From bd27b8132c458df5f6583369de2c90dd36ec2bbb Mon Sep 17 00:00:00 2001
From: bolliger32 <bolliger32@local>
Date: Mon, 3 Jun 2019 19:51:39 +0000
Subject: [PATCH 1/8] return returncode in runclaw

---
 src/python/clawutil/runclaw.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/python/clawutil/runclaw.py b/src/python/clawutil/runclaw.py
index 3f55be3..d3f08da 100755
--- a/src/python/clawutil/runclaw.py
+++ b/src/python/clawutil/runclaw.py
@@ -259,6 +259,8 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=None,
 
     if returncode != 0:
         print('==> runclaw: *** fortran returncode = ', returncode, '   aborting')
+        
+    return returncode
     
 
 #----------------------------------------------------------

From 1d44ea3a88b34a33666e76a98f00c35baa2e3601 Mon Sep 17 00:00:00 2001
From: bolliger32 <bolliger32@local>
Date: Tue, 4 Jun 2019 02:20:30 +0000
Subject: [PATCH 2/8] use subprocess for runclaw

---
 src/python/clawutil/runclaw.py | 29 +++++++++++++++++++++--------
 1 file changed, 21 insertions(+), 8 deletions(-)

diff --git a/src/python/clawutil/runclaw.py b/src/python/clawutil/runclaw.py
index d3f08da..8599a99 100755
--- a/src/python/clawutil/runclaw.py
+++ b/src/python/clawutil/runclaw.py
@@ -14,10 +14,13 @@
 import sys
 import glob
 import shutil
+import shlex
+import subprocess
 from clawpack.clawutil.claw_git_status import make_git_status_file
 
 def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=None, 
-            rundir=None, print_git_status=False, nohup=False, nice=None):
+            rundir=None, print_git_status=False, nohup=False, nice=None,
+            stdout=None, stderr=None):
     """
     Run the Fortran version of Clawpack using executable xclawcmd, which is
     typically set to 'xclaw', 'xamr', etc.
@@ -45,6 +48,10 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=None,
 
     If type(nice) is int, runs the code using "nice -n "
     with this nice value so it doesn't hog computer resources.
+    
+    if stdout or stderr are not None, they must be open python file handles.
+    The stdout and stderr from the call to CLAW_EXE will be written to
+    them.
 
     """
     
@@ -234,20 +241,26 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=None,
                 else:
                     cmd = "nohup time %s " % xclawcmd
                 print("\n==> Running with command:\n   ", cmd)
-                returncode = os.system(cmd)
             else:
                 if type(nice) is int:
                     cmd = "nice -n %s %s " % (nice,xclawcmd)
                 else:
                     cmd = xclawcmd
                 print("\n==> Running with command:\n   ", cmd)
-                returncode = os.system(cmd)
+            
+            cmd_split = shlex.split(cmd)
+            p = subprocess.Popen(cmd_split,
+                                 stdout=stdout,
+                                 stderr=stderr,
+                                 encoding='latin-1',
+                                 bufsize=1)
+            p.communicate()
     
-            if returncode == 0:
+            if p.returncode == 0:
                 print("\n==> runclaw: Finished executing\n")
             else:
                 print("\n ==> runclaw: *** Runtime error: return code = %s\n "\
-                        % returncode)
+                        % p.returncode)
             print('==> runclaw: Done executing %s via clawutil.runclaw.py' %\
                         xclawcmd)
             print('==> runclaw: Output is in ', outdir)
@@ -257,10 +270,10 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=None,
     
         os.chdir(startdir)
 
-    if returncode != 0:
-        print('==> runclaw: *** fortran returncode = ', returncode, '   aborting')
+    if p.returncode != 0:
+        print('==> runclaw: *** fortran returncode = ', p.returncode, '   aborting')
         
-    return returncode
+    return p.returncode
     
 
 #----------------------------------------------------------

From 50b31ce790b3da6a26ccb716a42ccefca8489e79 Mon Sep 17 00:00:00 2001
From: bolliger32 <bolliger32@local>
Date: Mon, 17 Jun 2019 02:53:57 +0000
Subject: [PATCH 3/8] clawutil threadsafe changes

