Repository: fulcrumgenomics/prymer (language: python)

Issue:
`OverlapDetector.filter()` should be made generic 
`OverlapDetector.filter` should be made generic so we can filter arbitrary subclasses of `Primer` without mypy raising a flag


Discussion / hints:

Fix patch:
diff --git a/poetry.lock b/poetry.lock
index a45a48a..d02ffe3 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -90,13 +90,13 @@ files = [
 
 [[package]]
 name = "build"
-version = "1.2.1"
+version = "1.2.2"
 description = "A simple, correct Python build frontend"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "build-1.2.1-py3-none-any.whl", hash = "sha256:75e10f767a433d9a86e50d83f418e83efc18ede923ee5ff7df93b6cb0306c5d4"},
-    {file = "build-1.2.1.tar.gz", hash = "sha256:526263f4870c26f26c433545579475377b2b7588b6f1eac76a001e873ae3e19d"},
+    {file = "build-1.2.2-py3-none-any.whl", hash = "sha256:277ccc71619d98afdd841a0e96ac9fe1593b823af481d3b0cea748e8894e0613"},
+    {file = "build-1.2.2.tar.gz", hash = "sha256:119b2fb462adef986483438377a13b2f42064a2a3a4161f24a0cca698a07ac8c"},
 ]
 
 [package.dependencies]
@@ -134,89 +134,89 @@ redis = ["redis (>=2.10.5)"]
 
 [[package]]
 name = "certifi"
-version = "2024.7.4"
+version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
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+    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
+    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
 ]
 
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 name = "cffi"
-version = "1.17.0"
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 description = "Foreign Function Interface for Python calling C code."
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
@@ -458,38 +458,38 @@ files = [
 
 [[package]]
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 optional = false
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+    {file = "cryptography-43.0.1.tar.gz", hash = "sha256:203e92a75716d8cfb491dc47c79e17d0d9207ccffcbcb35f598fbe463ae3444d"},
 ]
 
 [package.dependencies]
@@ -502,7 +502,7 @@ nox = ["nox"]
 pep8test = ["check-sdist", "click", "mypy", "ruff"]
 sdist = ["build"]
 ssh = ["bcrypt (>=3.1.5)"]
-test = ["certifi", "cryptography-vectors (==43.0.0)", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
+test = ["certifi", "cryptography-vectors (==43.0.1)", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
 test-randomorder = ["pytest-randomly"]
 
 [[package]]
@@ -640,19 +640,19 @@ typing_extensions = {version = ">=3.7.4", markers = "python_version < \"3.12\""}
 
 [[package]]
 name = "filelock"
-version = "3.15.4"
+version = "3.16.1"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.15.4-py3-none-any.whl", hash = "sha256:6ca1fffae96225dab4c6eaf1c4f4f28cd2568d3ec2a44e15a08520504de468e7"},
-    {file = "filelock-3.15.4.tar.gz", hash = "sha256:2207938cbc1844345cb01a5a95524dae30f0ce089eba5b00378295a17e3e90cb"},
+    {file = "filelock-3.16.1-py3-none-any.whl", hash = "sha256:2082e5703d51fbf98ea75855d9d5527e33d8ff23099bec374a134febee6946b0"},
+    {file = "filelock-3.16.1.tar.gz", hash = "sha256:c249fbfcd5db47e5e2d6d62198e565475ee65e4831e2561c8e313fa7eb961435"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-asyncio (>=0.21)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)", "virtualenv (>=20.26.2)"]
-typing = ["typing-extensions (>=4.8)"]
+docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4.1)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "diff-cover (>=9.2)", "pytest (>=8.3.3)", "pytest-asyncio (>=0.24)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.26.4)"]
+typing = ["typing-extensions (>=4.12.2)"]
 
 [[package]]
 name = "ghp-import"
@@ -673,13 +673,13 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "griffe"
-version = "1.1.1"
+version = "1.3.1"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "griffe-1.3.1-py3-none-any.whl", hash = "sha256:940aeb630bc3054b4369567f150b6365be6f11eef46b0ed8623aea96e6d17b19"},
+    {file = "griffe-1.3.1.tar.gz", hash = "sha256:3f86a716b631a4c0f96a43cb75d05d3c85975003c20540426c0eba3b0581c56a"},
 ]
 
 [package.dependencies]
@@ -687,33 +687,40 @@ colorama = ">=0.4"
 
 [[package]]
 name = "idna"
-version = "3.7"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 files = [
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+    {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"},
+    {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"},
 ]
 
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "importlib-metadata"
-version = "8.4.0"
+version = "8.5.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-zipp = ">=0.5"
+zipp = ">=3.20"
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
-test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
@@ -907,13 +914,13 @@ files = [
 
