Removes unnecessary external_context.py, clean Makefile & update de…

…pendencies. (mapping-commons#394)

* Removes unnecessary `external_context.py` and clean Makefile.

* Fixed get_external_jsonld_context()

* test change

* Moved scipy to extras

* Changed package dependencies from ^ to >= fixes mapping-commons#392

* flake8 ed

* ran poetry update and all work.

Makefile

@@ -20,7 +20,7 @@ schema/cliquesummary.py: schema/cliquesummary.yaml
 	gen-py-classes $< > $@
 schema/%.schema.json: .FORCE
 	wget $(SSSOM_JSON_SCHEMA) -O $@
-schema/sssom.external.context.jsonld:
+src/sssom/sssom.external.context.jsonld:
 	wget $(DEFAULT_PREFIX_MAP) -O $@
 schema/%.context.jsonld: .FORCE
 	wget $(SSSOM_JSONLD_CONTEXT) -O $@
@@ -33,28 +33,8 @@ test:
 	tox
 	sh tests/tests.sh
 
-src/sssom/external_context.py: schema/sssom.external.context.jsonld
-	echo "\"\"\"This module contains an autogenerated copy of the external SSSOM context.\"\"\"" > $@
-	echo "" >> $@
-	echo "# This is autogenerated and super hacky." >> $@
-	echo "sssom_external_context = \"\"\""  >> $@
-	cat $< >> $@
-	echo "\"\"\""  >> $@
-	black $@
-
-src/sssom/internal_context.py: schema/sssom.context.jsonld
-	echo "\"\"\"This module contains an autogenerated copy of the internal SSSOM context.\"\"\"" > $@
-	echo "" >> $@
-	echo "sssom_context = \"\"\""  >> $@
-	cat $< >> $@
-	echo "\"\"\""  >> $@
-
-deploy-dm: src/sssom/external_context.py src/sssom/internal_context.py
-	cp schema/sssom_datamodel.py src/sssom/
-	cp schema/sssom.context.jsonld src/sssom/
-	cp schema/sssom.external.context.jsonld src/sssom/
+deploy-dm: src/sssom/sssom.external.context.jsonld
 
-
 install:
 	pip install .[test,docs]
 

pyproject.toml

@@ -15,18 +15,18 @@ python = "^3.8"
 click = "*"
 importlib-metadata = ">=4.8.0"
 pyparsing = "^3.0.9"
-bioregistry = "^0.9.43"
-deprecation = "^2.1.0"
-linkml-runtime = "^1.5.3"
-networkx = "^3.1"
-pandas = "^2.0.2"
+bioregistry = ">=0.9.43"
+deprecation = ">=2.1.0"
+linkml-runtime = ">=1.5.3"
+networkx = ">=3.1"
+pandas = ">=2.0.2"
 pansql = "^0.0.1"
-pyyaml = "^6.0"
-rdflib = "^6.3.2"
-sparqlwrapper = "^2.0.0"
-sssom-schema = "^0.13.0"
-validators = "^0.20.0"
-scipy = "*"
+pyyaml = ">=6.0"
+rdflib = ">=6.3.2"
+sparqlwrapper = ">=2.0.0"
+sssom-schema = ">=0.13.0"
+validators = ">=0.20.0"
+scipy = {version = "*", extras = ["scipy"]}
 
 [tool.poetry.group.dev.dependencies]
 pytest = {version = ">=7.1.2"}

src/sssom/constants.py

@@ -14,6 +14,7 @@
 HERE = pathlib.Path(__file__).parent.resolve()
 
 SCHEMA_YAML = pkg_resources.resource_filename("sssom_schema", "schema/sssom_schema.yaml")
+EXTERNAL_CONTEXT = HERE / "sssom.external.context.jsonld"
 
 # SCHEMA_VIEW = package_schemaview("sssom_schema")
 

src/sssom/context.py

@@ -7,7 +7,8 @@
 
 import pkg_resources
 
-from .external_context import sssom_external_context
+from sssom.constants import EXTERNAL_CONTEXT
+
 from .typehints import Metadata, MetadataType, PrefixMap
 
 # HERE = pathlib.Path(__file__).parent.resolve()
@@ -41,7 +42,9 @@ def get_external_jsonld_context():
 
     :return: JSON-LD context
     """
-    return json.loads(sssom_external_context, strict=False)
+    with open(str(EXTERNAL_CONTEXT), "r") as f:
+        data = json.load(f, strict=False)
+    return data
 
 
 def get_built_in_prefix_map() -> PrefixMap:

tests/test_parsers.py

@@ -117,7 +117,7 @@ def test_parse_obographs(self):
             write_table(msdf, file)
         self.assertEqual(
             len(msdf.df),
-            9880,
+            9879,
             f"{self.obographs_file} has the wrong number of mappings.",
         )