Deprecate section option skip #1132

src/sos/syntax.py

@@ -8,7 +8,7 @@
 
 from typing import Callable
 SOS_TARGETS_OPTIONS = ['group_by', 'paired_with', 'pattern', 'group_with', 'for_each']
-SOS_INPUT_OPTIONS = ['filetype', 'concurrent']
+SOS_INPUT_OPTIONS = ['concurrent']
 SOS_OUTPUT_OPTIONS = []
 SOS_DEPENDS_OPTIONS = []
 SOS_RUNTIME_OPTIONS = ['workdir', 'concurrent', 'active', 'walltime', 'nodes',
@@ -18,7 +18,7 @@
                       'allow_error', 'tracked', 'stdout', 'stderr', 'default_env', 'env']
 
 SOS_DIRECTIVES = ['input', 'output', 'depends', 'task', 'parameter']
-SOS_SECTION_OPTIONS = ['skip', 'provides', 'shared', 'workdir']
+SOS_SECTION_OPTIONS = ['provides', 'shared', 'workdir']
 
 SOS_KEYWORDS = SOS_INPUT_OPTIONS + SOS_OUTPUT_OPTIONS + SOS_DEPENDS_OPTIONS + SOS_RUNTIME_OPTIONS \
     + SOS_ACTION_OPTIONS + SOS_DIRECTIVES + SOS_SECTION_OPTIONS

src/sos/workflow_executor.py

@@ -318,29 +318,6 @@ def init_dict(self) -> None:
                 if not key.startswith('__'):
                     env.sos_dict.set(key, value)
 
-    def skip(self, section: SoS_Step) -> bool:
-        if section.global_def:
-            try:
-                SoS_exec(section.global_def)
-            except subprocess.CalledProcessError as e:
-                raise RuntimeError(e.stderr)
-            except RuntimeError as e:
-                if env.verbosity > 2:
-                    sys.stderr.write(get_traceback())
-                raise RuntimeError(
-                    f'Failed to execute statements\n"{section.global_def}"\n{e}')
-        #
-        if 'skip' in section.options:
-            val_skip = section.options['skip']
-            if val_skip is None or val_skip is True:
-                env.logger.info(
-                    f'``{section.step_name(True)}`` is ``ignored`` due to skip option.')
-                return True
-            elif val_skip is not False:
-                raise RuntimeError(
-                    f'The value of section option skip can only be None, True or False, {val_skip} provided')
-        return False
-
     def match(self, target: BaseTarget, step: SoS_Step) -> Union[Dict[str, str], bool]:
         # for sos_step, we need to match step name
         if isinstance(target, sos_step):
@@ -442,8 +419,6 @@ def resolve_dangling_targets(self, dag: SoS_DAG, targets: Optional[sos_targets]=
                         default_input: sos_targets = sos_targets()
                         #
                         for idx, section in enumerate(sections):
-                            if self.skip(section):
-                                continue
                             res = analyze_section(section, default_input)
 
                             environ_vars = res['environ_vars']
@@ -634,8 +609,6 @@ def initialize_dag(self, targets: Optional[List[str]] = [], nested: bool = False
         default_input: sos_targets = sos_targets([])
         targets = sos_targets(targets)
         for idx, section in enumerate(self.workflow.sections):
-            if self.skip(section):
-                continue
             #
             res = analyze_section(section, default_input)
 

test/test_execute.py

@@ -960,30 +960,6 @@ def testLocalNamespace(self):
         self.assertEqual(env.sos_dict['shared'], 'c.txt')
         self.assertEqual(env.sos_dict['d'], 2)
 
-#
-#    def testCollectionOfErrors(self):
-#        '''Test collection of errors when running in dryrun mode.'''
-#        script = SoS_Script('''
-# [0]
-#depends: executable('a1')
-# [1: skip='blah']
-#depends: executable('a2')
-#
-# [2]
-#input: None
-#depends: executable('a3')
-# [3]
-#depends: executable('a4')
-#
-# ''')
-#        wf = script.workflow()
-#        # we should see a single error with 2 messages.
-#        # because 2 being on a separate branch will be executed but
-#        # the later steps will not be executed
-#        try:
-#            Base_Executor(wf).run(mode='dryrun')
-#        except Exception as e:
-#            self.assertEqual(len(e.errors), 3)
 
     def testDynamicOutput(self):
         '''Testing dynamic output'''

test/test_nested.py

@@ -347,7 +347,7 @@ def testIncludedNestedWorkFlow(self):
 if 'executed' not in locals():
     executed = []
 
