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Add __iter__ to TaxonomyIterator to satisfy Python iterator protocol #79

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Merged
audy merged 1 commit into from
Apr 13, 2026
+17 −3
Merged

Add __iter__ to TaxonomyIterator to satisfy Python iterator protocol #79

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4 changes: 4 additions & 0 deletions src/python.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -576,6 +576,10 @@ pub struct TaxonomyIterator {

#[pymethods]
impl TaxonomyIterator {
fn __iter__(slf: PyRef<Self>) -> PyRef<Self> {
slf
}

fn __next__(mut slf: PyRefMut<Self>, py: Python<'_>) -> PyResult<Option<String>> {
let traverse_preorder = true;
loop {
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16 changes: 13 additions & 3 deletions test_python.py
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Expand Up @@ -150,8 +150,16 @@ def test_json_internal_index(json_tax: Taxonomy):
] == [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]


def test_taxonomy_iterator_is_iterable(newick_tax):
it = iter(newick_tax)
assert iter(it) is it


def test_json_find_all_by_name(json_tax: Taxonomy):
assert sorted([n.id for n in json_tax.find_all_by_name("species 1.1")]) == ["10", "12"]
assert sorted([n.id for n in json_tax.find_all_by_name("species 1.1")]) == [
"10",
"12",
]


def test_json_edit_node_parent_updates_children(json_tax: Taxonomy):
Expand Down Expand Up @@ -475,7 +483,8 @@ def test_ncbi_edit_node_parent():
def test_ncbi_repr():
tax = Taxonomy.from_ncbi("tests/data/")
assert (
tax["562"].__repr__() == '<TaxonomyNode (id="562" rank="species" name="Escherichia coli")>'
tax["562"].__repr__()
== '<TaxonomyNode (id="562" rank="species" name="Escherichia coli")>'
)


Expand Down Expand Up @@ -511,7 +520,8 @@ def test_gtdb_invalid_format():


@pytest.mark.skipif(
not os.getenv("TAXONOMY_TEST_NCBI"), reason="Define TAXONOMY_TEST_NCBI to run NCBI test"
not os.getenv("TAXONOMY_TEST_NCBI"),
reason="Define TAXONOMY_TEST_NCBI to run NCBI test",
)
def test_latestncbi_load_latest_ncbi_taxonomy():
download("https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz")
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