refactor: extract CLI argv normalization

Author: 1613358894

tests/test_cli_config.py

@@ -0,0 +1,81 @@
+from __future__ import annotations
+
+import pytest
+
+from typetreeflow import cli
+from typetreeflow.cli_config import _normalize_command_argv as config_normalize_argv
+
+
+def test_cli_normalize_command_argv_compatibility_export():
+    assert cli._normalize_command_argv is config_normalize_argv
+
+
+def test_normalize_command_aliases_preserves_existing_rewrites():
+    assert config_normalize_argv(["doctor", "--strict"]) == (
+        ["--doctor", "--doctor-strict"],
+        False,
+        False,
+    )
+    assert config_normalize_argv(["status", "--outdir", "out"]) == (
+        ["--status", "--outdir", "out"],
+        False,
+        False,
+    )
+    assert config_normalize_argv(["next-step", "--json"]) == (
+        ["--next-step", "--json"],
+        False,
+        False,
+    )
+    assert config_normalize_argv(["package-results", "--include", "reports"]) == (
+        ["--package-results", "--include", "reports"],
+        False,
+        True,
+    )
+
+
+def test_normalize_verify_genus_aliases_policy_and_biosample_entrez():
+    assert config_normalize_argv(
+        [
+            "verify-genus",
+            "Fusobacterium",
+            "--policy",
+            "balanced",
+            "--enable-biosample-entrez",
+        ]
+    ) == (
+        [
+            "--acquire-genus",
+            "Fusobacterium",
+            "--dry-run",
+            "--selection-policy",
+            "balanced",
+            "--enrich-biosample",
+            "--enable-biosample-entrez",
+        ],
+        True,
+        False,
+    )
+
+
+def test_parse_args_handles_doctor_version_and_common_flags(tmp_path):
+    doctor_config = cli.parse_args(["doctor", "--strict", "--outdir", str(tmp_path)])
+    assert doctor_config.doctor is True
+    assert doctor_config.doctor_strict is True
+
+    with pytest.raises(SystemExit) as excinfo:
+        cli.parse_args(["--version"])
+    assert excinfo.value.code == 0
+
+    config = cli.parse_args(
+        [
+            "verify-genus",
+            "Aliivibrio",
+            "--policy=balanced",
+            "--outdir",
+            str(tmp_path / "verify"),
+        ]
+    )
+    assert config.verify_genus is True
+    assert config.acquire_genus == "Aliivibrio"
+    assert config.dry_run is True
+    assert config.selection_policy == "balanced"

typetreeflow/cli.py

@@ -16,8 +16,9 @@
     write_completion_summary,
 )
 from typetreeflow.completion_gaps import generate_completion_gap_reports
-from typetreeflow.config import AppConfig, ensure_real_action_allowed
+from typetreeflow.cli_config import _normalize_command_argv
 from typetreeflow.cli_parser import build_parser
+from typetreeflow.config import AppConfig, ensure_real_action_allowed
 from typetreeflow.delivery import package_results
 from typetreeflow.diagnostics import (
     build_doctor_report,
@@ -316,66 +317,6 @@ def parse_args(argv: list[str] | None = None) -> AppConfig:
     )
 
