Upversioned dependencies and fixed testing strategy

.github/workflows/python-app.yaml

@@ -15,16 +15,16 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install wheel
-        pip install flake8 pytest pandas pydotplus IPython colorutils networkx
+        pip install flake8 pytest pandas pydotplus IPython colorutils
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Test with pytest
       run: |

.gitignore

@@ -35,4 +35,6 @@ data/tic-tac-toe.xlsx
 cegpy-binder
 docs/_build/*
 .mypy
-build
+build
+.venv
+venv

requirements.txt

@@ -12,3 +12,4 @@ scipy>=1.7.0
 colorutils>=0.3.0
 xlsxwriter>=3.0.0
 tox>=4.2.8
+networkx>=3.2.1

setup.cfg

@@ -18,14 +18,14 @@ classifiers =
 package_dir =
     = src
 packages = find:
-python_requires = >=3.6
+python_requires= >=3.9
 install_requires =
     pandas >=1.3.0
     pydotplus >=2.0.2
     ipython >=7.25.0
     scipy >=1.7.0
     colorutils >=0.3.0
-    networkx >=2.6.3
+    networkx >=3.2.1
 
 license_files=
     LICENSE

src/tests/test_ceg.py

@@ -2,28 +2,26 @@
 # pylint: disable=protected-access
 import re
 from pathlib import Path
-from typing import Dict, List, Mapping, Tuple
+from typing import Dict, Mapping
 import unittest
 from unittest.mock import Mock, patch
 import networkx as nx
 import pandas as pd
-import pytest
-import pytest_mock
 from cegpy import StagedTree, ChainEventGraph
 from cegpy.graphs._ceg import (
     CegAlreadyGenerated,
     _merge_edge_data,
 )
 
 
-class TestMockedCEGMethods:
+class TestMockedCEGMethods(unittest.TestCase):
     """Tests that Mock functions in ChainEventGraph"""
 
     node_prefix = "w"
     sink_suffix = "∞"
     staged: StagedTree
 
-    def setup(self):
+    def setUp(self):
         """Test setup"""
         df_path = (
             Path(__file__)
@@ -34,12 +32,12 @@ def setup(self):
         self.staged = StagedTree(dataframe=pd.read_excel(df_path))
         self.staged.calculate_AHC_transitions()
 
-    def test_generate_argument(self, mocker: pytest_mock.MockerFixture):
+    @patch("cegpy.graphs._ceg.ChainEventGraph.generate", autospec=True)
+    def test_generate_argument(self, generate_mock: Mock):
         """When ChainEventGraph called with generate, the .generate()
         method is called."""
-        mocker.patch("cegpy.graphs._ceg.ChainEventGraph.generate")
-        ceg = ChainEventGraph(self.staged, generate=True)
-        ceg.generate.assert_called_once()  # pylint: disable=no-member
+        ChainEventGraph(self.staged, generate=True)
+        generate_mock.assert_called_once()  # pylint: disable=no-member
 
 
 class TestUnitCEG(unittest.TestCase):

src/tests/test_ceg_reducer.py

@@ -443,8 +443,8 @@ def test_str_out(self):
             assert str(node) in str_rep
 
 
-class TestReducedCEGTwo(object):
-    def setup(self):
+class TestReducedCEGTwo(unittest.TestCase):
+    def setUp(self):
         G = nx.MultiDiGraph()
         self.init_nodes = ["w0", "w1", "w2", "w3", "w4", "w5", "w6", "w_infinity"]
         self.init_edges = [

src/tests/test_event.py

@@ -38,8 +38,8 @@ def test_incorrect_sampling_zero_fails(self):
         )
 
 
-class TestEventTree:
-    def setup(self):
+class TestEventTree(unittest.TestCase):
+    def setUp(self):
         df_path = (
             Path(__file__)
             .resolve()
@@ -148,8 +148,8 @@ def test_node_colours(self) -> None:
         assert event_node_colours[0] == "lightgrey"
 
 
-class TestIntegration:
-    def setup(self):
+class TestIntegration(unittest.TestCase):
+    def setUp(self):
         # stratified dataset
         med_df_path = (
             Path(__file__)
@@ -198,8 +198,8 @@ def check_list_contains_strings(str_list) -> bool:
         assert isinstance(elem, str)
 
