Unit test fixing - remove network requirements

pyproject.toml

@@ -54,6 +54,44 @@ build-backend = "poetry.core.masonry.api"
 xfail_strict = true
 filterwarnings = "ignore::DeprecationWarning"
 markers = [
+    "ci: Tests that should run in continuous integration",
     "slow: Tests that take a long time",
     "db: Test that require access to our database",
+    "network: Tests that require network",
+    "text_mining: tests relating to text mining",
+    "cli: Test for command line interface",
+    "cpat: Tests for cpat",
+    "utils: utility tests",
+    # Database-specific markers
+    "crs: tests for crs",
+    "crw: tests for crw",
+    "dfam: tests for Dfam",
+    "ena: tests for ena",
+    "ensembl: tests for ensembl",
+    "epmc: tests for europepmc",
+    "expressionatlas: tests for Expression Atlas",
+    "genecards: tests for genecards",
+    "genecards_suite: tests for GeneCards Suite",
+    "generic: tests for generic json parser",
+    "gtrnadb: tests for gtrnadb",
+    "hgnc: tests for hgnc",
+    "intact: tests for intact",
+    "ncbi: tests for ncbi",
+    "ols: tests for ols",
+    "pdb: tests for pdb",
+    "pirbase: tests for pirbase",
+    "psi_mi: tests for psi_mi",
+    "psicquic: tests for psicquic",
+    "quickgo: tests for quickgo",
+    "refseq: tests for refseq",
+    "rfam: tests for rfam",
+    "rgd: tests for rgd",
+    "ribovision: tests for ribovision",
+    "r2dt: Tests for r2dt related functions",
+    "sequence_ontology: tests for the sequence ontology",
+    "so: tests for the sequence ontology",
+    "silva: tests for silva",
+    "tarbase: tests for tarbase",
+    "tmrna: tests for tmRNA",
+    "trna: Trna related tests",
 ]

pytest.ini

@@ -19,10 +19,13 @@ markers =
 
   crs: tests for crs
   crw: tests for crw
+  dfam: tests for Dfam
   ena: tests for ena
   ensembl: tests for ensembl
   epmc: tests for europepmc
+  expressionatlas: tests for Expression Atlas
   genecards: tests for genecards
+  genecards_suite: tests for GeneCards Suite
   generic: tests for generic json parser
   gtrnadb: tests for gtrnadb
   hgnc: tests for hgnc
@@ -39,7 +42,9 @@ markers =
   rgd: tests for rgd
   ribovision: tests for ribovision
   r2dt: Tests for r2dt related functions
+  sequence_ontology: tests for the sequence ontology
   so: tests for the sequence ontology
   silva: tests for silva
   tarbase: tests for tarbase
+  tmrna: tests for tmRNA
   trna: Trna related tests

tests/databases/ensembl/metadata/karyotypes_test.py

@@ -14,6 +14,7 @@
 """
 import asyncio
 import pytest
+from unittest.mock import Mock, patch
 
 from rnacentral_pipeline.databases.ensembl.metadata import karyotypes as karyo
 
@@ -22,9 +23,76 @@ def karyotype(domain, species):
     raw = asyncio.run(karyo.fetch(species, domain))
     return karyo.process(raw)
 
+
+# Mock data for Ensembl API responses
+HOMO_SAPIENS_RESPONSE = {
+    "default_coord_system_version": "GRCh38",
+    "top_level_region": [
+        # MT chromosome (no bands)
+        {
+            "coord_system": "chromosome",
+            "length": 16569,
+            "name": "MT"
+        },
+        # Y chromosome (with detailed cytogenetic bands)
+        {
+            "coord_system": "chromosome",
+            "name": "Y",
+            "length": 57227415,
+            "bands": [
+                {"stain": "acen", "id": "p11.1", "start": 10300001, "end": 10400000},
+                {"id": "p11.2", "stain": "gneg", "start": 600001, "end": 10300000},
+                {"id": "p11.31", "stain": "gpos50", "start": 300001, "end": 600000},
+                {"stain": "gneg", "id": "p11.32", "start": 1, "end": 300000},
+                {"start": 10400001, "end": 10600000, "id": "q11.1", "stain": "acen"},
+                {"stain": "gneg", "start": 10600001, "end": 12400000, "id": "q11.21"},
+                {"id": "q11.221", "end": 17100000, "start": 12400001, "stain": "gpos50"},
+                {"end": 19600000, "start": 17100001, "id": "q11.222", "stain": "gneg"},
+                {"stain": "gpos50", "id": "q11.223", "end": 23800000, "start": 19600001},
+                {"stain": "gneg", "id": "q11.23", "end": 26600000, "start": 23800001},
+                {"end": 57227415, "start": 26600001, "stain": "gvar", "id": "q12"},
+            ]
+        },
+        # 192 more regions would be here, but we only need MT and Y for tests
+    ] + [{"coord_system": "chromosome", "name": str(i), "length": 1000000} for i in range(1, 193)]
+}
+
+GLYCINE_MAX_RESPONSE = {
+    "default_coord_system_version": "Glycine_max_v2.1",
+    "top_level_region": [
+        {
+            "coord_system": "chromosome",
+            "name": "1",
+            "length": 56831624
+        }
+        # Would have 1189 more chromosomes, but we only need one for the test
+    ] + [{"coord_system": "chromosome", "name": str(i), "length": 1000000} for i in range(2, 1191)]
+}
+
+
+@pytest.fixture
+def mock_ensembl_api():
+    """Mock Ensembl REST API responses for karyotype data"""
+    def mock_get(url, **kwargs):
+        mock_response = Mock()
+        mock_response.raise_for_status = Mock()
+
+        # Match URL to return appropriate response
+        if "homo_sapiens" in url:
+            mock_response.json.return_value = HOMO_SAPIENS_RESPONSE
+        elif "glycine_max" in url:
+            mock_response.json.return_value = GLYCINE_MAX_RESPONSE
+        else:
+            raise ValueError(f"Unexpected URL in test: {url}")
+
+        return mock_response
+
+    with patch("rnacentral_pipeline.databases.ensembl.metadata.karyotypes.requests.get", side_effect=mock_get):
+        yield
+
+
 @pytest.mark.ensembl
-@pytest.mark.network
-def test_builds_empty_karyotype_for_missing_data():
+def test_builds_empty_karyotype_for_missing_data(mock_ensembl_api):
     _, found = karyotype("ensembl", "glycine_max")
     assert len(found) == 1190
     assert found["1"] == {
@@ -38,8 +106,7 @@ def test_builds_empty_karyotype_for_missing_data():
     }
 
 @pytest.mark.ensembl
-@pytest.mark.network
-def test_builds_with_known_bands():
+def test_builds_with_known_bands(mock_ensembl_api):
     _, found = karyotype("ensembl", "homo_sapiens")
     assert len(found) == 194
     assert found["MT"] == {