 
-def _normalize_command_argv(
-    argv: list[str] | None,
-) -> tuple[list[str] | None, bool, bool]:
-    raw_argv = list(sys.argv[1:] if argv is None else argv)
-    if raw_argv and raw_argv[0] == "doctor":
-        normalized = ["--doctor"]
-        for item in raw_argv[1:]:
-            if item == "--strict":
-                normalized.append("--doctor-strict")
-            else:
-                normalized.append(item)
-        return normalized, False, False
-    if raw_argv and raw_argv[0] == "status":
-        return ["--status", *raw_argv[1:]], False, False
-    if raw_argv and raw_argv[0] == "next-step":
-        return ["--next-step", *raw_argv[1:]], False, False
-    if raw_argv and raw_argv[0] == "package-results":
-        return ["--package-results", *raw_argv[1:]], False, True
-    if raw_argv and raw_argv[0] == "verify-release-genus":
-        if len(raw_argv) >= 2 and raw_argv[1] in {"-h", "--help"}:
-            return ["--help"], False, False
-        if len(raw_argv) < 2 or raw_argv[1].startswith("-"):
-            raise ValueError("verify-release-genus requires a GENUS argument.")
-        return ["--verify-release-genus", raw_argv[1], *raw_argv[2:]], False, False
-    if not raw_argv or raw_argv[0] != "verify-genus":
-        return argv, False, False
-    if len(raw_argv) >= 2 and raw_argv[1] in {"-h", "--help"}:
-        return ["--help"], False, False
-    if len(raw_argv) < 2 or raw_argv[1].startswith("-"):
-        raise ValueError("verify-genus requires a GENUS argument.")
-
-    genus = raw_argv[1]
-    normalized = ["--acquire-genus", genus, "--dry-run"]
-    remaining = raw_argv[2:]
-    index = 0
-    while index < len(remaining):
-        item = remaining[index]
-        if item == "--policy":
-            normalized.append("--selection-policy")
-            if index + 1 >= len(remaining):
-                raise ValueError(
-                    "--policy requires one of: strict, balanced, review-only, "
-                    "representative."
-                )
-            normalized.append(remaining[index + 1])
-            index += 2
-            continue
-        if item.startswith("--policy="):
-            normalized.append("--selection-policy=" + item.split("=", 1)[1])
-            index += 1
-            continue
-        if item == "--enable-biosample-entrez":
-            normalized.extend(["--enrich-biosample", item])
-            index += 1
-            continue
-        normalized.append(item)
-        index += 1
-    return normalized, True, False
-
-
 def _env_value(name: str) -> str | None:
     value = os.environ.get(name)
     if value is None:

typetreeflow/cli_config.py

@@ -0,0 +1,63 @@
+from __future__ import annotations
+
+import sys
+
+
+def _normalize_command_argv(
+    argv: list[str] | None,
+) -> tuple[list[str] | None, bool, bool]:
+    raw_argv = list(sys.argv[1:] if argv is None else argv)
+    if raw_argv and raw_argv[0] == "doctor":
+        normalized = ["--doctor"]
+        for item in raw_argv[1:]:
+            if item == "--strict":
+                normalized.append("--doctor-strict")
+            else:
+                normalized.append(item)
+        return normalized, False, False
+    if raw_argv and raw_argv[0] == "status":
+        return ["--status", *raw_argv[1:]], False, False
+    if raw_argv and raw_argv[0] == "next-step":
+        return ["--next-step", *raw_argv[1:]], False, False
+    if raw_argv and raw_argv[0] == "package-results":
+        return ["--package-results", *raw_argv[1:]], False, True
+    if raw_argv and raw_argv[0] == "verify-release-genus":
+        if len(raw_argv) >= 2 and raw_argv[1] in {"-h", "--help"}:
+            return ["--help"], False, False
+        if len(raw_argv) < 2 or raw_argv[1].startswith("-"):
+            raise ValueError("verify-release-genus requires a GENUS argument.")
+        return ["--verify-release-genus", raw_argv[1], *raw_argv[2:]], False, False
+    if not raw_argv or raw_argv[0] != "verify-genus":
+        return argv, False, False
+    if len(raw_argv) >= 2 and raw_argv[1] in {"-h", "--help"}:
+        return ["--help"], False, False
+    if len(raw_argv) < 2 or raw_argv[1].startswith("-"):
+        raise ValueError("verify-genus requires a GENUS argument.")
+
+    genus = raw_argv[1]
+    normalized = ["--acquire-genus", genus, "--dry-run"]
+    remaining = raw_argv[2:]
+    index = 0
+    while index < len(remaining):
+        item = remaining[index]
+        if item == "--policy":
+            normalized.append("--selection-policy")
+            if index + 1 >= len(remaining):
+                raise ValueError(
+                    "--policy requires one of: strict, balanced, review-only, "
+                    "representative."
+                )
+            normalized.append(remaining[index + 1])
+            index += 2
+            continue
+        if item.startswith("--policy="):
+            normalized.append("--selection-policy=" + item.split("=", 1)[1])
+            index += 1
+            continue
+        if item == "--enable-biosample-entrez":
+            normalized.extend(["--enrich-biosample", item])
+            index += 1
+            continue
+        normalized.append(item)
+        index += 1
+    return normalized, True, False