git: 527848251ff3 - main - biology/py-loompy: update 3.0.7 → 3.0.8

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=527848251ff358b4c1b873a5a009ba1c6980ea56

commit 527848251ff358b4c1b873a5a009ba1c6980ea56
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-06-08 19:29:34 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-06-08 19:50:40 +0000

    biology/py-loompy: update 3.0.7 → 3.0.8
---
 biology/py-loompy/Makefile                         | 16 ++++++++-----
 biology/py-loompy/distinfo                         |  6 ++---
 .../files/patch-tests_test__connection.py          | 26 ++++++++++++++++++++++
 .../patch-tests_test__file__attribute__manager.py  | 13 +++++++++++
 .../py-loompy/files/patch-tests_test__validator.py | 13 +++++++++++
 5 files changed, 65 insertions(+), 9 deletions(-)

diff --git a/biology/py-loompy/Makefile b/biology/py-loompy/Makefile
index 86b5253964a4..591cf8157082 100644
--- a/biology/py-loompy/Makefile
+++ b/biology/py-loompy/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	loompy
-DISTVERSION=	3.0.7
-PORTREVISION=	4
+DISTVERSION=	3.0.8
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -12,17 +11,22 @@ WWW=		https://loompy.org/
 LICENSE=	BSD2CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}click>0:devel/py-click@${PY_FLAVOR} \
+BUILD_DEPENDS=	${PY_SETUPTOOLS} \
+		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}click>0:devel/py-click@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}numba>0:devel/py-numba@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}numpy-groupies>0:math/py-numpy-groupies@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR}
 
 USES=		python
-USE_PYTHON=	distutils autoplist
+USE_PYTHON=	pep517 autoplist pytest
 
 NO_ARCH=	yes
 
+TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
+
+# tests as of 3.0.8: 8 passed, 1 failed
+
 .include <bsd.port.mk>
diff --git a/biology/py-loompy/distinfo b/biology/py-loompy/distinfo
index 633ef090896f..fbdb1a54a64d 100644
--- a/biology/py-loompy/distinfo
+++ b/biology/py-loompy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1646583060
-SHA256 (loompy-3.0.7.tar.gz) = b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4
-SIZE (loompy-3.0.7.tar.gz) = 4837617
+TIMESTAMP = 1780912743
+SHA256 (loompy-3.0.8.tar.gz) = c1f48d0bf21aa2bbdeee21a0577553cba9609d9435d7c32b687686bbb5869ca7
+SIZE (loompy-3.0.8.tar.gz) = 49618
diff --git a/biology/py-loompy/files/patch-tests_test__connection.py b/biology/py-loompy/files/patch-tests_test__connection.py
new file mode 100644
index 000000000000..193c3209614e
--- /dev/null
+++ b/biology/py-loompy/files/patch-tests_test__connection.py
@@ -0,0 +1,26 @@
+-- Fix tests for FreeBSD (don't delete temporary files on close, fix np.int).
+
+-- Fix np.int usage for NumPy 2.0+ compatibility.
+
+--- tests/test_connection.py.orig	2021-10-05 14:19:26 UTC
++++ tests/test_connection.py
+@@ -8,16 +8,16 @@ class LoomConnectionTests(TestCase):
+ 
+ class LoomConnectionTests(TestCase):
+     def setUp(self) -> None:
+-        self.file = NamedTemporaryFile(suffix=".loom")
++        self.file = NamedTemporaryFile(suffix=".loom", delete=False)
+         self.file.close()
+         loompy.create(
+             self.file.name,
+             np.random.random((5, 5)),
+             row_attrs={
+-                "key": np.fromiter(range(5), dtype=np.int)
++                "key": np.fromiter(range(5), dtype=int)
+             },
+             col_attrs={
+-                "key": np.fromiter(range(5), dtype=np.int)
++                "key": np.fromiter(range(5), dtype=int)
+             })
+ 
+     def tearDown(self) -> None:
diff --git a/biology/py-loompy/files/patch-tests_test__file__attribute__manager.py b/biology/py-loompy/files/patch-tests_test__file__attribute__manager.py
new file mode 100644
index 000000000000..dd50f169fc48
--- /dev/null
+++ b/biology/py-loompy/files/patch-tests_test__file__attribute__manager.py
@@ -0,0 +1,13 @@
+-- Fix tests for FreeBSD (don't delete temporary files on close, fix np.int).
+
+--- tests/test_file_attribute_manager.py.orig	2026-06-08 10:21:32 UTC
++++ tests/test_file_attribute_manager.py
+@@ -12,7 +12,7 @@ class GlobalAttributeManagerTests(TestCase):
+ 	VALUE_IN_FILE = np.arange(3)
+ 
+ 	def setUp(self):
+-		f = NamedTemporaryFile(suffix="loom")
++		f = NamedTemporaryFile(suffix="loom", delete=False)
+ 		f.close()
+ 		self.filename = f.name
+ 		self.file = h5py.File(f.name)
diff --git a/biology/py-loompy/files/patch-tests_test__validator.py b/biology/py-loompy/files/patch-tests_test__validator.py
new file mode 100644
index 000000000000..4fb215e41ba7
--- /dev/null
+++ b/biology/py-loompy/files/patch-tests_test__validator.py
@@ -0,0 +1,13 @@
+-- Fix tests for FreeBSD (don't delete temporary files on close, fix np.int).
+
+--- tests/test_validator.py.orig	2026-06-08 10:21:32 UTC
++++ tests/test_validator.py
+@@ -9,7 +9,7 @@ class LoomValidatorTests(TestCase):
+ 
+ class LoomValidatorTests(TestCase):
+     def test_file_with_empty_col_attrs_is_valid(self) -> None:
+-        f = NamedTemporaryFile(suffix=".loom")
++        f = NamedTemporaryFile(suffix=".loom", delete=False)
+         f.close()
+         loompy.create(f.name, np.zeros((5, 5)), {}, {})
+         try: