test skips/pyproject

pyproject.toml

@@ -42,9 +42,10 @@ dynamic = ["version"]
 [project.optional-dependencies]
 zarr = ["zarr>=2.12.0"]
 tqdm = ["tqdm>=4.41.0"]
-linkml = ["linkml-runtime>=1.5.0"]
-schemasheets = ["schemasheets>=0.1.23"]
-oaklib = ["oaklib>=0.5.12"]
+termset_reqs = ["linkml-runtime>=1.5.0",
+                "schemasheets>=0.1.23",
+                "oaklib>=0.5.12",
+                "yaml"]
 
 [project.urls]
 "Homepage" = "https://github.com/hdmf-dev/hdmf"

requirements-opt.txt

@@ -1,4 +1,7 @@
 # pinned dependencies that are optional. used to reproduce an entire development environment to use HDMF
 tqdm==4.65.0
 zarr==2.14.2
-linkml-runtime==1.5.0
+linkml-runtime>=1.5.0
+schemasheets>=0.1.23
+oaklib>=0.5.12
+yaml

src/hdmf/term_set.py

@@ -3,11 +3,6 @@
 import os
 from collections import namedtuple
 from .utils import docval
-from linkml_runtime.utils.schemaview import SchemaView
-from linkml_runtime.utils.schema_as_dict import schema_as_dict
-from schemasheets.schemamaker import SchemaMaker
-from oaklib.utilities.subsets.value_set_expander import ValueSetExpander
-
 
 
 class TermSet():
@@ -27,6 +22,15 @@ def __init__(self,
         """
         :param term_schema_path: The path to LinkML YAML enumeration schema
         """
+        try:
+            from linkml_runtime.utils.schemaview import SchemaView
+            from linkml_runtime.utils.schema_as_dict import schema_as_dict
+            from schemasheets.schemamaker import SchemaMaker
+            from oaklib.utilities.subsets.value_set_expander import ValueSetExpander
+        except ImportError:
+            msg = "Install TermSet requirements in pyproject.toml"
+            raise ValueError(msg)
+
         self.term_schema_path = term_schema_path
         self.schemasheets_folder = schemasheets_folder
 

tests/unit/expanded_example_dynamic_term_set.yaml

@@ -40,7 +40,6 @@ enums:
       include_self: false
       relationship_types:
       - rdfs:subClassOf
-
     permissible_values:
       CL:0000705:
         text: CL:0000705

tests/unit/test_term_set.py

@@ -7,60 +7,60 @@
 
 CUR_DIR = os.path.dirname(os.path.realpath(__file__))
 
-
 try:
     import linkml_runtime  # noqa: F401
-    LINKML_INSTALLED = True
+    import schemasheets
+    import oaklib
+
+    REQUIREMENTS_INSTALLED = TRUE
 except ImportError:
-    LINKML_INSTALLED = False
+    REQUIREMENTS_INSTALLED = False
 
 class TestTermSet(TestCase):
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_termset_setup(self):
         termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         self.assertEqual(list(termset.sources), ['NCBI_TAXON'])
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_view_set(self):
         termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         expected = ['Homo sapiens', 'Mus musculus', 'Ursus arctos horribilis', 'Myrmecophaga tridactyla']
         self.assertEqual(list(termset.view_set), expected)
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_termset_validate(self):
         termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         self.assertEqual(termset.validate('Homo sapiens'), True)
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_termset_validate_false(self):
         termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         self.assertEqual(termset.validate('missing_term'), False)
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_get_item(self):
         termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         self.assertEqual(termset['Homo sapiens'].id, 'NCBI_TAXON:9606')
         self.assertEqual(termset['Homo sapiens'].description, 'the species is human')
         self.assertEqual(termset['Homo sapiens'].meaning, 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606')
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_get_item_key_error(self):
         termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         with self.assertRaises(ValueError):
             termset['Homo Ssapiens']
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_view_set_sheets(self):
         folder = os.path.join(CUR_DIR, "test_term_set_input", "schemasheets")
         termset = TermSet(schemasheets_folder=folder)
         expected = ['ASTROCYTE', 'INTERNEURON', 'MICROGLIAL_CELL', 'MOTOR_NEURON', 'OLIGODENDROCYTE', 'PYRAMIDAL_NEURON']
         self.assertEqual(list(termset.view_set), expected)
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_enum_expander(self):
         termset = TermSet(term_schema_path='tests/unit/example_dynamic_term_set.yaml', dynamic=True)
         self.assertEqual(len(termset.view_set), 502)
-        remove_test_file('./expanded_example_dynamic_term_set.yaml')
+        remove_test_file('expanded_example_dynamic_term_set.yaml')