 
-class TestUsecase:
-    def setup(self):
+class TestUsecase(unittest.TestCase):
+    def setUp(self):
         # stratified dataset
         med_df_path = (
             Path(__file__)
@@ -232,88 +232,95 @@ def test_fall_cats_per_var(self):
 
 
 class TestChangingDataFrame:
-    def setup(self):
+    @pytest.fixture
+    def med_df(self):
         # stratified dataset
         med_df_path = (
             Path(__file__)
             .resolve()
             .parent.parent.joinpath("../data/medical_dm_modified.xlsx")
         )
-        self.med_s_z_paths = None
-        self.med_df = pd.read_excel(med_df_path)
-        self.med_et = EventTree(
-            dataframe=self.med_df, sampling_zero_paths=self.med_s_z_paths
-        )
 
+        return pd.read_excel(med_df_path)
+
+    @pytest.fixture
+    def med_et(self, med_df):
+        med_s_z_paths = None
+        med_et = EventTree(dataframe=med_df, sampling_zero_paths=med_s_z_paths)
+        return med_et
+
+    @pytest.fixture
+    def fall_df(self):
         # non-stratified dataset
         fall_df_path = (
             Path(__file__).resolve().parent.parent.joinpath("../data/Falls_Data.xlsx")
         )
+        return pd.read_excel(fall_df_path)
+
+    @pytest.fixture
+    def fall_et(self, fall_df):
         self.fall_s_z_paths = None
-        self.fall_df = pd.read_excel(fall_df_path)
-        self.fall_et = EventTree(
-            dataframe=self.fall_df, sampling_zero_paths=self.fall_s_z_paths
-        )
+        return EventTree(dataframe=fall_df, sampling_zero_paths=self.fall_s_z_paths)
 
-    def test_add_empty_column(self) -> None:
+    def test_add_empty_column(self, fall_et, med_df, med_et, fall_df) -> None:
         # adding empty column
-        med_empty_column_df = self.med_df
+        med_empty_column_df = med_df
         med_empty_column_df["extra"] = ""
         med_empty_column_et = EventTree(dataframe=med_empty_column_df)
-        assert med_empty_column_et.adj == self.med_et.adj
+        assert med_empty_column_et.adj == med_et.adj
 
-        fall_empty_column_df = self.fall_df
+        fall_empty_column_df = fall_df
         fall_empty_column_df["extra"] = ""
         fall_empty_column_et = EventTree(dataframe=fall_empty_column_df)
-        assert fall_empty_column_et.adj == self.fall_et.adj
+        assert fall_empty_column_et.adj == fall_et.adj
 
-    def test_add_NA_column(self) -> None:
+    def test_add_NA_column(self, fall_et, med_df, med_et, fall_df) -> None:
         # adding NA column
-        med_add_NA_df = self.med_df
+        med_add_NA_df = med_df
         med_add_NA_df["extra"] = np.nan
         med_add_NA_et = EventTree(dataframe=med_add_NA_df)
-        assert med_add_NA_et.adj == self.med_et.adj
+        assert med_add_NA_et.adj == med_et.adj
 
-        fall_add_NA_df = self.fall_df
+        fall_add_NA_df = fall_df
         fall_add_NA_df["extra"] = np.nan
         fall_add_NA_et = EventTree(dataframe=fall_add_NA_df)
-        assert fall_add_NA_et.adj == self.fall_et.adj
+        assert fall_add_NA_et.adj == fall_et.adj
 
-    def test_add_same_column(self) -> None:
+    def test_add_same_column(self, fall_et, med_df, med_et, fall_df) -> None:
         # adding column with no more information
-        med_add_same_df = self.med_df
+        med_add_same_df = med_df
         med_add_same_df["extra"] = "same for all"
         med_add_same_et = EventTree(dataframe=med_add_same_df)
-        assert len(med_add_same_et.leaves) == len(self.med_et.leaves)
+        assert len(med_add_same_et.leaves) == len(med_et.leaves)
 
-        fall_add_same_df = self.fall_df
+        fall_add_same_df = fall_df
         fall_add_same_df["extra"] = "same for all"
         fall_add_same_et = EventTree(dataframe=fall_add_same_df)
-        assert len(fall_add_same_et.leaves) == len(self.fall_et.leaves)
+        assert len(fall_add_same_et.leaves) == len(fall_et.leaves)
 