---
 src/python/clawutil/data.py    |  24 ++-
 src/python/clawutil/runclaw.py | 294 ++++++++++++++-------------------
 src/python/clawutil/test.py    |  43 +++--
 3 files changed, 167 insertions(+), 194 deletions(-)

diff --git a/src/python/clawutil/data.py b/src/python/clawutil/data.py
index dcfd915..edb18fd 100644
--- a/src/python/clawutil/data.py
+++ b/src/python/clawutil/data.py
@@ -14,6 +14,8 @@
 from __future__ import absolute_import
 from __future__ import print_function
 import os
+from inspect import signature
+
 try:
     from urllib.request import urlopen
 except ImportError:
@@ -458,7 +460,6 @@ def __init__(self, pkg, num_dim):
             import clawpack.amrclaw.data as amrclaw
 
             self.xclawcmd = 'xamr'
-            self.add_data(ClawInputData(num_dim),'clawdata')
             self.add_data(amrclaw.AmrclawInputData(self.clawdata),'amrdata')
             self.add_data(amrclaw.RegionData(num_dim=num_dim),'regiondata')
             self.add_data(amrclaw.GaugeData(num_dim=num_dim),'gaugedata')
@@ -517,16 +518,25 @@ def new_UserData(self,name,fname):
         return data
 
 
-    def write(self):
+    def write(self, out_dir = ''):
         r"""Write out each data objects in datalist """
         
         import clawpack.amrclaw.data as amrclaw
 
         for data_object in self.data_list:
+            # UserData doesn't naturally have an "out_file" parameter
+            if isinstance(data_object, UserData):
+                fname = data_object.__fname__
+            else:
+                try:
+                    fname = signature(data_object.write).parameters['out_file'].default
+                except:
+                    raise ValueError(type(data_object))
+            fpath = os.path.join(out_dir,fname)
             if isinstance(data_object, amrclaw.GaugeData):
-                data_object.write(self.clawdata.num_eqn, self.clawdata.num_aux)
+                data_object.write(self.clawdata.num_eqn, self.clawdata.num_aux, out_file=fpath)
             else:
-                data_object.write()
+                data_object.write(out_file=fpath)
 
 
 
@@ -841,6 +851,8 @@ def add_param(self,name,value,descr=''):
          descr_dict = self.__descr__
          descr_dict[name] = descr
 
-    def write(self,data_source='setrun.py'):
-        super(UserData,self).write(self.__fname__, data_source)
+    def write(self, data_source='setrun.py', out_file=None):
+        if out_file is None:
+            out_file = self.__fname__
+        super(UserData,self).write(out_file, data_source)
         self.close_data_file()
diff --git a/src/python/clawutil/runclaw.py b/src/python/clawutil/runclaw.py
index 8599a99..271f925 100755
--- a/src/python/clawutil/runclaw.py
+++ b/src/python/clawutil/runclaw.py
@@ -18,9 +18,19 @@
 import subprocess
 from clawpack.clawutil.claw_git_status import make_git_status_file
 
+# define an execution error class that returns a
+# message as well as the rest of the subprocess exceptions
+class ClawExeError(subprocess.CalledProcessError):
+    def __init__(self, msg, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.msg = msg
+        
+    def __str__(self):
+        return self.msg
+
 def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=None, 
             rundir=None, print_git_status=False, nohup=False, nice=None,
-            stdout=None, stderr=None):
+            xclawout=subprocess.PIPE, xclawerr=subprocess.PIPE):
     """
     Run the Fortran version of Clawpack using executable xclawcmd, which is
     typically set to 'xclaw', 'xamr', etc.
@@ -49,18 +59,17 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=None,
     If type(nice) is int, runs the code using "nice -n "
     with this nice value so it doesn't hog computer resources.
     
-    if stdout or stderr are not None, they must be open python file handles.
-    The stdout and stderr from the call to CLAW_EXE will be written to
-    them.
+    xclawout and xclawerr define the locations of stdout and stderr for the 
+    execution of CLAW_EXE. They should be strings to filepaths or open file
+    objects or ``subprocess.PIPE`` or ``subprocess.STDOUT``. To pass both
+    to the same file, specify ``xclawout`` as the filepath and 
+    ``xclawerr=subprocess.STDOUT``.
 
