Test failures

[yunesj]

testBasicCase2 (__main__.TestBasicUseCases) ... FAIL
testBasicCase2_WithGroups (__main__.TestBasicUseCases) ... FAIL

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FAIL: testBasicCase2 (__main__.TestBasicUseCases)
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Traceback (most recent call last):
  File "tests/test_configargparse.py", line 239, in testBasicCase2
    'positional arguments:\n'
AssertionError: Regexp didn't match: 'usage: .* \\[-h\\] --genome GENOME \\[-v\\] -g MY_CFG_FILE \\[-d DBSNP\\]\\s+\\[-f FRMT\\]\\s+vcf \\[vcf ...\\]\n\n(.+\\s+)(.+\\s+)(.+\\s+)(.+\\s+)(.+\\s+)(.+\\s+)(.+\\s+)(.+\\s+)(.+\\s+)positional arguments:\n  vcf \\s+ Variant file\\(s\\)\n\noptional arguments:\n  -h, --help \\s+ show this help message and exit\n  --genome GENOME \\s+ Path to genome file\n  -v\n  -g MY_CFG_FILE, --my-cfg-file MY_CFG_FILE\n  -d DBSNP, --dbsnp DBSNP\\s+\\[env var: DBSNP_PATH\\]\n  -f FRMT, --format FRMT\\s+\\[env var: OUTPUT_FORMAT\\]\n' not found in "usage: test_configargparse.py [-h] --genome GENOME [-v] -g MY_CFG_FILE\n                              [-d DBSNP] [-f FRMT]\n                              vcf [vcf ...]\n\nArgs that start with '--' (eg. --genome) can also be set in a config file\n(/etc/settings.ini or /home/jeff/.user_settings or\n/var/folders/jw/23sjzsn97lz8qj3kp4bg4pw00000gn/T/tmpUq7M1k or specified via\n-g). Config file syntax allows: key=value, flag=true, stuff=[a,b,c] (for\ndetails, see syntax at https://goo.gl/R74nmi). If an arg is specified in more\nthan one place, then commandline values override environment variables which\noverride config file values which override defaults.\n\npositional arguments:\n  vcf                   Variant file(s)\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --genome GENOME       Path to genome file\n  -v\n  -g MY_CFG_FILE, --my-cfg-file MY_CFG_FILE\n  -d DBSNP, --dbsnp DBSNP\n                        [env var: DBSNP_PATH]\n  -f FRMT, --format FRMT\n                        [env var: OUTPUT_FORMAT]\n"

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FAIL: testBasicCase2_WithGroups (__main__.TestBasicUseCases)
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Traceback (most recent call last):
  File "tests/test_configargparse.py", line 275, in testBasicCase2_WithGroups
    self.testBasicCase2(use_groups=True)
  File "tests/test_configargparse.py", line 253, in testBasicCase2
    'positional arguments:\n'
AssertionError: Regexp didn't match: 'usage: .* \\[-h\\] --genome GENOME \\[-v\\] -g MY_CFG_FILE \\[-d DBSNP\\]\\s+\\[-f FRMT\\]\\s+vcf \\[vcf ...\\]\n\n.+\\s+.+\\s+.+\\s+.+\\s+.+\\s+.+\\s+.+\\s+.+\\s+.+\\s+positional arguments:\n  vcf \\s+ Variant file\\(s\\)\n\noptional arguments:\n  -h, --help \\s+ show this help message and exit\n\ng1:\n  --genome GENOME \\s+ Path to genome file\n  -v\n  -g MY_CFG_FILE, --my-cfg-file MY_CFG_FILE\n\ng2:\n  -d DBSNP, --dbsnp DBSNP\\s+\\[env var: DBSNP_PATH\\]\n  -f FRMT, --format FRMT\\s+\\[env var: OUTPUT_FORMAT\\]\n' not found in "usage: test_configargparse.py [-h] --genome GENOME [-v] -g MY_CFG_FILE\n                              [-d DBSNP] [-f FRMT]\n                              vcf [vcf ...]\n\nArgs that start with '--' (eg. --genome) can also be set in a config file\n(/etc/settings.ini or /home/jeff/.user_settings or\n/var/folders/jw/23sjzsn97lz8qj3kp4bg4pw00000gn/T/tmp_leTr2 or specified via\n-g). Config file syntax allows: key=value, flag=true, stuff=[a,b,c] (for\ndetails, see syntax at https://goo.gl/R74nmi). If an arg is specified in more\nthan one place, then commandline values override environment variables which\noverride config file values which override defaults.\n\npositional arguments:\n  vcf                   Variant file(s)\n\noptional arguments:\n  -h, --help            show this help message and exit\n\ng1:\n  --genome GENOME       Path to genome file\n  -v\n  -g MY_CFG_FILE, --my-cfg-file MY_CFG_FILE\n\ng2:\n  -d DBSNP, --dbsnp DBSNP\n                        [env var: DBSNP_PATH]\n  -f FRMT, --format FRMT\n                        [env var: OUTPUT_FORMAT]\n"

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