update build config to pyproject.toml

pyproject.toml

@@ -1,7 +1,55 @@
-[build-system]
-requires = [
-    "setuptools>=42",
-    "wheel",
-    "setuptools_scm>=6.2"
+[project]
+name = "ga4gh.gks.metaschema"
+authors = [
+    {name = "Alex Wagner", email = "alex.wagner@nationwidechildrens.org"},
+]
+readme = "README.md"
+description = "GA4GH Genomic Knowledge Standards meta-schema tools"
+license = {file = "LICENSE"}
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Healthcare Industry",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
 ]
+keywords = [
+    "bioinformatics",
+    "ga4gh",
+    "genomics",
+    "hgvs",
+    "spdi",
+    "variation"
+]
+requires-python = ">=3.12"
+dynamic = ["version", "dependencies"]
+
+[project.urls]
+Homepage = "https://github.com/ga4gh/gks-metaschema"
+Documentation = "https://github.com/ga4gh/gks-metaschema"
+Changelog = "https://github.com/ga4gh/gks-metaschema/releases"
+Source = "https://github.com/ga4gh/gks-metaschema"
+"Bug Tracker" = "https://github.com/ga4gh/gks-metaschema/issues"
+
+[tool.setuptools.dynamic]
+dependencies = {file = [".requirements.txt"]}
+
+[tool.setuptools_scm]
+
+[project.scripts]
+jsy2js = "ga4gh.gks.metaschema.scripts.jsy2js:cli"
+source2jsy = "ga4gh.gks.metaschema.scripts.source2jsy:cli"
+y2t = "ga4gh.gks.metaschema.scripts.y2t:cli"
+source2mergedjsy = "ga4gh.gks.metaschema.scripts.source2mergedjsy:cli"
+source2splitjs = "ga4gh.gks.metaschema.scripts.source2splitjs:cli"
+source2classes = "ga4gh.gks.metaschema.scripts.source2classes:cli"
+
+[build-system]
+requires = ["setuptools>=65.3", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"

src/ga4gh/gks/metaschema/scripts/jsy2js.py

@@ -4,5 +4,9 @@
 import json
 import sys
 
-yaml_schema = yaml.load(sys.stdin, Loader=yaml.SafeLoader)
-json.dump(yaml_schema, sys.stdout, indent=3)
+def cli():
+    yaml_schema = yaml.load(sys.stdin, Loader=yaml.SafeLoader)
+    json.dump(yaml_schema, sys.stdout, indent=3)
+
+if __name__ == "__main__":
+    cli()

src/ga4gh/gks/metaschema/scripts/source2classes.py

@@ -13,8 +13,10 @@ def main(proc):
             continue
         print(cls)
 
-
-if __name__ == '__main__':
+def cli():
     args = parser.parse_args()
     p = YamlSchemaProcessor(Path(args.infile))
     main(p)
+
+if __name__ == '__main__':
+    cli()

src/ga4gh/gks/metaschema/scripts/source2jsy.py

@@ -4,6 +4,10 @@
 import sys
 from ga4gh.gks.metaschema.tools.source_proc import YamlSchemaProcessor
 
-source_file = pathlib.Path(sys.argv[1])
-p = YamlSchemaProcessor(source_file)
-p.js_yaml_dump(sys.stdout)
+def cli():
+    source_file = pathlib.Path(sys.argv[1])
+    p = YamlSchemaProcessor(source_file)
+    p.js_yaml_dump(sys.stdout)
+
+if __name__ == "__main__":
+    cli()

src/ga4gh/gks/metaschema/scripts/source2mergedjsy.py

@@ -4,7 +4,11 @@
 import sys
 from ga4gh.gks.metaschema.tools.source_proc import YamlSchemaProcessor
 
-source_file = pathlib.Path(sys.argv[1])
-p = YamlSchemaProcessor(source_file)
-p.merge_imported()
-p.js_yaml_dump(sys.stdout)
+def cli():
+    source_file = pathlib.Path(sys.argv[1])
+    p = YamlSchemaProcessor(source_file)
+    p.merge_imported()
+    p.js_yaml_dump(sys.stdout)
+
+if __name__ == "__main__":
+    cli()

src/ga4gh/gks/metaschema/scripts/source2splitjs.py

@@ -94,8 +94,10 @@ def split_defs_to_js(root_proc, mode='json'):
         with open(target_path, 'w') as f:
             json.dump(out_doc, f, indent=3, sort_keys=False)
 
-
-if __name__ == '__main__':
+def cli():
     args = parser.parse_args()
     p = YamlSchemaProcessor(Path(args.infile))
     split_defs_to_js(p)
+
+if __name__ == '__main__':
+    cli()

src/ga4gh/gks/metaschema/scripts/y2t.py

@@ -104,11 +104,13 @@ def main(proc_schema):
       - {resolve_cardinality(class_property_name, class_property_attributes, class_definition)}
       - {class_property_attributes.get('description', '')}""", file=f)
 
-
-if __name__ == "__main__":
+def cli():
     source_file = pathlib.Path(sys.argv[1])
     p = YamlSchemaProcessor(source_file)
     os.makedirs(p.def_fp, exist_ok=True)
     if p.defs is None:
         exit(0)
     main(p)
+
+if __name__ == "__main__":
+    cli()

tests/data/gnomAD/json/GnomadCAF

@@ -4,6 +4,32 @@
    "title": "GnomadCAF",
    "type": "object",
    "$defs": {
+      "GrpMaxFAF95": {
+         "description": "The group maximum filtering allele frequency at 95% CI",
+         "protectedClassOf": "GnomadCAF",
+         "type": "object",
+         "maturity": "draft",
+         "properties": {
+            "frequency": {
+               "type": "number"
+            },
+            "confidenceInterval": {
+               "type": "number",
+               "const": 0.95,
+               "default": 0.95
+            },
+            "groupId": {
+               "type": "string",
+               "description": "The genetic ancestry group from which the max frequency was calculated."
+            }
+         },
+         "required": [
+            "confidenceInterval",
+            "frequency",
+            "groupId"
+         ],
+         "additionalProperties": false
+      },
       "GnomadCafProperties": {
          "description": "Additional properties specific to the gnomAD CAF model.",
          "protectedClassOf": "GnomadCAF",
@@ -75,32 +101,6 @@
             }
          },
          "required": []
-      },
-      "GrpMaxFAF95": {
-         "description": "The group maximum filtering allele frequency at 95% CI",
-         "protectedClassOf": "GnomadCAF",
-         "type": "object",
-         "maturity": "draft",
-         "properties": {
-            "frequency": {
-               "type": "number"
-            },
-            "confidenceInterval": {
-               "type": "number",
-               "const": 0.95,
-               "default": 0.95
-            },
-            "groupId": {
-               "type": "string",
-               "description": "The genetic ancestry group from which the max frequency was calculated."
-            }
-         },
-         "required": [
-            "confidenceInterval",
-            "frequency",
-            "groupId"
-         ],
-         "additionalProperties": false
       }
    },
    "maturity": "draft",