addon r.mess: change to using format for python string formatting an …

…update email address
OSGeo · Jun 8, 2019 · ddd8bcc · ddd8bcc
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Showing 3 changed files with 126 additions and 11 deletions.
diff --git a/grass7/raster/r.mess/r.mess.html b/grass7/raster/r.mess/r.mess.html
@@ -152,7 +152,7 @@ <h2>REFERENCES</h2>
 
 <h2>AUTHOR</h2>
 
-Paulo van Breugel, paulo at ecodiv.org
+Paulo van Breugel, paulo at ecodiv.earth
 
 
 <p><i>Last changed: $Date$</i>
diff --git a/grass7/raster/r.mess/r.mess.py b/grass7/raster/r.mess/r.mess.py
@@ -4,7 +4,7 @@
 ########################################################################
 #
 # MODULE:       r.mess
-# AUTHOR(S):    Paulo van Breugel <p.vanbreugel AT gmail.com>
+# AUTHOR(S):    Paulo van Breugel <paulo ecodiv earth>
 # PURPOSE:      Calculate the multivariate environmental similarity
 #               surface (MESS) as proposed by Elith et al., 2010,
 #               Methods in Ecology & Evolution, 1(330–342).
@@ -201,8 +201,8 @@ def main(options, flags):
            reftype['max'] != 1):
             gs.fatal(_("The ref_rast map must be a binary raster,"
                        " i.e. it should contain only values 0 and 1 or 1 only"
-                       " (now the minimum is %d and maximum is %d)")
-                     % (reftype['min'], reftype['max']))
+                       " (now the minimum is {} and maximum is {})".
+                       format(reftype['min'], reftype['max'])))
 
     # old environmental layers & variable names
     REF = options['env']
@@ -222,8 +222,8 @@ def main(options, flags):
         raster_exists(PROJ)
         if len(PROJ) != len(REF) and len(PROJ) != 0:
             gs.fatal(_("The number of reference and predictor variables"
-                       " should be the same. You provided %d reference and %d"
-                       " projection variables") % (len(REF), len(PROJ)))
+                       " should be the same. You provided {} reference and {}"
+                       " projection variables".format(len(REF), len(PROJ))))
 
     # output layers
     opl = options['output']
@@ -368,7 +368,7 @@ def main(options, flags):
             gs.run_command("r.mask", quiet=True, flags="r")
 
         # Upload raster values and get value in python as frequency table
-        sql1 = "SELECT cat FROM %s" % tmpf0
+        sql1 = "SELECT cat FROM {}".format(str(tmpf0))
         cn = len(np.hstack(db.db_select(sql=sql1)))
         for m in xrange(len(REF)):
 
@@ -382,12 +382,12 @@ def main(options, flags):
             mid = str(m)
             laytype = gs.raster_info(REF[m])['datatype']
             if laytype == 'CELL':
-                columns = "envvar_%s integer" % mid
+                columns = "envvar_{} integer".format(str(mid))
             else:
                 columns = "envvar_%s double precision" % mid
             gs.run_command("v.db.addcolumn", map=tmpf0, columns=columns,
                            quiet=True)
-            sql2 = "UPDATE %s SET envvar_%s = NULL" % (tmpf0, mid)
+            sql2 = "UPDATE {} SET envvar_{} = NULL".format(str(tmpf0), str(mid))
             gs.run_command("db.execute", sql=sql2, quiet=True)
             coln = "envvar_%s" % mid
             gs.run_command("v.what.rast", quiet=True, map=tmpf0,
@@ -402,9 +402,9 @@ def main(options, flags):
 
             # Check for point without values
             if b < cn:
-                gs.info(_("Please note that there were %d points without "
+                gs.info(_("Please note that there were {} points without "
                           "value. This is probably because they are outside "
-                          "the computational region or mask") % (cn - b))
+                          "the computational region or mask".format((cn - b))))
 
