DOC: add typing to tests and reformat fixtures

pyproject.toml

@@ -106,11 +106,11 @@ dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 "tests/**/*.py" = [
     "S101", # asserts allowed in tests...
     "INP001", # __init__.py files are not required...
-    "ANN",
-    "N802",
-    "N803",
-    "SLF001",
-    "D"
+    "N802", # allow non snake_case function names for fixtures
+    "N803", # allow use of fixture constants
+    "SLF001", # private member access is useufl for testing
+    "FBT001", # allow bool pos args for parameterisation
+    "D", # don't require docstrings
 ]
 "noxfile.py" = [
     "S101", # asserts allowed in tests...

tests/conftest.py

@@ -1,8 +1,23 @@
 import pathlib
 
 import pytest
+from cogent3 import ArrayAlignment, load_aligned_seqs
 
 
 @pytest.fixture(scope="session")
-def DATA_DIR():
+def DATA_DIR() -> pathlib.Path:
     return pathlib.Path(__file__).parent / "data"
+
+
+@pytest.fixture()
+def three_otu(DATA_DIR: pathlib.Path) -> ArrayAlignment:
+    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
+    aln = aln.take_seqs(["Human", "Rhesus", "Mouse"])
+    return aln.omit_gap_pos(allowed_gap_frac=0)
+
+
+@pytest.fixture()
+def four_otu(DATA_DIR: pathlib.Path) -> ArrayAlignment:
+    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
+    aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Mouse"])
+    return aln.omit_gap_pos(allowed_gap_frac=0)

tests/test_app/test_app.py

@@ -1,33 +1,17 @@
-from pathlib import Path
-
 import piqtree2
 import pytest
-from cogent3 import ArrayAlignment, get_app, load_aligned_seqs, make_tree
+from cogent3 import ArrayAlignment, get_app, make_tree
 from piqtree2.model import DnaModel, Model
 
 
-@pytest.fixture()
-def three_otu(DATA_DIR: Path) -> ArrayAlignment:
-    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
-    aln = aln.take_seqs(["Human", "Rhesus", "Mouse"])
-    return aln.omit_gap_pos(allowed_gap_frac=0)
-
-
-@pytest.fixture()
-def four_otu(DATA_DIR: Path) -> ArrayAlignment:
-    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
-    aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Mouse"])
-    return aln.omit_gap_pos(allowed_gap_frac=0)
-
-
-def test_piqtree_phylo(four_otu: ArrayAlignment):
+def test_piqtree_phylo(four_otu: ArrayAlignment) -> None:
     expected = make_tree("(Human,Chimpanzee,(Rhesus,Mouse));")
     app = get_app("piqtree_phylo", model=Model(DnaModel.JC))
     got = app(four_otu)
     assert expected.same_topology(got)
 
 
-def test_piqtree_fit(three_otu: ArrayAlignment):
+def test_piqtree_fit(three_otu: ArrayAlignment) -> None:
     tree = make_tree(tip_names=three_otu.names)
     app = get_app("model", "JC69", tree=tree)
     expected = app(three_otu)
@@ -43,7 +27,7 @@ def test_piqtree_random_trees(
     num_taxa: int,
     tree_mode: piqtree2.TreeGenMode,
     num_trees: int,
-):
+) -> None:
     trees = piqtree2.random_trees(
         num_taxa,
         tree_mode,

tests/test_app/test_pickle.py

@@ -6,6 +6,6 @@
 from piqtree2._app import _ALL_APP_NAMES
 
 
-def test_pickle():
+def test_pickle() -> None:
     for app_name in _ALL_APP_NAMES:
         assert len(pickle.dumps(get_app(app_name))) > 0

tests/test_iqtree/test_build_tree.py

@@ -1,30 +1,26 @@
+from typing import Optional
+
 import piqtree2
 import pytest
-from cogent3 import load_aligned_seqs, make_tree
+from cogent3 import ArrayAlignment, make_tree
 from piqtree2.model import (
     DiscreteGammaModel,
     DnaModel,
     FreeRateModel,
     FreqType,
     Model,
+    RateModel,
     RateType,
 )
 
