MiniWDL does not properly support the POSIX regex standard

[stxue1]

The WDL spec says that regular expressions must be evaluated as POSIX ERE.

MiniWDL does attempt to support the POSIX standard:

miniwdl/WDL/StdLib.py

Line 74 in 475dd3f

pattern_re = regex.compile(pattern.value, flags=regex.POSIX) # pylint: disable=E1101

One of the character classes the POSIX standard supports is [:alpha:]

MiniWDL does not properly support the character classes. For example, in the WDL file below:

version 1.1

workflow test_sub {
  String string_to_sub = "word"

  output {
    String out = sub(string_to_sub, "[:alpha:]{4}", "4444")
  }
}

miniwdl returns:

{
  "dir": "/home/heaucques/Documents/wdl-conformance-tests/20240726_121643_test_sub",
  "outputs": {
    "test_sub.out": "word"
  }
}

I think this is due to the regex pypi library that miniwdl uses. While it says it supports the POSIX standard, the syntax is a little different than what is expected:
https://github.com/mrabarnett/mrab-regex?tab=readme-ov-file#posix-character-classes

Replacing [:alpha:] with [[:alpha:]] as per the regex documentation allows the substitution to work:

version 1.1

workflow test_sub {
  String string_to_sub = "word"

  output {
    String out = sub(string_to_sub, "[[:alpha:]]{4}", "4444")
  }
}

{
  "dir": "/home/heaucques/Documents/wdl-conformance-tests/20240726_121923_test_sub",
  "outputs": {
    "test_sub.out": "4444"
  }
}

The substitution unit test in the WDL spec depends on this behavior, meaning MiniWDL does not currently pass it:
https://github.com/openwdl/wdl/blob/9c0b9cf4586508a9e6260cc5c5e562e21f625aac/SPEC.md?plain=1#L6480-L6496