svn commit: r518470 - in head/biology/py-multiqc: . files

[Jason W. Bacon]

Author: jwb
Date: Tue Nov 26 16:25:08 2019
New Revision: 518470
URL: https://svnweb.freebsd.org/changeset/ports/518470

Log:
  biology/py-multiqc: Upgrade to 1.8
  
  Major enhancements including 6 new modules and improvements to existing modules
  Numerous minor fixes and enhancements
  
  Reported by:    portscout

Added:
  head/biology/py-multiqc/files/patch-multiqc_multiqc.py   (contents, props changed)
Deleted:
  head/biology/py-multiqc/files/patch-multiqc_utils_config.py
  head/biology/py-multiqc/files/patch-scripts_multiqc
Modified:
  head/biology/py-multiqc/Makefile
  head/biology/py-multiqc/distinfo

Modified: head/biology/py-multiqc/Makefile
==============================================================================
--- head/biology/py-multiqc/Makefile	Tue Nov 26 16:20:12 2019	(r518469)
+++ head/biology/py-multiqc/Makefile	Tue Nov 26 16:25:08 2019	(r518470)
@@ -1,7 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	multiqc
-DISTVERSION=	1.7
+DISTVERSION=	1.8
 CATEGORIES=	biology python
 MASTER_SITES=	CHEESESHOP
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -15,6 +15,7 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 RUN_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}click>0:devel/py-click@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}future>0.14.0:devel/py-future@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}coloredlogs>0:devel/py-coloredlogs@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}matplotlib>=2.1.1:math/py-matplotlib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}markdown>0:textproc/py-markdown@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR} \

Modified: head/biology/py-multiqc/distinfo
==============================================================================
--- head/biology/py-multiqc/distinfo	Tue Nov 26 16:20:12 2019	(r518469)
+++ head/biology/py-multiqc/distinfo	Tue Nov 26 16:25:08 2019	(r518470)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1569116068
-SHA256 (multiqc-1.7.tar.gz) = 02e6a7fac7cd9ed036dcc6c92b8f8bcacbd28983ba6be53afb35e08868bd2d68
-SIZE (multiqc-1.7.tar.gz) = 1168389
+TIMESTAMP = 1574697347
+SHA256 (multiqc-1.8.tar.gz) = ea7f3e320a8812a0d5a8778605f76ff4bb6ca5c3ed23d4269f0bac2159838f3e
+SIZE (multiqc-1.8.tar.gz) = 1657725

Added: head/biology/py-multiqc/files/patch-multiqc_multiqc.py
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/py-multiqc/files/patch-multiqc_multiqc.py	Tue Nov 26 16:25:08 2019	(r518470)
@@ -0,0 +1,30 @@
+--- multiqc/multiqc.py.orig	2019-11-25 15:53:22 UTC
++++ multiqc/multiqc.py
+@@ -11,16 +11,25 @@ from __future__ import print_function
+ 
+ import base64
+ import click
++import os
++import sys
++
++if 'LC_ALL' in os.environ and 'LANG' in os.environ:
++    import click
++else:
++    print('multiqc: LC_ALL and LANG must be set to a UTF-8 character set')
++    print('in your environment in order for the click module to function.')
++    print('E.g. export LC_ALL=en_US.UTF-8 or setenv LC_ALL en_US.UTF-8')
++    sys.exit()
++
+ from distutils import version
+ from distutils.dir_util import copy_tree
+ import errno
+ import io
+ import jinja2
+-import os
+ import re
+ import shutil
+ import subprocess
+-import sys
+ import tempfile
+ import traceback
+