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. I chose v0.29.1 as
the minimum supported version of referencing because that was the
version released alongside jsonschema 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

@@ -57,14 +57,15 @@
         "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.*",
         "networkx >= 2.5, <4",
         "numpy ==1.*",
         "packaging >=19.2",
         "pandas >=1.0.0, <3",
         "phylo-treetime >=0.11.2, <0.12",
         "pyfastx >=1.0.0, <3.0",
         "python_calamine >=0.2.0",
+        "referencing >=0.29.1, <1.0",
         "scipy ==1.*",
         "xopen[zstd] >=1.7.0, <3" # TODO: Deprecated, remove v1 support around November 2024
     ],