     """
-    
     from clawpack.clawutil.data import ClawData
     import os,glob,shutil,time
     verbose = True
-    xclawout = None
-    xclawerr = None
-
+    
     try:
         nice = int(nice)
     except:
@@ -88,7 +97,7 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=None,
 
     if outdir is None:
         outdir = '.'
-        
+
     if rundir is None:
         rundir = os.getcwd()
     rundir = os.path.abspath(rundir)
@@ -103,177 +112,120 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=None,
         clawdata = ClawData()
         clawdata.read(os.path.join(rundir,'claw.data'), force=True) 
         restart = clawdata.restart
-        #print '+++ From claw.data determined restart = %s' % restart
-
-    
-    #returncode = clawjob.runxclaw()
-
-    if 1:
-        startdir = os.getcwd()
-        xdir = os.path.abspath(startdir)
-        outdir = os.path.abspath(outdir)
-        rundir = os.path.abspath(rundir)
-        xclawcmd = os.path.join(xdir,xclawcmd)
         
+    xclawcmd = os.path.abspath(xclawcmd)
+
+    if os.path.isfile(outdir):
+        print("==> runclaw: Error: outdir specified is a file")
+        return
+
+    if (os.path.isdir(outdir) & (not overwrite)):
+        # copy the old outdir before possibly overwriting
+        tm = time.localtime(os.path.getmtime(outdir))
+        year = str(tm[0]).zfill(4)
+        month = str(tm[1]).zfill(2)
+        day = str(tm[2]).zfill(2)
+        hour = str(tm[3]).zfill(2)
+        minute = str(tm[4]).zfill(2)
+        second = str(tm[5]).zfill(2)
+        outdir_backup = outdir + '_%s-%s-%s-%s%s%s' \
+              % (year,month,day,hour,minute,second)
+        if verbose:
+            print("==> runclaw: Directory already exists: ",os.path.split(outdir)[1])
+            if restart:
+                print("==> runclaw: Copying directory to:      ",os.path.split(outdir_backup)[1])
+            else:
+                print("==> runclaw: Moving directory to:      ",os.path.split(outdir_backup)[1])
+            time.sleep(1)
+
         try:
-            os.chdir(xdir)
+            shutil.move(outdir,outdir_backup)
+            if restart:
+                shutil.copytree(outdir_backup,outdir)
         except:
-            raise Exception( "==> runclaw: Cannot change to directory xdir = %s" %xdir)
-            return 
-    
-    
-        if os.path.isfile(outdir):
-            print("==> runclaw: Error: outdir specified is a file")
-            return
-        
-        if (os.path.isdir(outdir) & (not overwrite)):
-            # copy the old outdir before possibly overwriting
-            tm = time.localtime(os.path.getmtime(outdir))
-            year = str(tm[0]).zfill(4)
-            month = str(tm[1]).zfill(2)
-            day = str(tm[2]).zfill(2)
-            hour = str(tm[3]).zfill(2)
-            minute = str(tm[4]).zfill(2)
-            second = str(tm[5]).zfill(2)
-            outdir_backup = outdir + '_%s-%s-%s-%s%s%s' \
-                  % (year,month,day,hour,minute,second)
-            if verbose:
-                print("==> runclaw: Directory already exists: ",os.path.split(outdir)[1])
-                if restart:
-                    print("==> runclaw: Copying directory to:      ",os.path.split(outdir_backup)[1])
-                else:
-                    print("==> runclaw: Moving directory to:      ",os.path.split(outdir_backup)[1])
-                time.sleep(1)
-            
-            try:
-                shutil.move(outdir,outdir_backup)
-                if restart:
-                    shutil.copytree(outdir_backup,outdir)
-            except:
-                print("==> runclaw: Could not move directory... copy already exists?")
-            
-            
-        if (not os.path.isdir(outdir)):
-            try:
-                os.mkdir(outdir)
-            except:
-                print("Cannot make directory ",outdir)
-                return
+            print("==> runclaw: Could not move directory... copy already exists?")
+
     
