git: ddb11fbe9778 - main - biology/py-macs3: Update to 3.0.1

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=ddb11fbe9778b0b8c66d0b7f77b0b16c2140634e

commit ddb11fbe9778b0b8c66d0b7f77b0b16c2140634e
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2024-02-28 13:26:03 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2024-02-28 13:29:15 +0000

    biology/py-macs3: Update to 3.0.1
    
    Minor bug fix release
    Changes: https://github.com/macs3-project/MACS/releases
---
 biology/py-macs3/Makefile                           |  4 ++--
 biology/py-macs3/distinfo                           |  6 +++---
 biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c |  2 +-
 biology/py-macs3/files/patch-pyproject.toml         |  9 +++++----
 biology/py-macs3/files/patch-requirements.txt       |  9 ++++++---
 biology/py-macs3/files/patch-setup.py               | 11 +----------
 6 files changed, 18 insertions(+), 23 deletions(-)

diff --git a/biology/py-macs3/Makefile b/biology/py-macs3/Makefile
index d2cad2892df4..6ad3d9000471 100644
--- a/biology/py-macs3/Makefile
+++ b/biology/py-macs3/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=		MACS3
 DISTVERSIONPREFIX=	v
-DISTVERSION=		3.0.0
+DISTVERSION=		3.0.1
 CATEGORIES=		biology python
 PKGNAMEPREFIX=		${PYTHON_PKGNAMEPREFIX}
 
@@ -42,7 +42,7 @@ post-stage:
 
 # FIXME: Some tests fail due to a py-threadpoolctl issue
 # https://github.com/joblib/threadpoolctl/pull/148
-do-test: deinstall install
+do-test: deinstall reinstall
 	@${RM} -rf ${WRKSRC}/temp
 	@cd ${WRKSRC}/test && ./cmdlinetest tag
 
diff --git a/biology/py-macs3/distinfo b/biology/py-macs3/distinfo
index 757e9bbaf640..b06631987784 100644
--- a/biology/py-macs3/distinfo
+++ b/biology/py-macs3/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1703890666
-SHA256 (macs3-project-MACS-v3.0.0_GH0.tar.gz) = faa7ec2ea1f47b8c4cd747f00f2754d0e40051fe44d81d229d0111e3dad34a1d
-SIZE (macs3-project-MACS-v3.0.0_GH0.tar.gz) = 197389439
+TIMESTAMP = 1708785426
+SHA256 (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 8a2f5b2dccfc255ea2fd5e54e0d6aa9c12f5ce83762b17b779ce2546ade860ce
+SIZE (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 197400439
diff --git a/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c b/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c
index d66d83f33606..e385ca2fc010 100644
--- a/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c
+++ b/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c
@@ -1,4 +1,4 @@
---- MACS3/fermi-lite/ksw.c.orig	2023-11-15 16:09:23 UTC
+--- MACS3/fermi-lite/ksw.c.orig	2024-02-24 15:09:33 UTC
 +++ MACS3/fermi-lite/ksw.c
 @@ -28,7 +28,7 @@
  
diff --git a/biology/py-macs3/files/patch-pyproject.toml b/biology/py-macs3/files/patch-pyproject.toml
index cf54cae8892f..15f55a86a701 100644
--- a/biology/py-macs3/files/patch-pyproject.toml
+++ b/biology/py-macs3/files/patch-pyproject.toml
@@ -1,6 +1,7 @@
---- pyproject.toml.orig	2024-01-06 15:00:01 UTC
+--- pyproject.toml.orig	2024-02-23 05:43:44 UTC
 +++ pyproject.toml
-@@ -1,2 +1,2 @@
+@@ -1,3 +1,3 @@
  [build-system]
--requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython~=3.0', 'hmmlearn>=0.3']
-+requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython>=0', 'hmmlearn>=0.3']
+-requires=['setuptools>=60.0', 'numpy>=1.24.2', 'scipy>=1.11.4', 'cykhash>=2.0,<3.0', 'Cython~=3.0', 'scikit-learn>=1.2.1', 'hmmlearn>=0.3']
++requires=['setuptools>=60.0', 'numpy>=1.24.2', 'scipy>=1.11.1', 'cykhash>=2.0,<3.0', 'Cython>=0', 'scikit-learn>=1.2.1', 'hmmlearn>=0.3']
+ 
diff --git a/biology/py-macs3/files/patch-requirements.txt b/biology/py-macs3/files/patch-requirements.txt
index 0c8106f79680..81c9a1f75f88 100644
--- a/biology/py-macs3/files/patch-requirements.txt
+++ b/biology/py-macs3/files/patch-requirements.txt
@@ -1,8 +1,11 @@
---- requirements.txt.orig	2024-01-06 14:55:53 UTC
+--- requirements.txt.orig	2024-02-23 05:43:44 UTC
 +++ requirements.txt
-@@ -1,4 +1,4 @@
+@@ -1,6 +1,6 @@
 -Cython~=3.0
 +Cython>=0
- numpy>=1.19
+ numpy>=1.24.2
+-scipy>=1.11.4
++scipy>=1.11.1
+ scikit-learn>=1.2.1
  hmmlearn>=0.3
  cykhash>=2.0,<3.0 
diff --git a/biology/py-macs3/files/patch-setup.py b/biology/py-macs3/files/patch-setup.py
index 58dde13ba2c2..f309f3139736 100644
--- a/biology/py-macs3/files/patch-setup.py
+++ b/biology/py-macs3/files/patch-setup.py
@@ -1,14 +1,5 @@
---- setup.py.orig	2023-11-15 16:09:23 UTC
+--- setup.py.orig	2024-02-24 14:39:02 UTC
 +++ setup.py
-@@ -40,7 +40,7 @@ classifiers =[\
- install_requires = [ "numpy>=1.19",
-                      "hmmlearn>=0.3",
-                      "cykhash>=2.0,<3.0",
--                     "Cython~=3.0" ]
-+                     "Cython>=0" ]
- 
- tests_requires = [ 'pytest' ]
- 
 @@ -70,7 +70,7 @@ def main():
  
      if not clang: