Made semsimian an optional dependency (#704)

* Made semsimian an optional dependency * latest version of semsimian * Address semsimian being optional dependency * formatted * updated message * formatted * Use TYPE_CHECKING * roll back init * formatted * add sesmimian as dependency in tox * duplicate * add semsimian install * add semsimian install * edit semsimian install * undo semsimian install * fixed semsimian mystery * semsimian as a group not an extra * optional semsimian possible solution * formatted * formatted * formatted * updated gitignore * corrected branch diff madness * don't initialize it to be None * formatted * Should fix the gh action error thanks @justaddcoffee * update pip dependency * cleanup+formatted * semsimian as extra not group * formatted * formatted * formatted * formatted
INCATools · Mar 14, 2024 · 8b9e6a3 · 8b9e6a3
1 parent b94123b
commit 8b9e6a3
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Showing 3 changed files with 7 additions and 6 deletions.
diff --git 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/pyproject.toml b/pyproject.toml
@@ -23,6 +23,7 @@ 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}
@@ -37,7 +38,6 @@ pysolr = "^3.9.0"
 eutils = ">=0.6.0"
 requests-cache = "^1.0.1"
 click = "*"
-semsimian = "^0.2.1"
 urllib3 = {version = "< 2", optional = true}
 pydantic = "*"
 jsonlines = "^4.0.0"
@@ -75,6 +75,7 @@ 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
@@ -6,8 +6,6 @@
 from dataclasses import dataclass, field
 from typing import ClassVar, Dict, Iterable, Iterator, List, Optional, Tuple, Union
 
-from semsimian import Semsimian
-
 from oaklib.datamodels.similarity import (
     BestMatch,
     TermInfo,
@@ -51,7 +49,7 @@ 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], Optional["Semsimian"]] = field(default_factory=dict)  # type: ignore # noqa
 
     def __post_init__(self):
         slug = self.resource.slug
@@ -81,13 +79,15 @@ def _get_semsimian_object(
         predicates: List[PRED_CURIE] = None,
         attributes: List[str] = None,
         resource_path: str = None,
-    ) -> Semsimian:
+    ) -> "Semsimian":  # type: ignore # noqa
         """
         Get Semsimian object from "semsimian_object_cache" or add a new one.
 
         :param predicates: collection of predicates, defaults to None
         :return: A Semsimian object.
         """
+        from semsimian import Semsimian
+
         predicates = tuple(sorted(predicates))
         if predicates not in self.semsimian_object_cache:
             # spo = [