[Biopython-dev] Biopython 1.66 release?

[Peter Cock]

Hi Ben,

I did a little reading about how to make an MSI file. Specifically
https://docs.python.org/2/distutils/builtdist.html suggested:

python setup.py bdist_msi

This worked fine on my old Windows XP machine for:

C:\Python33\python setup.py bdist_wininst
C:\Python34\python setup.py bdist_wininst

However Python 2.6 and 2.7 fail somewhat cryptically giving
me an incomplete MSI file:

> C:\Python27\python setup.py bdist_wininst
...
running install_egg_info
Writing build\bdist.win32\msi\Lib\site-packages\biopython-1.66-py2.7.egg-info
Traceback (most recent call last):
  File "setup.py", line 493, in <module>
    setup(**setup_args)
  File "c:\python27\lib\distutils\core.py", line 152, in setup
    dist.run_commands()
  File "c:\python27\lib\distutils\dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "c:\python27\lib\distutils\dist.py", line 972, in run_command
    cmd_obj.run()
  File "c:\python27\lib\distutils\command\bdist_msi.py", line 255, in run
    self.add_files()
  File "c:\python27\lib\distutils\command\bdist_msi.py", line 308, in add_files
    key = seen[afile] = dir.add_file(file)
  File "c:\python27\lib\msilib\__init__.py", line 340, in add_file
    short = self.make_short(file)
  File "c:\python27\lib\msilib\__init__.py", line 299, in make_short
    assert file not in self.short_names
AssertionError

>From a little debugging this was a bug in the standard library
where Bio/Entrez/DTDs/MMDB.dtd and MMDB.mod.dtd are
both mapped to the upper case short name MMDB.DTD, without
noticing the middle part of the filename. i.e.

http://bugs.python.org/issue1128

This should have been fixed as part of:

http://bugs.python.org/issue7639

It looks like I need to update to Python 2.7.2 or later for the fix, but
it may never have been addressed in an official Python 2.6.x
release (I could backport this if required).

Leaving those problematic builds aside, do you think I should
upload these 32-bit MSI files for Biopython 1.66?

Peter

On Thu, Oct 22, 2015 at 9:58 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Thanks Ben,
>
> This has all changed since back when I used Windows - you're
> perhaps in a good position to take charge of Biopython on Windows?
>
> Peter
>
> On Thu, Oct 22, 2015 at 7:23 PM, Ben Fulton <ben at benfulton.net> wrote:
>> I installed the Python 2.7 version successfully on Windows. Building an MSI
>> might be advisable instead of an exe, though; on Windows 8 I get:
>>
>> "Windows protected your PC. Windows SmartScreen prevented an unrecognized
>> app from starting. Running this app might put your PC at risk"
>>
>> To install it you have to click "More info", which tells you that the
>> publisher is unknown and has a button that says "Run anyway".
>>