-        try:
-            os.chdir(outdir)
-        except:
-            print('==> runclaw: *** Error in runxclaw: cannot move to outdir = ',\
-                  outdir)
-            raise
+    os.makedirs(outdir, exist_ok=True)
+
+    if print_git_status not in [False,'False']:
+        # create files claw_git_status.txt and claw_git_diffs.txt in
+        # outdir:
+        make_git_status_file(outdir=outdir)
+
+    # old fort.* files to be removed for new run?
+    fortfiles = glob.glob(os.path.join(outdir,'fort.*'))
+    # also need to remove gauge*.txt output files now that the gauge
+    # output is no longer in fort.gauge  (but don't remove new gauges.data)
+    gaugefiles = glob.glob(os.path.join(outdir,'gauge*.txt'))
+
+    if (overwrite and (not restart)):
+        # remove any old versions:
+        if verbose:
+            print("==> runclaw: Removing all old fort/gauge files in ", outdir)
+        for file in fortfiles + gaugefiles:
+            os.remove(file)
+    elif restart:
+        if verbose:
+            print("==> runclaw: Restart: leaving original fort/gauge files in ", outdir)
+    else:
+        # this should never be reached: 
+        # if overwrite==False then outdir has already been moved
+        if len(fortfiles+gaugefiles) > 1:
+            print("==> runclaw: *** Remove fort.* and gauge*.txt")
+            print("  from output directory %s and try again," % outdir)
+            print("  or use overwrite=True in call to runclaw")
+            print("  e.g., by setting OVERWRITE = True in Makefile")
             return
-    
-        if print_git_status not in [False,'False']:
-            # create files claw_git_status.txt and claw_git_diffs.txt in
-            # outdir:
-            make_git_status_file()
-
-        # old fort.* files to be removed for new run?
-        fortfiles = glob.glob(os.path.join(outdir,'fort.*'))
-        # also need to remove gauge*.txt output files now that the gauge
-        # output is no longer in fort.gauge  (but don't remove new gauges.data)
-        gaugefiles = glob.glob(os.path.join(outdir,'gauge*.txt'))
-
-        if (overwrite and (not restart)):
-            # remove any old versions:
-            if verbose:
-                print("==> runclaw: Removing all old fort/gauge files in ", outdir)
-            for file in fortfiles + gaugefiles:
-                os.remove(file)
-        elif restart:
-            if verbose:
-                print("==> runclaw: Restart: leaving original fort/gauge files in ", outdir)
+
+    datafiles = glob.glob(os.path.join(rundir,'*.data'))
+    if datafiles == ():
+        print("==> runclaw: Warning: no data files found in directory ",rundir)
+    else:
+        if rundir != outdir:
+            for file in datafiles:
+                shutil.copy(file,os.path.join(outdir,os.path.basename(file)))
+
+    # execute command to run fortran program:
+    if nohup:
+        # run in nohup mode:
+        print("\n==> Running in nohup mode, output will be sent to:")
+        print("      %s/nohup.out" % outdir)
+        if type(nice) is int:
+            cmd = "nohup time nice -n %s %s " % (nice,xclawcmd)
         else:
-            # this should never be reached: 
-            # if overwrite==False then outdir has already been moved
-            if len(fortfiles+gaugefiles) > 1:
-                print("==> runclaw: *** Remove fort.* and gauge*.txt")
-                print("  from output directory %s and try again," % outdir)
-                print("  or use overwrite=True in call to runclaw")
-                print("  e.g., by setting OVERWRITE = True in Makefile")
-                return
-            
-        
-        try:
-            os.chdir(rundir)
-        except:
-            raise Exception("Cannot change to directory %s" % rundir)
-            return 
-    
-        datafiles = glob.glob('*.data')
-        if datafiles == ():
-            print("==> runclaw: Warning: no data files found in directory ",rundir)
+            cmd = "nohup time %s " % xclawcmd
+        print("\n==> Running with command:\n   ", cmd)
+    else:
+        if type(nice) is int:
+            cmd = "nice -n %s %s " % (nice,xclawcmd)
         else:
-            if rundir != outdir:
-                for file in datafiles:
-                    shutil.copy(file,os.path.join(outdir,file))
-    
-        if xclawout:
-            xclawout = open(xclawout,'wb')
-        if xclawerr:
-            xclawerr = open(xclawerr,'wb')
-    
-        os.chdir(outdir)
-    
-        #print "\nIn directory outdir = ",outdir,"\n"
-    
-        # execute command to run fortran program:
-    
-        try:
-            #print "\nExecuting ",xclawcmd, "  ...  "
-            #pclaw = subprocess.Popen(xclawcmd,stdout=xclawout,stderr=xclawerr)
-            #print '+++ pclaw started'
-                #pclaw.wait()   # wait for code to run
-            #returncode = pclaw.returncode
-            #print '+++ pclaw done'
-            
-            if nohup:
-                # run in nohup mode:
-                print("\n==> Running in nohup mode, output will be sent to:")
-                print("      %s/nohup.out" % outdir)
-                if type(nice) is int:
-                    cmd = "nohup time nice -n %s %s " % (nice,xclawcmd)
-                else:
-                    cmd = "nohup time %s " % xclawcmd
-                print("\n==> Running with command:\n   ", cmd)
-            else:
-                if type(nice) is int:
-                    cmd = "nice -n %s %s " % (nice,xclawcmd)
-                else:
-                    cmd = xclawcmd
-                print("\n==> Running with command:\n   ", cmd)
-            
-            cmd_split = shlex.split(cmd)
-            p = subprocess.Popen(cmd_split,
-                                 stdout=stdout,
-                                 stderr=stderr,
-                                 encoding='latin-1',
-                                 bufsize=1)
-            p.communicate()
-    
-            if p.returncode == 0:
-                print("\n==> runclaw: Finished executing\n")
-            else:
-                print("\n ==> runclaw: *** Runtime error: return code = %s\n "\
-                        % p.returncode)
-            print('==> runclaw: Done executing %s via clawutil.runclaw.py' %\
-                        xclawcmd)
-            print('==> runclaw: Output is in ', outdir)
-            
-        except:
-            raise Exception("Could not execute command %s" % xclawcmd)
+            cmd = xclawcmd
+        print("\n==> Running with command:\n   ", cmd)
+
+    cmd_split = shlex.split(cmd)
+    if isinstance(xclawout,str):
+        xclawout = open(xclawout,'w', encoding='utf-8')
+    if isinstance(xclawerr,str):
+        xclawerr = open(xclawerr,'w', encoding='utf-8')
+    try:
+        p = subprocess.run(cmd_split,
+                           cwd=outdir,
+                           stdout=xclawout,
+                           stderr=xclawerr,
+                           encoding='utf-8',
+                           bufsize=1,
+                           check=True)
+    except subprocess.CalledProcessError as cpe:
+        raise ClawExeError('error', cpe.returncode, cpe.cmd,
+                           output=cpe.output, 
+                           stderr=cpe.stderr) from cpe
     
