add function generate argument parser

and modified plain test to work with it. other tests still need to be
updated though.

bfps/__init__.py

@@ -51,3 +51,41 @@ from .fluid_converter import fluid_converter
 from .fluid_resize import fluid_resize
 from .NavierStokes import NavierStokes
 
+import argparse
+
+def get_parser(base_class = NavierStokes,
+               n = 32,
+               ncpu = 2,
+               precision = 'single',
+               simname = 'test',
+               work_dir = './',
+               njobs = 1):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--run', dest = 'run', action = 'store_true')
+    parser.add_argument('-n',
+            type = int, dest = 'n',
+            default = n)
+    parser.add_argument('--ncpu',
+            type = int, dest = 'ncpu',
+            default = ncpu)
+    parser.add_argument('--precision',
+            type = str, dest = 'precision',
+            default = precision)
+    parser.add_argument('--simname',
+            type = str, dest = 'simname',
+            default = simname)
+    parser.add_argument('--wd',
+            type = str, dest = 'work_dir',
+            default = work_dir)
+    parser.add_argument('--njobs',
+            type = int, dest = 'njobs',
+            default = njobs)
+    c = base_class()
+    for k in sorted(c.parameters.keys()):
+        parser.add_argument(
+                '--{0}'.format(k),
+                type = type(c.parameters[k]),
+                dest = k,
+                default = c.parameters[k])
+    return parser
+

bfps/base.py

@@ -101,6 +101,11 @@ class base(object):
             for k in data_file['parameters'].keys():
                 self.parameters[k] = data_file['parameters/' + k].value
         return None
+    def pars_from_namespace(self, opt):
+        new_pars = vars(opt)
+        for k in self.parameters.keys():
+            self.parameters[k] = new_pars[k]
+        return None
     def get_coord(self, direction):
         assert(direction == 'x' or direction == 'y' or direction == 'z')
         return np.arange(.0, self.parameters['n' + direction])*2*np.pi / self.parameters['n' + direction]

tests/test_base.py

@@ -22,42 +22,19 @@
 
 import os
 import subprocess
-import argparse
 import pickle
 
-import numpy as np
-from mpl_toolkits.mplot3d import axes3d
-import matplotlib.pyplot as plt
-import h5py
-
 import bfps
 from bfps import fluid_resize
 
-parser = argparse.ArgumentParser()
-parser.add_argument('--run', dest = 'run', action = 'store_true')
+parser = bfps.get_parser()
 parser.add_argument('--initialize', dest = 'initialize', action = 'store_true')
-parser.add_argument('-n',
-        type = int, dest = 'n', default = 64)
 parser.add_argument('--iteration',
         type = int, dest = 'iteration', default = 0)
-parser.add_argument('--ncpu',
-        type = int, dest = 'ncpu', default = 2)
-parser.add_argument('--nsteps',
-        type = int, dest = 'nsteps', default = 16)
-parser.add_argument('--njobs',
-        type = int, dest = 'njobs', default = 1)
-parser.add_argument('--nparticles',
-        type = int, dest = 'nparticles', default = 8)
 parser.add_argument('--neighbours',
         type = int, dest = 'neighbours', default = 3)
 parser.add_argument('--smoothness',
         type = int, dest = 'smoothness', default = 2)
-parser.add_argument('--wd',
-        type = str, dest = 'work_dir', default = 'data')
-parser.add_argument('--precision',
-        type = str, dest = 'precision', default = 'single')
-parser.add_argument('--multiplejob',
-        dest = 'multiplejob', action = 'store_true')
 
 def double(opt):
     old_simname = 'N{0:0>3x}'.format(opt.n)
@@ -100,7 +77,7 @@ def launch(
     c = code_class(
             work_dir = opt.work_dir,
             fluid_precision = opt.precision)
-    assert((opt.nsteps % 4) == 0)
+    c.pars_from_namespace(opt)
     c.parameters['nx'] = opt.n
     c.parameters['ny'] = opt.n
     c.parameters['nz'] = opt.n
@@ -109,11 +86,9 @@ def launch(
     else:
         c.parameters['nu'] = nu
     c.parameters['dt'] = 5e-3 * (64. / opt.n)
-    c.parameters['niter_todo'] = opt.nsteps
-    c.parameters['niter_out'] = opt.nsteps
     c.parameters['niter_part'] = 1
     c.parameters['famplitude'] = 0.2
-    c.parameters['nparticles'] = opt.nparticles
+    if c.parameters['nparticles'] > 0:
         c.add_particles(kcut = 'fs->kM/2',
                         integration_steps = 1, neighbours = opt.neighbours, smoothness = opt.smoothness)
         c.add_particles(integration_steps = 1, neighbours = opt.neighbours, smoothness = opt.smoothness)

tests/test_plain.py

@@ -21,6 +21,12 @@
 
 from test_base import *
 
+import numpy as np
+import matplotlib.pyplot as plt
+
+parser.add_argument('--multiplejob',
+        dest = 'multiplejob', action = 'store_true')
+
 def plain(opt):
     wd = opt.work_dir
     opt.work_dir = wd + '/N{0:0>3x}_1'.format(opt.n)
@@ -30,7 +36,7 @@ def plain(opt):
         return None
     opt.work_dir = wd + '/N{0:0>3x}_2'.format(opt.n)
     opt.njobs *= 2
-    opt.nsteps /= 2
+    opt.niter_todo /= 2
     c1 = launch(opt)
     c1.compute_statistics()
     # plot energy and enstrophy

tox_plain.ini

@@ -9,7 +9,7 @@ changedir =
     {envtmpdir}
 commands =
     cp -r {toxinidir}/tests {envtmpdir}
-    python tests/test_plain.py -n 256 --run --initialize --ncpu 8 --nsteps 8 --precision single --wd "data/single"
-    #python tests/test_plain.py -n 32 --run --initialize --ncpu 2 --nsteps 64 --precision single --wd "data/single"
-    #python tests/test_plain.py -n 32 --run --initialize --ncpu 2 --nsteps 64 --precision double --wd "data/double"
+    #python tests/test_plain.py -n 256 --run --initialize --ncpu 8 --niter_todo 8 --precision single --wd "data/single"
+    python tests/test_plain.py -n 32 --run --initialize --multiplejob --ncpu 2 --nparticles 16 --niter_todo 64 --precision single --wd "data/single"
+    python tests/test_plain.py -n 32 --run --initialize --multiplejob --ncpu 2 --nparticles 16 --niter_todo 64 --precision double --wd "data/double"