Out of Place GEOS ATS (#6)

* Removing unused code, fixing reports

* Using dataclass in geos_ats.reporting

* Updating the reporting dataclass for geos_ats

* Adding an error for tests without restart or curve checks

* Fixing curve check paths

* Adding duplicate test check

geos_ats_package/geos_ats/command_line_parsers.py

@@ -40,7 +40,11 @@ def build_command_line_parser():
 
     parser.add_argument( "geos_bin_dir", type=str, help="GEOS binary directory." )
 
-    parser.add_argument( "-w", "--workingDir", type=str, help="Initial working directory" )
+    parser.add_argument( "ats_target", type=str, help="ats file" )
+
+    parser.add_argument( "-w", "--workingDir", type=str, help="Root working directory" )
+
+    parser.add_argument( "-b", "--baselineDir", type=str, help="Root baseline directory" )
 
     action_names = ','.join( action_options.keys() )
     parser.add_argument( "-a", "--action", type=str, default="run", help=f"Test actions options ({action_names})" )
@@ -89,6 +93,8 @@ def build_command_line_parser():
 
     parser.add_argument( "-l", "--logs", type=str, default=None )
 
+    parser.add_argument( "-f", "--allow-failed-tests", default=False, action='store_true' )
+
     parser.add_argument(
         "--failIfTestsFail",
         action="store_true",
@@ -98,8 +104,6 @@ def build_command_line_parser():
 
     parser.add_argument( "-n", "-N", "--numNodes", type=int, default="2" )
 
-    parser.add_argument( "ats_targets", type=str, nargs='*', help="ats files or directories." )
-
     return parser
 
 
@@ -127,6 +131,13 @@ def parse_command_line_arguments( args ):
         print( f"Selected verbose option ({verbose}) not recognized" )
         exit_flag = True
 
+    # Paths
+    if not options.workingDir:
+        options.workingDir = os.path.basename( options.ats_target )
+
+    if not options.baselineDir:
+        options.baselineDir = options.workingDir
+
     # Print detailed information
     if options.detail:
         for option_type, details in zip( [ 'action', 'check' ], [ action_options, check_options ] ):
@@ -139,22 +150,3 @@ def parse_command_line_arguments( args ):
         quit()
 
     return options
-
-
-def patch_parser( parser ):
-
-    def add_option_patch( *xargs, **kwargs ):
-        """
-        Convert type string to actual type instance
-        """
-        tmp = kwargs.get( 'type', str )
-        type_map = { 'string': str }
-        if isinstance( tmp, str ):
-            if tmp in type_map:
-                tmp = type_map[ tmp ]
-            else:
-                tmp = locate( tmp )
-        kwargs[ 'type' ] = tmp
-        parser.add_argument( *xargs, **kwargs )
-
-    parser.add_option = add_option_patch

geos_ats_package/geos_ats/configuration_record.py

@@ -167,7 +167,7 @@ def initializeConfig( configFile, configOverride, options ):
     geos_atsdir = os.path.realpath( os.path.dirname( __file__ ) )
 
     # configfile
-    config.add( "testbaseline_dir", str, "", "Base directory that contains all the baselines" )
+    config.add( "testbaseline_directory", str, "", "Base directory that contains all the baselines" )
 
     config.add( "geos_bin_dir", str, "", "Directory that contains 'geos' and related executables." )
 
@@ -194,11 +194,6 @@ def initializeConfig( configFile, configOverride, options ):
     config.add( "report_doc_remake", bool, False,
                 "Remake test documentation, even if it already exists (used with html reports)" )
 
-    config.add( "report_text", bool, True, "True if you want text results to be generated with the report action" )
-    config.add( "report_text_file", str, "test_results.txt", "Location to write the text report" )
-    config.add( "report_text_echo", bool, True, "If True, echo the report to stdout" )
-    config.add( "report_wait", bool, False, "Wait until all tests are complete before reporting" )
-
     config.add( "report_ini", bool, True, "True if you want ini results to be generated with the report action" )
     config.add( "report_ini_file", str, "test_results.ini", "Location to write the ini report" )
 
@@ -213,10 +208,6 @@ def initializeConfig( configFile, configOverride, options ):
     config.add( "checkmessages_never_ignore_regexp", type( [] ), [ "not yet implemented" ],
                 "Regular expression to not ignore in all checkmessages steps." )
 
-    config.add( "report_timing", bool, False, "True if you want timing file to be generated with the report action" )
-    config.add( "report_timing_overwrite", bool, False,
-                "True if you want timing file to overwrite existing timing file rather than augment it" )
-
     # timing and priority
     config.add( "priority", str, "equal", "Method of prioritization of tests: [\"equal\", \"processors\",\"timing\"]" )
     config.add( "timing_file", str, "timing.txt", "Location of timing file" )

geos_ats_package/geos_ats/environment_setup.py

@@ -4,20 +4,24 @@
 import argparse
 
 
-def setup_ats( src_path, build_path, ats_xargs, ats_machine, ats_machine_dir ):
+def setup_ats( src_path, build_path, baseline_dir, working_dir, ats_xargs, ats_machine, ats_machine_dir ):
     bin_dir = os.path.join( build_path, "bin" )
     geos_ats_fname = os.path.join( bin_dir, "run_geos_ats" )
-    ats_dir = os.path.abspath( os.path.join( src_path, "integratedTests", "tests", "allTests" ) )
     test_path = os.path.join( build_path, "integratedTests" )
     link_path = os.path.join( test_path, "integratedTests" )
     run_script_fname = os.path.join( test_path, "geos_ats.sh" )
     log_dir = os.path.join( test_path, "TestResults" )
+    baseline_dir = os.path.abspath( baseline_dir )
+    working_dir = os.path.abspath( working_dir )
+    ats_main_file = os.path.abspath( os.path.join( src_path, 'inputFiles', 'main.ats' ) )
 
