got tests to load

pydra/design/shell.py

@@ -328,7 +328,13 @@ def make(
                 input_helps=input_helps,
                 output_helps=output_helps,
             )
-            class_name = re.sub(r"[^\w]", "_", executable) if not name else name
+            if name:
+                class_name = name
+            else:
+                class_name = (
+                    "_".join(executable) if isinstance(executable, list) else executable
+                )
+                class_name = re.sub(r"[^\w]", "_", class_name)
             if class_name[0].isdigit():
                 class_name = f"_{class_name}"
 
@@ -457,10 +463,19 @@ def parse_command_line_template(
     else:
         assert outputs is None
         outputs = {}
-    parts = template.split(maxsplit=1)
-    if len(parts) == 1:
-        return template, inputs, outputs
-    executable, args_str = parts
+    parts = template.split()
+    executable = []
+    for i, part in enumerate(parts, start=1):
+        if part.startswith("<") or part.startswith("-"):
+            break
+        executable.append(part)
+    if not executable:
+        raise ValueError(f"Found no executable in command line template: {template}")
+    if len(executable) == 1:
+        executable = executable[0]
+    if i == len(parts):
+        return executable, inputs, outputs
+    args_str = " ".join(parts[i:])
     tokens = re.split(r"\s+", args_str.strip())
     arg_pattern = r"<([:a-zA-Z0-9_,\|\-\.\/\+]+(?:\?|=[^>]+)?)>"
     opt_pattern = r"--?[a-zA-Z0-9_]+"

pydra/engine/tests/test_environments.py

@@ -4,13 +4,10 @@
 from ..task import ShellTask
 from ..submitter import Submitter
 from ..specs import (
-    ShellSpec,
-    SpecInfo,
     File,
 )
+from pydra.design import shell
 from .utils import no_win, need_docker, need_singularity
-
-import attr
 import pytest
 
 
@@ -176,33 +173,22 @@ def test_singularity_1_subm(tmp_path, plugin):
 
 def create_shelly_inputfile(tempdir, filename, name, executable):
     """creating a task with a simple input_spec"""
-    my_input_spec = SpecInfo(
-        name="Input",
-        fields=[
-            (
-                "file",
-                attr.ib(
-                    type=File,
-                    metadata={
-                        "position": 1,
-                        "help_string": "files",
-                        "mandatory": True,
-                        "argstr": "",
-                    },
-                ),
-            )
-        ],
-        bases=(ShellSpec,),
-    )
+    inputs = [
+        shell.arg(
+            name="file",
+            type=File,
+            position=1,
+            help_string="files",
+            mandatory=True,
+            argstr="",
+        )
+    ]
 
     kwargs = {} if filename is None else {"file": filename}
-    shelly = ShellTask(
-        name=name,
-        executable=executable,
-        cache_dir=makedir(tempdir, name),
-        input_spec=my_input_spec,
-        **kwargs,
-    )
+    shelly = shell.define(
+        executable,
+        input=inputs,
+    )(**kwargs)
     return shelly
 
 
@@ -363,35 +349,25 @@ def test_docker_fileinp_st(tmp_path):
 
 def create_shelly_outputfile(tempdir, filename, name, executable="cp"):
     """creating a task with an input_spec that contains a template"""
-    my_input_spec = SpecInfo(
-        name="Input",
-        fields=[
-            (
-                "file_orig",
-                attr.ib(
-                    type=File,
-                    metadata={"position": 2, "help_string": "new file", "argstr": ""},
-                ),
-            ),
-            (
-                "file_copy",
-                attr.ib(
-                    type=str,
-                    metadata={
-                        "output_file_template": "{file_orig}_copy",
-                        "help_string": "output file",
-                        "argstr": "",
-                    },
-                ),
-            ),
-        ],
-        bases=(ShellSpec,),
-    )
+    my_input_spec = [
+        shell.arg(
+            name="file_orig",
+            type=File,
+            position=2,
+            help_string="new file",
+            argstr="",
+        ),
+        shell.arg(
+            name="file_copy",
+            type=str,
+            output_file_template="{file_orig}_copy",
+            help_string="output file",
+            argstr="",
+        ),
+    ]
 
     kwargs = {} if filename is None else {"file_orig": filename}
-    shelly = ShellTask(
-        name=name,
-        executable=executable,
+    shelly = shell.define(executable)(
         cache_dir=makedir(tempdir, name),
         input_spec=my_input_spec,
         **kwargs,