-        os.chdir(startdir)
+    print('==> runclaw: Done executing %s via clawutil.runclaw.py' %\
+                xclawcmd)
+    print('==> runclaw: Output is in ', outdir)
 
-    if p.returncode != 0:
-        print('==> runclaw: *** fortran returncode = ', p.returncode, '   aborting')
-        
-    return p.returncode
+    return p
     
 
 #----------------------------------------------------------
diff --git a/src/python/clawutil/test.py b/src/python/clawutil/test.py
index bddde4a..5c0289c 100644
--- a/src/python/clawutil/test.py
+++ b/src/python/clawutil/test.py
@@ -25,6 +25,7 @@
 import clawpack.pyclaw.gauges as gauges
 import clawpack.pyclaw.solution as solution
 import clawpack.clawutil.claw_git_status as claw_git_status
+from clawpack.clawutil import runclaw
 
 # Support for WIP decorator
 from functools import wraps
@@ -214,28 +215,36 @@ def write_rundata_objects(self, path=None):
 
         if path is None:
             path = self.temp_path
-
-        orig_path = os.getcwd()
-        os.chdir(path)
-        self.rundata.write()
-        os.chdir(orig_path)
+        self.rundata.write(out_dir=path)
 
 
     def run_code(self):
         r"""Run test code given an already compiled executable"""
 