-    # Create a symbolic link to test directory
+    # Create a symbolic link to working directory
+    for d in [ baseline_dir, working_dir, test_path ]:
+        os.makedirs( d, exist_ok=True )
     if os.path.islink( link_path ):
         print( 'integratedTests symlink already exists' )
     else:
-        os.symlink( ats_dir, link_path )
+        os.symlink( working_dir, link_path )
 
     # Build extra arguments that should be passed to ATS
     joined_args = [ ' '.join( x ) for x in ats_xargs ]
@@ -30,7 +34,9 @@ def setup_ats( src_path, build_path, ats_xargs, ats_machine, ats_machine_dir ):
     # Write the bash script to run ats.
     with open( run_script_fname, "w" ) as g:
         g.write( "#!/bin/bash\n" )
-        g.write( f"{geos_ats_fname} {bin_dir} --workingDir {ats_dir} --logs {log_dir} {ats_args} \"$@\"\n" )
+        g.write(
+            f"{geos_ats_fname} {bin_dir} {ats_main_file} --workingDir {working_dir} --baselineDir {baseline_dir} --logs {log_dir} {ats_args} \"$@\"\n"
+        )
 
     # Make the script executable
     st = os.stat( run_script_fname )
@@ -46,6 +52,8 @@ def main():
     parser = argparse.ArgumentParser( description="Setup ATS script" )
     parser.add_argument( "src_path", type=str, help="GEOS src path" )
     parser.add_argument( "build_path", type=str, help="GEOS build path" )
+    parser.add_argument( "baseline_dir", type=str, help="GEOS test baseline root directory" )
+    parser.add_argument( "working_dir", type=str, help="GEOS test working root directory" )
     parser.add_argument( "--ats",
                          nargs='+',
                          default=[],
@@ -54,7 +62,8 @@ def main():
     parser.add_argument( "--machine", type=str, default='', help="ATS machine name" )
     parser.add_argument( "--machine-dir", type=str, default='', help="ATS machine directory" )
     options, unkown_args = parser.parse_known_args()
-    setup_ats( options.src_path, options.build_path, options.ats, options.machine, options.machine_dir )
+    setup_ats( options.src_path, options.build_path, options.baseline_dir, options.working_dir, options.ats,
+               options.machine, options.machine_dir )
 
 
 if __name__ == '__main__':

geos_ats_package/geos_ats/helpers/curve_check.py

@@ -275,20 +275,17 @@ def compare_time_history_curves( fname, baseline, curve, tolerance, output, outp
     # Generate script-based curve
     if script_instructions and ( len( data ) > 0 ):
         data[ 'script' ] = {}
-        try:
-            for script, fn, p, s in script_instructions:
-                k = location_strings[ p ]
-                data[ 'script' ][ f'{p} Time' ] = data[ 'target' ][ f'{p} Time' ]
-                key = f'{p} {k}'
-                key2 = f'{p}'
-                if s != DEFAULT_SET_NAME:
-                    key += f' {s}'
-                    key2 += f' {s}'
-                data[ 'script' ][ key ] = data[ 'target' ][ key ]
-                data[ 'script' ][ key2 ] = evaluate_external_script( script, fn, data[ 'target' ] )
-                data_sizes[ p ][ s ][ 'script' ] = list( np.shape( data[ 'script' ][ key2 ] ) )
-        except Exception as e:
-            errors.append( str( e ) )
+        for script, fn, p, s in script_instructions:
+            k = location_strings[ p ]
+            data[ 'script' ][ f'{p} Time' ] = data[ 'target' ][ f'{p} Time' ]
+            key = f'{p} {k}'
+            key2 = f'{p}'
+            if s != DEFAULT_SET_NAME:
+                key += f' {s}'
+                key2 += f' {s}'
+            data[ 'script' ][ key ] = data[ 'target' ][ key ]
+            data[ 'script' ][ key2 ] = evaluate_external_script( script, fn, data[ 'target' ] )
+            data_sizes[ p ][ s ][ 'script' ] = list( np.shape( data[ 'script' ][ key2 ] ) )
 
     # Reshape data if necessary so that they have a predictable number of dimensions
     for k in data.keys():

geos_ats_package/geos_ats/machines/batchGeosatsMoab.py

@@ -1,8 +1,8 @@
 #BATS:batchGeosatsMoab  batchGeosatsMoab BatchGeosatsMoab -1
 
 from ats import machines, configuration, log, atsut, times, AtsTest  # type: ignore[import]
-import subprocess, sys, os, shlex, time, socket, re
-import utils, batchTemplate  # type: ignore[import]
+import subprocess, sys, os, time, socket, re
+import utils  # type: ignore[import]
 from batch import BatchMachine  # type: ignore[import]
 import logging