require spatialist>=0.17.0 and adapt to new interface

Author: johntruckenbrodt

environment-dev.yml

@@ -16,7 +16,7 @@ dependencies:
   - pyyaml
   - requests
   - shapely
-  - spatialist>=0.16.2
+  - spatialist>=0.17.0
   - sqlalchemy>=1.4,<2.0
   - sqlalchemy-utils>=0.37,<0.42
   - coverage

environment.yml

@@ -16,6 +16,6 @@ dependencies:
   - pyyaml
   - requests
   - shapely
-  - spatialist>=0.16.2
+  - spatialist>=0.17.0
   - sqlalchemy>=1.4,<2.0
   - sqlalchemy-utils>=0.37,<0.42

pyroSAR/examine.py

@@ -439,7 +439,7 @@ def __init__(self):
                                  getattr(self, 'home')).group('version')
 
         try:
-            out, err = run(['which', 'gdal-config'], void=False)
+            returncode, out, err = run(['which', 'gdal-config'], void=False)
             gdal_config = out.strip('\n')
             self.gdal_config = gdal_config
         except sp.CalledProcessError:

pyroSAR/gamma/auxil.py

@@ -452,7 +452,7 @@ def process(cmd, outdir=None, logfile=None, logpath=None,
     # create an environment containing the locations of all GAMMA submodules to be passed to the subprocess calls
     gammaenv = os.environ.copy()
     gammaenv['GAMMA_HOME'] = gamma_home
-    out, err = run([ExamineGamma().gdal_config, '--datadir'], void=False)
+    returncode, out, err = run([ExamineGamma().gdal_config, '--datadir'], void=False)
     gammaenv['GDAL_DATA'] = out.strip()
     for module in ['DIFF', 'DISP', 'IPTA', 'ISP', 'LAT']:
         loc = os.path.join(gammaenv['GAMMA_HOME'], module)
@@ -464,7 +464,8 @@ def process(cmd, outdir=None, logfile=None, logpath=None,
                     gammaenv['PATH'] += os.pathsep + subloc
 
     # execute the command
-    out, err = run(cmd, outdir=outdir, logfile=log, inlist=inlist, void=False, errorpass=True, env=gammaenv)
+    returncode, out, err = run(cmd, outdir=outdir, logfile=log, inlist=inlist,
+                               void=False, errorpass=True, env=gammaenv)
     gammaErrorHandler(out, err)
     if not void:
         return out, err

pyroSAR/snap/auxil.py

@@ -108,7 +108,7 @@ def parse_node(name, use_existing=True):
 
             cmd = [gpt, operator, '-h']
 
-            out, err = run(cmd=cmd, void=False)
+            returncode, out, err = run(cmd=cmd, void=False)
 
             if re.search('Unknown operator', out + err):
                 raise RuntimeError("unknown operator '{}'".format(operator))

requirements.txt

@@ -8,6 +8,6 @@ psycopg2
 pyyaml
 requests
 shapely
-spatialist>=0.16.2
+spatialist>=0.17.0
 sqlalchemy-utils>=0.37,<0.42
 sqlalchemy>=1.4,<2.0