TST: add tests for command execution

tests/test_gbintk.py

@@ -0,0 +1,88 @@
+import pathlib
+import pytest
+import subprocess
+
+
+__author__ = "Vijini Mallawaarachchi"
+__credits__ = ["Vijini Mallawaarachchi"]
+
+
+DATADIR = pathlib.Path(__file__).parent / "data"
+
+
+@pytest.fixture(scope="session")
+def tmp_dir(tmpdir_factory):
+    return tmpdir_factory.mktemp("tmp")
+
+
+@pytest.fixture(autouse=True)
+def workingdir(tmp_dir, monkeypatch):
+    """set the working directory for all tests"""
+    monkeypatch.chdir(tmp_dir)
+
+
+def exec_command(cmnd, stdout=subprocess.PIPE, stderr=subprocess.PIPE):
+    """executes shell command and returns stdout if completes exit code 0
+
+    Parameters
+    ----------
+
+    cmnd : str
+      shell command to be executed
+    stdout, stderr : streams
+      Default value (PIPE) intercepts process output, setting to None
+      blocks this."""
+
+    proc = subprocess.Popen(cmnd, shell=True, stdout=stdout, stderr=stderr)
+    out, err = proc.communicate()
+    if proc.returncode != 0:
+        raise RuntimeError(f"FAILED: {cmnd}\n{err}")
+    return out.decode("utf8") if out is not None else None
+
+
+def test_gbintk():
+    """test gbintk"""
+    cmd = "gbintk"
+    exec_command(cmd)
+
+
+def test_gbintk_version():
+    """test gbintk version"""
+    cmd = "gbintk --version"
+    exec_command(cmd)
+
+
+def test_gbintk_graphbin():
+    """test gbintk graphbin"""
+    cmd = "gbintk graphbin"
+    exec_command(cmd)
+
+
+def test_gbintk_graphbin2():
+    """test gbintk graphbin2"""
+    cmd = "gbintk graphbin2"
+    exec_command(cmd)
+
+
+def test_gbintk_metacoag():
+    """test gbintk metacoag"""
+    cmd = "gbintk metacoag"
+    exec_command(cmd)
+
+
+def test_gbintk_prepare():
+    """test gbintk prepare"""
+    cmd = "gbintk prepare"
+    exec_command(cmd)
+
+
+def test_gbintk_visualise():
+    """test gbintk visualise"""
+    cmd = "gbintk visualise"
+    exec_command(cmd)
+
+
+def test_gbintk_evaluate():
+    """test gbintk evaluate"""
+    cmd = "gbintk evaluate"
+    exec_command(cmd)