= The Situation =

I wrote a script using Biopython which read a file containing a bunch of Genbank accession numbers, and downloaded the Genbank records:
{{{
#!python
### gentest.py

from Bio import GenBank

gi_list = ['AF339445', 'AF339444', 'AF339443', 'AF339442', 'AF339441']
record_parser = GenBank.FeatureParser()             # GenBank file parser
ncbi_dict = GenBank.NCBIDictionary(parser = record_parser,
                                   database = "nucleotide") # Dict for accessing NCBI

count = 1
for accession in gi_list:
    print "Accessing GenBank for %s... (%d/%d)" % (accession, count, len(gi_list))
    try:
        record = ncbi_dict[accession]           # Get record as SeqRecord
        RECORDS.append(record)                  # Put records in local list
    except:
        print "Accessing record %s failed" % accession


    count += 1
}}}

This worked fine as a script, but when I attempted to turn it into a Windows executable with py2exe and the setup.py script: 

{{{
#!python
### setup.py

from distutils.core import setup
import py2exe, sys

setup (name = "gentest",
       version = "0.10",
       url = r'http://bioinf.scri.sari.ac.uk/lp/index.shtml',
       author = "Leighton Pritchard",
       console = ["gentest.py"])
}}}

with the command {{{python setup.py py2exe}}}, attempting to run the resulting gentest.exe would throw an error.

= The Error =

This is the error thrown on running the executable:

{{{Traceback (most recent call last):
  File "gentest.py", line 1, in ?
  File "Bio\__init__.pyc", line 68, in ?
  File "Bio\__init__.pyc", line 55, in _load_registries
WindowsError: [Errno 3] The system cannot find the path specified: 
  'E:\\Data\\CVSWorkspace\\genbank2excel\\genbank2excel\\dist\\library.zip\\Bio\\config/*.*'}}}

= The Problem =

== Location of Bio.config ==
With help from Thomas Heller on the Python-Win32 mailing list, the problem was identified.  When the Bio package is imported, {{{Bio/__init__.py}}} imports a number of modules from the Bio.config module using the {{{_load_registries}}} function.  The first problem occurs in line 52: (file version 1.21 from CVS)

{{{
#!python
    x = os.listdir(
        os.path.dirname(__import__("Bio.config", {}, {}, ["Bio"]).__file__))
}}}

Under normal script-like execution, the {{{os.path.dirname}}} call returns a string indicating a location accessible through the filesystem via {{{os.listdir}}}.  However, py2exe uses new import hooks (via the builtin zipimport hook), described in PEP 302, so the location returned by the {{{os.path.dirname}}} call is located within the shared zip archive that py2exe creates.  As a result, {{{os.listdir}}} fails, and the above error is thrown.

== Module extensions ==
The arrangement with py2exe's shared zipfile causes problems further down the function.  The {{{_load_registries}}} function expects that modules will have the .py extension, rather than the .pyc extension that the compiled files (all that are included in the zipfile) use.  

{{{
#!python
    x = filter(lambda x: not x.startswith("_") and x.endswith(".py"), x)
    x = map(lambda x: x[:-3], x)            # chop off '.py'
}}}

Zipfile modules within Bio.config are thus not loaded.

= The Solution =

== Existing code ==
The code to be changed for the {{{_load_registries}}} method is (lines 50-55 in Bio/__init__.py CVS version 1.21)

{{{
#!python
    # Load the registries.  Look in all the '.py' files in Bio.config
    # for Registry objects.  Save them all into the local namespace.
    x = os.listdir(
        os.path.dirname(__import__("Bio.config", {}, {}, ["Bio"]).__file__))
    x = filter(lambda x: not x.startswith("_") and x.endswith(".py"), x)
    x = map(lambda x: x[:-3], x)            # chop off '.py'
}}}

Which obtains a list of modules, (for later import as Bio.config.module_name).

Since we cannot obtain the list of modules with this code, we need to provide an alternative way of generating the list when the modules are in the shared zipfile.

== Processing the zipfile ==

Firstly, we must determine whether the imported module comes from a zipfile, or is a straightforward import.  This is done by checking for the {{{.__loader__}}} attribute with {{{if hasattr(config_imports, '__loader__'):}}}

Next, we need to obtain the list of module files for Bio.config.  These are all found within the Bio/config folder, so we can filter the filenames in the shared zipfile using the {{{x = [zipfiles[file][0] for file in zipfiles.keys() if 'Bio\\config' in file]}}} list comprehension.

The filenames in this list are absolute paths, so we can grab just the filename with another list comprehension
{{{x = [name.split('\\')[-1] for name in x]}}}.

We have to lose the extensions from these filenames, too.  These are all .pyc files, so we can use a modification of the existing code's map and lambda {{{x = map(lambda x: x[:-4], x)}}}. [Note: we could easily combine the last two steps, but I keep them separate for clarity].

We now have the required list of module filenames.

Putting the steps together, and combining with the original code, we have:

{{{
#!python
    # Load the registries.  Look in all the '.py' files in Bio.config
    # for Registry objects.  Save them all into the local namespace.
    # Import code changed to allow for compilation with py2exe from distutils
    config_imports = __import__("Bio.config", {}, {}, ["Bio"])  # Import Bio.config
    if hasattr(config_imports, '__loader__'):                   # Is it in zipfile?
        zipfiles = __import__("Bio.config", {}, {}, ["Bio"]).__loader__._files
        x = [zipfiles[file][0] for file in zipfiles.keys() \
             if 'Bio\\config' in file]
        x = [name.split('\\')[-1] for name in x]# get filename
        x = map(lambda x: x[:-4], x)            # chop off '.pyc'
    else:                           # Not in zipfile, get files normally
        x = os.listdir(
            os.path.dirname(config_imports.__file__))
        x = filter(lambda x: not x.startswith("_") and x.endswith(".py"), x)
        x = map(lambda x: x[:-3], x)            # chop off '.py'
}}}

Compilation with the original setup.py script and {{{python setup.py py2exe}}} then ran smoothly, apart from a couple of missing modules which had no impact on the running of the executable.

= Update =
The changes have now (3rd Feb 04) been incorporated into the Biopython source in CVS.