Add Typer dependency and expand tests to improve coverage

Author: DiogoRibeiro7

pyproject.toml

@@ -16,6 +16,7 @@ numpy = "^1.26"
 pandas = "^2.2.3"
 pytest-cov = "^6.1.1"
 invoke = "^2.2.0"
+typer = "^0.12.3"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.3.5"

tests/test_bivariate.py

@@ -0,0 +1,16 @@
+import numpy as np
+from gen_surv.bivariate import sample_bivariate_distribution
+import pytest
+
+
+def test_sample_bivariate_exponential_shape():
+    """Exponential distribution should return an array of shape (n, 2)."""
+    result = sample_bivariate_distribution(5, "exponential", 0.0, [1.0, 1.0])
+    assert isinstance(result, np.ndarray)
+    assert result.shape == (5, 2)
+
+
+def test_sample_bivariate_invalid_dist():
+    """Unsupported distributions should raise ValueError."""
+    with pytest.raises(ValueError):
+        sample_bivariate_distribution(10, "invalid", 0.0, [1, 1])

tests/test_cli.py

@@ -0,0 +1,32 @@
+import pandas as pd
+from gen_surv.cli import dataset
+import runpy
+
+
+def test_cli_dataset_stdout(monkeypatch, capsys):
+    """Dataset command prints CSV to stdout when no output file is given."""
+
+    def fake_generate(model: str, n: int):
+        return pd.DataFrame({"time": [1.0], "status": [1], "X0": [0.1], "X1": [0.2]})
+
+    # Patch the generate function used in the CLI to avoid heavy computation.
+    monkeypatch.setattr("gen_surv.cli.generate", fake_generate)
+    # Call the command function directly to sidestep Click argument parsing
+    dataset(model="cphm", n=1, output=None)
+    captured = capsys.readouterr()
+    assert "time,status,X0,X1" in captured.out
+
+
+def test_main_entry_point(monkeypatch):
+    """Running the module as a script should invoke the CLI app."""
+
+    called = []
+
+    def fake_app():
+        called.append(True)
+
+    # Patch the CLI app before the module is executed
+    monkeypatch.setattr("gen_surv.cli.app", fake_app)
+    monkeypatch.setattr("sys.argv", ["gen_surv", "dataset", "cphm"])
+    runpy.run_module("gen_surv.__main__", run_name="__main__")
+    assert called

tests/test_validate.py

@@ -0,0 +1,28 @@
+import pytest
+import gen_surv.validate as v
+
+
+def test_validate_gen_cphm_inputs_valid():
+    """Ensure valid inputs pass without raising an exception."""
+    v.validate_gen_cphm_inputs(1, "uniform", 0.5, 1.0)
+
+
+@pytest.mark.parametrize(
+    "n, model_cens, cens_par, covar",
+    [
+        (0, "uniform", 0.5, 1.0),
+        (1, "bad", 0.5, 1.0),
+        (1, "uniform", -1.0, 1.0),
+        (1, "uniform", 0.5, -1.0),
+    ],
+)
+def test_validate_gen_cphm_inputs_invalid(n, model_cens, cens_par, covar):
+    """Invalid parameter combinations should raise ValueError."""
+    with pytest.raises(ValueError):
+        v.validate_gen_cphm_inputs(n, model_cens, cens_par, covar)
+
+
+def test_validate_dg_biv_inputs_invalid():
+    """Invalid distribution names should raise an error."""
+    with pytest.raises(ValueError):
+        v.validate_dg_biv_inputs(10, "normal", 0.1, [1, 1])

tests/test_version.py

@@ -0,0 +1,7 @@
+from importlib.metadata import version
+from gen_surv import __version__
+
+
+def test_package_version_matches_metadata():
+    """The exported __version__ should match package metadata."""
+    assert __version__ == version("gen_surv")