 
-@pytest.fixture()
-def four_otu(DATA_DIR):
-    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
-    aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Mouse"])
-    return aln.omit_gap_pos(allowed_gap_frac=0)
-
-
 def check_build_tree(
-    four_otu,
-    dna_model,
-    freq_type=None,
-    invariable_sites=None,
-    rate_model=None,
-):
+    four_otu: ArrayAlignment,
+    dna_model: DnaModel,
+    freq_type: Optional[FreqType] = None,
+    invariable_sites: Optional[bool] = None,
+    rate_model: Optional[RateModel] = None,
+) -> None:
     expected = make_tree("(Human,Chimpanzee,(Rhesus,Mouse));")
 
     model = Model(
@@ -46,15 +42,15 @@ def check_build_tree(
 @pytest.mark.parametrize("dna_model", list(DnaModel)[:22])
 @pytest.mark.parametrize("freq_type", list(FreqType))
 def test_non_lie_build_tree(
-    four_otu,
-    dna_model,
-    freq_type,
-):
+    four_otu: ArrayAlignment,
+    dna_model: DnaModel,
+    freq_type: FreqType,
+) -> None:
     check_build_tree(four_otu, dna_model, freq_type)
 
 
 @pytest.mark.parametrize("dna_model", list(DnaModel)[22:])
-def test_lie_build_tree(four_otu, dna_model):
+def test_lie_build_tree(four_otu: ArrayAlignment, dna_model: DnaModel) -> None:
     check_build_tree(four_otu, dna_model)
 
 
@@ -70,7 +66,12 @@ def test_lie_build_tree(four_otu, dna_model):
         FreeRateModel(6),
     ],
 )
-def test_rate_model_build_tree(four_otu, dna_model, invariable_sites, rate_model):
+def test_rate_model_build_tree(
+    four_otu: ArrayAlignment,
+    dna_model: DnaModel,
+    invariable_sites: Optional[bool],
+    rate_model: RateModel,
+) -> None:
     check_build_tree(
         four_otu,
         dna_model,

tests/test_iqtree/test_fit_tree.py

@@ -1,16 +1,9 @@
 import piqtree2
 import pytest
-from cogent3 import get_app, load_aligned_seqs, make_tree
+from cogent3 import ArrayAlignment, get_app, make_tree
 from piqtree2.model import DnaModel, Model
 
 
-@pytest.fixture()
-def three_otu(DATA_DIR):
-    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
-    aln = aln.take_seqs(["Human", "Rhesus", "Mouse"])
-    return aln.omit_gap_pos(allowed_gap_frac=0)
-
-
 @pytest.mark.parametrize(
     ("iq_model", "c3_model"),
     [
@@ -22,7 +15,7 @@ def three_otu(DATA_DIR):
         (DnaModel.F81, "F81"),
     ],
 )
-def test_fit_tree(three_otu, iq_model, c3_model):
+def test_fit_tree(three_otu: ArrayAlignment, iq_model: DnaModel, c3_model: str) -> None:
     tree_topology = make_tree(tip_names=three_otu.names)
     app = get_app("model", c3_model, tree=tree_topology)
     expected = app(three_otu)

tests/test_iqtree/test_robinson_foulds.py

@@ -3,7 +3,7 @@
 from numpy.testing import assert_array_equal
 
 
-def test_robinson_foulds():
+def test_robinson_foulds() -> None:
     tree1 = "(A,B,(C,D));"
     tree2 = "(A,C,(B,D));"
     pairwise_distances = piqtree2.robinson_foulds(tree1, tree2)

tests/test_iqtree/test_segmentation_fault.py

@@ -4,10 +4,10 @@
 from cogent3 import make_aligned_seqs, make_tree
 from piqtree2 import TreeGenMode, build_tree, fit_tree, random_trees
 from piqtree2.exceptions import IqTreeError
-from piqtree2.model import DiscreteGammaModel, DnaModel, FreeRateModel, Model
+from piqtree2.model import DiscreteGammaModel, DnaModel, FreeRateModel, Model, RateModel
 
 
-def test_two_build_random_trees():
+def test_two_build_random_trees() -> None:
     """
     Calling build tree twice followed by random trees with a bad input
     used to result in a Segmentation Fault in a previous version.
@@ -21,7 +21,7 @@ def test_two_build_random_trees():
         random_trees(2, TreeGenMode.BALANCED, 3, 1)
 
 
-def test_two_fit_random_trees():
+def test_two_fit_random_trees() -> None:
     """
     Calling fit tree twice followed by random trees with a bad input
     used to result in a Segmentation Fault in a previous version.
@@ -36,17 +36,17 @@ def test_two_fit_random_trees():
         random_trees(2, TreeGenMode.BALANCED, 3, 1)
 