-        runclaw_cmd = " ".join((
-                            "cd %s ;" % self.temp_path,
-                            "python",
-                            "$CLAW/clawutil/src/python/clawutil/runclaw.py",
-                            self.executable_name,
-                            self.temp_path,
-                            "True",
-                            "False",
-                            self.temp_path))
-        subprocess.check_call(runclaw_cmd, stdout=self.stdout, 
-                                           stderr=self.stderr,
-                                           shell=True)
+#         runclaw_cmd = " ".join((
+#                             "cd %s ;" % self.temp_path,
+#                             "python",
+#                             "$CLAW/clawutil/src/python/clawutil/runclaw.py",
+#                             self.executable_name,
+#                             self.temp_path,
+#                             "True",
+#                             "False",
+#                             self.temp_path,
+#                             os.path.join(self.temp_path,'geoclaw.out'),
+#                             os.path.join(self.temp_path,'geoclaw.err')))
+        this_dir = os.getcwd()
+        os.chdir(self.temp_path)
+        runclaw.runclaw(xclawcmd=os.path.join(self.temp_path,self.executable_name),
+                        rundir=self.temp_path,
+                        outdir=self.temp_path,
+                        overwrite=True,
+                        restart=False,
+                        xclawout=self.stdout,
+                        xclawerr=self.stderr)
+        os.chdir(this_dir)
+#         subprocess.check_call(runclaw_cmd, stdout=self.stdout, 
+#                                            stderr=self.stderr,
+#                                            shell=True)
         self.stdout.flush()
         self.stderr.flush()
 

From faf1f0112d6f3928e0971b2cd4da65005b3bb424 Mon Sep 17 00:00:00 2001
From: bolliger32 <bolliger32@local>
Date: Mon, 17 Jun 2019 02:57:55 +0000
Subject: [PATCH 4/8] chdir in test

---
 src/python/clawutil/test.py | 26 ++++++++------------------
 1 file changed, 8 insertions(+), 18 deletions(-)

diff --git a/src/python/clawutil/test.py b/src/python/clawutil/test.py
index 5c0289c..76a181f 100644
--- a/src/python/clawutil/test.py
+++ b/src/python/clawutil/test.py
@@ -220,19 +220,8 @@ def write_rundata_objects(self, path=None):
 
     def run_code(self):
         r"""Run test code given an already compiled executable"""
-
-#         runclaw_cmd = " ".join((
-#                             "cd %s ;" % self.temp_path,
-#                             "python",
-#                             "$CLAW/clawutil/src/python/clawutil/runclaw.py",
-#                             self.executable_name,
-#                             self.temp_path,
-#                             "True",
-#                             "False",
-#                             self.temp_path,
-#                             os.path.join(self.temp_path,'geoclaw.out'),
-#                             os.path.join(self.temp_path,'geoclaw.err')))
-        this_dir = os.getcwd()
+        
+        cwd = os.getcwd()
         os.chdir(self.temp_path)
         runclaw.runclaw(xclawcmd=os.path.join(self.temp_path,self.executable_name),
                         rundir=self.temp_path,
@@ -241,10 +230,8 @@ def run_code(self):
                         restart=False,
                         xclawout=self.stdout,
                         xclawerr=self.stderr)
-        os.chdir(this_dir)
-#         subprocess.check_call(runclaw_cmd, stdout=self.stdout, 
-#                                            stderr=self.stderr,
-#                                            shell=True)
+        os.chdir(cwd)
+        
         self.stdout.flush()
         self.stderr.flush()
 
@@ -264,12 +251,15 @@ def runTest(self, save=False, indices=(2, 3)):
         """
 
         # Write out data files
+        cwd = os.getcwd()
+        os.chdir(self.temp_path)
         self.load_rundata()
         self.write_rundata_objects()
 
         # Run code
         self.run_code()
-
+        os.chdir(cwd)
+        
         # Perform tests
         # Override this class to perform data checks, as is this class will
         # simply check that a test runs to completion

From 4147443b3cd477fd25919bc978c9487d44e81b2d Mon Sep 17 00:00:00 2001
From: bolliger32 <bolliger32@local>
Date: Mon, 17 Jun 2019 03:32:29 +0000
Subject: [PATCH 5/8] switch test chdir location

---
 src/python/clawutil/test.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/src/python/clawutil/test.py b/src/python/clawutil/test.py
index 76a181f..55fd5ad 100644
--- a/src/python/clawutil/test.py
+++ b/src/python/clawutil/test.py
@@ -215,14 +215,17 @@ def write_rundata_objects(self, path=None):
 
         if path is None:
             path = self.temp_path
+        # need to cwd b/c setrun.py files contain
+        # relative paths to topofiles and fgmax files
+        cwd = os.getcwd()
+        os.chdir(path)
         self.rundata.write(out_dir=path)
+        os.chdir(cwd)
 
 
     def run_code(self):
         r"""Run test code given an already compiled executable"""
-        
-        cwd = os.getcwd()
-        os.chdir(self.temp_path)
+
         runclaw.runclaw(xclawcmd=os.path.join(self.temp_path,self.executable_name),
                         rundir=self.temp_path,
                         outdir=self.temp_path,
@@ -230,7 +233,6 @@ def run_code(self):
                         restart=False,
                         xclawout=self.stdout,
                         xclawerr=self.stderr)
-        os.chdir(cwd)
         
         self.stdout.flush()
         self.stderr.flush()
@@ -251,14 +253,11 @@ def runTest(self, save=False, indices=(2, 3)):
         """
 