             # Set region to env_proj layers (if different from env) and remove
             # mask (if set above)

diff --git a/grass7/raster/r.mess/tests/r_mess_tests.txt b/grass7/raster/r.mess/tests/r_mess_tests.txt
@@ -0,0 +1,115 @@
+#-----------------------------------------------------------------------
+# Test 1 - same area, without mask
+#-----------------------------------------------------------------------
+g.remove type=raster pattern=Ex_* -f
+g.region raster=bio1
+r.mess2 env=bio1,bio12,bio15 \
+        output=Ex_01
+r.mess2 -c -k -m -n env=bio1,bio12,bio15 \
+        ref_rast=ppa \
+        output=Ex_02
+r.mess2 -c -k -m -n \
+        env=bio1,bio12,bio15 \
+        env_proj=IPSL_bio1,IPSL_bio12,IPSL_bio15 \
+        output=Ex_03
+r.mess2 -c -k -m -n \
+        env=bio1,bio12,bio15 \
+        ref_vect=sample_locations@mess \
+        output=Ex_04
+r.mess2 -c -k -m -n env=bio1,bio12,bio15 \
+        env_proj=IPSL_bio1,IPSL_bio12,IPSL_bio15 \
+        ref_vect=sample_locations@mess \
+        output=Ex_05
+
+#-----------------------------------------------------------------------
+# Test 2 - same area, with mask
+#-----------------------------------------------------------------------
+g.remove type=raster pattern=Ex_* -f
+g.region raster=bio1
+r.mask raster=pnvmap
+r.mess2 env=bio1,bio12,bio15 \
+        output=Ex_06
+r.mask raster=pnvmap
+r.mess2 -c -k -m -n env=bio1,bio12,bio15 \
+        ref_rast=ppa \
+        output=Ex_07
+r.mask raster=pnvmap
+r.mess2 -c -k -m -n \
+        env=bio1,bio12,bio15 \
+        env_proj=IPSL_bio1,IPSL_bio12,IPSL_bio15 \
+        output=Ex_08
+r.mask raster=pnvmap
+r.mess2 -c -k -m -n \
+        env=bio1,bio12,bio15 \
+        ref_vect=sample_locations@mess \
+        output=Ex_09
+r.mask raster=pnvmap
+r.mess2 -c -k -m -n env=bio1,bio12,bio15 \
+        env_proj=IPSL_bio1,IPSL_bio12,IPSL_bio15 \
+        ref_vect=sample_locations@mess \
+        output=Ex_10
+
+#-----------------------------------------------------------------------
+# Test 3 - different reference and projection area, without mask
+#-----------------------------------------------------------------------
+g.remove type=raster pattern=Ex_* -f
+r.mask -r
+g.region raster=bio1
+r.mess2 -c -k -m -n \
+        env=bio1,bio12,bio15 \
+        env_proj=bio1_Eth,bio12_Eth,bio15_Eth \
+        output=Ex_11
+g.region raster=bio1
+r.mess2 -c -k -m -n \
+        env=bio1,bio12,bio15 \
+        env_proj=bio1_Eth,bio12_Eth,bio15_Eth \
+        ref_rast=ppa \
+        output=Ex_12
+g.region raster=bio1
+r.mess2 -c -k -m -n \
+        env=bio1,bio12,bio15 \
+        env_proj=bio1_Eth,bio12_Eth,bio15_Eth \
+        ref_vect=sample_locations@mess \
+        output=Ex_13
+
+# Test 3 - different reference and projection area, with mask
+#-----------------------------------------------------------------------
+g.remove type=raster pattern=Ex_* -f
+g.region raster=bio1
+r.mask raster=pnvmap
+r.mess2 -c -k -m -n \
+        env=bio1,bio12,bio15 \
+        env_proj=bio1_Eth,bio12_Eth,bio15_Eth \
+        output=Ex_14
+g.region raster=bio1
+r.mask raster=pnvmap
+r.mess2 -c -k -m -n \
+        env=bio1,bio12,bio15 \
+        env_proj=bio1_Eth,bio12_Eth,bio15_Eth \
+        ref_rast=ppa \
+        output=Ex_15
+g.region raster=bio1
+r.mask raster=pnvmap
+r.mess2 -c -k -m -n \
+        env=bio1,bio12,bio15 \
+        env_proj=bio1_Eth,bio12_Eth,bio15_Eth \
+        ref_vect=sample_locations@mess \
+        output=Ex_16
+
+# Test 4 - Compare tests that should give the same results
+#-----------------------------------------------------------------------
+g.region raster=bio1
+r.mask -r
+r.mess2 -c -k -m -n env=bio1,bio12,bio15 \
+        ref_rast=ppa \
+        output=Ex_02
+
+r.mask raster=ppa
+r.mess2 -c -k -m -n env=bio1,bio12,bio15 output=Ex_17
+
+
+
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