tests: speed up the slowest tests (--durations=0)

Author: mr-c

schema_salad/tests/test_codegen_errors.py

@@ -1,6 +1,8 @@
 """Tests of helpful error messages."""
 
 import importlib
+import os
+import shutil
 from collections.abc import MutableSequence
 from pathlib import Path
 from typing import Any, Optional, cast
@@ -16,7 +18,7 @@
 from .util import cwl_file_uri, get_path
 
 
-def test_error_message1(tmp_path: Path) -> None:
+def test_error_message1(cwl_v1_0: Any) -> None:
     t = "test_schema/test1.cwl"
     match = r"""^.*test1\.cwl:2:1:\s+Object\s+`.*test1\.cwl`\s+is\s+not\s+valid\s+because:
 \s+\*\s+missing\s+required\s+field\s+`inputs`
@@ -25,19 +27,19 @@ def test_error_message1(tmp_path: Path) -> None:
     path = get_path("tests/" + t)
     assert path.exists()
     with pytest.raises(ValidationException, match=match):
-        load_document_by_uri(tmp_path, path)
+        load_document_by_uri(cwl_v1_0, path)
 
 
-def test_error_message2(tmp_path: Path) -> None:
+def test_error_message2(cwl_v1_0: Any) -> None:
     t = "test_schema/test2.cwl"
     match = r"""^.*test2\.cwl:2:1:\s+Field\s+`class`\s+contains\s+undefined\s+reference\s+to\s+`file://.+/schema_salad/tests/test_schema/xWorkflow`$"""
     path = get_path("tests/" + t)
     assert path.exists()
     with pytest.raises(ValidationException, match=match):
-        load_document_by_uri(tmp_path, path)
+        load_document_by_uri(cwl_v1_0, path)
 
 
-def test_error_message4(tmp_path: Path) -> None:
+def test_error_message4(cwl_v1_0: Any) -> None:
     t = "test_schema/test4.cwl"
     match = r"""^.*test4.cwl:2:1:\s+Object\s+`.*test4.cwl`\s+is\s+not\s+valid\s+because:
 .*test4\.cwl:6:1:\s+the\s+`outputs`\s+field\s+is\s+not\s+valid\s+because:
@@ -48,10 +50,10 @@ def test_error_message4(tmp_path: Path) -> None:
     path = get_path("tests/" + t)
     assert path.exists()
     with pytest.raises(ValidationException, match=match):
-        load_document_by_uri(tmp_path, path)
+        load_document_by_uri(cwl_v1_0, path)
 
 
-def test_error_message5(tmp_path: Path) -> None:
+def test_error_message5(cwl_v1_0: Any) -> None:
     t = "test_schema/test5.cwl"
     match = r"""^.*test5\.cwl:2:1:\s+Object\s+`.*test5\.cwl`\s+is\s+not\s+valid\s+because:
 .+test5\.cwl:8:1:\s+the\s+`steps`\s+field\s+is\s+not\s+valid\s+because:
@@ -60,10 +62,10 @@ def test_error_message5(tmp_path: Path) -> None:
     path = get_path("tests/" + t)
     assert path.exists()
     with pytest.raises(ValidationException, match=match):
-        load_document_by_uri(tmp_path, path)
+        load_document_by_uri(cwl_v1_0, path)
 
 
-def test_error_message6(tmp_path: Path) -> None:
+def test_error_message6(cwl_v1_0: Any) -> None:
     t = "test_schema/test6.cwl"
     match = r"""\*\s+tried\s+`CommandLineTool`\s+but
 \s+missing\s+required\s+field\s+`class`
@@ -74,10 +76,10 @@ def test_error_message6(tmp_path: Path) -> None:
     path = get_path("tests/" + t)
     assert path.exists()
     with pytest.raises(ValidationException, match=match):
-        load_document_by_uri(tmp_path, path)
+        load_document_by_uri(cwl_v1_0, path)
 
