Various test updates needed for pydantic v2:

- Reorder imports for better isolation
- Additional test cases for schema functionality

Author: BenjaminCharmes

pydatalab/tests/apps/test_chat.py

@@ -1,7 +1,6 @@
-from pydatalab.apps.chat import ChatBlock
-
-
 def test_chatblock():
+    from pydatalab.apps.chat import ChatBlock
+
     chat = ChatBlock(item_id="test")
     chat.data["model"] = "langchain-debug"
 

pydatalab/tests/apps/test_echem_block.py

@@ -1,18 +1,13 @@
 from pathlib import Path
 
 import pytest
-from navani.echem import echem_file_loader
-
-from pydatalab.apps.echem.utils import (
-    compute_gpcl_differential,
-    filter_df_by_cycle_index,
-    reduce_echem_cycle_sampling,
-)
 
 
 @pytest.fixture
 def echem_dataframe():
     """Yields example echem data as a dataframe."""
+    from navani.echem import echem_file_loader
+
     df = echem_file_loader(
         Path(__file__)
         .parent.joinpath(
@@ -38,15 +33,27 @@ def echem_dataframe():
 
 @pytest.fixture
 def reduced_echem_dataframe(echem_dataframe):
+    from pydatalab.apps.echem.utils import (
+        reduce_echem_cycle_sampling,
+    )
+
     return reduce_echem_cycle_sampling(echem_dataframe, 100)
 
 
 @pytest.fixture
 def reduced_and_filtered_echem_dataframe(reduced_echem_dataframe):
+    from pydatalab.apps.echem.utils import (
+        filter_df_by_cycle_index,
+    )
+
     return filter_df_by_cycle_index(reduced_echem_dataframe)
 
 
 def test_reduce_size(echem_dataframe):
+    from pydatalab.apps.echem.utils import (
+        reduce_echem_cycle_sampling,
+    )
+
     original_size = echem_dataframe.shape[0]
     for size in (1, 10, int(0.5 * len(echem_dataframe)), len(echem_dataframe)):
         number_of_cycles = echem_dataframe["half cycle"].nunique()
@@ -57,6 +64,10 @@ def test_reduce_size(echem_dataframe):
 
 
 def test_compute_gpcl_differential(reduced_and_filtered_echem_dataframe):
+    from pydatalab.apps.echem.utils import (
+        compute_gpcl_differential,
+    )
+
     df = reduced_and_filtered_echem_dataframe
 
     dqdv_results = compute_gpcl_differential(df)
@@ -67,13 +78,20 @@ def test_compute_gpcl_differential(reduced_and_filtered_echem_dataframe):
 
 
 def test_filter_df_by_cycle_index(reduced_echem_dataframe):
+    from pydatalab.apps.echem.utils import (
+        filter_df_by_cycle_index,
+    )
+
     cycle_lists = ([1, 2, 3], [4.0, 6.0, 10.0], [-1, 5, 2])
     for cycle_list in cycle_lists:
         filtered_df = filter_df_by_cycle_index(reduced_echem_dataframe, cycle_list)
         assert {int(i) for i in filtered_df["full cycle"]}.issubset({int(i) for i in cycle_list})
 
 
 def test_plot(reduced_echem_dataframe):
+    from pydatalab.apps.echem.utils import (
+        compute_gpcl_differential,
+    )
     from pydatalab.bokeh_plots import double_axes_echem_plot
 
     layout = double_axes_echem_plot(reduced_echem_dataframe)

pydatalab/tests/apps/test_ftir_block.py

@@ -2,15 +2,15 @@
 
 import pytest
 
-from pydatalab.apps.ftir import FTIRBlock
-
 
 @pytest.fixture
 def data_files():
     return (Path(__file__).parent.parent.parent / "example_data" / "FTIR").glob("*")
 
 
 def test_load(data_files):
+    from pydatalab.apps.ftir import FTIRBlock
+
     for f in data_files:
         df = FTIRBlock.parse_ftir_asp(f)
         assert len(df) == 1932
@@ -25,6 +25,8 @@ def test_load(data_files):
 
 
 def test_plot(data_files):
+    from pydatalab.apps.ftir import FTIRBlock
+
     f = next(data_files)
     ftir_data = FTIRBlock.parse_ftir_asp(f)
     layout = FTIRBlock._format_ftir_plot(ftir_data)

pydatalab/tests/apps/test_nmr.py

@@ -4,9 +4,6 @@
 
 import pytest
 
-from pydatalab.apps.nmr.blocks import NMRBlock
-from pydatalab.apps.nmr.utils import read_bruker_1d, read_jcamp_dx_1d
-
 
 def _extract_example(filename, _dir):
     with zipfile.ZipFile(filename, "r") as zip_ref:
@@ -64,6 +61,8 @@ def nmr_2d_matpass_example(tmpdir, nmr_2d_matpass_path):
 
 
 def test_bruker_reader_solution(nmr_1d_solution_example):
+    from pydatalab.apps.nmr.utils import read_bruker_1d
+
     df, a_dic, topspin_title, shape = read_bruker_1d(nmr_1d_solution_example)
     assert df is not None
     assert a_dic
@@ -72,6 +71,8 @@ def test_bruker_reader_solution(nmr_1d_solution_example):
 
