fix killing simulation in non-local folder, fix testing finished plots, add documentation in Readme, stop leaving open a lot of file handles, add testing for 3.6

Author: nhoening

README.rst

@@ -11,7 +11,7 @@ but StoSim takes over a lot of tedious work from there on. StoSim can
 * analyse the results with graphical plots and T-tests (it is easy to analyse results made with specific parameter settings)
 * back up code and results (to be able to go back to important milestones)
 
-You can find extensive documentation at http://www.nicolashoening.de/stosim/ and example simulations in the "example" folder.
+You can find tutorials and extensive documentation at http://stosim.nicolashoening.de and example simulations in the "example" folder.
 
 
 Installation/Dependencies
@@ -40,9 +40,18 @@ Running a simulation: A quick overview
 Place an experiment configuration (stosim.conf) and your simulation code in a folder of your choice (see basic example in the examples folder).
 Call::
 
-    stosim --folder <path-to-your-experiment-folder>
+    stosim
+    
+This assumes that you placed a configuration file describing your jobs (called `stosim.conf`) in the current folder.
+It also assumes you want to run the jobs, and in addition perform T-Tests and make plots (if stosim.conf says how). So the above command is synonymous to::
+
+    stosim --folder . --run --ttests --plots
 
-You can leave the --folder option away if stosim.conf is in the current directory.
 The results will be put in the "data" directory, in your folder 
-(but if you like the plotting capabilities of StoSim you might never have to look there).
+(but if you like the plotting/analysis capabilities of StoSim you might never have to look there).
+
+One more example, where you know your stosim.conf is in a different folder and you only want to run::
+
+    stosim --folder <path-to-your-experiment-folder> --run
 
+There are more features, e.g. `--more` to add more stochastic runs, `--list` to inspect data or `--snapshot` to make a snapshots of results at a given time that can be loaded back later. Do check out the tutorials where you can learn more. 

stosim/__init__.py

@@ -1 +1 @@
-__version__ = '0.2.20'
+__version__ = '0.2.22'

stosim/analysis/harvester.py

@@ -65,13 +65,11 @@ def collect_values(filepath, delim, outfile_name, cols=[], selector='all'):
     vals = []
     files = [f for f in os.listdir(filepath) if f.endswith('.dat')]
     for f in files:
-        tmp = open('%s/%s' % (filepath, f), 'r')
-        vals.extend(selector(tmp, cols, delim))
-    out = open(outfile_name, 'w')
-    for v in vals:
-        out.write('%s' % str(v))
-    out.close()
-
+        with open('%s/%s' % (filepath, f), 'r') as tmp:
+            vals.extend(selector(tmp, cols, delim))
+    with open(outfile_name, 'w') as out:
+        for v in vals:
+            out.write('%s' % str(v))
 
 
 # ---- selectors ----

stosim/sim/commands.py

@@ -58,8 +58,8 @@ def run(simfolder):
         copy("{}/jobs/{}".format(simfolder, job),
              "{}/jobqueue".format(fjd_dir))
     dispatch_cmd = 'fjd-dispatcher --project {} --end_when_jobs_are_done '\
-                   ' --callback "stosim --kill" --interval {}'\
-                   .format(sim_name, utils.get_interval(simfolder))
+                   ' --callback "stosim --folder {} --kill" --interval {}'\
+                   .format(sim_name, simfolder, utils.get_interval(simfolder))
 
     # now decide if recruiting is done in a local network or on a PBS cluster
     scheduler = utils.get_scheduler(simfolder)

stosim/tests/test_integration.py

@@ -57,7 +57,11 @@ def test_data(self):
 
     def test_plots(self):
         assert(os.path.exists('{}/plots'.format(self.edir)))
-        assert(os.listdir('{}/plots'.format(self.edir)) == self.plots)
+        plots_made = os.listdir('{}/plots'.format(self.edir))
+        plots_expected = self.plots
+        plots_made.sort()
+        plots_expected.sort()
+        assert(plots_made == plots_expected)
 
 
 class TestSubsimExample(TestBasicExample):

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist=py27,py33
+envlist=py27,py36
 
 [testenv]
 deps=