tests: increase pytest coverage

tests/primer3/test_primer3_input.py

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+import pytest
+
+from prymer.api import Span
+from prymer.api import Strand
+from prymer.api.minoptmax import MinOptMax
+from prymer.primer3 import DesignLeftPrimersTask
+from prymer.primer3 import DesignPrimerPairsTask
+from prymer.primer3 import DesignRightPrimersTask
+from prymer.primer3 import Primer3Input
+from prymer.primer3.primer3_input_tag import Primer3InputTag
+from prymer.primer3.primer3_parameters import PrimerAndAmpliconParameters
+from prymer.primer3.primer3_parameters import ProbeParameters
+from prymer.primer3.primer3_task import PickHybProbeOnly
+from prymer.primer3.primer3_task import Primer3TaskType
+from prymer.primer3.primer3_weights import PrimerAndAmpliconWeights
+from prymer.primer3.primer3_weights import ProbeWeights
+
+
+@pytest.fixture
+def valid_primer_amplicon_params() -> PrimerAndAmpliconParameters:
+    return PrimerAndAmpliconParameters(
+        amplicon_sizes=MinOptMax(min=200, opt=250, max=300),
+        amplicon_tms=MinOptMax(min=55.0, opt=60.0, max=65.0),
+        primer_sizes=MinOptMax(min=18, opt=21, max=27),
+        primer_tms=MinOptMax(min=55.0, opt=60.0, max=65.0),
+        primer_gcs=MinOptMax(min=45.0, opt=55.0, max=60.0),
+    )
+
+
+@pytest.fixture
+def valid_probe_params() -> ProbeParameters:
+    return ProbeParameters(
+        probe_sizes=MinOptMax(min=18, opt=22, max=30),
+        probe_tms=MinOptMax(min=65.0, opt=70.0, max=75.0),
+        probe_gcs=MinOptMax(min=45.0, opt=55.0, max=60.0),
+    )
+
+
+@pytest.fixture
+def valid_primer_weights() -> PrimerAndAmpliconWeights:
+    return PrimerAndAmpliconWeights()
+
+
+@pytest.fixture
+def valid_probe_weights() -> ProbeWeights:
+    return ProbeWeights(probe_wt_hairpin_th=100.0)
+
+
+@pytest.mark.parametrize(
+    "task_type",
+    [
+        DesignRightPrimersTask(),
+        DesignLeftPrimersTask(),
+        DesignPrimerPairsTask(),
+    ],
+)
+def test_primer_design_only_valid(
+    valid_primer_amplicon_params: PrimerAndAmpliconParameters,
+    task_type: Primer3TaskType,
+    valid_primer_weights: PrimerAndAmpliconWeights,
+) -> None:
+    test_design_region = Span(refname="chr1", start=1, end=500, strand=Strand.POSITIVE)
+    test_target = Span(refname="chr1", start=200, end=300, strand=Strand.POSITIVE)
+    test_input = Primer3Input(
+        target=test_target,
+        primer_weights=valid_primer_weights,
+        task=task_type,
+        primer_and_amplicon_params=valid_primer_amplicon_params,
+    )
+    mapped_dict = test_input.to_input_tags(design_region=test_design_region)
+    assert len(mapped_dict.keys()) == 46
+
+
+@pytest.mark.parametrize(
+    "task_type", [DesignRightPrimersTask(), DesignLeftPrimersTask(), DesignPrimerPairsTask()]
+)
+def test_primer_design_only_raises(
+    task_type: Primer3TaskType, valid_primer_weights: PrimerAndAmpliconWeights
+) -> None:
+    test_target = Span(refname="chr1", start=200, end=300, strand=Strand.POSITIVE)
+    with pytest.raises(ValueError, match="Primer3 requires at least one set of parameters"):
+        Primer3Input(
+            target=test_target,
+            primer_weights=valid_primer_weights,
+            task=task_type,
+            primer_and_amplicon_params=None,
+        )
+
+
+def test_probe_design_only_valid(
+    valid_probe_params: ProbeParameters, valid_probe_weights: ProbeWeights
+) -> None:
