Merge pull request #28 from jeromekelleher/lowlevel-tests

Initial start on cpython interface testing

.github/workflows/ci.yml

@@ -7,8 +7,8 @@ on:
       - main
 
 jobs:
-  test:
-    name: Test
+  python_test:
+    name: Python tests
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -42,30 +42,32 @@ jobs:
         run: |
           pytest
 
-  packaging:
-    name: Packaging
+  c_python_test:
+    name: CPython interface tests
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
-      - name: Install dependencies
+      - name: Install system dependencies
+        run: |
+          sudo apt install -y gcovr
+      - name: Install python dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install build twine validate-pyproject[all]
-      - name: Check and install package
+          python -m pip install numpy pytest
+      - name: Build module with coverage
         run: |
-          validate-pyproject pyproject.toml
-          python -m build
-          python -m twine check --strict dist/*
-          python -m pip install dist/*.whl
-      - name: Check vcztools CLI
+          # Build the extension module in-place so pytest can find it
+          CFLAGS="--coverage" python3 setup.py build_ext --inplace
+      - name: Run tests
         run: |
-          vcztools --help
-          # Make sure we don't have ``vcztools`` in the CWD
-          cd tests
-          python -m vcztools --help
+          pytest -vs tests/test_cpython_interface.py
+      - name: Show coverage
+        run: |
+          gcovr --filter vcztools
 
   c_test:
     name: C tests
@@ -88,7 +90,33 @@ jobs:
         run: |
           ninja -C build coverage-text
           cat build/meson-logs/coverage.txt
-      - name: Valgrind 
+      - name: Valgrind
         working-directory: ./lib
         run: |
           valgrind --leak-check=full --error-exitcode=1 ./build/tests
+
+  packaging:
+    name: Packaging
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build twine validate-pyproject[all]
+      - name: Check and install package
+        run: |
+          validate-pyproject pyproject.toml
+          python -m build
+          python -m twine check --strict dist/*
+          python -m pip install dist/*.whl
+      - name: Check vcztools CLI
+        run: |
+          vcztools --help
+          # Make sure we don't have ``vcztools`` in the CWD
+          cd tests
+          python -m vcztools --help
+

tests/test_cpython_interface.py

@@ -0,0 +1,53 @@
+import pytest
+import numpy as np
+
+from vcztools import _vcztools
+
+FIXED_FIELD_NAMES = ["chrom", "pos", "id", "qual", "ref", "alt", "filter"]
+
+
+def example_fixed_data(num_variants, num_samples=0):
+    chrom = np.array(["X"] * num_variants, dtype="S")
+    pos = np.arange(num_variants, dtype=np.int32)
+    id = np.array(["."] * num_variants, dtype="S").reshape((num_variants, 1))
+    ref = np.array(["A"] * num_variants, dtype="S")
+    alt = np.array(["T"] * num_variants, dtype="S").reshape((num_variants, 1))
+    qual = np.arange(num_variants, dtype=np.float32)
+    filter_ = np.ones(num_variants, dtype=bool).reshape((num_variants, 1))
+    filter_id = np.array(["PASS"], dtype="S")
+    return {
+        "chrom": chrom,
+        "pos": pos,
+        "id": id,
+        "qual": qual,
+        "ref": ref,
+        "alt": alt,
+        "filter": filter_,
+        "filter_ids": filter_id,
+    }
+
+
+class TestTypeChecking:
+    @pytest.mark.parametrize("name", FIXED_FIELD_NAMES)
+    def test_field_incorrect_length(self, name):
+        num_variants = 5
+        data = example_fixed_data(num_variants)
+        data[name] = data[name][1:]
+        with pytest.raises(ValueError, match=f"Array {name.upper()} must have "):
+            _vcztools.VcfEncoder(num_variants, 0, **data)
+
+    @pytest.mark.parametrize("name", FIXED_FIELD_NAMES)
+    def test_field_incorrect_dtype(self, name):
+        num_variants = 5
+        data = example_fixed_data(num_variants)
+        data[name] = np.zeros(data[name].shape, dtype=np.int64)
+        with pytest.raises(ValueError, match=f"Wrong dtype for {name.upper()}"):
+            _vcztools.VcfEncoder(num_variants, 0, **data)
+
+    @pytest.mark.parametrize("name", FIXED_FIELD_NAMES)
+    def test_field_incorrect_type(self, name):
+        num_variants = 5
+        data = example_fixed_data(num_variants)
+        data[name] = "A Python string"
+        with pytest.raises(TypeError, match=f"must be numpy.ndarray"):
+            _vcztools.VcfEncoder(num_variants, 0, **data)

vcztools/_vcztoolsmodule.c

@@ -119,7 +119,7 @@ VcfEncoder_store_fixed_array(VcfEncoder *self, PyArrayObject *array, const char
         goto out;
     }
     if (PyArray_DTYPE(array)->type_num != type) {
-        PyErr_Format(PyExc_ValueError, "Array %s is not of the correct type", name);
+        PyErr_Format(PyExc_ValueError, "Wrong dtype for %s", name);
         goto out;
     }
 
@@ -189,7 +189,7 @@ VcfEncoder_init(VcfEncoder *self, PyObject *args, PyObject *kwds)
         goto out;
     }
 
-    /* NOTE: we generalise this pattern for CHROM also to save a bit of time
+    /* NOTE: we could generalise this pattern for CHROM also to save a bit of time
      * in building numpy String arrays */
     assert(PyArray_CheckExact(filter_ids));
     if (!PyArray_CHKFLAGS(filter_ids, NPY_ARRAY_IN_ARRAY)) {
@@ -209,7 +209,7 @@ VcfEncoder_init(VcfEncoder *self, PyObject *args, PyObject *kwds)
     if (VcfEncoder_add_array(self, "IDS/", "FILTER", filter_ids) != 0) {
         goto out;
     }
-    if (VcfEncoder_store_fixed_array(self, filter, "filter", NPY_BOOL, 2, num_variants)
+    if (VcfEncoder_store_fixed_array(self, filter, "FILTER", NPY_BOOL, 2, num_variants)
         != 0) {
         goto out;
     }