doc, admin and script updates

.gitignore

@@ -4,6 +4,6 @@ build/
 dist/
 cache/
 .eggs/
-tmpdata/
+data/
 .Rproj.user
 apikey.sh

README.md

@@ -1,4 +1,4 @@
-*[this documentation refers to a non-current revision of this software and will be updated accordingly]*
+*[this documentation is in the process of being updated to reflect the current codebase...]*
 
 # Household Microsynthesis
 
@@ -24,9 +24,9 @@ pip3 install git+git://github.com/virgesmith/UKCensusAPI.git
 ```
 - [humanleague](https://github.com/virgesmith/humanleague)
 ```
-pip3 install git+git://github.com/virgesmith/humanleague.git@1.0.1
+pip3 install git+git://github.com/virgesmith/humanleague.git
 ```
-NB Ensure you install the version 1.0.1 of humanleague. Later versions have breaking changes and/or are under heavy development.
+NB Ensure you install humanleague version 2 or higher - this package uses features that are not available in earlier versions.
 
 ### Installation and Testing
 ```
@@ -38,10 +38,11 @@ NB Ensure you install the version 1.0.1 of humanleague. Later versions have brea
 ```
 scripts/run_microsynth.py <region(s)> <resolution>
 ```
-where region can be a one or more local authorities (or one of England, EnglandWales, GB, UK) and resolution can be one of: LA, MSOA, LSOA, OA. If there are spaces in the former, enclose the argument in quotes, e.g.
+where region can be a one or more local authorities (or one of England, EnglandWales, GB, UK), specified by either name or ONS/GSS code (e.g. E09000001). If there are spaces in the former, enclose the argument in quotes, e.g.
 ```
-scripts/run_microsynth.py "City of London" OA
+scripts/run_microsynth.py "City of London" OA11
 ```
+Resolution can be one of: LA, MSOA11, LSOA11, OA11. 
 
 # Overview
 

batch.sh

@@ -1,5 +1,10 @@
 #!/bin/bash
 
+if [ ! -f ./apikey.sh ]; then
+  echo "api key not found. Please specify your Nomisweb API key in ./apikey.sh, e.g.:"
+  echo "export NOMIS_API_KEY=0x0123456789abcdef0123456789abcdef01234567"
+  exit 1
+fi
 . ./apikey.sh
 
 source activate testenv1
@@ -32,11 +37,11 @@ E09000022 E09000023 E09000024 E09000025 E09000026 E09000027 E09000028 E09000029
 W06000004 W06000005 W06000006 W06000008 W06000009 W06000010 W06000011 W06000012 W06000013 W06000014 W06000015 W06000016 W06000018 W06000019 W06000020 \
 W06000021 W06000022 W06000023 W06000024"
 
+resolution="OA11"
 
+# max run time (NB Birmingham takes longest at ~6h)
 qsub_params="-l h_rt=8:0:0"
 
-resolution="OA11"
-
 for region in $regions; do
   outfile="hh_"$region"_"$resolution".csv"
   if [ ! -f $outfile ]; then

requirements.txt

@@ -1,3 +1,3 @@
 distutils_pytest
-git+git://github.com/virgesmith/humanleague.git@1.0.1
+git+git://github.com/virgesmith/humanleague.git
 git+git://github.com/virgesmith/UKCensusAPI.git

setup.py

@@ -7,7 +7,7 @@ def readme():
     return f.read()
 
 setup(name='household_microsynth',
-  version='0.1',
+  version='0.0.1',
   description='Household microsynthesis',
   long_description=readme(),
   url='https://github.com/nismod/household_microsynth',
@@ -17,7 +17,7 @@ def readme():
   packages=['household_microsynth'],
   zip_safe=False,
   install_requires=['distutils_pytest', 'humanleague', 'ukcensusapi'],
-  dependency_links=['git+git://github.com/virgesmith/humanleague.git#egg=humanleague-1.0',
+  dependency_links=['git+git://github.com/virgesmith/humanleague.git#egg=humanleague',
                     'git+git://github.com/virgesmith/UKCensusAPI.git#egg=ukcensusapi'],
   test_suite='nose.collector',
   tests_require=['nose'],

single.sh

@@ -1,12 +1,20 @@
 #!/bin/bash
 
-# single job submission
-
-# TODO pass (and check) args from cmd line
+# single job submission - args from cmd line
+if [ "$#" -ne 2 ]; then
+  echo "Usage: $0 <region(s)> <resolution>"
+  echo   e.g. $0 E09000001 OA11
+  exit 1
+fi
 
-region=W06000016
-resolution=OA11
+region=$1
+resolution=$2
 
+if [ ! -f ./apikey.sh ]; then
+  echo "api key not found. Please specify your Nomisweb API key in ./apikey.sh, e.g.:"
+  echo "export NOMIS_API_KEY=0x0123456789abcdef0123456789abcdef01234567"
+  exit 1
+fi
 . ./apikey.sh
 
 source activate testenv1