Rename check.py to runcheck and use execfile

Huge speedup!

CHANGES.rst

@@ -1,6 +1,27 @@
 Release notes
 #############
 
+Version 3.5.0
+=============
+
+- Added new classes for MesoNh, Symp張onie and WW3 models
+- Added cfgui: graphical user interface to ConfigMgr
+- Added support for 4D interpolation to grid2xy
+- Added linear4dto1dxx
+- Add tcompress, bound_ops and haversine to vcmq
+- Rename check.py to runcheck
+- Fix kinetic_energy: bad indexes
+- Fix cfgm merging
+- Fix vacumm.misc.file.strfsize
+- Fix OceanDataset.get_mld density issue
+- Fix missing datetime import for tfind
+- Fix ConfigManager warning when default value is not scalar
+- Fix fix xml text nodes load
+- Fix Logger defaults
+- Fix Object class logging funcName
+- Fix spherical variogram
+- Fix imports in basemap
+- Fix cdtime validator in config
 
 Version 3.4.1
 =============

lib/python/vacumm/misc/file.py

@@ -151,9 +151,9 @@ def rollover(filepath, count=1, suffix='.%d', keep=True, verbose=False):
 def strfsize(size, fmt=None, unit=None, si=False, suffix=True):
     '''
     Format a size in bytes using the appropriate unit multiplicator (Ko, Mo, Kio, Mio)
-    
+
     :Params:
-    
+
         * **size**:
             the size in bytes
         * **fmt**:
@@ -163,15 +163,15 @@ def strfsize(size, fmt=None, unit=None, si=False, suffix=True):
             use an auto determinated unit if None, or the given one among %s
         * **si**:
             whether to use SI (International System) units (10^3, ...) or binary units (2^10, ...)
-    
+
     :Return: a string
     '''
-    
+
     units_dict = _si_size_units if si else _size_units
     units = reversed(_sorted_si_size_units if si else _sorted_size_units)
     unit_suffix = 'o' if si else 'io'
     size = float(size)
-    
+
     fmt_unit, fmt_ratio = '', 1
     if unit is None:
         for unit, threshold in units:
@@ -183,7 +183,7 @@ def strfsize(size, fmt=None, unit=None, si=False, suffix=True):
         if unit not in units_dict:
             raise ValueError('Invalid unit, must be one of: %s'%(_strfsize_doc_sorted_units))
         fmt_unit, fmt_ratio = unit, units_dict[unit]
-    
+
     fmt_size = size / fmt_ratio
     if fmt is None:
         fmt = '%(size).3f %(unit)s' if float(fmt_size) % 1 else '%(size)d %(unit)s'
@@ -201,7 +201,7 @@ def strpsize(size, si=False):
     :Params:
 
         - **size**: the size string (eg. "1Ko", "1Kio", "2 Mo", " 10 Go"
-        - **si**: when unit does not ends with 'io' force interpretation as 
+        - **si**: when unit does not ends with 'io' force interpretation as
                   International System units (10^3, ...) instead of binary units (2^10, ...)
 
     :Return: the float number of bytes

scripts/tutorials/Makefile

@@ -1,4 +1,4 @@
 all: checks
 
-checks: check.py
-	python check.py
+checks: runcheck
+	python runcheck

scripts/tutorials/bathy.bathy.gridded.base.py

@@ -1,4 +1,7 @@
 # -*- coding: utf8 -*-
+
+import pylab as P
+
 # Récupération d'une bathy sous la forme d'une variable cdat
 import cdms2
 cdms2.axis.latitude_aliases.append('y')
@@ -35,8 +38,8 @@
 
