House keeping - fix broken test

.gitignore

@@ -23,3 +23,7 @@ test/repository/variables/model.xml.bak1
 test/repository/variables/model.xml.bak2
 ../test/grass_location/PERMANENT/.bashrc
 *.pyc
+grass-modules/**/*.tmp.html
+grass-modules/**/OBJ*
+*.swp
+*.un~

README.md

@@ -1,36 +1,27 @@
-# MDiG - Modular Dispersal in GIS
+# mdig - Modular Dispersal in GIS
 
-## Requirements
+## Setup
 
-- [**GRASS 6.4RC5**](http://grass.itc.it/download/index.php) or later, hasn't been tested with the new GRASS 7.0.
-  In particular, we recommend an SVN snapshot as RC5 has an annoying
-  g.region issue that can be confusing for new users.
-- [**GDAL 1.6.0**](http://trac.osgeo.org/gdal/wiki/DownloadingGdalBinaries) or later (earlier versions have bugs)
-  Although it is a GRASS requirement instead of a direct MDiG one, stuff can
-  break if you have earlier buggy versions.
-
-- ImageMagick's convert utility (imagemagick)
-- [lxml](http://codespeak.net/lxml/) and its dependency, the [Gnome XML library](http://xmlsoft.org/)
-- GNU Scientific Library (libgsl, libgsl0-dev) http://www.gnu.org/software/gsl/
-
-    sudo apt-get install \
-       gsl-bin libgsl0-dev bc libxml2 libxml2-dev python-lxml python-imaging-tk \
-       python-scipy python-matplotlib python-numpy python-configobj python-paste \
-       python-simplejson imagemagick
-
-- Python dependencies 
+    sudo apt-get install grass grass-dev
+    sudo apt-get install libxml2 libxml2-dev gsl-bin libgsl0-dev imagemagick bc
 
+    # Numpy and scipy are potentially finicky, so safest to install them separate
+    # and in order:
+    mkvirtualenv mdig
+    pip install numpy
+    pip install scipy
+    # Rest of python dependencies should be fine, ensure you are in mdig root dir
     pip install -r requirements.txt
 
-## Compile modules
+That's the core mdig simulation manager, but to install the custom GRASS
+modules that are particularly useful for people modelling dispersal:
 
-Change into MDiG's grass-module dir
+    cd grass-modules
+    sudo make MODULE_TOPDIR=/usr/lib/grass64
 
-    cd mdig/grass-modules
+Or if you installed GRASS from source, you can do something like:
 
-and run:
-
-    export GRASS_SRC=~/src/grass63_release
+    export GRASS_SRC=~/src/grass64_release
     make -S MODULE_TOPDIR=$GRASS_SRC
     cd $GRASS_SRC
     make install
@@ -41,3 +32,9 @@ These are the requests that I've had for MDiG to support:
 
 * [PRIORITY] Keep track of area treated by management strategies.
 
+## Troubleshooting
+
+Older versions of requirements have some bugs to be aware of:
+
+* GRASS 6.4RC5 has an annoying g.region issue that can be confusing for new users.
+* GDAL <1.6.0 or later, earlier versions can run into segfaults.

TESTING

@@ -1,25 +1,19 @@
-If you wish to run the unit tests for MDiG while developing code, then install
-nosetests for python which is a testing framework, and optionally "coverage"
-which is to measure the code coverage of tests:
+If you wish to run the unit tests for MDiG while developing code, then go to
+the mdig program directory ('mdig/' from the root of the source) and run:
 
- easy_install nose coverage paste
-
-Then if you go to the mdig program directory (mdig/ from the root of the source)
-and run:
-
- nosetests -v
+    nosetests -v
 
 Or to run with code coverage analysis:
 
- nosetests -v --with-coverage
+    nosetests -v --with-coverage
 
 You'll run a bunch of tests to check everything's working correctly.
 