         # Write out data files
-        cwd = os.getcwd()
-        os.chdir(self.temp_path)
         self.load_rundata()
         self.write_rundata_objects()
 
         # Run code
         self.run_code()
-        os.chdir(cwd)
         
         # Perform tests
         # Override this class to perform data checks, as is this class will

From 36f1cca529dcecbf89a38a64451e76fdc884aa7a Mon Sep 17 00:00:00 2001
From: bolliger32 <bolliger32@local>
Date: Mon, 17 Jun 2019 05:37:40 +0000
Subject: [PATCH 6/8] remove chdir b/c now in write methods

---
 src/python/clawutil/test.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/src/python/clawutil/test.py b/src/python/clawutil/test.py
index 55fd5ad..45e2eef 100644
--- a/src/python/clawutil/test.py
+++ b/src/python/clawutil/test.py
@@ -215,12 +215,7 @@ def write_rundata_objects(self, path=None):
 
         if path is None:
             path = self.temp_path
-        # need to cwd b/c setrun.py files contain
-        # relative paths to topofiles and fgmax files
-        cwd = os.getcwd()
-        os.chdir(path)
         self.rundata.write(out_dir=path)
-        os.chdir(cwd)
 
 
     def run_code(self):

From 00d322a3b6a35c5db0336c64018bbda07b139f13 Mon Sep 17 00:00:00 2001
From: bolliger32 <bolliger32@local>
Date: Mon, 17 Jun 2019 06:15:50 +0000
Subject: [PATCH 7/8] remove unnecessary try except

---
 src/python/clawutil/data.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/python/clawutil/data.py b/src/python/clawutil/data.py
index edb18fd..276a0df 100644
--- a/src/python/clawutil/data.py
+++ b/src/python/clawutil/data.py
@@ -528,10 +528,7 @@ def write(self, out_dir = ''):
             if isinstance(data_object, UserData):
                 fname = data_object.__fname__
             else:
-                try:
-                    fname = signature(data_object.write).parameters['out_file'].default
-                except:
-                    raise ValueError(type(data_object))
+                fname = signature(data_object.write).parameters['out_file'].default
             fpath = os.path.join(out_dir,fname)
             if isinstance(data_object, amrclaw.GaugeData):
                 data_object.write(self.clawdata.num_eqn, self.clawdata.num_aux, out_file=fpath)

From 10edc50de410eeaa768932af89540cee45476d27 Mon Sep 17 00:00:00 2001
From: bolliger32 <bolliger32@local>
Date: Wed, 19 Jun 2019 03:33:01 +0000
Subject: [PATCH 8/8] fix buffering

---
 src/python/clawutil/runclaw.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/python/clawutil/runclaw.py b/src/python/clawutil/runclaw.py
index 271f925..8d8f4d3 100755
--- a/src/python/clawutil/runclaw.py
+++ b/src/python/clawutil/runclaw.py
@@ -205,16 +205,17 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=None,
 
     cmd_split = shlex.split(cmd)
     if isinstance(xclawout,str):
-        xclawout = open(xclawout,'w', encoding='utf-8')
+        xclawout = open(xclawout,'w', encoding='utf-8',
+                        buffering=1)
     if isinstance(xclawerr,str):
-        xclawerr = open(xclawerr,'w', encoding='utf-8')
+        xclawerr = open(xclawerr,'w', encoding='utf-8',
+                        buffering=1)
     try:
         p = subprocess.run(cmd_split,
                            cwd=outdir,
                            stdout=xclawout,
                            stderr=xclawerr,
                            encoding='utf-8',
-                           bufsize=1,
                            check=True)
     except subprocess.CalledProcessError as cpe:
         raise ClawExeError('error', cpe.returncode, cpe.cmd,