 # Plots
 from matplotlib import rc ; rc('font', size=9);rc('axes', titlesize=9)
-kwplot = dict(resolution=None, show=False, colorbar=False, contour=False, 
-    top=.97, hspace=.25, bottom=.03, right=.98, 
+kwplot = dict(resolution=None, show=False, colorbar=False, contour=False,
+    top=.97, hspace=.25, bottom=.03, right=.98,
     autoresize=False, vmax=bathy_orig.max(), vmin=bathy_orig.min())
 # - colormap
 from vacumm.misc.color import auto_cmap_topo, land
@@ -52,3 +55,4 @@
 # - sauvegarde
 from vacumm.misc.plot import savefigs
 savefigs(__file__)
+P.close()

scripts/tutorials/bathy.bathy.gridded.merging.py

@@ -1,4 +1,6 @@
 # -*- coding: utf8 -*-
+import pylab as P
+
 # Création de bathymétries fictives à partir de Smith and Sandwell
 import cdms2
 from vacumm.config import data_sample
@@ -44,4 +46,4 @@
 add_grid(grid_large, color='r', **kwgrid)
 add_grid(var_small.getGrid(), color='#00ff00', **kwgrid)
 savefigs(__file__)
-
+P.close()

scripts/tutorials/bathy.bathy.xyz.base.py

@@ -67,7 +67,7 @@
 # Extraction d'une sous-zone (xmin,ymin...) avec marge
 xyz_up = xyz.clip(zone=(None, None, None, 48.3), margin=2)
 # - si None, valeurs limites internes (i.e xyz.xmin(), ...)
-# - margin : marge relative en unite de resolution 
+# - margin : marge relative en unite de resolution
 #   -> ici : ymax = 48.3 + xyz.resol()[1]*2
 
 # Sauvegarde
@@ -82,17 +82,18 @@
 P.figure(figsize=(4.5, 8))
 P.rc('font', size=8)
 P.subplots_adjust(top=.95, hspace=.25, left=.1, bottom=.05, right=.98)
-m = map2(lon=(xc-xr, xc+xr), lat=(yc-yr, yc+yr), proj='merc', 
-    subplot=311, autoresize=0, resolution='f', show=False, drawmeridians_rotation=45, 
+m = map2(lon=(xc-xr, xc+xr), lat=(yc-yr, yc+yr), proj='merc',
+    subplot=311, autoresize=0, resolution='f', show=False, drawmeridians_rotation=45,
     ticklabel_size=9, xhide=True)
-kwplot = dict(vmin=xyz.get_zmin(False), vmax=xyz.get_zmax(False), 
+kwplot = dict(vmin=xyz.get_zmin(False), vmax=xyz.get_zmax(False),
     m=m, show=False, colorbar=False)
 # - xyz
 xyz.plot(size=10, mode='both', masked_alpha=.1, **kwplot)
 # - interpole manuellement
 kwplot.update(autoresize=0, ticklabel_size=9)
 map2(gridded_manual, subplot=312, xhide=True, title='Sur grille manuelle', **kwplot)
 # - interpole auto
-map2(gridded_auto, subplot=313, title='Sur grille auto', savefigs=__file__, **kwplot)
+map2(gridded_auto, subplot=313, title='Sur grille auto', savefigs=__file__,
+    close=True, **kwplot)
 #P.show()
 

scripts/tutorials/bathy.bathy.xyz.bathybank.py

@@ -1,5 +1,5 @@
 # Creation de fausses bathymetries xyz
-import numpy as N,  os
+import numpy as N,  os, pylab as P
 from vacumm.bathy.bathy import XYZBathy,  XYZBathyBank
 # - fonction generatrice
 def gene_bathy(xc, yc, r, n):
@@ -44,7 +44,7 @@ def gene_bathy(xc, yc, r, n):
 
 # Suppression d'une bathy
 bank.remove('south')
-#  on peut aussi utiliser: 
+#  on peut aussi utiliser:
 #  >>> bank -= 'south'
 #  >>> bank -= bsouth
 #  >>> del bank['south']
@@ -53,5 +53,6 @@ def gene_bathy(xc, yc, r, n):
 bsouth = bank['north'].load()
 
 # Plot de l'ensemble
-bank.plot(size=15,  map_proj='cyl', map_res=None, savefigs=__file__, 
+bank.plot(size=15,  map_proj='cyl', map_res=None, savefigs=__file__,
     savefigs_pdf=True, show=False)
+P.close()

scripts/tutorials/bathy.bathy.xyz.merging.py

@@ -24,7 +24,7 @@ def gene_bathy(xc, yc, xr, yr, n=500, amp=30.):
 import pylab as P ; P.figure(figsize=(5., 8.5)) ; P.subplot(311)
 P.rcParams['font.size'] = 9
 P.subplots_adjust(bottom=.03, top=.97, hspace=.25)
-kwplot = dict(show=False, colorbar=False,map_res=None, margin=0., map_autoresize=0, 
+kwplot = dict(show=False, colorbar=False,map_res=None, margin=0., map_autoresize=0,
     xmin=xyz.xmin, xmax=xyz.xmax, ymin=xyz.ymin, ymax=xyz.ymax)
 xyz.plot(title='Fusion directe', **kwplot)
 