+    test_design_region = Span(refname="chr1", start=1, end=500, strand=Strand.POSITIVE)
+    test_target = Span(refname="chr1", start=200, end=300, strand=Strand.POSITIVE)
+    test_input = Primer3Input(
+        target=test_target,
+        probe_weights=valid_probe_weights,
+        task=PickHybProbeOnly(),
+        probe_params=valid_probe_params,
+        primer_and_amplicon_params=None,
+    )
+    mapped_dict = test_input.to_input_tags(design_region=test_design_region)
+    assert mapped_dict[Primer3InputTag.PRIMER_PICK_INTERNAL_OLIGO] == 1
+    assert mapped_dict[Primer3InputTag.PRIMER_INTERNAL_WT_HAIRPIN_TH] == 100.0
+
+    assert len(mapped_dict.keys()) == 29
+
+    # test instantiation of default `ProbeWeights` when they are not provided
+    altered_input = Primer3Input(
+        target=test_target,
+        probe_weights=None,
+        task=PickHybProbeOnly(),
+        probe_params=valid_probe_params,
+        primer_and_amplicon_params=None,
+    )
+    altered_mapped_dict = altered_input.to_input_tags(design_region=test_target)
+    assert altered_mapped_dict[Primer3InputTag.PRIMER_INTERNAL_WT_HAIRPIN_TH] == 1.0
+
+
+def test_probe_design_only_raises(valid_probe_weights: ProbeWeights) -> None:
+    test_target = Span(refname="chr1", start=200, end=300, strand=Strand.POSITIVE)
+    with pytest.raises(ValueError, match="Primer3 requires at least one set"):
+        Primer3Input(
+            target=test_target,
+            probe_weights=valid_probe_weights,
+            task=PickHybProbeOnly(),
+            primer_and_amplicon_params=None,
+        )
+
+
+@pytest.mark.parametrize(
+    "task_type",
+    [
+        DesignRightPrimersTask(),
+        DesignLeftPrimersTask(),
+        DesignPrimerPairsTask(),
+        PickHybProbeOnly(),
+    ],
+)
+def test_no_params_given_raises(
+    valid_primer_weights: PrimerAndAmpliconWeights, task_type: Primer3TaskType
+) -> None:
+    test_target = Span(refname="chr1", start=200, end=300, strand=Strand.POSITIVE)
+    with pytest.raises(ValueError, match="Primer3 requires at least one set"):
+        Primer3Input(
+            target=test_target,
+            primer_weights=valid_primer_weights,
+            task=task_type,
+            primer_and_amplicon_params=None,
+            probe_params=None,
+        )
+
+
+@pytest.mark.parametrize(
+    "task_type, expected_req_primer_amplicon_params, expected_req_probe_params",
+    [
+        (DesignPrimerPairsTask(), True, False),
+        (DesignRightPrimersTask(), True, False),
+        (DesignLeftPrimersTask(), True, False),
+        (PickHybProbeOnly(), False, True),
+    ],
+)
+def test_requires_params_sets(
+    task_type: Primer3TaskType,
+    valid_probe_params: ProbeParameters,
+    valid_primer_amplicon_params: PrimerAndAmpliconParameters,
+    valid_primer_weights: PrimerAndAmpliconWeights,
+    valid_probe_weights: ProbeWeights,
+    expected_req_primer_amplicon_params: bool,
+    expected_req_probe_params: bool,
+) -> None:
+    test_target = Span(refname="chr1", start=200, end=300, strand=Strand.POSITIVE)
+    test_input = Primer3Input(
+        target=test_target,
+        primer_weights=valid_primer_weights,
+        probe_weights=valid_probe_weights,
+        task=task_type,
+        probe_params=valid_probe_params,
+        primer_and_amplicon_params=valid_primer_amplicon_params,
+    )
+    assert test_input.task.requires_probe_params == expected_req_probe_params
+    assert test_input.task.requires_primer_amplicon_params == expected_req_primer_amplicon_params