 
-def test_error_message7(tmp_path: Path) -> None:
+def test_error_message7(cwl_v1_0: Any) -> None:
     t = "test_schema/test7.cwl"
     match = r"""^.*test7\.cwl:2:1:\s+Object\s+`.*test7\.cwl`\s+is\s+not\s+valid\s+because:
 .*test7\.cwl:8:1:\s+the\s+`steps`\s+field\s+is\s+not\s+valid\s+because:
@@ -88,10 +90,10 @@ def test_error_message7(tmp_path: Path) -> None:
     path = get_path("tests/" + t)
     assert path.exists()
     with pytest.raises(ValidationException, match=match):
-        load_document_by_uri(tmp_path, path)
+        load_document_by_uri(cwl_v1_0, path)
 
 
-def test_error_message8(tmp_path: Path) -> None:
+def test_error_message8(cwl_v1_0: Any) -> None:
     t = "test_schema/test8.cwl"
     match = r"""^.*test8.cwl:2:1:\s+Object\s+`.*test8.cwl`\s+is\s+not\s+valid\s+because:
 .*test8\.cwl:8:1:\s+the\s+`steps`\s+field\s+is\s+not\s+valid\s+because:
@@ -103,10 +105,10 @@ def test_error_message8(tmp_path: Path) -> None:
     path = get_path("tests/" + t)
     assert path.exists()
     with pytest.raises(ValidationException, match=match):
-        load_document_by_uri(tmp_path, path)
+        load_document_by_uri(cwl_v1_0, path)
 
 
-def test_error_message9(tmp_path: Path) -> None:
+def test_error_message9(cwl_v1_0: Any) -> None:
     t = "test_schema/test9.cwl"
     match = r"""^.*test9.cwl:2:1:\s+Object\s+`.*test9.cwl`\s+is\s+not\s+valid\s+because:
 .*test9\.cwl:8:1:\s+the\s+`steps`\s+field\s+is\s+not\s+valid\s+because:
@@ -118,10 +120,10 @@ def test_error_message9(tmp_path: Path) -> None:
     path = get_path("tests/" + t)
     assert path.exists()
     with pytest.raises(ValidationException, match=match):
-        load_document_by_uri(tmp_path, path)
+        load_document_by_uri(cwl_v1_0, path)
 
 
-def test_error_message10(tmp_path: Path) -> None:
+def test_error_message10(cwl_v1_0: Any) -> None:
     t = "test_schema/test10.cwl"
     match = r"""^.*test10\.cwl:2:1:\s+Object\s+`.*test10\.cwl`\s+is\s+not\s+valid\s+because:
 .*test10\.cwl:8:1:\s+the\s+`steps`\s+field\s+is\s+not\s+valid\s+because:
@@ -133,10 +135,10 @@ def test_error_message10(tmp_path: Path) -> None:
     path = get_path("tests/" + t)
     assert path.exists()
     with pytest.raises(ValidationException, match=match):
-        load_document_by_uri(tmp_path, path)
+        load_document_by_uri(cwl_v1_0, path)
 
 
-def test_error_message11(tmp_path: Path) -> None:
+def test_error_message11(cwl_v1_0: Any) -> None:
     t = "test_schema/test11.cwl"
     match = r"""^.*test11\.cwl:2:1:\s+Object\s+`.*test11.cwl`\s+is\s+not\s+valid\s+because:
 .*test11\.cwl:8:1:\s+the\s+`steps`\s+field\s+is\s+not\s+valid\s+because:
@@ -146,11 +148,10 @@ def test_error_message11(tmp_path: Path) -> None:
     path = get_path("tests/" + t)
     assert path.exists()
     with pytest.raises(ValidationException, match=match):
-        load_document_by_uri(tmp_path, path)
+        load_document_by_uri(cwl_v1_0, path)
 
 
-# `loadContents`,\s+`position`,\s+`prefix`,\s+`separate`,\s+`itemSeparator`,\s+`valueFrom`,\s+`shellQuote`
-def test_error_message15(tmp_path: Path) -> None:
+def test_error_message15(cwl_v1_0: Any) -> None:
     t = "test_schema/test15.cwl"
     match = r"""^.*test15\.cwl:3:1:\s+Object\s+`.*test15\.cwl`\s+is\s+not\s+valid\s+because:
 .*test15\.cwl:6:1:\s+the\s+`inputs`\s+field\s+is\s+not\s+valid\s+because:
@@ -163,10 +164,12 @@ def test_error_message15(tmp_path: Path) -> None:
     path = get_path("tests/" + t)
     assert path.exists()
     with pytest.raises(ValidationException, match=match):
-        load_document_by_uri(tmp_path, path)
+        load_document_by_uri(cwl_v1_0, path)
 