 [[package]]
 name = "mkdocs"
-version = "1.6.0"
+version = "1.6.1"
 description = "Project documentation with Markdown."
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "mkdocs-1.6.1-py3-none-any.whl", hash = "sha256:db91759624d1647f3f34aa0c3f327dd2601beae39a366d6e064c03468d35c20e"},
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 ]
 
 [package.dependencies]
@@ -1015,13 +1022,13 @@ mkdocs = ">=1.0.3"
 
 [[package]]
 name = "mkdocs-material"
-version = "9.5.32"
+version = "9.5.35"
 description = "Documentation that simply works"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "mkdocs_material-9.5.35.tar.gz", hash = "sha256:0d233d7db067ac896bf22ee7950eebf2b1eaf26c155bb27382bf4174021cc117"},
 ]
 
 [package.dependencies]
@@ -1069,13 +1076,13 @@ mkdocs = ">=1.2"
 
 [[package]]
 name = "mkdocs-table-reader-plugin"
-version = "3.0.1"
+version = "3.1.0"
 description = "MkDocs plugin to directly insert tables from files into markdown."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1112,129 +1119,138 @@ python-legacy = ["mkdocstrings-python-legacy (>=0.2.1)"]
 
 [[package]]
 name = "mkdocstrings-python"
-version = "1.10.8"
+version = "1.10.9"
 description = "A Python handler for mkdocstrings."
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "mkdocstrings_python-1.10.9-py3-none-any.whl", hash = "sha256:cbe98710a6757dfd4dff79bf36cb9731908fb4c69dd2736b15270ae7a488243d"},
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 ]
 
 [package.dependencies]
 griffe = ">=0.49"
+mkdocs-autorefs = ">=1.0"
 mkdocstrings = ">=0.25"
 
 [[package]]
 name = "more-itertools"
-version = "10.4.0"
+version = "10.5.0"
 description = "More routines for operating on iterables, beyond itertools"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "msgpack"
-version = "1.0.8"
+version = "1.1.0"
 description = "MessagePack serializer"
 optional = false
 python-versions = ">=3.8"
 files = [
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@@ -1330,14 +1346,19 @@ files = [
 
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+version = "0.5.7"
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 python-versions = "*"
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+lint = ["black"]
+
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@@ -1451,19 +1472,19 @@ testing = ["pytest", "pytest-cov", "wheel"]
 
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 [[package]]
 name = "pluggy"
@@ -1764,13 +1785,13 @@ six = ">=1.5"
 
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+version = "2024.2"
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 [package.extras]
@@ -1982,90 +2003,105 @@ full = ["numpy"]
 
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+    {file = "watchdog-5.0.2-pp39-pypy39_pp73-macosx_10_15_x86_64.whl", hash = "sha256:901ee48c23f70193d1a7bc2d9ee297df66081dd5f46f0ca011be4f70dec80dab"},
+    {file = "watchdog-5.0.2-pp39-pypy39_pp73-macosx_11_0_arm64.whl", hash = "sha256:638bcca3d5b1885c6ec47be67bf712b00a9ab3d4b22ec0881f4889ad870bc7e8"},
+    {file = "watchdog-5.0.2-py3-none-manylinux2014_aarch64.whl", hash = "sha256:5597c051587f8757798216f2485e85eac583c3b343e9aa09127a3a6f82c65ee8"},
+    {file = "watchdog-5.0.2-py3-none-manylinux2014_armv7l.whl", hash = "sha256:53ed1bf71fcb8475dd0ef4912ab139c294c87b903724b6f4a8bd98e026862e6d"},
+    {file = "watchdog-5.0.2-py3-none-manylinux2014_i686.whl", hash = "sha256:29e4a2607bd407d9552c502d38b45a05ec26a8e40cc7e94db9bb48f861fa5abc"},
+    {file = "watchdog-5.0.2-py3-none-manylinux2014_ppc64.whl", hash = "sha256:b6dc8f1d770a8280997e4beae7b9a75a33b268c59e033e72c8a10990097e5fde"},
+    {file = "watchdog-5.0.2-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:d2ab34adc9bf1489452965cdb16a924e97d4452fcf88a50b21859068b50b5c3b"},
+    {file = "watchdog-5.0.2-py3-none-manylinux2014_s390x.whl", hash = "sha256:7d1aa7e4bb0f0c65a1a91ba37c10e19dabf7eaaa282c5787e51371f090748f4b"},
+    {file = "watchdog-5.0.2-py3-none-manylinux2014_x86_64.whl", hash = "sha256:726eef8f8c634ac6584f86c9c53353a010d9f311f6c15a034f3800a7a891d941"},
+    {file = "watchdog-5.0.2-py3-none-win32.whl", hash = "sha256:bda40c57115684d0216556671875e008279dea2dc00fcd3dde126ac8e0d7a2fb"},
+    {file = "watchdog-5.0.2-py3-none-win_amd64.whl", hash = "sha256:d010be060c996db725fbce7e3ef14687cdcc76f4ca0e4339a68cc4532c382a73"},
+    {file = "watchdog-5.0.2-py3-none-win_ia64.whl", hash = "sha256:3960136b2b619510569b90f0cd96408591d6c251a75c97690f4553ca88889769"},
+    {file = "watchdog-5.0.2.tar.gz", hash = "sha256:dcebf7e475001d2cdeb020be630dc5b687e9acdd60d16fea6bb4508e7b94cf76"},
 ]
 
