Use jsonschema ≥4.18.0 and new referencing library

In v4.18.0, jsonschema.RefResolver was deprecated in favor of the new
referencing library.¹ The intro² and API³ docs were helpful in
determining the necessary changes.

I've tested that our new usage is not backwards compatible with v4.17.3,
so I've updated the minimum requirement to v4.18.0.

Mismatches are now a "PointerToNowhere" error instead of an
"Unresolvable JSON pointer" error. It shows the entire schema JSON in
the output which can seem unnecessarily verbose, but I think it's fine
since this is only intended to show on internal errors with the schema.

¹ https://github.com/python-jsonschema/jsonschema/blob/93e0caa5752947ec77333da81a634afe41a022ed/CHANGELOG.rst#v4180
² https://python-jsonschema.readthedocs.io/en/stable/referencing/#introduction-to-the-referencing-api
³ https://referencing.readthedocs.io/en/stable/api/#referencing.Registry.with_contents

augur/validate.py

@@ -9,6 +9,7 @@
 import jsonschema.exceptions
 import re
 from itertools import groupby
+from referencing import Registry
 from textwrap import indent
 from typing import Iterable, Union
 from augur.data import as_file
@@ -48,8 +49,8 @@ def load_json_schema(path, refs=None):
         for k, v in refs.items():
             with as_file(v) as file, open_file(file, "r") as fh:
                 schema_store[k] = json.load(fh)
-        resolver = jsonschema.RefResolver.from_schema(schema,store=schema_store)
-        schema_validator = Validator(schema, resolver=resolver)
+        registry = Registry().with_contents(schema_store.items())
+        schema_validator = Validator(schema, registry=registry)
     else:
         schema_validator = Validator(schema)
 

setup.py

@@ -57,7 +57,8 @@
         "cvxopt >=1.1.9, ==1.*",
         "importlib_resources >=5.3.0; python_version < '3.11'",
         "isodate ==0.6.*",
-        "jsonschema >=3.0.0, ==3.*",
+        "jsonschema >=4.18.0, ==4.*",
+        "referencing >=0.30.0",
         "networkx >= 2.5, <4",
         "numpy ==1.*",
         "packaging >=19.2",