nebius/SWE-bench-extra huggingface dataset:
Repository: fair-workflows/nanopub

Issue:
Deprecation warning coming from click
When running test: ```tests/test_setup_profile.py::test_provided_keypair_copied_to_nanopub_dir```
There is a deprecation warning:
```
/usr/local/lib/python3.9/site-packages/click/core.py:1048: DeprecationWarning: Parameter callbacks take 3 args, (ctx, param, value). The 2-arg style is deprecated and will be removed in 8.0.
    value, args = param.handle_parse_result(ctx, opts, args)
```

Comments:

Patch:
diff --git a/nanopub/setup_nanopub_profile.py b/nanopub/setup_nanopub_profile.py
index 6c98360..93b6750 100755
--- a/nanopub/setup_nanopub_profile.py
+++ b/nanopub/setup_nanopub_profile.py
@@ -21,10 +21,11 @@ RSA = 'RSA'
 ORCID_ID_REGEX = r'^https://orcid.org/(\d{4}-){3}\d{3}(\d|X)$'
 
 
-def validate_orcid_id(ctx, orcid_id: str):
+def validate_orcid_id(ctx, param, orcid_id: str):
     """
     Check if valid ORCID iD, should be https://orcid.org/ + 16 digit in form:
-        https://orcid.org/0000-0000-0000-0000
+        https://orcid.org/0000-0000-0000-0000. ctx and param are
+        necessary `click` callback arguments
     """
     if re.match(ORCID_ID_REGEX, orcid_id):
         return orcid_id


Test patch:
diff --git a/tests/test_setup_profile.py b/tests/test_setup_profile.py
index 7b1998f..34ad3cc 100644
--- a/tests/test_setup_profile.py
+++ b/tests/test_setup_profile.py
@@ -103,7 +103,7 @@ def test_validate_orcid_id():
     valid_ids = ['https://orcid.org/1234-5678-1234-5678',
                  'https://orcid.org/1234-5678-1234-567X']
     for orcid_id in valid_ids:
-        assert validate_orcid_id(ctx=None, orcid_id=orcid_id) == orcid_id
+        assert validate_orcid_id(ctx=None, param=None, orcid_id=orcid_id) == orcid_id
 
     invalid_ids = ['https://orcid.org/abcd-efgh-abcd-efgh',
                    'https://orcid.org/1234-5678-1234-567',
@@ -112,4 +112,4 @@ def test_validate_orcid_id():
                    '0000-0000-0000-0000']
     for orcid_id in invalid_ids:
         with pytest.raises(ValueError):
-            validate_orcid_id(ctx=None, orcid_id=orcid_id)
+            validate_orcid_id(ctx=None, param=None, orcid_id=orcid_id)