Merge pull request #29 from pythonhealthdatascience/dev

Dev

Author: amyheather

.lintr

@@ -0,0 +1,2 @@
+linters: linters_with_defaults(object_usage_linter = NULL)
+exclusions: "pages/code"

.pylintrc

@@ -0,0 +1,2 @@
+[main]
+check-quote-consistency = yes

CONTRIBUTING.md

@@ -2,6 +2,14 @@
 
 This file is for contributors. It describes how the `stars-testing-intro` site is set-up and quality controlled.
 
+## Linting
+
+Simply run from terminal:
+
+```
+bash lint.sh
+```
+
 ## Example code
 
 The example code is contained in `examples`.

DESCRIPTION

@@ -4,6 +4,7 @@ Imports:
     devtools
     DT
     knitr
+    lintr
     patrick
     reticulate
     rmarkdown

_quarto.yml

@@ -26,12 +26,13 @@ website:
           - pages/write_basic_test.qmd
           - pages/run_tests.qmd
           - pages/parametrising_tests.qmd
+          - pages/temp_mock.qmd
       - section: Types of test
         contents:
           - pages/smoke_tests.qmd
           - pages/unit_tests.qmd
-          - pages/functional_tests.qmd
-          - pages/back_tests.qmd
+          - pages/system_tests.qmd
+          - pages/regression_tests.qmd
       - pages/break.qmd
       - pages/test_coverage.qmd
       - pages/github_actions.qmd

assets/styles.css

@@ -45,6 +45,18 @@
   padding: 1em 1em 0.2em 1em;
   margin-bottom: 1em;
 }
+.box-green {
+  background-color: #d3ebba;
+  border-radius: 8px;
+  padding: 1em 1em 0.2em 1em;
+  margin-bottom: 1em;
+}
+.box-red {
+  background-color: #fbcbca;
+  border-radius: 8px;
+  padding: 1em 1em 0.2em 1em;
+  margin-bottom: 1em;
+}
 
 /* Add space before H2 + H3 */
 h2 {

examples/python_package/tests/test_data_mock.py

@@ -0,0 +1,31 @@
+"""
+Using mocking to provide CSV data to a test
+"""
+
+import pandas as pd
+
+from waitingtimes.patient_analysis import import_patient_data
+
+def test_mocking(monkeypatch):
+    """Providing data to a test via mocking"""
+
+    # Create sample patient data
+    testdata = pd.DataFrame(
+        [["p1", "2024-01-01", "08:00", "2024-01-01", "09:00"]],
+        columns=[
+            "PATIENT_ID", "ARRIVAL_DATE", "ARRIVAL_TIME",
+            "SERVICE_DATE", "SERVICE_TIME",
+        ],
+    )
+
+    # Define a fake CSV reader that just returns our DataFrame
+    def mock_read_csv(path):
+        return testdata
+
+    # Temporarily replace pd.read_csv with our fake version
+    monkeypatch.setattr(pd, "read_csv", mock_read_csv)
+
+    # Call the function with any path - it does not matter - it will use the
+    # mocked reader, and pd.read_csv is never actually called
+    df = import_patient_data("does_not_matter.csv")
+    assert not df.empty

examples/python_package/tests/test_data_real.py

@@ -0,0 +1,17 @@
+"""
+Importing a real data file to a test
+"""
+
+from pathlib import Path
+
+from waitingtimes.patient_analysis import import_patient_data
+
+def test_real_data_file():
+    """Importing a real data file to a test"""
+
+    # Path to example test data
+    csv_path = Path(__file__).parent.joinpath("data/patient_data.csv")
+
+    # Load the data and check it was read
+    df = import_patient_data(csv_path)
+    assert not df.empty

examples/python_package/tests/test_data_temp.py

@@ -0,0 +1,27 @@
+"""
+Using temporary file to provide CSV to a test
+"""
+
+import pandas as pd
+
+from waitingtimes.patient_analysis import import_patient_data
+
+def test_temporary_file(tmp_path):
+    """Providing data to a test via a temporary file"""
+
+    # Create sample patient data
+    testdata = pd.DataFrame(
+        [["p1", "2024-01-01", "08:00", "2024-01-01", "09:00"]],
+        columns=[
+            "PATIENT_ID", "ARRIVAL_DATE", "ARRIVAL_TIME",
+            "SERVICE_DATE", "SERVICE_TIME",
+        ],
+    )
+
+    # Create a temporary CSV file
+    csv_path = tmp_path / "patients.csv"
+    testdata.to_csv(csv_path, index=False)
+
+    # Load the data and check it was read
+    df = import_patient_data(csv_path)
+    assert not df.empty

…amples/python_package/tests/test_back.py …/python_package/tests/test_regression.pyexamples/python_package/tests/test_back.py renamed to examples/python_package/tests/test_regression.py examples/python_package/tests/test_back.py renamed to examples/python_package/tests/test_regression.py

@@ -1,5 +1,5 @@
 """
-Back testing.
+Regression testing.
 """
 
 from pathlib import Path