 
-@pytest.mark.parametrize("rate_type_class", [DiscreteGammaModel, FreeRateModel])
+@pytest.mark.parametrize("rate_model_class", [DiscreteGammaModel, FreeRateModel])
 @pytest.mark.parametrize("categories", [0, -4])
-def test_two_invalid_models(rate_type_class, categories):
+def test_two_invalid_models(rate_model_class: type[RateModel], categories: int) -> None:
     """
     Calling build_tree multiple times with an invalid
     model has resulted in a Segmentation Fault.
     """
     aln = make_aligned_seqs({"a": "GGG", "b": "GGC", "c": "AAC", "d": "AAA"})
 
     with pytest.raises(IqTreeError):
-        _ = build_tree(aln, Model(DnaModel.JC, rate_type=rate_type_class(categories)))
+        _ = build_tree(aln, Model(DnaModel.JC, rate_type=rate_model_class(categories)))
 
     with pytest.raises(IqTreeError):
-        _ = build_tree(aln, Model(DnaModel.JC, rate_type=rate_type_class(categories)))
+        _ = build_tree(aln, Model(DnaModel.JC, rate_type=rate_model_class(categories)))

tests/test_iqtree/test_tree_yaml.py

@@ -1,10 +1,12 @@
+from typing import Any
+
 import pytest
 from piqtree2.exceptions import ParseIqTreeError
 from piqtree2.iqtree._tree import _process_tree_yaml
 
 
 @pytest.fixture()
-def newick_not_in_candidates():
+def newick_not_in_candidates() -> dict[str, Any]:
     # The newick string does not appear in the CandidateSet
     return {
         "CandidateSet": {
@@ -36,6 +38,6 @@ def newick_not_in_candidates():
     }
 
 
-def test_newick_not_in_candidates(newick_not_in_candidates):
+def test_newick_not_in_candidates(newick_not_in_candidates: dict[str, Any]) -> None:
     with pytest.raises(ParseIqTreeError):
         _ = _process_tree_yaml(newick_not_in_candidates, ["a", "b", "c"])

tests/test_model/test_freq_type.py

@@ -1,11 +1,11 @@
 from piqtree2.model import FreqType
 
 
-def test_number_of_descriptions():
+def test_number_of_descriptions() -> None:
     assert len(FreqType) == len(FreqType._descriptions())
 
 
-def test_descriptions_exist():
+def test_descriptions_exist() -> None:
     for freq_type in FreqType:
         # Raises an error if description not present
         _ = freq_type.description

tests/test_model/test_options.py

@@ -1,15 +1,20 @@
 # testing the display of functions
+from typing import Optional
+
 import pytest
 from piqtree2 import available_freq_type, available_models, available_rate_type
-from piqtree2.model import AaModel, DnaModel, FreqType
+from piqtree2.model import AaModel, DnaModel, FreqType, SubstitutionModel
 from piqtree2.model._rate_type import ALL_BASE_RATE_TYPES
 
 
 @pytest.mark.parametrize(
     ("model_class", "model_type"),
     [(None, None), (DnaModel, "dna"), (AaModel, "protein")],
 )
-def test_num_available_models(model_class, model_type):
+def test_num_available_models(
+    model_class: Optional[SubstitutionModel],
+    model_type: Optional[str],
+) -> None:
     table = available_models(model_type)
     total_models = (
         len(DnaModel) + len(AaModel) if model_class is None else len(model_class)
@@ -22,7 +27,10 @@ def test_num_available_models(model_class, model_type):
     ("model_fetch", "model_type"),
     [(None, None), ("dna", "nucleotide"), ("protein", "protein")],
 )
-def test_available_models_types(model_fetch, model_type):
+def test_available_models_types(
+    model_fetch: Optional[str],
+    model_type: Optional[str],
+) -> None:
     table = available_models(model_fetch)
 
     if model_type is None:
@@ -33,15 +41,15 @@ def test_available_models_types(model_fetch, model_type):
             assert check_model_type[0] == model_type
 
 
-def test_num_freq_type():
+def test_num_freq_type() -> None:
     table = available_freq_type()
     total_freq_types = len(FreqType)
 
     assert total_freq_types > 0
     assert table.shape[0] == total_freq_types
 
 
-def test_num_rate_type():
+def test_num_rate_type() -> None:
     table = available_rate_type()
     total_rate_types = len(ALL_BASE_RATE_TYPES)
 

tests/test_model/test_rate_type.py

@@ -1,8 +1,10 @@
+from typing import Optional
+
 import pytest
 from piqtree2.model import DiscreteGammaModel, FreeRateModel, RateModel, RateType
 
 
-def test_rate_model_uninstantiable():
+def test_rate_model_uninstantiable() -> None:
     with pytest.raises(TypeError):
         _ = RateModel()
 
@@ -27,10 +29,10 @@ def test_rate_model_uninstantiable():
     ],
 )
 def test_invariable_sites(
-    invariable_sites,
-    rate_model,
-    iqtree_str,
-):
+    invariable_sites: bool,
+    rate_model: Optional[RateModel],
+    iqtree_str: str,
+) -> None:
     model = RateType(invariable_sites=invariable_sites, model=rate_model)
     assert model.iqtree_str() == iqtree_str