Merge branch '17-tests-not-running-in-rust' into 'main'

Run all tests in using Rust classes, and refactor the tests in classes

Closes #17

See merge request pydisk/examples/vizitig!12

vizitig/api/main.py

@@ -111,6 +111,7 @@ async def find_with_query(name: str, query: str) -> list[int]:
     except ParseError as E:
         raise QueryError(detail=str(E), status_code=402)
 
+
 @app.get(
     path="/graphs/{name}/find/subseq/{seq}",
     status_code=status.HTTP_200_OK,
@@ -141,7 +142,8 @@ async def find_one_kmer(name: str, seq: str) -> int:
         raise NodeNotFoundException(detail=seq, status_code=404)
     except Exception as E:
         raise HTTPException(
-            status_code=500, detail=f"Error in retrieving sequence. {E}",
+            status_code=500,
+            detail=f"Error in retrieving sequence. {E}",
         )
 
 

vizitig/tests/test_typing.py

 from pytest import mark
 
 from vizitig.types import DNAPython, KmerPython, Nucleotide
+from vizibridge import Kmer, DNA
 
 sequences_and_revcomp = [
     ("ATCGTAGCTGATCG", "CGATCAGCTACGAT"),
@@ -57,74 +58,83 @@ kmer_eq = [
     ("TACA", KmerPython(0, 4), False),
 ]
 
