exclude slow tests by default, keep them in ci

.github/workflows/test.yaml

@@ -54,7 +54,7 @@ jobs:
           MPLBACKEND: agg
           PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
-        run: coverage run -m pytest -v --color=yes
+        run: coverage run -m pytest "" -v --color=yes
       - name: Report coverage
         run: coverage report
       - name: Upload coverage

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+markers =
+    slow: marks tests as slow (deselect with '-m "not slow"')
+addopts = -m "not slow"

tests/test_dt/test_dt.py

@@ -13,6 +13,7 @@ def duckdb_connection():
     con.close()
 
 
+@pytest.mark.slow
 def test_mimic_iv_omop(tmp_path):
     duckdb_connection = duckdb.connect()
     ed.dt.mimic_iv_omop(data_path=tmp_path, backend_handle=duckdb_connection)
@@ -22,6 +23,7 @@ def test_mimic_iv_omop(tmp_path):
     duckdb_connection.close()
 
 
+@pytest.mark.slow
 def test_gibleed_omop(tmp_path):
     duckdb_connection = duckdb.connect()
     ed.dt.gibleed_omop(data_path=tmp_path, backend_handle=duckdb_connection)
@@ -31,6 +33,7 @@ def test_gibleed_omop(tmp_path):
     duckdb_connection.close()
 
 
+@pytest.mark.slow
 def test_synthea27nj_omop(tmp_path):
     duckdb_connection = duckdb.connect()
     ed.dt.synthea27nj_omop(data_path=tmp_path, backend_handle=duckdb_connection)
@@ -40,6 +43,7 @@ def test_synthea27nj_omop(tmp_path):
     duckdb_connection.close()
 
 
+@pytest.mark.slow
 def test_physionet2012():
     edata = ed.dt.physionet2012()
     assert edata.shape == (11988, 38)