-[b_1: skip=False, shared='executed']
+[b_1: shared='executed']
 executed.append(step_name)
 input: 'a.txt', 'b.txt', group_by='single'
 sos_run('A', shared='executed')
@@ -371,7 +371,7 @@ def testIncludedNestedWorkFlow(self):
 if 'executed' not in locals():
     executed = []
 
-[b_1: skip=False, shared='executed']
+[b_1: shared='executed']
 executed.append('g.' + step_name)
 input: 'a.txt', 'b.txt', group_by='single'
 sos_run('k.A', shared='executed')

test/test_parser.py

@@ -55,7 +55,7 @@
 
 var3 = 'a'
 
-[section_3, *_4 : shared='var4', skip ]
+[section_3, *_4 : shared='var4']
 output:
 	var2,
 	var3
@@ -119,11 +119,6 @@ def testWorkflows(self):
         self.assertEqual(sorted(script.workflows), [
                          '', 'human', 'mouse'])
         script = SoS_Script('''[0]\n[*_1]\n[human_1]\n[mouse_2]\n[s*_2]''')
-        self.assertEqual(sorted(script.workflows), [
-                         '', 'human', 'mouse'])
-        # skip option is not effective at parsing time
-        script = SoS_Script(
-            '''[0]\n[*_1]\n[human_1]\n[mouse_2:skip]\n[s*_2]''')
         self.assertEqual(sorted(script.workflows), [
                          '', 'human', 'mouse'])
         # unnamed
@@ -147,32 +142,14 @@ def testTypeHint(self):
         # action
         SoS_Script('''a : expand='${ }' ''')
 
-    def testSkipStep(self):
-        '''Test the skip option to skip certain steps'''
-        script = SoS_Script('''
-parameter: skip = 0
-
-[0: shared={'a':'var'}, skip=skip==0]
-var = 0
-
-[1: shared={'b': 'var'}, skip=skip==1]
-var = 1
-
-''')
-        wf = script.workflow()
-        Base_Executor(wf, args=['--skip', '0']).run()
-        self.assertEqual(env.sos_dict['b'], 1)
-        #
-        Base_Executor(wf, args=['--skip', '1']).run()
-        self.assertEqual(env.sos_dict['a'], 0)
 
     def testSections(self):
         '''Test section definitions'''
         # bad names
         for badname in ['56_1', '_a', 'a_', '1x', '*', '?']:
             self.assertRaises(ParsingError, SoS_Script, '[{}]'.format(badname))
         # bad options
-        for badoption in ['ss', 'skip a', 'skip:_', 'skip, skip']:
+        for badoption in ['ss']:
             self.assertRaises(ParsingError, SoS_Script,
                               '[0:{}]'.format(badoption))
         # allowed names
@@ -193,8 +170,6 @@ def testSections(self):
         SoS_Script('''[a_1]\n[a_3]\n[b*_1]''')
         #
         # global section
-        self.assertRaises(ParsingError, SoS_Script,
-                          '''[global: skip]''')
         self.assertRaises(ParsingError, SoS_Script,
                           '''[global, step_10]''')
 

test/test_utils.py

@@ -102,7 +102,7 @@ def testAccessedVars(self):
         self.assertEqual(accessed_vars('''a = "C" + f"{D}"'''), {'a', 'D'})
         self.assertEqual(accessed_vars(
             '''a = 1 + f"{D + 20:f}" '''), {'a', 'D'})
-        self.assertEqual(accessed_vars('''k, "a.txt", "b.txt", skip=True, par=f(something) '''), {
+        self.assertEqual(accessed_vars('''k, "a.txt", "b.txt", par=f(something) '''), {
                          'k', 'f', 'something', '__NULLFUNC__'})
         # this is a complicated case because the actual variable depends on the
         # result of an expression... However, in the NO-evaluation case, this is