test: test coverage of __init__.py

pybwa/__init__.py

@@ -6,14 +6,13 @@
 from pybwa.libbwamem import *  # noqa: F403
 
 
-def get_include() -> list[str]:
+def _get_include() -> list[str]:
     """return a list of include directories."""
     dirname = os.path.abspath(os.path.join(os.path.dirname(__file__)))
 
-    #
     # Header files may be stored in different relative locations
     # depending on installation mode (e.g., `python setup.py install`,
-    # `python setup.py develop`. The first entry in each list is
+    # `python setup.py develop`). The first entry in each list is
     # where develop-mode headers can be found.
     #
     pybwa_possibilities = [
@@ -31,18 +30,15 @@ def get_include() -> list[str]:
     return includes
 
 
-def get_defines() -> list[str]:
+def _get_defines() -> list[str]:
     """return a list of defined compilation parameters."""
     return []
 
 
-def get_libraries() -> list[str]:
+def _get_libraries() -> list[str]:
     """return a list of libraries to link against."""
-    # Note that this list does not include libcsamtools.so as there are
-    # numerous name conflicts with libchtslib.so.
     dirname = os.path.abspath(os.path.join(os.path.dirname(__file__)))
-    # pybwa_libs = ['libbwaaln', 'libbwaindex', 'libbwamem']
-    pybwa_libs = ["libbwaindex"]
+    pybwa_libs = ["libbwaaln", "libbwaindex", "libbwamem"]
 
     so = sysconfig.get_config_var("EXT_SUFFIX")
     return [os.path.join(dirname, x + so) for x in pybwa_libs]

tests/_test_libbwaindex.pyxbld

@@ -4,7 +4,7 @@ def make_ext(modname, pyxfilename):
     import pybwa
     return Extension(name = modname,
                      sources = [pyxfilename],
-                     include_dirs = pybwa.get_include(),
+                     include_dirs = pybwa._get_include(),
                      extra_compile_args = [
                          "-Wno-unused-result",
                          "-Wno-unreachable-code",
@@ -15,4 +15,4 @@ def make_ext(modname, pyxfilename):
                          "-Wno-sign-compare",
                          "-Wno-error=declaration-after-statement"
                      ],
-                     define_macros = pybwa.get_defines())
+                     define_macros = pybwa._get_defines())

tests/test_pybwa.py

@@ -0,0 +1,21 @@
+from pathlib import Path
+
+import pybwa
+
+
+def test_get_includes() -> None:
+    names = [Path(p).name for p in pybwa._get_include()]
+    assert names == ["pybwa", "bwa"]
+
+
+def test_get_defines() -> None:
+    assert pybwa._get_defines() == []
+
+
+def test_get_libraries() -> None:
+    names = [Path(p).name for p in pybwa._get_libraries()]
+    assert names == [
+        "libbwaaln.cpython-311-darwin.so",
+        "libbwaindex.cpython-311-darwin.so",
+        "libbwamem.cpython-311-darwin.so",
+    ]