-
-@mark.parametrize("kmer, okmer, is_eq", kmer_eq)
-def test_kmer_eq(kmer: str, okmer: KmerPython, is_eq: bool):
-    assert (KmerPython.from_dna(DNAPython(kmer)) == okmer) == is_eq
-
-
-@mark.parametrize("kmer, nucleotide, rkmer", kmers_add_left)
-def test_kmer_class_add_left(kmer: str, nucleotide: Nucleotide, rkmer: str):
-    K = KmerPython.from_dna(DNAPython(kmer))
-    K.add_left_nucleotid(nucleotide)
-    RK = KmerPython.from_dna(DNAPython(kmer))
-    assert K == RK
-
-
-@mark.parametrize("kmer, nucleotide, rkmer", kmers_add_right)
-def test_kmer_class_add_right(kmer: str, nucleotide: Nucleotide, rkmer: str):
-    K = KmerPython.from_dna(DNAPython(kmer))
-    K.add_right_nucleotid(nucleotide)
-    RK = KmerPython.from_dna(DNAPython(kmer))
-    assert K == RK
-
-
-@mark.parametrize("seq", sequences)
-def test_DNAPython_builder(seq: str):
-    assert str(DNAPython(seq)) == seq
-
-
-@mark.parametrize("seq, rseq", sequences_and_revcomp)
-def test_kmer_class_reverse_complement(seq: str, rseq: str):
-    assert KmerPython.from_dna(
-        DNAPython(seq),
-    ).reverse_complement() == KmerPython.from_dna(DNAPython(rseq))
-
-
-@mark.parametrize("kmer, c_kmer", kmers_and_canonical)
-def test_kmer_class_canonical(kmer: str, c_kmer: str):
-    assert KmerPython.from_dna(DNAPython(kmer)).canonical() == KmerPython.from_dna(
-        DNAPython(c_kmer),
-    )
-
-
-def test_kmer_class_enum_kmer():
-    assert list(DNAPython("ACTG")) == [i for i in "ACTG"]
-
-
-def test_dna_class_enum_canonical_kmer():
-    assert list(DNAPython("ACTG").enum_canonical_kmer(2)) == [
-        KmerPython.from_dna(DNAPython("AC")),
-        KmerPython.from_dna(DNAPython("AG")),
-        KmerPython.from_dna(DNAPython("CA")),
-    ]
-
-
-@mark.parametrize("seq", sequences)
-def test_dna_class_enum_kmer_returns_right_kmer_count(seq: str):
-    for m in range(len(seq)):
-        assert len(list(DNAPython(seq).enum_kmer(m))) + m - 1 == len(seq)
-
-
-@mark.parametrize("seq", sequences)
-def test_dna_class_enum_canonical_kmer_returns_right_kmer_count(seq: str):
-    for m in range(1, len(seq)):
-        assert len(list(DNAPython(seq).enum_canonical_kmer(m))) + m - 1 == len(seq)
-
-
-@mark.parametrize("seq", sequences)
-def test_dna_class_canonicality_of_enum_canonical_kmer(seq: str):
-    for m in range(1, len(seq)):
-        assert all(
-            kmer.is_canonical() for kmer in DNAPython(seq).enum_canonical_kmer(m)
+kmer_types = [(KmerPython, DNAPython), (Kmer, DNA)]
+
+
+class TestKmer:
+    @mark.parametrize("kmer, okmer, is_eq", kmer_eq)
+    def test_kmer_eq(self, kmer: str, okmer: KmerPython, is_eq: bool):
+        assert (KmerPython.from_dna(DNAPython(kmer)) == okmer) == is_eq
+
+    @mark.parametrize("kmer, nucleotide, rkmer", kmers_add_left)
+    @mark.parametrize("Kmer, DNA", kmer_types)
+    def test_kmer_class_add_left(
+        self, kmer: str, nucleotide: Nucleotide, rkmer: str, Kmer, DNA
+    ):
+        K = Kmer.from_dna(DNA(kmer))
+        K.add_left_nucleotid(nucleotide)
+        RK = Kmer.from_dna(DNA(kmer))
+        assert K == RK
+
+    @mark.parametrize("kmer, nucleotide, rkmer", kmers_add_right)
+    @mark.parametrize("Kmer, DNA", kmer_types)
+    def test_kmer_class_add_right(
+        self, kmer: str, nucleotide: Nucleotide, rkmer: str, Kmer, DNA
+    ):
+        K = Kmer.from_dna(DNA(kmer))
+        K.add_right_nucleotid(nucleotide)
+        RK = Kmer.from_dna(DNA(kmer))
+        assert K == RK
+
+    @mark.parametrize("seq, rseq", sequences_and_revcomp)
+    @mark.parametrize("Kmer, DNA", kmer_types)
+    def test_kmer_class_reverse_complement(self, seq: str, rseq: str, Kmer, DNA):
+        assert Kmer.from_dna(
+            DNA(seq),
+        ).reverse_complement() == Kmer.from_dna(DNA(rseq))
+
+    @mark.parametrize("kmer, c_kmer", kmers_and_canonical)
+    @mark.parametrize("Kmer, DNA", kmer_types)
+    def test_kmer_class_canonical(self, kmer: str, c_kmer: str, Kmer, DNA):
+        assert Kmer.from_dna(DNA(kmer)).canonical() == Kmer.from_dna(
+            DNA(c_kmer),
         )
+
+    @mark.parametrize("Kmer, DNA", kmer_types)
+    def test_kmer_class_enum_kmer(self, Kmer, DNA):
+        assert list(DNA("ACTG")) == [i for i in "ACTG"]
+
+
+class TestDNA:
+    @mark.parametrize("seq", sequences)
+    @mark.parametrize("Kmer, DNA", kmer_types)
+    def test_DNAPython_builder(self, seq: str, Kmer, DNA):
+        assert str(DNA(seq)) == seq
+
+    @mark.parametrize("Kmer, DNA", kmer_types)
+    def test_dna_class_enum_canonical_kmer(self, Kmer, DNA):
+        assert list(DNA("ACTG").enum_canonical_kmer(2)) == [
+            Kmer.from_dna(DNA("AC")),
+            Kmer.from_dna(DNA("AG")),
+            Kmer.from_dna(DNA("CA")),
+        ]
+
+    @mark.parametrize("seq", sequences)
+    @mark.parametrize("Kmer, DNA", kmer_types)
+    def test_dna_class_enum_kmer_returns_right_kmer_count(self, seq: str, Kmer, DNA):
+        for m in range(1, len(seq)):
+            assert len(list(DNA(seq).enum_kmer(m))) + m - 1 == len(seq)
+
+    @mark.parametrize("seq", sequences)
+    @mark.parametrize("Kmer, DNA", kmer_types)
+    def test_dna_class_enum_canonical_kmer_returns_right_kmer_count(
+        self, seq: str, Kmer, DNA
+    ):
+        for m in range(1, len(seq)):
+            assert len(list(DNA(seq).enum_canonical_kmer(m))) + m - 1 == len(seq)
+
+    @mark.parametrize("seq", sequences)
+    @mark.parametrize("Kmer, DNA", kmer_types)
+    def test_dna_class_canonicality_of_enum_canonical_kmer(self, seq: str, Kmer, DNA):
+        for m in range(1, len(seq)):
+            assert all(kmer.is_canonical() for kmer in DNA(seq).enum_canonical_kmer(m))