add integration test

Author: dsmutin

pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+markers =
+    integration: end-to-end pipeline run (requires BLAST, primer3, bash scripts; slow)

tests/test_pipeline_general_integration.py

@@ -0,0 +1,91 @@
+# MIT License
+#
+# Copyright (c) 2025 CTLab-ITMO
+#
+# Authors: Daniil Smutin, Aleksandr Serdiukov, Vitalii Dravgelis, Artem Ivanov,
+# Aleksei Zabashta, Sergey Muravyov, and the CTLab-ITMO university team.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+"""Integration test equivalent to repo root test.sh (general FISH dataset)."""
+
+import shutil
+import subprocess
+import sys
+from pathlib import Path
+
+import pytest
+
+PROJECT_ROOT = Path(__file__).resolve().parent.parent
+
+
+def _require_blast_tools():
+    for cmd in ("makeblastdb", "blastn"):
+        if shutil.which(cmd) is None:
+            pytest.skip(f"{cmd} not on PATH")
+
+
+@pytest.mark.integration
+def test_pipeline_general_fish_from_test_sh(tmp_path):
+    """Mirror test.sh: small general run with visualization and AI enabled."""
+    _require_blast_tools()
+
+    output = tmp_path / "output"
+    cmd = [
+        sys.executable,
+        str(PROJECT_ROOT / "pipeline.py"),
+        "-i",
+        str(PROJECT_ROOT / "data/test/general/test.fna"),
+        "-o",
+        str(output),
+        "-tb",
+        str(PROJECT_ROOT / "data/test/general/fasta_base/true_base"),
+        "-fb",
+        str(PROJECT_ROOT / "data/test/general/fasta_base/false_base_1"),
+        str(PROJECT_ROOT / "data/test/general/fasta_base/false_base_2"),
+        "-a",
+        "FISH",
+        "--PRIMER_PICK_PRIMER",
+        "5",
+        "--PRIMER_NUM_RETURN",
+        "5",
+        "-N",
+        "3",
+        "--visualize",
+        "True",
+        "--AI",
+        "True",
+    ]
+
+    result = subprocess.run(
+        cmd,
+        cwd=PROJECT_ROOT,
+        capture_output=True,
+        text=True,
+    )
+    if result.returncode != 0:
+        pytest.fail(
+            f"pipeline.py exited {result.returncode}\n"
+            f"--- stdout ---\n{result.stdout}\n--- stderr ---\n{result.stderr}"
+        )
+
+    assert (output / "modeling_results.tsv").is_file()
+    assert (output / "output_dedegenerated.fa").is_file()
+    assert (output / "visualizations").is_dir()
+    assert any((output / "visualizations").iterdir())