 [package.extras]
@@ -2429,18 +2464,22 @@ test = ["pytest"]
 
 [[package]]
 name = "zipp"
-version = "3.20.0"
+version = "3.20.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.20.0-py3-none-any.whl", hash = "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"},
-    {file = "zipp-3.20.0.tar.gz", hash = "sha256:0145e43d89664cfe1a2e533adc75adafed82fe2da404b4bbb6b026c0157bdb31"},
+    {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
+    {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"},
 ]
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [metadata]
 lock-version = "2.0"
diff --git a/prymer/offtarget/offtarget_detector.py b/prymer/offtarget/offtarget_detector.py
index eb3a9b8..1773042 100644
--- a/prymer/offtarget/offtarget_detector.py
+++ b/prymer/offtarget/offtarget_detector.py
@@ -82,6 +82,7 @@
 from types import TracebackType
 from typing import Optional
 from typing import Self
+from typing import TypeVar
 
 from ordered_set import OrderedSet
 
@@ -93,6 +94,8 @@
 from prymer.offtarget.bwa import BwaResult
 from prymer.offtarget.bwa import Query
 
+PrimerType = TypeVar("PrimerType", bound=Primer)
+
 
 @dataclass(init=True, frozen=True)
 class OffTargetResult:
@@ -188,7 +191,7 @@ def __init__(
         self._keep_spans: bool = keep_spans
         self._keep_primer_spans: bool = keep_primer_spans
 
-    def filter(self, primers: list[Primer]) -> list[Primer]:
+    def filter(self, primers: list[PrimerType]) -> list[PrimerType]:
         """Filters an iterable of Primers to return only those that have less than
         `max_primer_hits` mappings to the genome."""
         results: dict[str, BwaResult] = self.mappings_of(primers)
@@ -282,13 +285,13 @@ def _build_off_target_result(
 
         return result
 
-    def mappings_of(self, primers: list[Primer]) -> dict[str, BwaResult]:
+    def mappings_of(self, primers: list[PrimerType]) -> dict[str, BwaResult]:
         """Function to take a set of primers and map any that are not cached, and return mappings
         for all of them.  Note: the genomics sequence of the returned mappings are on the opposite
         strand of that of the strand of the primer.  I.e. we map the complementary bases (reversed)
         to that of the primer."""
 
-        primers_to_map: list[Primer]
+        primers_to_map: list[PrimerType]
         if not self._cache_results:
             primers_to_map = primers
         else:


Test patch:
diff --git a/tests/offtarget/test_offtarget.py b/tests/offtarget/test_offtarget.py
index f1c809c..43e7b9e 100644
--- a/tests/offtarget/test_offtarget.py
+++ b/tests/offtarget/test_offtarget.py
@@ -1,3 +1,4 @@
+from dataclasses import dataclass
 from pathlib import Path
 
 import pytest
@@ -228,3 +229,29 @@ def test_to_amplicons(
     with _build_detector(ref_fasta=ref_fasta, cache_results=cache_results) as detector:
         actual = detector._to_amplicons(lefts=[left], rights=[right], max_len=250)
         assert actual == expected, test_id
+
+
+def test_generic_filter(ref_fasta: Path) -> None:
+    """
+    This test isn't intended to validate any runtime assertions, but is a minimal example for the
+    type checker to ensure that we can apply `OffTargetDetector.filter()` to arbitrary subclases of
+    `Primer`.
+    """
+
+    @dataclass(frozen=True)
+    class CustomPrimer(Primer):
+        foo: str = "foo"
+
+    # fmt: off
+    primers: list[CustomPrimer] = [
+        CustomPrimer(bases="AAAA", tm=37, penalty=0, span=Span(refname="chr1", start=1, end=4), foo="bar"),  # noqa: E501
+        CustomPrimer(bases="TTTT", tm=37, penalty=0, span=Span(refname="chr2", start=1, end=4), foo="qux"),  # noqa: E501
+    ]
+    # fmt: on
+
+    with _build_detector(ref_fasta=ref_fasta) as detector:
+        # Here we are validating that we can both
+        # 1. Pass a list of a `Primer` subclass to `filter()` and
+        # 2. Return a list of the same type.
+        # NB: we're ignoring the unused value error because we want to check the type hint
+        filtered_primers: list[CustomPrimer] = detector.filter(primers)  # noqa: F841