Test update

Author: standage

CHANGELOG.md

@@ -10,6 +10,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ### Fixed
 - Bug with handling marker vs. locus identifiers when running `mhpl8r seq` (#190).
+- Bug with writing output to terminal for some commands (#191).
 
 
 ## [0.8.4] 2024-09-16

microhapulator/cli/sim.py

@@ -59,8 +59,9 @@ def main(args):
     profile = mhapi.sim(frequencies, seed=args.seed)
     with mhopen(args.out, "w") as fh:
         profile.dump(fh)
-        message = "profile JSON written to {:s}".format(fh.name)
-        print("[MicroHapulator::sim]", message, file=sys.stderr)
+        if hasattr(fh, "name"):
+            message = "profile JSON written to {:s}".format(fh.name)
+            print("[MicroHapulator::sim]", message, file=sys.stderr)
     if args.haplo_seq:
         index = MicrohapIndex.from_files(args.markers, fasta_path=args.sequences)
         index.validate()

microhapulator/tests/test_cli.py

@@ -11,16 +11,59 @@
 # -------------------------------------------------------------------------------------------------
 # -----------------------------------------------------------------------------
 
-import microhapulator
+from microhapulator import open as mhopen
+from microhapulator.cli import main
 from microhapulator.tests import data_file
 import pytest
 
 
 def test_microhapulator_open():
     thefile = data_file("refr/three-loci-refr.fasta")
-    with microhapulator.open(thefile, "r") as filehandle:
+    with mhopen(thefile, "r") as filehandle:
         filecontents = filehandle.read()
         assert len(filecontents.strip().split("\n")) == 6
-    with pytest.raises(ValueError, match=r'invalid mode "p"') as ve:
-        with microhapulator.open(thefile, "p") as filehandle:
+    with pytest.raises(ValueError, match=r'invalid mode "p"'):
+        with mhopen(thefile, "p") as filehandle:
             pass
+
+
+# These parameters and the following two test functions are mostly just smoke tests to make sure
+# the code doesn't go up in flames when data is written to stdout.
+# @pytest.fixture(params=[
+#     ("diff", [data_file("prof/euramer-sim-gt.json"), data_file("prof/euramer-inf-gt.json")]),
+#     ("dist", [data_file("prof/euramer-sim-gt.json"), data_file("prof/euramer-inf-gt.json")]),
+#     ("sim", [data_file("pashtun-sim/tiny-panel-multidef-freq.tsv")]),
+#     ("unite", [data_file("prof/swedish-mom.json"), data_file("prof/swedish-dad.json")]),
+# ])
+# def stdout_regress_param(request):
+#     return request.param
+#
+#
+# def test_regression_stdout(stdout_regress_param, capsys, tmp_path):
+#     command, infiles = stdout_regress_param
+#     main([command, *infiles, "-o", outfile])
+#     terminal = capsys.readouterr()
+#     assert terminal.out == ""
+#     main([command, *infiles])
+#     assert terminal.out != ""
+
+
+@pytest.mark.parametrize(
+    "command, infiles",
+    [
+        ("diff", [data_file("prof/euramer-sim-gt.json"), data_file("prof/euramer-inf-gt.json")]),
+        ("dist", [data_file("prof/euramer-sim-gt.json"), data_file("prof/euramer-inf-gt.json")]),
+        ("sim", [data_file("freq/korea-5loc-freq.tsv")]),
+        ("unite", [data_file("prof/swedish-mom.json"), data_file("prof/swedish-dad.json")]),
+    ],
+)
+def test_regression_output_file(command, infiles, capsys, tmp_path):
+    # This is mostly just a smoke test to make sure the code doesn't go up in flames when data is
+    # written to stdout.
+    outfile = str(tmp_path / "output.data")
+    main([command, *infiles, "-o", outfile])
+    terminal = capsys.readouterr()
+    assert terminal.out == ""
+    main([command, *infiles])
+    terminal = capsys.readouterr()
+    assert terminal.out != ""