@@ -53,13 +53,13 @@ def gene_bathy(xc, yc, xr, yr, n=500, amp=30.):
 merger.plot(mode='value', title='Merger : valeurs', **kwplot)
 # - cluster
 P.subplot(313)
-merger.plot(mode='cluster', size=10, title='Merger : cluster', marker='o', 
+merger.plot(mode='cluster', size=10, title='Merger : cluster', marker='o',
     legend_loc='upper left', savefigs=__file__, savefigs_pdf=True, **kwplot)
-    
+
 # On recupere le tout dans un xyz
 merged_xyz = merger.get_xyz(long_name='Merged')
 
 # On peut donc le sauvegarder
 merged_xyz.save(__file__[:-2]+'merged.xyz')
-
+P.close()
 

scripts/tutorials/bathy.shorelines.compare.py

@@ -14,9 +14,9 @@
     m='auto', show=False)
 
 # Fin de plot
-from pylab import show, legend, title
+from pylab import show, legend, title, close
 from vacumm.misc.plot import savefigs
 legend()
 title("Ushant shorelines")
 savefigs(__file__, pdf=True)
-
+close()

scripts/tutorials/bathy.shorelines.readplot.py

@@ -4,7 +4,7 @@
 from vcmq import code_base_name
 
 m = map2(lat=(48.41, 48.49), lon=(-5.15, -5), show=False,
-    fillcontinents=False, drawcoastlines=False, figsize=(5.5, 4), 
+    fillcontinents=False, drawcoastlines=False, figsize=(5.5, 4),
      bgcolor=ocean, left=.12, top=.9)
 
 # Fichier au 1/25000eme avec selection de la zone de la carte
@@ -28,8 +28,9 @@
     xx, yy = poly.boundary.transpose() # coordonnees
     P.fill(xx, yy, alpha=.5, facecolor='g', linewidth=0) # coloriage
 
-# Fin du trace 
-from pylab import show, title
+# Fin du trace
+from pylab import show, title, close
 from vacumm.misc.plot import savefigs
 title('Trait de cote SHOM/IGN 1/25000')
 savefigs(code_base_name(ext='png'), pdf=True)
+close()

scripts/tutorials/bathy.shorelines.sealevel.py

@@ -1,4 +1,6 @@
 # -*- coding: utf8 -*-
+import pylab as P
+
 # Definition de la region de travail Bretagne
 zone = (-6.5, 47.2, -2, 49.05)
 
@@ -11,3 +13,4 @@
 
 # Plot
 xyz.plot(size=10, savefigs=__file__, show=False)#, savefigs_pdf=True)
+P.close()

scripts/tutorials/data.misc.sigma.py

@@ -46,7 +46,8 @@
 # Plot
 kw = dict(show=False, vmin=10, vmax=14, xhide='auto', add_grid=True, ymax=0)
 section2(data_in[0, :, 10], yaxis=depths_in[0, :, 10], subplot=211, title='Sigma', **kw)
-s = section2(data_out[0, :, 10], subplot=212, title='Z', savefigs=__file__, **kw)
+s = section2(data_out[0, :, 10], subplot=212, title='Z', savefigs=__file__,
+    close=True, **kw)
 
 # Sauvegarde
 outfile = __file__[:-2]+'nc'

scripts/tutorials/general.scripts.level1.py

@@ -32,7 +32,7 @@
 print 'plot'
 map2(mld, proj='merc', figsize=(6, 4), autoresize=0,
     fill='pcolormesh',  contour=False, show=False,
-    colorbar_shrink=0.7, right=1, savefigs=__file__)
+    colorbar_shrink=0.7, right=1, savefigs=__file__, close=True)
 
 
 print 'Done'