optional = false python-versions = "~=3.6" files = [ @@ -6064,7 +5819,6 @@ url = ["furl (>=0.4.1)"] name = "sqlite-fts4" version = "1.0.3" description = "Python functions for working with SQLite FTS4 search" -category = "main" optional = true python-versions = "*" files = [ @@ -6079,7 +5833,6 @@ test = ["pytest"] name = "sqlite-migrate" version = "0.1b0" description = "A simple database migration system for SQLite, based on sqlite-utils" -category = "main" optional = true python-versions = "*" files = [ @@ -6097,7 +5850,6 @@ test = ["black", "mypy", "pytest", "ruff"] name = "sqlite-utils" version = "3.36" description = "CLI tool and Python library for manipulating SQLite databases" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -6124,7 +5876,6 @@ tui = ["trogon"] name = "sssom" version = "0.4.4" description = "Operations on SSSOM mapping tables" -category = "main" optional = false python-versions = ">=3.8,<4.0" files = [ @@ -6152,7 +5903,6 @@ validators = ">=0.20.0" name = "sssom-schema" version = "0.15.0" description = "SSSOM is a Simple Standard for Sharing Ontology Mappings." -category = "main" optional = false python-versions = ">=3.7.6,<4.0.0" files = [ @@ -6168,7 +5918,6 @@ mkdocs-mermaid2-plugin = ">=0.6.0,<0.7.0" name = "stack-data" version = "0.6.3" description = "Extract data from python stack frames and tracebacks for informative displays" -category = "dev" optional = false python-versions = "*" files = [ @@ -6188,7 +5937,6 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] name = "tabulate" version = "0.9.0" description = "Pretty-print tabular data" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -6203,7 +5951,6 @@ widechars = ["wcwidth"] name = "terminado" version = "0.18.0" description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -6225,7 +5972,6 @@ typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"] name = "threadpoolctl" version = "3.3.0" description = "threadpoolctl" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -6237,7 +5983,6 @@ files = [ name = "tinycss2" version = "1.2.1" description = "A tiny CSS parser" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -6256,7 +6001,6 @@ test = ["flake8", "isort", "pytest"] name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -6268,7 +6012,6 @@ files = [ name = "tornado" version = "6.4" description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." -category = "dev" optional = false python-versions = ">= 3.8" files = [ @@ -6289,7 +6032,6 @@ files = [ name = "tox" version = "4.14.1" description = "tox is a generic virtualenv management and test command line tool" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -6317,7 +6059,6 @@ testing = ["build[virtualenv] (>=1.0.3)", "covdefaults (>=2.3)", "detect-test-po name = "tqdm" version = "4.66.2" description = "Fast, Extensible Progress Meter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -6338,7 +6079,6 @@ telegram = ["requests"] name = "traitlets" version = "5.14.1" description = "Traitlets Python configuration system" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -6354,7 +6094,6 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0, name = "types-python-dateutil" version = "2.8.19.20240106" description = "Typing stubs for python-dateutil" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -6366,7 +6105,6 @@ files = [ name = "typing-extensions" version = "4.10.0" description = "Backported and Experimental Type Hints for Python 3.8+" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -6378,7 +6116,6 @@ files = [ name = "tzdata" version = "2024.1" description = "Provider of IANA time zone data" -category = "main" optional = false python-versions = ">=2" files = [ @@ -6390,7 +6127,6 @@ files = [ name = "unidecode" version = "1.3.8" description = "ASCII transliterations of Unicode text" -category = "main" optional = true python-versions = ">=3.5" files = [ @@ -6402,7 +6138,6 @@ files = [ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -6417,7 +6152,6 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "url-normalize" version = "1.4.3" description = "URL normalization for Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -6432,7 +6166,6 @@ six = "*" name = "urllib3" version = "1.26.18" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -6449,7 +6182,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "validators" version = "0.22.0" description = "Python Data Validation for Humans™" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -6472,7 +6204,6 @@ tooling-extras = ["pyaml (>=23.7.0)", "pypandoc-binary (>=1.11)", "pytest (>=7.4 name = "virtualenv" version = "20.25.1" description = "Virtual Python Environment builder" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -6493,7 +6224,6 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess name = "watchdog" version = "4.0.0" description = "Filesystem events monitoring" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -6535,7 +6265,6 @@ watchmedo = ["PyYAML (>=3.10)"] name = "wcwidth" version = "0.2.13" description = "Measures the displayed width of unicode strings in a terminal" -category = "dev" optional = false python-versions = "*" files = [ @@ -6547,7 +6276,6 @@ files = [ name = "webcolors" version = "1.13" description = "A library for working with the color formats defined by HTML and CSS." