py-pybigwig: Python access to bigWig files using libBigWig

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Dec 18 21:05:49 2023 -0600
Changeset:	6f8278a4c24ec9a404a991219eb462d4517038fd

Modified Files:
	Makefile
Added Files:
	py-pybigwig/DESCR
	py-pybigwig/Makefile
	py-pybigwig/PLIST
	py-pybigwig/distinfo
	py-pybigwig/patches/patch-libBigWig_bwValues.c

Log Message:
py-pybigwig: Python access to bigWig files using libBigWig

A python extension, written in C, for quick access to bigBed files and
access to and creation of bigWig files. This extension uses libBigWig
for local and remote file access.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=6f8278a4c24ec9a404a991219eb462d4517038fd

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                                       |  1 +
 py-pybigwig/DESCR                              |  3 +++
 py-pybigwig/Makefile                           | 21 +++++++++++++++++
 py-pybigwig/PLIST                              | 14 ++++++++++++
 py-pybigwig/distinfo                           |  6 +++++
 py-pybigwig/patches/patch-libBigWig_bwValues.c | 31 ++++++++++++++++++++++++++
 6 files changed, 76 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index e6b2ecb94d..1a5e622c53 100644
--- a/Makefile
+++ b/Makefile
@@ -4215,6 +4215,7 @@ SUBDIR+=	py-py4j
 SUBDIR+=	py-pyaiml
 SUBDIR+=	py-pyamf
 SUBDIR+=	py-pyamg
+SUBDIR+=	py-pybigwig
 SUBDIR+=	py-pybitbucket
 SUBDIR+=	py-pycifrw
 SUBDIR+=	py-pydelay
diff --git a/py-pybigwig/DESCR b/py-pybigwig/DESCR
new file mode 100644
index 0000000000..d69a6a12fd
--- /dev/null
+++ b/py-pybigwig/DESCR
@@ -0,0 +1,3 @@
+A python extension, written in C, for quick access to bigBed files and
+access to and creation of bigWig files. This extension uses libBigWig
+for local and remote file access.
diff --git a/py-pybigwig/Makefile b/py-pybigwig/Makefile
new file mode 100644
index 0000000000..33eadecd1a
--- /dev/null
+++ b/py-pybigwig/Makefile
@@ -0,0 +1,21 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Mon Dec 18 20:44:18 CST 2023               #
+###########################################################
+
+DISTNAME=	pyBigWig-0.3.22
+PKGNAME=	${PYPKGPREFIX}-pyBigWig-0.3.22
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_PYPI:=p/pyBigWig/}
+
+OWNER=		bacon%NetBSD.org@localhost
+HOMEPAGE=	https://pypi.org/project/pyBigWig/
+COMMENT=	Python access to bigWig files using libBigWig
+LICENSE=	mit
+
+.include "../../lang/python/egg.mk"
+.include "../../www/curl/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/py-pybigwig/PLIST b/py-pybigwig/PLIST
new file mode 100644
index 0000000000..cb50e7ad64
--- /dev/null
+++ b/py-pybigwig/PLIST
@@ -0,0 +1,14 @@
+@comment $NetBSD$
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/pyBigWig.so
+${PYSITELIB}/pyBigWigTest/__init__.py
+${PYSITELIB}/pyBigWigTest/__init__.pyc
+${PYSITELIB}/pyBigWigTest/__init__.pyo
+${PYSITELIB}/pyBigWigTest/test.bigBed
+${PYSITELIB}/pyBigWigTest/test.bw
+${PYSITELIB}/pyBigWigTest/test.py
+${PYSITELIB}/pyBigWigTest/test.pyc
+${PYSITELIB}/pyBigWigTest/test.pyo
diff --git a/py-pybigwig/distinfo b/py-pybigwig/distinfo
new file mode 100644
index 0000000000..f67c6f3847
--- /dev/null
+++ b/py-pybigwig/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+BLAKE2s (pyBigWig-0.3.22.tar.gz) = 05ef15d553161285b2268b7d84774797276740c79772c559dea82c3d20e81e03
+SHA512 (pyBigWig-0.3.22.tar.gz) = e1974f43a0cb1f7f1f010e130971ca3c1ec6882071a2617002ee6ec441820daf3c1f5ef930f9cc3662bd320279a50e04765c0bf8ee040eb0e7c857f966c86c40
+Size (pyBigWig-0.3.22.tar.gz) = 73864 bytes
+SHA1 (patch-libBigWig_bwValues.c) = a180ebf1e84dea7074b79318b4f1ce445df376d5
diff --git a/py-pybigwig/patches/patch-libBigWig_bwValues.c b/py-pybigwig/patches/patch-libBigWig_bwValues.c
new file mode 100644
index 0000000000..9407479f87
--- /dev/null
+++ b/py-pybigwig/patches/patch-libBigWig_bwValues.c
@@ -0,0 +1,31 @@
+$NetBSD$
+
+--- libBigWig/bwValues.c.orig	2023-12-16 13:51:54 UTC
++++ libBigWig/bwValues.c
+@@ -5,7 +5,7 @@
+ #include <zlib.h>
+ #include <errno.h>
+ 
+-static uint32_t roundup(uint32_t v) {
++static uint32_t bigwig_roundup(uint32_t v) {
+     v--;
+     v |= v >> 1;
+     v |= v >> 2;
+@@ -346,7 +346,7 @@ static bwOverlappingIntervals_t *pushIntervals(bwOverl
+ //Returns NULL on error, in which case o has been free()d
+ static bwOverlappingIntervals_t *pushIntervals(bwOverlappingIntervals_t *o, uint32_t start, uint32_t end, float value) {
+     if(o->l+1 >= o->m) {
+-        o->m = roundup(o->l+1);
++        o->m = bigwig_roundup(o->l+1);
+         o->start = realloc(o->start, o->m * sizeof(uint32_t));
+         if(!o->start) goto error;
+         o->end = realloc(o->end, o->m * sizeof(uint32_t));
+@@ -366,7 +366,7 @@ static bbOverlappingEntries_t *pushBBIntervals(bbOverl
+ 
+ static bbOverlappingEntries_t *pushBBIntervals(bbOverlappingEntries_t *o, uint32_t start, uint32_t end, char *str, int withString) {
+     if(o->l+1 >= o->m) {
+-        o->m = roundup(o->l+1);
++        o->m = bigwig_roundup(o->l+1);
+         o->start = realloc(o->start, o->m * sizeof(uint32_t));
+         if(!o->start) goto error;
+         o->end = realloc(o->end, o->m * sizeof(uint32_t));