added tests and coverage

.github/workflows/ci.yml

@@ -21,3 +21,7 @@ jobs:
         - name: Run tests
           run: |
               make coverage
+        - name: Upload coverage reports to Codecov
+          uses: codecov/[email protected]
+          with:
+            token: ${{ secrets.CODECOV_TOKEN }}

peakipy/cli/main.py

@@ -441,28 +441,6 @@ def select_specified_planes(plane, peakipy_data):
     return plane_numbers, peakipy_data
 
 
-def select_specified_planes(plane, peakipy_data):
-    plane_numbers = np.arange(peakipy_data.data.shape[peakipy_data.dims[0]])
-    # only fit specified planes
-    if plane:
-        inds = [i for i in plane]
-        data_inds = [
-            (i in inds) for i in range(peakipy_data.data.shape[peakipy_data.dims[0]])
-        ]
-        plane_numbers = np.arange(peakipy_data.data.shape[peakipy_data.dims[0]])[
-            data_inds
-        ]
-        peakipy_data.data = peakipy_data.data[data_inds]
-        print(
-            "[yellow]Using only planes {plane} data now has the following shape[/yellow]",
-            peakipy_data.data.shape,
-        )
-        if peakipy_data.data.shape[peakipy_data.dims[0]] == 0:
-            print("[red]You have excluded all the data![/red]", peakipy_data.data.shape)
-            exit()
-    return plane_numbers, peakipy_data
-
-
 def exclude_specified_planes(exclude_plane, peakipy_data):
     plane_numbers = np.arange(peakipy_data.data.shape[peakipy_data.dims[0]])
     # do not fit these planes
@@ -566,6 +544,10 @@ def unpack_xy_bounds(xy_bounds, peakipy_data):
             xy_bounds = list(xy_bounds)
             xy_bounds[0] = xy_bounds[0] * peakipy_data.pt_per_ppm_f2
             xy_bounds[1] = xy_bounds[1] * peakipy_data.pt_per_ppm_f1
+        case _:
+            raise TypeError(
+                "xy_bounds should be a tuple (<x_bounds_ppm>, <y_bounds_ppm>)"
+            )
     return xy_bounds
 
 

test/test_main.py

@@ -9,8 +9,12 @@
 from peakipy.cli.main import (
     get_vclist,
     check_for_include_column_and_add_if_missing,
+    check_data_shape_is_consistent_with_dims,
     select_specified_planes,
     exclude_specified_planes,
+    remove_excluded_peaks,
+    warn_if_trying_to_fit_large_clusters,
+    unpack_xy_bounds,
     validate_plane_selection,
     validate_sample_count,
     unpack_plotting_colors,
@@ -32,6 +36,8 @@ class PeakipyData:
     df: pd.DataFrame = field(default_factory=lambda: pd.DataFrame())
     data: np.array = field(default_factory=lambda: np.zeros((4, 10, 20)))
     dims: list = field(default_factory=lambda: [0, 1, 2])
+    pt_per_ppm_f2 = 10
+    pt_per_ppm_f1 = 20
 
 
 def test_get_vclist(actual_vclist):
@@ -47,6 +53,13 @@ def test_get_vclist_none():
     assert args == expected_args
 
 
+def test_get_vclist_error():
+    vclist = "vclist"
+    args = {}
+    with pytest.raises(Exception):
+        get_vclist(vclist, args)
+
+
 def test_check_for_include_column():
     peakipy_data = PeakipyData(pd.DataFrame())
     peakipy_data = check_for_include_column_and_add_if_missing(peakipy_data)
@@ -68,6 +81,14 @@ def test_select_specified_planes_2():
     assert peakipy_data.data.shape == (2, 10, 20)
 
 
+def test_select_specified_planes_all_planes_excluded(capsys):
+    plane = [10]
+    with pytest.raises(SystemExit):
+        select_specified_planes(plane, PeakipyData())
+    captured = capsys.readouterr()
+    assert "" in captured.err
+
+
 def test_exclude_specified_planes():
     plane = None
     expected_plane_numbers = np.arange(4)
@@ -83,6 +104,66 @@ def test_exclude_specified_planes_2():
     assert peakipy_data.data.shape == (2, 10, 20)
 
 
+def test_exclude_specified_planes_all_planes_excluded(capsys):
+    plane = [0, 1, 2, 3]
+    with pytest.raises(SystemExit):
+        exclude_specified_planes(plane, PeakipyData())
+    captured = capsys.readouterr()
+    assert "" in captured.err
+
+
+def test_remove_excluded_peaks():
+    actual_dict = dict(
+        include=["yes", "yes", "no"],
+        peak=[1, 2, 3],
+        INDEX=[0, 1, 2],
+        ASS=["one", "two", "three"],
+        X_PPM=[1, 2, 3],
+        Y_PPM=[1, 2, 3],
+        CLUSTID=[1, 2, 3],
+        MEMCNT=[1, 1, 1],
+    )
+    expected_dict = {k: v[:-1] for k, v in actual_dict.items()}
+    actual_df = pd.DataFrame(actual_dict)
+    expected_df = pd.DataFrame(expected_dict)
+    peakipy_data = PeakipyData(df=actual_df)
+    pd.testing.assert_frame_equal(remove_excluded_peaks(peakipy_data).df, expected_df)
+
+
+def test_warn_if_trying_to_fit_large_clusters():
+    max_cluster_size = 7
+    df = pd.DataFrame(dict(MEMCNT=[1, 6], CLUSTID=[0, 1]))
+    peakipy_data = PeakipyData(df=df)
+    assert (
+        warn_if_trying_to_fit_large_clusters(max_cluster_size, peakipy_data)
+        == max_cluster_size
+    )
+
+
+def test_warn_if_trying_to_fit_large_clusters_none():
+    max_cluster_size = None
+    df = pd.DataFrame(dict(MEMCNT=[1, 12], CLUSTID=[0, 1]))
+    peakipy_data = PeakipyData(df=df)
+    assert warn_if_trying_to_fit_large_clusters(max_cluster_size, peakipy_data) == 12
+
+
+def test_unpack_xy_bounds_case_00():
+    xy_bounds = (0, 0)
+    result = unpack_xy_bounds(xy_bounds, PeakipyData())
+    assert result == None
+
+
+def test_unpack_xy_bounds_case_xy():
+    xy_bounds = (1, 2)
+    result = unpack_xy_bounds(xy_bounds, PeakipyData())
+    assert result == [10, 40]
+
+
+def test_unpack_xy_bounds_invalid_input():
+    with pytest.raises(TypeError):
+        unpack_xy_bounds(None, PeakipyData())
+
+
 class MockPseudo3D:
     def __init__(self, n_planes):
         self.n_planes = n_planes
@@ -195,3 +276,9 @@ def test_invalid_clusters():
     fits = pd.DataFrame({"clustid": [1, 2, 3]})
     with pytest.raises(SystemExit):
         get_fit_data_for_selected_peak_clusters(fits, [4, 5, 6])
+
+
+def test_check_data_shape_is_consistent_with_dims():
+    peakipy_data = PeakipyData(data=np.zeros((4, 10)))
+    with pytest.raises(SystemExit):
+        check_data_shape_is_consistent_with_dims(peakipy_data)