Add INSDC yml and fix makefile

Makefile

@@ -1,15 +1,13 @@
 .PHONY : docs
 docs :
 	rm -rf docs/build/
-	sphinx-autobuild -b html --watch my_package/ docs/source/ docs/build/
+	sphinx-autobuild -b html --watch convast/ docs/source/ docs/build/
 
 .PHONY : run-checks
 run-checks :
-	isort --check .
 	black --check .
 	ruff check .
-	mypy .
-	CUDA_VISIBLE_DEVICES='' pytest -v --color=yes --doctest-modules tests/ my_package/
+	pytest -v --color=yes --doctest-modules tests/ convast/
 
 .PHONY : build
 build :

convast/schema/ena_insdc_format.yml

@@ -0,0 +1,38 @@
+id: https://w3id.org/linkml/examples/personinfo
+name: INSDC_AST_fields
+prefixes:
+  linkml: https://w3id.org/linkml/
+  personinfo: https://w3id.org/linkml/examples/personinfo
+imports:
+  - linkml:types
+default_range: string
+default_prefix: INSDC_AST_fields
+
+classes:
+  ENA:
+    attributes:
+      bioSample_ID:
+      antibiotic_name:
+      resistance_phenotype:
+      measurement_sign:
+      measurement:
+      measurement_units:
+      laboratory_typing_method:
+      platform:
+      ast_standard:
+      breakpoint_version:
+      species:
+
+  NCBI:
+    attributes:
+      bisample_accession:
+      antibiotic:
+      resistance_phenotype:
+      measurement_sign:
+      measurement:
+      measurement_units:
+      laboratory_typing_method:
+      laboratory_typing_platform:
+      vendor:
+      laboratory_typing_method_version_or_reagent:
+      testing_standard:

pyproject.toml

@@ -31,7 +31,8 @@ Changelog = "https://github.com/pha4ge/convast/blob/main/CHANGELOG.md"
 [project.optional-dependencies]
 dev = [
     "ruff",
-    "black>=23.0,<24.0",
+    "black",
+    "pylint",
     "pytest",
     "pytest-cov",
     "twine>=1.11.0",