Add --keep-invalid Flag for LCA

environment.yaml

@@ -10,5 +10,5 @@ dependencies:
  - pytest>=5.4
  - pytest-cov>=2.8
  - pytest-xdist>=1.31
- - taxonkit>=0.8
+ - taxonkit>=0.16.0
  - wget>=1.20

pytaxonkit.py

@@ -1046,6 +1046,7 @@ def lca(
     multi=False,
     skip_deleted=False,
     skip_unfound=False,
+    keep_invalid=False,
     threads=None,
     data_dir=None,
     debug=False,
@@ -1063,6 +1064,8 @@ def lca(
         Ignore deleted taxids and compute LCA with the remaining taxa
     skip_unfound : bool, default False
         Ignore taxids not found in the taxonomy database and compute LCA with the remaining taxa
+    keep_invalid: bool, default False
+        Returns 0 when all taxids have been skipped from `skip_deleted` or `skip_unfound`
     threads : int
         Override the default taxonkit threads setting
     data_dir : str, default None
@@ -1096,6 +1099,8 @@ def lca(
         arglist.append("--skip-deleted")
     if skip_unfound:
         arglist.append("--skip-unfound")
+    if keep_invalid:
+        arglist.append("--keep-invalid")
     if threads:
         arglist.extend(("--threads", validate_threads(threads)))
     if data_dir:
@@ -1134,6 +1139,15 @@ def test_lca_unfound(capsys):
     assert "taxonkit lca --skip-unfound" in terminal.err
 
 
+def test_lca_keep_invalid(capsys):
+    assert lca([11111111], skip_deleted=True, skip_unfound=True) == None
+    assert lca([22222222], skip_deleted=True, skip_unfound=True) == None
+    assert lca([11111111], skip_deleted=True, skip_unfound=True, keep_invalid=True) == 0
+    assert lca([11111111, 22222222], skip_deleted=True, skip_unfound=True, keep_invalid=True, debug=True) == 0
+    terminal = capsys.readouterr()
+    assert "taxonkit lca --skip-deleted --skip-unfound --keep-invalid" in terminal.err
+
+
 @pytest.mark.parametrize(
     "domulti, ids,result",
     [