 
-def load_document_by_uri(tmp_path: Path, path: Path) -> Any:
+@pytest.fixture(scope="session")
+def cwl_v1_0(tmp_path_factory: pytest.TempPathFactory) -> Any:
+    tmp_path = tmp_path_factory.mktemp("cwl_v1_0_pycode")
     src_target = tmp_path / "cwl_v1_0.py"
     python_codegen(cwl_file_uri, src_target)
     spec = importlib.util.spec_from_file_location("cwl_v1_0", src_target)
@@ -175,11 +178,13 @@ def load_document_by_uri(tmp_path: Path, path: Path) -> Any:
     temp_cwl_v1_0 = importlib.util.module_from_spec(spec)
     spec.loader.exec_module(temp_cwl_v1_0)
     cwl_v1_0: Any = temp_cwl_v1_0
+    yield cwl_v1_0
+    shutil.rmtree(os.path.join(tmp_path))
 
-    path_uri = path.resolve().as_uri()
 
+def load_document_by_uri(cwl_v1_0: Any, path: Path) -> Any:
+    path_uri = path.resolve().as_uri()
     baseuri = path_uri
-
     loadingOptions = cwl_v1_0.LoadingOptions(fileuri=baseuri)
 
     with open(path) as file:

schema_salad/tests/test_pickling.py

@@ -10,7 +10,7 @@
 from schema_salad import ref_resolver, schema
 from schema_salad.avro.schema import Names, RecordSchema
 
-from .util import get_data_uri
+from .util import cwl_file_uri
 
 
 def test_recordschema_pickle() -> None:
@@ -30,7 +30,6 @@ def test_loader_pickle() -> None:
 
 
 def test_extend_and_specialize_enums(tmp_path: Path) -> None:
-    cwl_file_uri = get_data_uri("tests/test_schema/CommonWorkflowLanguage.yml")
     _, avsc_names, _, _ = schema.load_schema(cwl_file_uri)
     print(avsc_names)
     print(pickle.loads(pickle.dumps(avsc_names)))

schema_salad/tests/test_real_cwl/bio-cwl-tools/picard_CreateSequenceDictionary.cwl

@@ -36,7 +36,6 @@ inputs:
 - doc: Input reference fasta or fasta.gz [synonymous with -R]
   id: REFERENCE
   type: File
-  format: edam:format_1929  # FASTA
   inputBinding:
     valueFrom: REFERENCE=$(self.basename)
 - doc: Put into AS field of sequence dictionary entry if supplied [synonymous with
@@ -177,7 +176,6 @@ arguments:
 outputs:
   sequences_with_dictionary:
     type: File
-    format: edam:format_2573  # SAM
     secondaryFiles:
       - ^.dict
       - .fai?
@@ -189,7 +187,3 @@ outputs:
     outputBinding:
       glob: $(inputs.REFERENCE.nameroot).dict
 
-$namespaces:
-  edam: http://edamontology.org/
-$schemas:
-  - http://edamontology.org/EDAM_1.18.owl

schema_salad/tests/test_schema.py

@@ -3,9 +3,7 @@
 
 from schema_salad import schema
 
-from .util import get_data_uri
-
-cwl_file_uri = get_data_uri("tests/test_schema/CommonWorkflowLanguage.yml")
+from .util import cwl_file_uri
 
 
 def test_extend_and_specialize_enums(tmp_path: Path) -> None:

tox.ini

@@ -10,7 +10,7 @@ envlist =
 skip_missing_interpreters = True
 
 [pytest]
-addopts=-n auto
+addopts=-n auto --dist=loadscope
 testpaths=schema_salad/tests
 
 [gh-actions]