-    def test_add_same_column_int(self) -> None:
+    def test_add_same_column_int(self, fall_et, med_df, med_et, fall_df) -> None:
         # adding column with no more information
-        med_add_same_df = self.med_df
+        med_add_same_df = med_df
         med_add_same_df["extra"] = 1
         med_add_same_et = EventTree(dataframe=med_add_same_df)
         try:
             med_add_same_et.create_figure("et_fig_path.pdf")
         except InvocationException:
             pass
-        assert len(med_add_same_et.leaves) == len(self.med_et.leaves)
+        assert len(med_add_same_et.leaves) == len(med_et.leaves)
 
-        fall_add_same_df = self.fall_df
+        fall_add_same_df = fall_df
         fall_add_same_df["extra"] = 1
         fall_add_same_et = EventTree(dataframe=fall_add_same_df)
         try:
             fall_add_same_et.create_figure("et_fig_path.pdf")
         except InvocationException:
             pass
-        assert len(fall_add_same_et.leaves) == len(self.fall_et.leaves)
+        assert len(fall_add_same_et.leaves) == len(fall_et.leaves)
 
 
-class TestMissingLabels:
-    def setup(self):
+class TestMissingLabels(unittest.TestCase):
+    def setUp(self):
         array = [
             np.array(["1", "NotANum", "Recover"]),
             np.array(["1", "Trt1", "NotANum"]),
@@ -525,8 +532,8 @@ def test_complete_case_reduction(self) -> None:
         assert df_et.dataframe.equals(expected_df) is True
 
 
-class TestVariablesFiltered:
-    def setup(self):
+class TestVariablesFiltered(unittest.TestCase):
+    def setUp(self):
         array = [
             np.array(["1", "NotANum", "Recover"]),
             np.array(["1", "Trt1", "NotANum"]),
@@ -535,7 +542,7 @@ def setup(self):
             np.array(["1", "Trt1", "Recover"]),
             np.array(["1", "Trt2", "Recover"]),
             np.array(["1", "Trt2", "Dont Recover"]),
-            np.array(["1", np.NaN, "Dont Recover"]),
+            np.array(["1", np.nan, "Dont Recover"]),
         ]
 
         self.df = pd.DataFrame(array)
@@ -562,8 +569,8 @@ def test_pd_nans_filtered_with_missing(self) -> None:
         assert df_et.categories_per_variable == expected_categories
 
 
-class TestStageColours:
-    def setup(self):
+class TestStageColours(unittest.TestCase):
+    def setUp(self):
         array = [
             np.array(["1", "NotANum", "Recover"]),
             np.array(["1", "Trt1", "NotANum"]),
@@ -572,7 +579,7 @@ def setup(self):
             np.array(["1", "Trt1", "Recover"]),
             np.array(["1", "Trt2", "Recover"]),
             np.array(["1", "Trt2", "Dont Recover"]),
-            np.array(["1", np.NaN, "Dont Recover"]),
+            np.array(["1", np.nan, "Dont Recover"]),
         ]
 
         self.df = pd.DataFrame(array)

src/tests/test_staged.py

@@ -16,37 +16,23 @@
 class TestLogging:
     """Tests logging in stagedtree"""
 
-    def setup(self):
-        """Test setup"""
-        # pylint: disable=attribute-defined-outside-init
-        # stratified dataset
+    @pytest.fixture
+    def med_st(self):
         med_df_path = (
             Path(__file__)
             .resolve()
             .parent.parent.joinpath("../data/medical_dm_modified.xlsx")
         )
-        self.med_s_z_paths = None
-        self.med_df = pd.read_excel(med_df_path)
-        self.med_st = StagedTree(
-            dataframe=self.med_df, sampling_zero_paths=self.med_s_z_paths
-        )
-
-        # non-stratified dataset
-        fall_df_path = (
-            Path(__file__).resolve().parent.parent.joinpath("../data/Falls_Data.xlsx")
-        )
-        self.fall_s_z_paths = None
-        self.fall_df = pd.read_excel(fall_df_path)
-        self.fall_st = StagedTree(
-            dataframe=self.fall_df,
-            sampling_zero_paths=self.fall_s_z_paths,
-        )
+        med_s_z_paths = None
+        med_df = pd.read_excel(med_df_path)
+        med_st = StagedTree(dataframe=med_df, sampling_zero_paths=med_s_z_paths)
+        return med_st
 
-    def test_run_ahc_before_figure(self) -> None:
+    def test_run_ahc_before_figure(self, med_st) -> None:
         """Tests expected error message is in the log when running without
         running AHC"""
         try:
-            self.med_st.create_figure()
+            med_st.create_figure()
 
         except (InvocationException):
             pass