-Note - currently only basic tests are run, more rigarous tests are
-needed (although this has been greatly improved over the last year):
-* More model files that more thoroughly test the potential model types.
+Note - currently only basic tests are run, more rigorous tests are needed
+(although this has been greatly improved over the last year):
+
+* Additional model files that more thoroughly test the potential model types.
 * More coverage in unit tests for components within MDiG.
 * Comparison of the output maps from various models versus what the expected map
   should look like. For modules, create before and after maps and make sure they
   have no difference,implement as a shell script to be run within GRASS.
-

mdig/mdig/config.py

@@ -102,18 +102,20 @@ def find_grass_base_dir():
             opts = glob.glob(os.path.join(os.environ['OSGEO4W_ROOT'],'apps\\grass\\grass-*'))
     else:
         opts = glob.glob('/usr/local/grass-*')
-    if len(opts) > 0: return opts[-1]
-    else: return None
+        opts.extend(glob.glob('/usr/lib/grass*'))
+    if len(opts) > 0:
+        return opts[-1]
 
 def find_grassdb_dir():
     # TODO find from GRASS environment if it exists
     # find from guessing /home/user/src/mdig/test
     my_path = os.path.normpath(os.path.join(home_dir, '..', 'src/mdig/test'))
-    if os.path.isdir(my_path): return my_path
+    if os.path.isdir(my_path):
+        return my_path
     if 'OSGEO4W_ROOT' in os.environ:
         my_path = os.path.normpath(os.path.join(os.environ['OSGEO4W_ROOT'], 'src/mdig/test'))
-        if os.path.isdir(my_path): return my_path
-    return None
+        if os.path.isdir(my_path):
+            return my_path
 
 def find_location_dir():
     # TODO find from GRASS environment if it exists
@@ -127,7 +129,6 @@ def find_location_dir():
             if os.path.isdir(d) and \
                     os.path.isdir(os.path.join(d,'PERMANENT')):
                 return os.path.basename(d)
-    return None
 
 class MDiGConfig(ConfigObj):
 
@@ -311,7 +312,8 @@ def prompt_for_config(self,section,k,fresh):
         if section in MDiGConfig.required \
                 and k in MDiGConfig.required[section]:
             guess = MDiGConfig.required[section][k]
-        if guess: guess = guess() # guess should be a callable
+        if guess:
+            guess = guess() # guess should be a callable
         if not fresh:
             print "While setting up config, required parameter %s:%s was missing" % (section,k)
         is_done = False

mdig/mdig/grass.py

@@ -24,8 +24,6 @@
 import logging
 import random
 import re
-import signal
-import pdb
 import subprocess
 from subprocess import Popen
 import StringIO
@@ -251,7 +249,6 @@ def init_pid_specific_files(self):
         os.environ["GISRC"]=gisrc_fn
 
     def get_version_from_dir(self):
-        import re
         if sys.platform == 'win32':
             # TODO - place this in config and make NSIS script write it
             self.grass_version = "6.4.0svn"
@@ -260,7 +257,7 @@ def get_version_from_dir(self):
             try:
                 x=re.match(r'grass-(\d\.\d\.[\d\w]+)', end_bit)
                 self.grass_version = x.groups()[0]
-            except IndexError, e:
+            except (IndexError, AttributeError):
                 self.grass_version = "6.4.0svn"
         return self.grass_version
 

mdig/mdig/tests/__init__.py

@@ -19,6 +19,7 @@ def setup():
     # Copy test repository
     c = config.get_config()
     c['GRASS']['GISBASE'] = config.find_grass_base_dir()
+    assert c['GRASS']['GISBASE'], "Couldn't find GRASS GISBASE"
     global test_dir
     test_dir = tempfile.mkdtemp(prefix="mdig_test_")
     end_part = os.path.split(c['GRASS']['GISDBASE'])[1]

mdig/mdig/tests/mdig.conf

@@ -8,7 +8,7 @@ GRASS_HTML_BROWSER = firefox
 GRASS_MESSAGE_FORMAT = silent
 GRASS_GNUPLOT = gnuplot -persist
 MAPSET = PERMANENT
-GISBASE = c:\\mdig
+GISBASE = /usr/lib/grass64
 GISDBASE = ../test
 GRASS_TRUECOLOR = TRUE
 GRASS_PAGER = cat

requirements.txt

@@ -5,6 +5,8 @@ python-dateutil<2.0
 numpy
 scipy
 matplotlib
-imagetk
+pillow
+nose
+coverage
 paste
-
+mock