Index: head/biology/py-multiqc/Makefile =================================================================== --- head/biology/py-multiqc/Makefile (revision 518469) +++ head/biology/py-multiqc/Makefile (revision 518470) @@ -1,36 +1,37 @@ # $FreeBSD$ PORTNAME= multiqc -DISTVERSION= 1.7 +DISTVERSION= 1.8 CATEGORIES= biology python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Aggregate bioinformatics analysis reports across samples and tools LICENSE= GPLv3 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} \ ${PYTHON_PKGNAMEPREFIX}requests>:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}simplejson>0:devel/py-simplejson@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Jinja2>=2.9:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}lzstring>0:archivers/py-lzstring@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}spectra>=0.0.10:graphics/py-spectra@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}colormath>0:math/py-colormath@${PY_FLAVOR} USES= python USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes post-patch: @${RM} ${WRKSRC}/multiqc/utils/config.py.orig .include Index: head/biology/py-multiqc/distinfo =================================================================== --- head/biology/py-multiqc/distinfo (revision 518469) +++ head/biology/py-multiqc/distinfo (revision 518470) @@ -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 Index: head/biology/py-multiqc/files/patch-scripts_multiqc =================================================================== --- head/biology/py-multiqc/files/patch-scripts_multiqc (revision 518469) +++ head/biology/py-multiqc/files/patch-scripts_multiqc (nonexistent) @@ -1,32 +0,0 @@ ---- scripts/multiqc.orig 2018-12-21 17:29:54 UTC -+++ scripts/multiqc -@@ -6,18 +6,26 @@ - 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 pkg_resources - import re - import shutil - import subprocess --import sys - import tempfile - import traceback - Property changes on: head/biology/py-multiqc/files/patch-scripts_multiqc ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/py-multiqc/files/patch-multiqc_utils_config.py =================================================================== --- head/biology/py-multiqc/files/patch-multiqc_utils_config.py (revision 518469) +++ head/biology/py-multiqc/files/patch-multiqc_utils_config.py (nonexistent) @@ -1,41 +0,0 @@ ---- multiqc/utils/config.py.orig 2019-09-22 13:24:47 UTC -+++ multiqc/utils/config.py -@@ -42,13 +42,13 @@ MULTIQC_DIR = os.path.dirname(os.path.realpath(inspect - # Default MultiQC config - searchp_fn = os.path.join( MULTIQC_DIR, 'utils', 'config_defaults.yaml') - with open(searchp_fn) as f: -- configs = yaml.load(f) -+ configs = yaml.load(f, Loader=yaml.FullLoader) - for c, v in configs.items(): - globals()[c] = v - # Module filename search patterns - searchp_fn = os.path.join( MULTIQC_DIR, 'utils', 'search_patterns.yaml') - with open(searchp_fn) as f: -- sp = yaml.load(f) -+ sp = yaml.load(f, Loader=yaml.FullLoader) - - # Other defaults that can't be set in YAML - data_tmp_dir = '/tmp' # will be overwritten by core script -@@ -118,7 +118,7 @@ def mqc_load_config(yaml_config): - if os.path.isfile(yaml_config): - try: - with open(yaml_config) as f: -- new_config = yaml.load(f) -+ new_config = yaml.load(f, Loader=yaml.FullLoader) - logger.debug("Loading config settings from: {}".format(yaml_config)) - mqc_add_config(new_config, yaml_config) - except (IOError, AttributeError) as e: -@@ -132,11 +132,11 @@ def mqc_load_config(yaml_config): - def mqc_cl_config(cl_config): - for clc_str in cl_config: - try: -- parsed_clc = yaml.load(clc_str) -+ parsed_clc = yaml.load(clc_str, Loader=yaml.FullLoader) - # something:var fails as it needs a space. Fix this (a common mistake) - if isinstance(parsed_clc, str) and ':' in clc_str: - clc_str = ': '.join(clc_str.split(':')) -- parsed_clc = yaml.load(clc_str) -+ parsed_clc = yaml.load(clc_str, Loader=yaml.FullLoader) - assert(isinstance(parsed_clc, dict)) - except yaml.scanner.ScannerError as e: - logger.error("Could not parse command line config: {}\n{}".format(clc_str, e)) Property changes on: head/biology/py-multiqc/files/patch-multiqc_utils_config.py ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/py-multiqc/files/patch-multiqc_multiqc.py =================================================================== --- head/biology/py-multiqc/files/patch-multiqc_multiqc.py (nonexistent) +++ head/biology/py-multiqc/files/patch-multiqc_multiqc.py (revision 518470) @@ -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 + Property changes on: head/biology/py-multiqc/files/patch-multiqc_multiqc.py ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property