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

4 files changed, 9 insertions, 51 deletions

diff --git a/biology/py-multiqc/Makefile b/biology/py-multiqc/Makefile
index ff2051382123..2fd85fae288f 100644
--- a/biology/py-multiqc/Makefile
+++ b/biology/py-multiqc/Makefile
@@ -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} \
diff --git a/biology/py-multiqc/distinfo b/biology/py-multiqc/distinfo
index adbaecddc9c9..78a63fadeadd 100644
--- a/biology/py-multiqc/distinfo
+++ b/biology/py-multiqc/distinfo
@@ -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
diff --git a/biology/py-multiqc/files/patch-scripts_multiqc b/biology/py-multiqc/files/patch-multiqc_multiqc.py
index 34eef2e89279..d1a670b3bb56 100644
--- a/biology/py-multiqc/files/patch-scripts_multiqc
+++ b/biology/py-multiqc/files/patch-multiqc_multiqc.py
@@ -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
diff --git a/biology/py-multiqc/files/patch-multiqc_utils_config.py b/biology/py-multiqc/files/patch-multiqc_utils_config.py
deleted file mode 100644
index 707b510672f0..000000000000
--- a/biology/py-multiqc/files/patch-multiqc_utils_config.py
+++ /dev/null
@@ -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))