fix tests

PGScatalog · Sep 11, 2023 · 8cddbc7 · 8cddbc7
1 parent 68c6165
commit 8cddbc7
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Showing 3 changed files with 4 additions and 6 deletions.
diff --git a/pgscatalog_utils/download/download_scorefile.py b/pgscatalog_utils/download/download_scorefile.py
@@ -47,7 +47,7 @@ def download_scorefile() -> None:
             f"Setting user agent to {config.PGSC_CALC_VERSION} for PGS Catalog API queries")
     else:
         config.PGSC_CALC_VERSION = f"pgscatalog_utils/{version}"
-        logger.warn(f"No user agent set, defaulting to {config.PGSC_CALC_VERSION}")
+        logger.warning(f"No user agent set, defaulting to {config.PGSC_CALC_VERSION}")
 
     config.OUTDIR = pathlib.Path(args.outdir).resolve()
     logger.info(f"Download directory: {config.OUTDIR}")

diff --git a/tests/test_combine.py b/tests/test_combine.py
@@ -33,7 +33,7 @@ def test_fail_combine(scorefiles, tmp_path_factory):
 
 @pytest.fixture
 def _n_variants(pgs_accessions):
-    result = CatalogQuery(CatalogCategory.SCORE, accession=pgs_accessions, pgsc_calc_version=None).get()[0]
+    result = CatalogQuery(CatalogCategory.SCORE, accession=pgs_accessions).get()[0]
     json = result.response
     n: list[int] = jq.compile("[.results][][].variants_number").input(json).all()
     return sum(n)
diff --git a/tests/test_download.py b/tests/test_download.py
@@ -92,13 +92,11 @@ def test_download_trait(tmp_path):
 
 def test_query_publication():
     # publications are relatively static
-    query: list[CatalogResult] = CatalogQuery(CatalogCategory.PUBLICATION, accession="PGP000001",
-                                              pgsc_calc_version=None).get()
+    query: list[CatalogResult] = CatalogQuery(CatalogCategory.PUBLICATION, accession="PGP000001").get()
     assert not query[0].pgs_ids.difference({'PGS000001', 'PGS000002', 'PGS000003'})
 
 
 def test_query_trait():
     # new scores may be added to traits in the future
-    query: list[CatalogResult] = CatalogQuery(CatalogCategory.TRAIT, accession="EFO_0004329",
-                                              pgsc_calc_version=None).get()
+    query: list[CatalogResult] = CatalogQuery(CatalogCategory.TRAIT, accession="EFO_0004329").get()
     assert not {'PGS001901', 'PGS002115'}.difference(query[0].pgs_ids)