Respect solver configuration precedence

src/optitype/cli.py

@@ -89,7 +89,6 @@ def main():
 @click.option(
     "--solver",
     type=click.Choice(["glpk", "cbc", "cplex"]),
-    default="glpk",
     envvar="OPTITYPE_SOLVER",
     help="ILP solver to use. Default: glpk.",
 )
@@ -189,7 +188,8 @@ def run(
     pipeline_config.razers3_args = razers3_args
     pipeline_config.yara_args = yara_args
     pipeline_config.mapping_threads = threads
-    pipeline_config.solver = solver
+    if solver is not None:
+        pipeline_config.solver = solver
     pipeline_config.ilp_threads = ilp_threads
     pipeline_config.delete_bam = not keep_bam
 
@@ -200,7 +200,7 @@ def run(
         click.echo(f"Sequence type: {seq_type}")
         click.echo(f"Output directory: {outdir}")
         click.echo(f"Mapper: {mapper}")
-        click.echo(f"Solver: {solver}")
+        click.echo(f"Solver: {pipeline_config.solver}")
         click.echo()
 
     try:

tests/test_cli.py

@@ -1,7 +1,7 @@
 """Tests for CLI interface."""
 
 from pathlib import Path
-from unittest.mock import patch
+from unittest.mock import MagicMock, patch
 
 from click.testing import CliRunner
 
@@ -33,6 +33,43 @@ def test_cli_run_help():
         assert expected in result.output
 
 
+def test_cli_solver_precedence(tmp_path):
+    """CLI/env solver values override config, which overrides the built-in default."""
+    config_file = tmp_path / "config.ini"
+    config_file.write_text("[ilp]\nsolver=cbc\n")
+    cases = [
+        ("config", ["-c", str(config_file)], None, "cbc"),
+        ("command-line", ["-c", str(config_file), "--solver", "glpk"], None, "glpk"),
+        ("cli-over-env", ["-c", str(config_file), "--solver", "glpk"], "cplex", "glpk"),
+        ("environment", ["-c", str(config_file)], "cplex", "cplex"),
+        ("default", [], None, "glpk"),
+    ]
+
+    runner = CliRunner()
+    pipeline_result = MagicMock(output_csv="result.tsv", output_plot="coverage.pdf")
+    pipeline_result.result_4digit.iloc.__getitem__.return_value = {"nof_reads": 0, "obj": 0}
+    for name, extra_args, env_solver, expected in cases:
+        args = [
+            "run",
+            "-i",
+            str(Path(__file__)),
+            "--dna",
+            "-o",
+            str(tmp_path / name),
+            "-v",
+            *extra_args,
+        ]
+        with (
+            patch("optitype.cli.shutil.which", return_value=None),
+            patch("optitype.pipeline.run_pipeline", return_value=pipeline_result) as run_pipeline,
+        ):
+            result = runner.invoke(main, args, env={"OPTITYPE_SOLVER": env_solver})
+
+        assert result.exit_code == 0, result.output
+        assert run_pipeline.call_args.kwargs["config"].solver == expected
+        assert f"Solver: {expected}" in result.output
+
+
 def test_cli_check_deps():
     """Test that check-deps command works."""
     runner = CliRunner()