New PaSh version

.github/workflows/black.yaml

@@ -0,0 +1,12 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable
+        with:
+          options: "--extend-exclude 'evaluations/'"

compiler/annotations_utils/util_cmd_invocations.py

@@ -1,24 +1,43 @@
 from pash_annotations.datatypes.BasicDatatypes import Flag, ArgStringType, Operand
 from pash_annotations.datatypes.BasicDatatypesWithIO import OptionWithIO
 from pash_annotations.datatypes.CommandInvocationInitial import CommandInvocationInitial
-from pash_annotations.annotation_generation.datatypes.InputOutputInfo import InputOutputInfo
-from pash_annotations.annotation_generation.datatypes.ParallelizabilityInfo import ParallelizabilityInfo
-from pash_annotations.annotation_generation.datatypes.CommandProperties import CommandProperties
-from pash_annotations.annotation_generation.AnnotationGeneration import get_input_output_info_from_cmd_invocation, \
-    get_parallelizability_info_from_cmd_invocation
-from pash_annotations.datatypes.CommandInvocationWithIOVars import CommandInvocationWithIOVars
+from pash_annotations.annotation_generation.datatypes.InputOutputInfo import (
+    InputOutputInfo,
+)
+from pash_annotations.annotation_generation.datatypes.ParallelizabilityInfo import (
+    ParallelizabilityInfo,
+)
+from pash_annotations.annotation_generation.datatypes.CommandProperties import (
+    CommandProperties,
+)
+from pash_annotations.annotation_generation.AnnotationGeneration import (
+    get_input_output_info_from_cmd_invocation,
+    get_parallelizability_info_from_cmd_invocation,
+)
+from pash_annotations.datatypes.CommandInvocationWithIOVars import (
+    CommandInvocationWithIOVars,
+)
 
 from definitions.ir.arg import Arg
 
 # for typing
 from pash_annotations.datatypes.CommandInvocationPrefix import CommandInvocationPrefix
 
-from shell_ast.ast_util import  string_to_argument, redir_stdout_to_file, redir_file_to_stdin, make_command
+from shell_ast.ast_util import (
+    string_to_argument,
+    redir_stdout_to_file,
+    redir_file_to_stdin,
+    make_command,
+)
+
 
 def get_command_invocation_prefix_from_dfg_node(dfg_node):
-    return CommandInvocationPrefix(cmd_name = dfg_node.com_name,
-                                   flag_option_list = dfg_node.flag_option_list,
-                                   positional_config_list = dfg_node.positional_config_list)
+    return CommandInvocationPrefix(
+        cmd_name=dfg_node.com_name,
+        flag_option_list=dfg_node.flag_option_list,
+        positional_config_list=dfg_node.positional_config_list,
+    )
+
 
 # TODO: ideally methods in the respective classes but requires refactoring of parsing infrastructure
 # TODO: isn't this `to_ast`?
@@ -48,55 +67,70 @@ def to_node_cmd_inv_with_io_vars(cmd_inv, edges, redirs, assignments):
     node = make_command(cmd_asts, redirections=new_redirs, assignments=assignments)
     return node
 
+
 def to_ast_flagoption(flagoption, edges):
     if isinstance(flagoption, Flag):
         return [string_to_argument(flagoption.get_name())]
-    elif isinstance(flagoption, OptionWithIO): # retype to IOVar
+    elif isinstance(flagoption, OptionWithIO):  # retype to IOVar
         opt_name_ast = string_to_argument(flagoption.get_name())
         opt_arg_ast = translate_io_var_if_applicable(flagoption.get_arg(), edges)
         return [opt_name_ast, opt_arg_ast]
 
+
 def to_ast_operand(operand, edges):
     if isinstance(operand, Operand):
         return translate_io_var_if_applicable(operand.get_name(), edges)
     return translate_io_var_if_applicable(operand, edges)
 
+
 def translate_io_var_if_applicable(pot_io_var, edges):
     # TODO: this is currently a hack but eventually every possible type gets their own to_ast-function
     if isinstance(pot_io_var, int):
         return dereference_io_var(pot_io_var, edges)
     elif isinstance(pot_io_var, ArgStringType):
         return to_ast_arg_string_type(pot_io_var)
     elif isinstance(pot_io_var, CommandInvocationWithIOVars):
-        assert(False)
+        assert False
         # only happens as r-wrapped node
         return to_node_cmd_inv_with_io_vars(pot_io_var, edges, [], [])
     elif isinstance(pot_io_var, Arg):
         return pot_io_var.to_ast()
     else:
         raise Exception("Unhandled type for operand in to_ast!")
 
