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biology/py-multiqc: Upgrade to 1.8

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Major enhancements including 6 new modules and improvements to existing modules
Numerous minor fixes and enhancements

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2019-11-26 16:25:08 +00:00
parent 698e8c8201
commit 795a4fecb2
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=518470
4 changed files with 9 additions and 51 deletions
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3
biology/py-multiqc/Makefile
View File

@ -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} \

6
biology/py-multiqc/distinfo
View File

@ -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

10
biology/py-multiqc/files/patch-scripts_multiqc → biology/py-multiqc/files/patch-multiqc_multiqc.py
View File

@ -1,10 +1,9 @@
--- scripts/multiqc.orig 2018-12-21 17:29:54 UTC
+++ scripts/multiqc
@@ -6,18 +6,26 @@
from __future__ import print_function
--- 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 click
+import os
+import sys
+
@ -22,7 +21,6 @@
import io
import jinja2
-import os
import pkg_resources
import re
import shutil
import subprocess

41
biology/py-multiqc/files/patch-multiqc_utils_config.py
View File

@ -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))