[Biopython-dev] Martel changes

[Andrew Dalke]

Me to Jeff:
>What do you define as punctuation?

Duh!  I see there's a "string.punctuation".
"Punctuation" added to CVS.

Also added:
  Digits == \d+
  Word == \w+
  Spaces == same as \s+ except not including newline
  Unprintable == AnyBut(string.printable)

These all take an optional name and attributes for a Group.

Changed "Integer" to "[+-]?\d+" (It had been the same
as what Digits is now.)

Removed SignedInteger.

Added a new type of Expression -- NullOp.  This simplified
the implementation of Time.py

New submodule "Time.py" for building patterns and/or expressions
for parsing strings.  Has a full regression test and docstring.

Added "LAX" as a new way to handle "simple" XML records.
Docstring may need some updating.  (It's too late for me to
think clearly enough to tell if the documentation is reasonable.)
Also, additional documentation on the topic, which I send earlier
today to c.l.py, is attached to this email.

Bug fixed! - someone in personal email pointed out the named
group backreferences ("(?P=name)" construct) weren't working.
Turned out I didn't even have a regression test for that
case.  Both problems now fixed.

Regression tests added for all the new code.  All tests pass.

Some cleanup here and there.

Excepting that it would be nice if others could check that
my new code (and changes) really does work, I'm ready for
a new release.  Even ready for a new Martel release.

                    Andrew
                    dalke at dalkescientific.com

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From: "Andrew Dalke" <dalke at dalkescientific.com>
Subject: Re: XML parsing besides SAX and DOM
Date: Fri, 14 Dec 2001 14:13:06 -0700
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