+
 def to_ast_arg_string_type(arg_string_type):
-    return arg_string_type.get_name().arg_char_list # is of type Arg
+    return arg_string_type.get_name().arg_char_list  # is of type Arg
+
 
 # assumes io_var is an edge id
 def dereference_io_var(io_var, edges):
     fid, _, _ = edges[io_var]
     return fid.to_ast()
 
-def get_input_output_info_from_cmd_invocation_util(cmd_invocationInitial : CommandInvocationInitial) -> InputOutputInfo:
+
+def get_input_output_info_from_cmd_invocation_util(
+    cmd_invocationInitial: CommandInvocationInitial,
+) -> InputOutputInfo:
     return get_input_output_info_from_cmd_invocation(cmd_invocationInitial)
 
-def get_parallelizability_info_from_cmd_invocation_util(cmd_invocationInitial : CommandInvocationInitial) -> ParallelizabilityInfo:
+
+def get_parallelizability_info_from_cmd_invocation_util(
+    cmd_invocationInitial: CommandInvocationInitial,
+) -> ParallelizabilityInfo:
     return get_parallelizability_info_from_cmd_invocation(cmd_invocationInitial)
 
+
 def construct_property_container_from_list_of_properties(list_properties):
     return CommandProperties(dict(list_properties))
 
+
 # this function is needed to wrap a node in `r_wrap`
-def to_arg_from_cmd_inv_with_io_vars_without_streaming_inputs_or_outputs_for_wrapping(cmd_inv, edges):
+def to_arg_from_cmd_inv_with_io_vars_without_streaming_inputs_or_outputs_for_wrapping(
+    cmd_inv, edges
+):
     # we already expand here
-    whole_cmd = Arg.string_to_arg("\'")
+    whole_cmd = Arg.string_to_arg("'")
     arg_cmd_name = Arg.string_to_arg(cmd_inv.cmd_name)
     arg_flagoptions = []
     for flagoption in cmd_inv.flag_option_list:
@@ -107,9 +141,10 @@ def to_arg_from_cmd_inv_with_io_vars_without_streaming_inputs_or_outputs_for_wra
     all_cmd_parts_arg.extend(arg_operands)
     for part in all_cmd_parts_arg:
         whole_cmd.concatenate(part)
-    whole_cmd.concatenate(Arg.string_to_arg("\'"))
+    whole_cmd.concatenate(Arg.string_to_arg("'"))
     return whole_cmd
 
+
 def to_arg_flagoption(flagoption, edges):
     if isinstance(flagoption, Flag):
         return [Arg.string_to_arg(flagoption.get_name())]
@@ -118,11 +153,13 @@ def to_arg_flagoption(flagoption, edges):
         opt_arg_arg = translate_io_var_to_arg_if_applicable(flagoption.get_arg(), edges)
         return [opt_name_arg, opt_arg_arg]
 
+
 def to_arg_operand(operand, edges):
     if isinstance(operand, Operand):
         return translate_io_var_to_arg_if_applicable(operand.get_name(), edges)
     return translate_io_var_to_arg_if_applicable(operand, edges)
 
+
 def translate_io_var_to_arg_if_applicable(pot_io_var, edges):
     if isinstance(pot_io_var, int):
         return Arg(dereference_io_var(pot_io_var, edges))

compiler/annotations_utils/util_file_descriptors.py

@@ -1,18 +1,21 @@
 from util import log
 from definitions.ir.resource import FileResource, Resource, FileDescriptorResource
-from pash_annotations.datatypes.BasicDatatypesWithIO import FileNameWithIOInfo, StdDescriptorWithIOInfo
+from pash_annotations.datatypes.BasicDatatypesWithIO import (
+    FileNameWithIOInfo,
+    StdDescriptorWithIOInfo,
+)
 
 
 def resource_from_file_descriptor(file_descriptor) -> Resource:
     if isinstance(file_descriptor, FileNameWithIOInfo):
         arg = file_descriptor.get_name()
-        log(f'filedes name: {file_descriptor.get_name()}')
-        log(f'filedes name type: {type(file_descriptor.get_name())}')
-        log(f'arg: {arg}')
+        log(f"filedes name: {file_descriptor.get_name()}")
+        log(f"filedes name type: {type(file_descriptor.get_name())}")
+        log(f"arg: {arg}")
         return FileResource(file_descriptor.get_name())
     elif isinstance(file_descriptor, StdDescriptorWithIOInfo):
         resource = ("fd", file_descriptor.get_type().value)
         return FileDescriptorResource(resource)
     else:
-        assert(False)
+        assert False
         # unreachable

compiler/annotations_utils/util_parsing.py

@@ -3,9 +3,20 @@
 from definitions.ir.arg import Arg
 
 from pash_annotations.datatypes.CommandInvocationInitial import CommandInvocationInitial
-from pash_annotations.datatypes.BasicDatatypes import Option, ArgStringType, Flag, Operand
-from pash_annotations.parser.parser import parse, get_set_of_all_flags, get_dict_flag_to_primary_repr, get_set_of_all_options, \
-    get_dict_option_to_primary_repr, are_all_individually_flags
+from pash_annotations.datatypes.BasicDatatypes import (
+    Option,
+    ArgStringType,
+    Flag,
+    Operand,
+)
+from pash_annotations.parser.parser import (
+    parse,
+    get_set_of_all_flags,
+    get_dict_flag_to_primary_repr,
+    get_set_of_all_options,
+    get_dict_option_to_primary_repr,
+    are_all_individually_flags,
+)
 from pash_annotations.parser.util_parser import get_json_data
 
 
@@ -18,40 +29,51 @@ def merge_to_single_string_with_space(list_str):
     else:
         return " ".join(list_str)
 
