[Biopython-dev] README and python3

[Tiago Antão]

This was a local installation (on my home dir). As soon as I noticed
the problem I just removed 2to3 (as I had others - more recent). But
the python from which it was installed reports

>>> print sys.version_info

(2, 6, 0, 'final', 0)

2010/10/28 Peter <biopython at maubp.freeserve.co.uk>:
> 2010/10/27 Tiago Antão <tiagoantao at gmail.com>:
>> Hi,
>>
>> Just a minor issue with the README and python3.
>> The option --nofix does not exist in 2to3 for the 2.x version. So that
>> line will not work if the 2to3 happens to be from Python 2.X (can
>> happen if you have several versions installed).
>>
>
> Hi Tiago,
>
> Can you work out which version of 2to3 lacks the --nofix (or -x)
> option, and which version of Python it came from?
>
> The (Apple provided) Python 2.6.1 on my Mac seems to have
> a 2to3 with the --nofix option, and I don't have Python 3 installed
> on this machine. In addition to running 2to3 as a command line
> script, you can call the library from within Python:
>
> $ python2.6
> Python 2.6.1 (r261:67515, Feb 11 2010, 00:51:29)
> [GCC 4.2.1 (Apple Inc. build 5646)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from lib2to3.main import main
>>>> main("lib2to3.fixes", ["--help"])
> Usage: refactor.py [options] file|dir ...
>
> Options:
>  -h, --help            show this help message and exit
>  -d, --doctests_only   Fix up doctests only
>  -f FIX, --fix=FIX     Each FIX specifies a transformation; default: all
>  -x NOFIX, --nofix=NOFIX
>                        Prevent a fixer from being run.
>  -l, --list-fixes      List available transformations (fixes/fix_*.py)
>  -p, --print-function  Modify the grammar so that print() is a function
>  -v, --verbose         More verbose logging
>  -w, --write           Write back modified files
>  -n, --nobackups       Don't write backups for modified files.
>
> Likewise on our Linux server the 2to3 from Python 2.6.6, 2.7 and
> 3.1.2 all seem to have it:
>
> $ python2.6
> Python 2.6.6 (r266:84292, Aug 31 2010, 16:21:14)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from lib2to3.main import main
>>>> main("lib2to3.fixes", ["--help"])
> Usage: 2to3 [options] file|dir ...
>
> Options:
>  -h, --help            show this help message and exit
>  -d, --doctests_only   Fix up doctests only
>  -f FIX, --fix=FIX     Each FIX specifies a transformation; default: all
>  -j PROCESSES, --processes=PROCESSES
>                        Run 2to3 concurrently
>  -x NOFIX, --nofix=NOFIX
>                        Prevent a fixer from being run.
>  -l, --list-fixes      List available transformations
>  -p, --print-function  Modify the grammar so that print() is a function
>  -v, --verbose         More verbose logging
>  --no-diffs            Don't show diffs of the refactoring
>  -w, --write           Write back modified files
>  -n, --nobackups       Don't write backups for modified files.
>
> $ python2.7
> Python 2.7 (r27:82500, Jul 13 2010, 14:02:41)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from lib2to3.main import main
>>>> main("lib2to3.fixes", ["--help"])
> Usage: 2to3 [options] file|dir ...
>
> Options:
>  -h, --help            show this help message and exit
>  -d, --doctests_only   Fix up doctests only
>  -f FIX, --fix=FIX     Each FIX specifies a transformation; default: all
>  -j PROCESSES, --processes=PROCESSES
>                        Run 2to3 concurrently
>  -x NOFIX, --nofix=NOFIX
>                        Prevent a fixer from being run.
>  -l, --list-fixes      List available transformations
>  -p, --print-function  Modify the grammar so that print() is a function
>  -v, --verbose         More verbose logging
>  --no-diffs            Don't show diffs of the refactoring
>  -w, --write           Write back modified files
>  -n, --nobackups       Don't write backups for modified files.
>
>
> $ python3.1
> Python 3.1.2 (r312:79147, Jul 15 2010, 12:43:37)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from lib2to3.main import main
>>>> main("lib2to3.fixes", ["--help"])
> Usage: 2to3 [options] file|dir ...
>
> Options:
>  -h, --help            show this help message and exit
>  -d, --doctests_only   Fix up doctests only
>  -f FIX, --fix=FIX     Each FIX specifies a transformation; default: all
>  -j PROCESSES, --processes=PROCESSES
>                        Run 2to3 concurrently
>  -x NOFIX, --nofix=NOFIX
>                        Prevent a fixer from being run.
>  -l, --list-fixes      List available transformations (fixes/fix_*.py)
>  -p, --print-function  Modify the grammar so that print() is a function
>  -v, --verbose         More verbose logging
>  --no-diffs            Don't show diffs of the refactoring
>  -w, --write           Write back modified files
>  -n, --nobackups       Don't write backups for modified files.
>
>
> Note that we *need* the --nofix option for the conversion of
> Bio.Phylo to work (it uses long as an argument name,
> short longitude).
>
> Peter
>



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