Git commit from Python with GitPython delete files committed from command line

Here is the code I use to create a new file and commit it :

# We are inside a home-made class, using GitPython
# So self.repo is a Repo() object from GitPython module

def set_content(self, path, content, commit_msg=None):
    """ Add new content in ``path``. """

    # Create the stream
    stream = StringIO(content.encode('utf-8'))
    stream.seek(0, 2)
    streamlen = stream.tell()
    stream.seek(0)

    istream = IStream('blob', streamlen, stream)

    # Add it to the repository object database
    self.repo.odb.store(istream)

    # Create the corresponding Blob object
    blob = Blob(self.repo, istream.binsha, 0100644, path.encode('utf-8'))

    # Commit
    self.repo.index.add([IndexEntry.from_blob(blob)])

    if not commit_msg:
        commit_msg = ugettext(u'Update Wiki: {0}').format(path).encode('utf-8')

    self.repo.index.commit(commit_msg)

    # Update internal informations
    self.parse()

It works just fine.

The problem comes when I commit in the git repository from the git command line :

• commit from set_content()
• commit from set_content()
• commit from command line
• new commit from set_content() : files committed by the previous commit are deleted.

I can't understand where is the mistake.

If someone is able to help me, thanks :)