How can I code a 'zoom to layer' applied to a vector layer when I build a QGIS standalone Python application?

Question

I am trying to code a standalone QGIS application that is able to print a composed map that zooms in the same layer every time I call it. The feature that have to be zoomed in change its location when is regenerated so my map application has to zoom in to a different place when I call it. I have been preparing an Atlas composer but when I call the print Python function it keeps the same area, it does not zoom to the chosen Atlas Layer. Another possibility is to zoom in to my layer every time I call the mapper, but I can't achieve it. I am adapting a code I found in the following Git repo without success: https://github.com/rjspiers/qgis-standalone-map-export

from qgis.core import *
import sys

print 'Hello from QGIS'

from qgis.core import (QgsProject, QgsComposition, QgsApplication, QgsProviderRegistry)
from qgis.gui import QgsMapCanvas, QgsLayerTreeMapCanvasBridge
from PyQt4.QtCore import QFileInfo, QObject
from PyQt4.QtXml import QDomDocument


gui_flag = True
app = QgsApplication(sys.argv, gui_flag)

# Make sure QGIS_PREFIX_PATH is set in your env if needed!
app.initQgis()

# project.qgs
project_path = r'D:\Fmesalessimulation\Simulator\qgis-standalone-map-export-master\smartfee_map.qgs'  # absolute filepath example: 'C:/folder/subfolder/project.qgs'

# template.qpt
template_path = r'D:\Fmesalessimulation\Simulator\qgis-standalone-map-export-master\smartfee_maptemplate.qpt'

#LayerIds
unused = 'BOUGHT_PAYS_DIFF20170130111140143'
sailedthrough = 'BOUGHT_UNITS20170130111140159'
optimalunits = 'PAYS_UNITS20170130111140165'
boundingbox = 'BOUNDING_BOX20170130111140161'


def make_pdf():
    canvas = QgsMapCanvas()
    # Load our project
    QgsProject.instance().read(QFileInfo(project_path))

    # Set canvas extent
    # canvas.setExtent(QgsRectangle(xmin, ymin, xmax, ymax))

    # Load layers here if they are not already in the project
    for layer in QgsMapLayerRegistry.instance().mapLayers().values():
        if layer.name() == 'BOUNDING_BOX':
            lyr = layer
            break
    # lyr.setSubsetString(filter_expression)
    #################
    list_layers = []
    for f in lyr.getFeatures():
        if f['unit_name'] != '':
            list_layers.append(f.id())
    print list_layers
    lyr.setSelectedFeatures(list_layers)
    box = lyr.boundingBoxOfSelected()
    lyr.setSelectedFeatures([])
    canvas.setExtent(box)
    canvas.refresh()
    canvas.show()
    #################
    # bridge used in standalone script: http://docs.qgis.org/testing/en/docs/pyqgis_developer_cookbook/loadproject.html
    bridge = QgsLayerTreeMapCanvasBridge(
        QgsProject.instance().layerTreeRoot(), canvas)
    bridge.setCanvasLayers()

    # Check data providers load ok
    print('Provider List')
    print(QgsProviderRegistry.instance().providerList())

    # Print layer validity - I've had some trouble with some wms layers
    for layer in QgsMapLayerRegistry.instance().mapLayers().values():
        print(layer.name())
        print(layer.isValid())

    template_file = file(template_path)
    template_content = template_file.read()
    template_file.close()
    document = QDomDocument()
    document.setContent(template_content)
    composition = QgsComposition(canvas.mapSettings())
    # You can use this to replace any string like this [key]
    # in the template with a new value. e.g. to replace
    # [date] pass a map like this {'date': '1 Jan 2012'}
    substitution_map = {'title': 'PyQGIS test'}
    # substitution_map = ''
    composition.loadFromTemplate(document, substitution_map)
    # You must set the id in the template
    map_item = composition.getComposerItemById('Main Map')
    map_item.setMapCanvas(canvas)
    map_item.zoomToExtent(canvas.extent())
    # You must set the id in the template
    legend_item = composition.getComposerItemById('Legend')
    legend_item.updateLegend()
    composition.refreshItems()
    composition.exportAsPDF(r'D:\Fmesalessimulation\Simulator\OUTPUT\JPG\PaysComparison.pdf')
    QgsProject.instance().clear()

make_pdf()