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -6563,7 +6291,6 @@ tests = ["pytest", "pytest-cov"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -category = "dev" optional = false python-versions = "*" files = [ @@ -6575,7 +6302,6 @@ files = [ name = "websocket-client" version = "1.7.0" description = "WebSocket client for Python with low level API options" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -6592,7 +6318,6 @@ test = ["websockets"] name = "werkzeug" version = "3.0.1" description = "The comprehensive WSGI web application library." -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -6610,7 +6335,6 @@ watchdog = ["watchdog (>=2.3)"] name = "widgetsnbextension" version = "4.0.10" description = "Jupyter interactive widgets for Jupyter Notebook" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -6622,7 +6346,6 @@ files = [ name = "wrapt" version = "1.16.0" description = "Module for decorators, wrappers and monkey patching." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -6702,7 +6425,6 @@ files = [ name = "yarl" version = "1.9.4" description = "Yet another URL library" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -6806,7 +6528,6 @@ multidict = ">=4.0" name = "zipp" version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -6823,9 +6544,9 @@ docs = [] gilda = ["gilda", "urllib3"] llm = ["aiohttp", "llm"] seaborn = [] +semsimian = ["semsimian"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0.0" -content-hash = "704a1092e360f697bbea171d07f9d93d7e165cc22569fb7499074178cea4a812" - +content-hash = "f20c9dca2ff33ce80f395bb9e6346ab1df5a3af388483dd1c54424aee499fb52" diff --git a/pyproject.toml b/pyproject.toml index 603c3bd10..5da57ad33 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,6 +22,7 @@ semsql = ">=0.3.1" kgcl-schema = "^0.6.5" funowl = ">=0.2.0" gilda = {version = ">=1.0.0", optional = true} +semsimian = {version = ">=0.1.0", optional = true} kgcl-rdflib = "0.5.0" llm = {version = "*", optional = true} aiohttp = {version = "*", optional = true} @@ -57,10 +58,6 @@ tox = "*" [tool.poetry.group.dev.dependencies] seaborn = "^0.12.2" - -[tool.poetry.group.semsimian.dependencies] -semsimian = "^0.2.13" - [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" @@ -75,6 +72,7 @@ docs = ["Sphinx", "sphinx-rtd-theme", "sphinxcontrib-mermaid", "sphinx-copybutto gilda = ["scipy", "gilda", "urllib3"] llm = ["llm", "aiohttp"] seaborn = ["seaborn"] +semsimian = ["semsimian"] [tool.black] line-length = 100 diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 6b962cf7b..86aa74b27 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -31,8 +31,6 @@ from oaklib.types import CURIE, PRED_CURIE Semsimian: Optional["Semsimian"] = None # type: ignore -if TYPE_CHECKING: - from semsimian import Semsimian wrapped_adapter: BasicOntologyInterface = None @@ -100,6 +98,9 @@ def _get_semsimian_object( :param predicates: collection of predicates, defaults to None :return: A Semsimian object. """ + global Semsimian + if Semsimian is None: + from semsimian import Semsimian predicates = tuple(sorted(predicates)) if predicates not in self.semsimian_object_cache: # spo = [ From af0e1f3efc050ab2aa39e45efdfbb3433f335d5e Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 11 Mar 2024 11:28:44 -0500 Subject: [PATCH 27/33] update pip dependency --- poetry.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/poetry.lock b/poetry.lock index 900402fda..e1ef6ae21 100644 --- a/poetry.lock +++ b/poetry.lock @@ -3885,7 +3885,7 @@ xmp = ["defusedxml"] name = "pip" version = "24.0" description = "The PyPA recommended tool for installing Python packages." -optional = true +optional = false python-versions = ">=3.7" files = [ {file = "pip-24.0-py3-none-any.whl", hash = "sha256:ba0d021a166865d2265246961bec0152ff124de910c5cc39f1156ce3fa7c69dc"}, @@ -6549,4 +6549,4 @@ semsimian = ["semsimian"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0.0" -content-hash = "f20c9dca2ff33ce80f395bb9e6346ab1df5a3af388483dd1c54424aee499fb52" +content-hash = "713640c06be41afbef1ccf4af02e4fafc2cff9763382660a0e31be5cd7b54136" From d3803e772fecd12963bcd7907d24b6822f316a8a Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 11 Mar 2024 11:33:25 -0500 Subject: [PATCH 28/33] cleanup+formatted --- poetry.lock | 4 ++-- .../semsimian/semsimian_implementation.py | 12 +----------- 2 files changed, 3 insertions(+), 13 deletions(-) diff --git a/poetry.lock b/poetry.lock index e1ef6ae21..900402fda 100644 --- a/poetry.lock +++ b/poetry.lock @@ -3885,7 +3885,7 @@ xmp = ["defusedxml"] name = "pip" version = "24.0" description = "The PyPA recommended tool for installing Python packages." -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "pip-24.0-py3-none-any.whl", hash = "sha256:ba0d021a166865d2265246961bec0152ff124de910c5cc39f1156ce3fa7c69dc"}, @@ -6549,4 +6549,4 @@ semsimian = ["semsimian"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0.0" -content-hash = "713640c06be41afbef1ccf4af02e4fafc2cff9763382660a0e31be5cd7b54136" +content-hash = "f20c9dca2ff33ce80f395bb9e6346ab1df5a3af388483dd1c54424aee499fb52" diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 86aa74b27..48bcdbeb8 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -4,17 +4,7 @@ import logging import math from dataclasses import dataclass, field -from typing import ( - TYPE_CHECKING, - ClassVar, - Dict, - Iterable, - Iterator, - List, - Optional, - Tuple, - Union, -) +from typing import ClassVar, Dict, Iterable, Iterator, List, Optional, Tuple, Union from oaklib.datamodels.similarity import ( BestMatch, From 2bcfb86133a1dd59633b54cecb567e3bc64d112f Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 11 Mar 2024 15:14:03 -0500 Subject: [PATCH 29/33] semsimian as extra not group --- .github/workflows/main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 4da9615a5..4b0bd9ddf 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -88,7 +88,7 @@ jobs: # install your root project, if required #---------------------------------------------- - name: Install library - run: poetry install --no-interaction --extras "gilda" --with semsimian + run: poetry install --no-interaction --extras "gilda semsimian" - name: Get Gilda resources run: | From 415b217df041b0d5430f4a1176d0b05759b555a3 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 12 Mar 2024 16:43:02 -0500 Subject: [PATCH 30/33] formatted --- .../semsimian/semsimian_implementation.py | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 48bcdbeb8..bda4a7014 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -20,8 +20,6 @@ from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface from oaklib.types import CURIE, PRED_CURIE -Semsimian: Optional["Semsimian"] = None # type: ignore - wrapped_adapter: BasicOntologyInterface = None __all__ = [ @@ -51,7 +49,7 @@ class SemSimianImplementation(SearchInterface, SemanticSimilarityInterface, OboG SemanticSimilarityInterface.information_content_scores, ] - semsimian_object_cache: Dict[Tuple[PRED_CURIE], Optional[Semsimian]] = field(default_factory=dict) # type: ignore + semsimian_object_cache: Dict[Tuple[PRED_CURIE], Optional["Semsimian"]] = field(default_factory=dict) # type: ignore def __post_init__(self): slug = self.resource.slug @@ -81,16 +79,15 @@ def _get_semsimian_object( predicates: List[PRED_CURIE] = None, attributes: List[str] = None, resource_path: str = None, - ) -> Semsimian: + ) -> "Semsimian": # type: ignore """ Get Semsimian object from "semsimian_object_cache" or add a new one. :param predicates: collection of predicates, defaults to None :return: A Semsimian object. """ - global Semsimian - if Semsimian is None: - from semsimian import Semsimian + from semsimian import Semsimian + predicates = tuple(sorted(predicates)) if predicates not in self.semsimian_object_cache: # spo = [ From 7f14f285fd240f2e6de0fcf563072e5c4e8042e5 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 12 Mar 2024 16:45:21 -0500 Subject: [PATCH 31/33] formatted --- .../implementations/semsimian/semsimian_implementation.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index bda4a7014..df6ae970e 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -49,7 +49,7 @@ class SemSimianImplementation(SearchInterface, SemanticSimilarityInterface, OboG SemanticSimilarityInterface.information_content_scores, ] - semsimian_object_cache: Dict[Tuple[PRED_CURIE], Optional["Semsimian"]] = field(default_factory=dict) # type: ignore + semsimian_object_cache: Dict[Tuple[PRED_CURIE], Optional["Semsimian"]] = field(default_factory=dict) # type: ignore # noqa def __post_init__(self): slug = self.resource.slug @@ -79,7 +79,7 @@ def _get_semsimian_object( predicates: List[PRED_CURIE] = None, attributes: List[str] = None, resource_path: str = None, - ) -> "Semsimian": # type: ignore + ) -> "Semsimian": # type: ignore # noqa """ Get Semsimian object from "semsimian_object_cache" or add a new one. From 582f5a583c8c01d91fc3390b3991517c6d3c2542 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 12 Mar 2024 16:45:28 -0500 Subject: [PATCH 32/33] formatted --- .../implementations/semsimian/semsimian_implementation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index df6ae970e..c84769f29 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -79,7 +79,7 @@ def _get_semsimian_object( predicates: List[PRED_CURIE] = None, attributes: List[str] = None, resource_path: str = None, - ) -> "Semsimian": # type: ignore # noqa + ) -> "Semsimian": # type: ignore # noqa """ Get Semsimian object from "semsimian_object_cache" or add a new one. From efd88582c70fc5758b72be05eab119cf1259cd89 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 13 Mar 2024 21:24:36 -0500 Subject: [PATCH 33/33] formatted --- .../implementations/semsimian/semsimian_implementation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index c84769f29..df6ae970e 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -79,7 +79,7 @@ def _get_semsimian_object( predicates: List[PRED_CURIE] = None, attributes: List[str] = None, resource_path: str = None, - ) -> "Semsimian": # type: ignore # noqa + ) -> "Semsimian": # type: ignore # noqa """ Get Semsimian object from "semsimian_object_cache" or add a new one.