+
 def get_command_invocation(command, options) -> CommandInvocationInitial:
     command_as_string: str = format_arg_chars(command)
-    options_and_operands_as_string: str = merge_to_single_string_with_space([format_arg_chars(option) for option in options])
-    command_invocation_as_string: str = f'{command_as_string} {options_and_operands_as_string}'
+    options_and_operands_as_string: str = merge_to_single_string_with_space(
+        [format_arg_chars(option) for option in options]
+    )
+    command_invocation_as_string: str = (
+        f"{command_as_string} {options_and_operands_as_string}"
+    )
     command_invocation: CommandInvocationInitial = parse(command_invocation_as_string)
     return command_invocation
 
+
 def get_ast_for_flagoption(flagoption):
     result = string_to_argument(flagoption.get_name())
     if isinstance(flagoption, Option):
         # TODO: add argument here as well but eventually also fid
         assert False
     return result
 
+
 def get_ast_for_argstringtype(arg):
     return string_to_argument(arg.get_name())
 
+
 # TODO: this is a hack to fix the wrong parsing of "
 def fix_parsing_newline(arg):
-    if arg.get_name() == '\\n':
+    if arg.get_name() == "\\n":
         return ArgStringType(r'"\n"')
     else:
         return arg
 
 
-def parse_arg_list_to_command_invocation(command, flags_options_operands) -> CommandInvocationInitial:
-
+def parse_arg_list_to_command_invocation(
+    command, flags_options_operands
+) -> CommandInvocationInitial:
     cmd_name = format_arg_chars(command)
     json_data = get_json_data(cmd_name)
 
     set_of_all_flags: Set[str] = get_set_of_all_flags(json_data)
     dict_flag_to_primary_repr: dict[str, str] = get_dict_flag_to_primary_repr(json_data)
     set_of_all_options: Set[str] = get_set_of_all_options(json_data)
-    dict_option_to_primary_repr: dict[str, str] = get_dict_option_to_primary_repr(json_data)
+    dict_option_to_primary_repr: dict[str, str] = get_dict_option_to_primary_repr(
+        json_data
+    )
     # we keep the Arg for everything but flag and option names
 
     # parse list of command invocation terms
@@ -61,20 +83,30 @@ def parse_arg_list_to_command_invocation(command, flags_options_operands) -> Com
         potential_flag_or_option_arg = flags_options_operands[i]
         potential_flag_or_option_name = format_arg_chars(potential_flag_or_option_arg)
         if potential_flag_or_option_name in set_of_all_flags:
-            flag_name_as_string: str = dict_flag_to_primary_repr.get(potential_flag_or_option_name, potential_flag_or_option_name)
+            flag_name_as_string: str = dict_flag_to_primary_repr.get(
+                potential_flag_or_option_name, potential_flag_or_option_name
+            )
             flag: Flag = Flag(flag_name_as_string)
             flag_option_list.append(flag)
-        elif (potential_flag_or_option_name in set_of_all_options) and ((i+1) < len(flags_options_operands)):
-            option_name_as_string: str = dict_option_to_primary_repr.get(potential_flag_or_option_name, potential_flag_or_option_name)
-            option_arg_as_arg: Arg = Arg(flags_options_operands[i+1])
+        elif (potential_flag_or_option_name in set_of_all_options) and (
+            (i + 1) < len(flags_options_operands)
+        ):
+            option_name_as_string: str = dict_option_to_primary_repr.get(
+                potential_flag_or_option_name, potential_flag_or_option_name
+            )
+            option_arg_as_arg: Arg = Arg(flags_options_operands[i + 1])
             option = Option(option_name_as_string, option_arg_as_arg)
             flag_option_list.append(option)
             i += 1  # since we consumed another term for the argument
-        elif potential_flag_or_option_name == "-": # switch to operand mode (interpreted as hyphen-stdin)
+        elif (
+            potential_flag_or_option_name == "-"
+        ):  # switch to operand mode (interpreted as hyphen-stdin)
             break
-        elif are_all_individually_flags(potential_flag_or_option_name, set_of_all_flags):
+        elif are_all_individually_flags(
+            potential_flag_or_option_name, set_of_all_flags
+        ):
             for split_el in list(potential_flag_or_option_name[1:]):
-                flag: Flag = Flag(f'-{split_el}')
+                flag: Flag = Flag(f"-{split_el}")
                 flag_option_list.append(flag)
         else:
             break  # next one is Operand, and we keep these in separate list
@@ -85,7 +117,9 @@ def parse_arg_list_to_command_invocation(command, flags_options_operands) -> Com
     # if parsed_elements_list[i] == '--':
     #     i += 1
 
-    operand_list = [Operand(Arg(operand_arg)) for operand_arg in flags_options_operands[i:]]
+    operand_list = [
+        Operand(Arg(operand_arg)) for operand_arg in flags_options_operands[i:]
+    ]
     # log("type of operand_list[0].get_name()", type(operand_list[0].get_name()))   can only be used if there are operands
 
     return CommandInvocationInitial(cmd_name, flag_option_list, operand_list)