move some tests inside proper test suite to help with coverage

.github/workflows/ci.yml

@@ -35,13 +35,7 @@ jobs:
 
     - name: Tests
       run: |
-        ceci tests/test.yml
-        ceci --dry-run tests/test.yml
-        ceci --flow-chart test-flow.png tests/test.yml
-        test -f test-flow.png
         pytest --cov=ceci
-        # add a test with the memory monitor and profiling switched on
-        python3 -m ceci_example PZEstimationPipe   --DM=./tests/inputs/dm.txt   --fiducial_cosmology=./tests/inputs/fiducial_cosmology.txt   --config=./tests/config.yml   --photoz_pdfs=./tests/outputs/photoz_pdfs.txt --memmon=1 --cprofile=profile.stats
 
 
     - name: Upload coverage to Codecov

ceci_example/example_stages.py

@@ -32,6 +32,7 @@ class PZEstimationPipe(PipelineStage):
     name = "PZEstimationPipe"
     inputs = [("DM", TextFile), ("fiducial_cosmology", TextFile)]
     outputs = [("photoz_pdfs", TextFile)]
+    parallel = False
 
     def run(self):
         for inp, _ in self.inputs:

tests/test_executables.py

@@ -0,0 +1,22 @@
+import pytest
+import subprocess
+import os
+
+def test_executable():
+    subprocess.check_call(["ceci", "tests/test.yml"])
+
+def test_dry_run():
+    subprocess.check_call(["ceci", "--dry-run", "tests/test.yml",])
+
+def test_flow_chart_run():
+    subprocess.check_call(["ceci", "--flow-chart", "test-flow.png", "tests/test.yml",])
+    assert os.path.exists("test-flow.png")
+
+def test_profiling_and_memmon_flags():
+    cmd = "python3 -m ceci_example PZEstimationPipe   --DM=./tests/inputs/dm.txt   --fiducial_cosmology=./tests/inputs/fiducial_cosmology.txt   --config=./tests/config.yml   --photoz_pdfs=./tests/outputs/photoz_pdfs.txt --memmon=1 --cprofile=profile.stats"
+    subprocess.check_call(cmd.split())
+
+def test_misuse_mpi():
+    cmd = "python3 -m ceci_example PZEstimationPipe --mpi"
+    with pytest.raises(subprocess.CalledProcessError):
+        subprocess.check_call(cmd.split())