Run example pipelines via pytest instead and check abundance output

.github/workflows/python-tests.yml

@@ -39,12 +39,3 @@ jobs:
       run: |
         micromamba install pytest
         pytest
-    - name: "Run example: full length"
-      run: |
-        python emu abundance example/full_length.fa
-    - name: "Run example: short-read fwd+rev"
-      run: |
-        python emu abundance --type sr example/short_read_f.fq example/short_read_r.fq
-    - name: "Run example: short-read fwd only"
-      run:
-        python emu abundance --type sr example/short_read_f.fq

tests/test_emu_cli.py

@@ -0,0 +1,48 @@
+import pytest
+import subprocess
+import os
+import pandas as pd
+
+
+@pytest.mark.parametrize(
+    "emu_command, abundance_file, expected_abundancies",
+    [
+        (
+            "./emu abundance --db emu_database --output-dir test_results example/full_length.fa",
+            "test_results/full_length_rel-abundance.tsv",
+            {
+                "Sphingobacterium puteale": 0.5,
+                "Mycobacterium saskatchewanense": 0.25,
+                "Streptococcus sobrinus": 0.25,
+            },
+        ),
+        (
+            "./emu abundance --db emu_database --output-dir test_results --type sr example/short_read_f.fq",
+            "test_results/short_read_f_rel-abundance.tsv",
+            {
+                "Staphylococcus hominis": 1.0,
+            },
+        ),
+        (
+            "./emu abundance --db emu_database --output-dir test_results --type sr example/short_read_f.fq example/short_read_r.fq",
+            "test_results/short_read_f-short_read_r_rel-abundance.tsv",
+            {
+                "Staphylococcus aureus": 1.0 / 3,
+                "Salmonella enterica": 1.0 / 3,
+                "Enterococcus columbae": 1.0 / 3,
+            },
+        ),
+    ],
+)
+def test_full_length_example(emu_command, abundance_file, expected_abundancies):
+    if os.path.exists(abundance_file):
+        os.remove(abundance_file)
+
+    subprocess.check_output(emu_command, shell=True)
+
+    assert os.path.exists(abundance_file)
+
+    df = abundance_df = pd.read_csv(abundance_file, sep="\t")
+
+    for species, expected_abundance in expected_abundancies.items():
+        assert df[df["species"] == species].iloc[0]["abundance"] == expected_abundance