 
 def test_bruker_reader_solid(nmr_1d_solid_example):
+    from pydatalab.apps.nmr.utils import read_bruker_1d
+
     df, a_dic, topspin_title, shape = read_bruker_1d(nmr_1d_solid_example)
     assert df is not None
     assert a_dic
@@ -80,6 +81,8 @@ def test_bruker_reader_solid(nmr_1d_solid_example):
 
 
 def test_bruker_reader_2D(nmr_2d_matpass_example):
+    from pydatalab.apps.nmr.utils import read_bruker_1d
+
     df, a_dic, topspin_title, shape = read_bruker_1d(nmr_2d_matpass_example)
     assert df is None
     assert a_dic
@@ -90,6 +93,8 @@ def test_bruker_reader_2D(nmr_2d_matpass_example):
 def test_nmr_block(
     nmr_1d_solution_path, nmr_1d_solution_path_renamed, nmr_1d_solid_path, nmr_2d_matpass_path
 ):
+    from pydatalab.apps.nmr.blocks import NMRBlock
+
     block = NMRBlock(item_id="nmr-block")
     block.processed_data, block.data["metadata"] = block.read_bruker_nmr_data(nmr_1d_solid_path)
     assert block.data["metadata"]["topspin_title"].split("\n")[0] == "7Li 40 kHz 40 C hahn-echo"
@@ -124,6 +129,9 @@ def test_nmr_block(
 
 
 def test_read_jcamp_1h_1d(nmr_jcamp_1h_path):
+    from pydatalab.apps.nmr.blocks import NMRBlock
+    from pydatalab.apps.nmr.utils import read_jcamp_dx_1d
+
     df, dic, title, shape = read_jcamp_dx_1d(nmr_jcamp_1h_path)
     assert df is not None
     assert dic[".OBSERVENUCLEUS"]
@@ -136,6 +144,9 @@ def test_read_jcamp_1h_1d(nmr_jcamp_1h_path):
 
 
 def test_read_jcamp_13c_1d(nmr_jcamp_13c_path):
+    from pydatalab.apps.nmr.blocks import NMRBlock
+    from pydatalab.apps.nmr.utils import read_jcamp_dx_1d
+
     df, dic, title, shape = read_jcamp_dx_1d(nmr_jcamp_13c_path)
     assert df is not None
     assert dic[".OBSERVENUCLEUS"]

pydatalab/tests/apps/test_plugins.py

@@ -1,10 +1,11 @@
 # Load block types first to avoid circular dependency issues
-from pydatalab.apps import BLOCK_TYPES, BLOCKS, load_block_plugins
 
 
 def test_load_insitu_nmr_plugin():
     from datalab_app_plugin_insitu import InsituBlock
 
+    from pydatalab.apps import BLOCK_TYPES, BLOCKS, load_block_plugins
+
     plugins = load_block_plugins()
 
     assert plugins["insitu-nmr"] == InsituBlock
@@ -16,6 +17,8 @@ def test_load_insitu_nmr_plugin():
 def test_load_insitu_uvvis_plugin():
     from datalab_app_plugin_insitu import UVVisInsituBlock
 
+    from pydatalab.apps import BLOCK_TYPES, BLOCKS, load_block_plugins
+
     plugins = load_block_plugins()
 
     assert plugins["insitu-uvvis"] == UVVisInsituBlock

pydatalab/tests/apps/test_raman.py

@@ -3,8 +3,6 @@
 import numpy as np
 import pytest
 
-from pydatalab.apps.raman.blocks import RamanBlock
-
 
 @pytest.fixture
 def wdf_example():
@@ -24,6 +22,8 @@ def renishaw_txt_example():
 
 
 def test_load_wdf(wdf_example):
+    from pydatalab.apps.raman.blocks import RamanBlock
+
     df, metadata, y_options = RamanBlock.load(wdf_example)
     assert all(y in df.columns for y in y_options)
     assert df.shape == (1011, 11)
@@ -45,6 +45,8 @@ def test_load_wdf(wdf_example):
 
 
 def test_load_renishaw_txt(renishaw_txt_example):
+    from pydatalab.apps.raman.blocks import RamanBlock
+
     with pytest.warns(UserWarning, match="Unable to find wavenumber unit"):
         with pytest.warns(UserWarning, match="Unable to find wavenumber offset"):
             df, metadata, y_options = RamanBlock.load(renishaw_txt_example)
@@ -61,6 +63,8 @@ def test_load_renishaw_txt(renishaw_txt_example):
 
 
 def test_load_labspec_txt(labspec_txt_example):
+    from pydatalab.apps.raman.blocks import RamanBlock
+
     df, metadata, y_options = RamanBlock.load(labspec_txt_example)
     assert all(y in df.columns for y in y_options)
     assert df.shape == (341, 11)

pydatalab/tests/apps/test_tabular.py

@@ -1,26 +1,32 @@
 import pytest
 
-from pydatalab.blocks.common import TabularDataBlock
-
 
 def test_load_raman_txt(example_data_dir):
+    from pydatalab.blocks.common import TabularDataBlock
+
     with pytest.warns(UserWarning):
         df = TabularDataBlock.load(example_data_dir / "raman" / "raman_example.txt")
     assert df.shape == (1011, 2)
 
 
 def test_load_labspec_raman_txt(example_data_dir):
+    from pydatalab.blocks.common import TabularDataBlock
+
     with pytest.warns(UserWarning):
         df = TabularDataBlock.load(example_data_dir / "raman" / "labspec_raman_example.txt")
     assert df.shape == (341, 2)
 
 
 def test_simple_csv(example_data_dir):
+    from pydatalab.blocks.common import TabularDataBlock
+
     df = TabularDataBlock.load(example_data_dir / "csv" / "simple.csv")
     assert df.shape == (2, 3)
     assert df.columns.tolist() == ["test", "test2", "test3"]
 
 
 def test_simple_xlsx(example_data_dir):
+    from pydatalab.blocks.common import TabularDataBlock
+
     df = TabularDataBlock.load(example_data_dir / "csv" / "simple.xlsx")
     assert df.shape == (4, 4)

pydatalab/tests/apps/test_uvvis.py

@@ -3,16 +3,16 @@
 
 import pytest
 
-from pydatalab.apps.uvvis import UVVisBlock
-from pydatalab.apps.uvvis.utils import find_absorbance, parse_uvvis_txt
-
 
 @pytest.fixture
 def data_files():
     return (Path(__file__).parent.parent.parent / "example_data" / "UV-Vis").glob("*")
 
 
 def test_load(data_files):
+    from pydatalab.apps.uvvis import UVVisBlock
+    from pydatalab.apps.uvvis.utils import parse_uvvis_txt
+
     logging.info("Testing UV-Vis data loading")
     for f in data_files:
         logging.info(f"Testing file: {f}")
@@ -30,6 +30,9 @@ def test_find_absorbance(
     reference_file="1908047U1_0000.Raw8.TXT",
     sample_files=["1908047U1_0001.Raw8.txt", "1908047U1_0060.Raw8.txt"],
 ):
+    from pydatalab.apps.uvvis import UVVisBlock
+    from pydatalab.apps.uvvis.utils import find_absorbance, parse_uvvis_txt
+
     # Tests two specific sample files with one reference file, will fail if files aren't present in the example data
     reference_path = (
         Path(__file__).parent.parent.parent / "example_data" / "UV-Vis" / reference_file
@@ -62,6 +65,9 @@ def test_plot(
     reference_file="1908047U1_0000.Raw8.TXT",
     sample_files=["1908047U1_0001.Raw8.txt", "1908047U1_0060.Raw8.txt"],
 ):
+    from pydatalab.apps.uvvis import UVVisBlock
+    from pydatalab.apps.uvvis.utils import find_absorbance, parse_uvvis_txt
+
     reference_path = (
         Path(__file__).parent.parent.parent / "example_data" / "UV-Vis" / reference_file
     )

pydatalab/tests/apps/test_xrd_block.py

@@ -2,19 +2,21 @@
 
 import pytest
 
-from pydatalab.apps.xrd.blocks import XRDBlock
-
 XRD_DATA_FILES = list((Path(__file__).parent.parent.parent / "example_data" / "XRD").glob("*"))
 
 
 @pytest.mark.parametrize("f", XRD_DATA_FILES)
 def test_load(f):
+    from pydatalab.apps.xrd.blocks import XRDBlock
+
     if f.suffix in XRDBlock.accepted_file_extensions:
         df, y_options, metadata = XRDBlock.load_pattern(f)
         assert all(y in df.columns for y in y_options)
 
 
 def test_event():
+    from pydatalab.apps.xrd.blocks import XRDBlock
+
     block = XRDBlock(item_id="test-id")
     assert block.data["wavelength"] == 1.54060
     block.process_events({"event_name": "set_wavelength", "wavelength": 1.0})
@@ -28,6 +30,8 @@ def test_event():
 
 @pytest.mark.parametrize("f", XRD_DATA_FILES)
 def test_single_plots(f):
+    from pydatalab.apps.xrd.blocks import XRDBlock
+
     if f.suffix in XRDBlock.accepted_file_extensions:
         block = XRDBlock(item_id="test")
         block.generate_xrd_plot(f)

pydatalab/tests/conftest.py

@@ -4,7 +4,7 @@
 import pytest
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(autouse=True, scope="session")
 def monkeypatch_session():
     from _pytest.monkeypatch import MonkeyPatch
 
@@ -13,13 +13,13 @@ def monkeypatch_session():
     m.undo()
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(autouse=True, scope="session")
 def secret_key():
     """Fixture to provide a secret key for testing purposes."""
     return hashlib.sha512(b"test").hexdigest()
 
 
-@pytest.fixture(scope="session", autouse=True)
+@pytest.fixture(autouse=True)
 def override_environment_variables(monkeypatch_session, secret_key):
     """Override the secret key and other environment variables that will
     otherwise fallover outside of testing mode.