map.xml

<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE Map[]>
<Map srs="+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0.0 +k=1.0 +units=m +nadgrids=@null +wktext +no_defs +over" background-color="white">


<Style name="countries" filter-mode="first">
  <Rule>
    <PolygonSymbolizer fill="blue" />
  </Rule>
</Style>
<Layer name="countries"
  srs="+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0.0 +k=1.0 +units=m +nadgrids=@null +wktext +no_defs +over">
    <StyleName>countries</StyleName>
    <Datasource>
       <Parameter name="file"><![CDATA[data/82945364-10m-admin-0-countries.shp]]></Parameter>
       <Parameter name="type"><![CDATA[shape]]></Parameter>
<!--
       <Parameter name="file"><![CDATA[data/broke.json]]></Parameter>
       <Parameter name="type"><![CDATA[ogr]]></Parameter>
       <Parameter name="layer_by_index"><![CDATA[0]]></Parameter>
-->
    </Datasource>
  </Layer>

<Style name="shoreline300" filter-mode="first">
  <Rule>
    <PolygonSymbolizer fill="red" />
  </Rule>
</Style>
<Layer name="shoreline300"
  srs="+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0.0 +k=1.0 +units=m +nadgrids=@null +wktext +no_defs +over">
    <StyleName>shoreline300</StyleName>
    <Datasource>
       <Parameter name="file"><![CDATA[data/shoreline_300.shp]]></Parameter>
       <Parameter name="type"><![CDATA[shape]]></Parameter>
    </Datasource>
  </Layer>

</Map>

test.py

import mapnik

m = mapnik.Map(512,512)
mapnik.load_map(m,'z18/map.xml')

# /Users/dane/Documents/MapBox/project/z18/layers/countries/

# z17, works
# http://localhost:20008/tile/z18/17/20990/45795.png?updated=1328918555000
extent = [ -13619855.447965845,
  6035467.753397517,
  -13619243.951739565,
  6036079.249623798 ]

# z18, busted
# http://localhost:20008/tile/z18/18/41981/91591.png?updated=1328918555000
extent = [ -13619855.447965845,
  6035467.753397517,
  -13619549.699852705,
  6035773.501510657 ]


box = mapnik.Box2d(*extent)
m.zoom_to_box(box)
mapnik.render_to_file(m,'missing.png')

import os
os.system('open missing.png')