diff --git a/biology/py-pyrodigal/Makefile b/biology/py-pyrodigal/Makefile
index abc88d6fac82..37d361e11acc 100644
--- a/biology/py-pyrodigal/Makefile
+++ b/biology/py-pyrodigal/Makefile
@@ -1,32 +1,34 @@
 PORTNAME=	pyrodigal
-DISTVERSION=	3.6.3
+DISTVERSION=	3.7.1
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Python binding for Prodigal, an ORF finder for genomes and metagenomes
 WWW=		https://pyrodigal.readthedocs.io/en/stable/ \
 		https://github.com/althonos/pyrodigal
 
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/COPYING
 
 BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}scikit-build-core>0:devel/py-scikit-build-core@${PY_FLAVOR}
 TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}archspec>0:devel/py-archspec@${PY_FLAVOR}
 
 USES=		cmake:indirect python
 USE_PYTHON=	autoplist concurrent cython pep517 pytest
 
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
 
 xpost-build:
 	@cd ${BUILD_WRKSRC} && ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py build_ext --inplace
 
 post-install:
 	@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pyrodigal/lib${PYTHON_TAG}.so
 
-do-test: # as of 3.6.3 this doesn't work: https://github.com/althonos/pyrodigal/issues/63
-	@cd ${TEST_WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -vv
+do-test:
+	@cd ${TEST_WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest pyrodigal.tests -vv
+
+# tests as of 3.7.1: Ran 99 tests in 2.562s
 
 .include <bsd.port.mk>
diff --git a/biology/py-pyrodigal/distinfo b/biology/py-pyrodigal/distinfo
index 19c6cf076683..fff71ed871e4 100644
--- a/biology/py-pyrodigal/distinfo
+++ b/biology/py-pyrodigal/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1731398873
-SHA256 (pyrodigal-3.6.3.tar.gz) = 3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78
-SIZE (pyrodigal-3.6.3.tar.gz) = 3589356
+TIMESTAMP = 1777547296
+SHA256 (pyrodigal-3.7.1.tar.gz) = 0262fc5b5fd0b16c18eb3eb9b6079e1590e6d838c3f8431c46d9027c8e67f600
+SIZE (pyrodigal-3.7.1.tar.gz) = 3676370
diff --git a/biology/py-pyrodigal/files/patch-pyproject.toml b/biology/py-pyrodigal/files/patch-pyproject.toml
deleted file mode 100644
index 097ac58992f9..000000000000
--- a/biology/py-pyrodigal/files/patch-pyproject.toml
+++ /dev/null
@@ -1,12 +0,0 @@
-- workaround for https://github.com/althonos/pyrodigal/issues/69
-
---- pyproject.toml.orig	2025-03-03 20:52:28 UTC
-+++ pyproject.toml
-@@ -12,7 +12,6 @@ authors = [
- authors = [
-   { name = "Martin Larralde", email = "martin.larralde@embl.de" },
- ]
--platform = "any"
- keywords = ["bioinformatics", "genome", "orf", "gene", "prodigal"]
- classifiers = [
-     "Development Status :: 5 - Production/Stable",