pydra/engine/tests/test_helpers.py

@@ -5,7 +5,6 @@
 import platform
 import typing as ty
 import pytest
-import attrs
 import cloudpickle as cp
 from unittest.mock import Mock
 from fileformats.generic import Directory, File
@@ -20,7 +19,6 @@
     parse_format_string,
 )
 from pydra.utils.hash import hash_function
-from ..core import Workflow
 
 
 def test_save(tmpdir):

pydra/engine/tests/test_helpers_file.py

@@ -5,7 +5,7 @@
 from unittest.mock import Mock
 import pytest
 from fileformats.generic import File
-from ..specs import SpecInfo, ShellSpec
+from ..specs import ShellSpec
 from ..task import ShellTask
 from ..helpers_file import (
     ensure_list,

pydra/engine/tests/test_nipype1_convert.py

@@ -1,76 +1,56 @@
 import typing as ty
 import pytest
+from pathlib import Path
+from pydra.engine.specs import ShellOutputs, ShellSpec
+from fileformats.generic import File
+from pydra.design import shell
 
 
-from ..task import ShellTask
-from ..specs import ShellOutputs, ShellSpec, SpecInfo, File
+def find_txt(output_dir: Path) -> File:
+    files = list(output_dir.glob("*.txt"))
+    assert len(files) == 1
+    return files[0]
 
-interf_input_spec = SpecInfo(
-    name="Input", fields=[("test", ty.Any, {"help_string": "test"})], bases=(ShellSpec,)
-)
-interf_output_spec = SpecInfo(
-    name="Output", fields=[("test_out", File, "*.txt")], bases=(ShellOutputs,)
-)
 
+interf_inputs = [shell.arg(name="test", type=ty.Any, help_string="test")]
+interf_outputs = [shell.out(name="test_out", type=File, callable=find_txt)]
 
-class Interf_1(ShellTask):
-    """class with customized input/output specs"""
 
-    input_spec = interf_input_spec
-    output_spec = interf_output_spec
+Interf_1 = shell.define(inputs=interf_inputs, outputs=interf_outputs)
+Interf_2 = shell.define("testing command", inputs=interf_inputs, outputs=interf_outputs)
 
 
-class Interf_2(ShellTask):
-    """class with customized input/output specs and executables"""
+@shell.define
+class Interf_3(ShellSpec["Interf_3.Outputs"]):
+    """class with customized input and executables"""
 
-    input_spec = interf_input_spec
-    output_spec = interf_output_spec
-    executable = "testing command"
+    executable = ["testing", "command"]
 
+    in_file: str = shell.arg(help_string="in_file", argstr="{in_file}")
 
-class Interf_3(ShellTask):
-    """class with customized input and executables"""
+    @shell.outputs
+    class Outputs(ShellOutputs):
+        pass
 
-    input_spec = SpecInfo(
-        name="Input",
-        fields=[
-            (
-                "in_file",
-                str,
-                {"help_string": "in_file", "argstr": "'{in_file}'"},
-            )
-        ],
-        bases=(ShellSpec,),
-    )
-    executable = "testing command"
 
-
-class TouchInterf(ShellTask):
+@shell.define
+class TouchInterf(ShellSpec["TouchInterf.Outputs"]):
     """class with customized input and executables"""
 
-    input_spec = SpecInfo(
-        name="Input",
-        fields=[
-            (
-                "new_file",
-                str,
-                {
-                    "help_string": "new_file",
-                    "argstr": "",
-                    "output_file_template": "{new_file}",
-                },
-            )
-        ],
-        bases=(ShellSpec,),
+    new_file: str = shell.outarg(
+        help_string="new_file", argstr="", path_template="{new_file}"
     )
     executable = "touch"
 
+    @shell.outputs
+    class Outputs(ShellOutputs):
+        pass
+
 
 def test_interface_specs_1():
     """testing if class input/output spec are set properly"""
-    task = Interf_1(executable="ls")
-    assert task.input_spec == interf_input_spec
-    assert task.output_spec == interf_output_spec
+    task_spec = Interf_1(executable="ls")
+    assert task.Outputs == Interf_1.Outputs
 
 
 def test_interface_specs_2():

pydra/engine/tests/test_node_task.py

@@ -25,7 +25,7 @@
 )
 
 from ..core import Task
-from ..specs import StateArray
+from pydra.utils.typing import StateArray
 from ..submitter import Submitter
 
 

pydra/engine/tests/test_numpy_examples.py

@@ -7,7 +7,6 @@
 
 
 from ..submitter import Submitter
-from ..core import Workflow
 from pydra.mark import task, annotate
 from .utils import identity
 from pydra.utils.hash import hash_function

pydra/engine/tests/test_profiles.py

@@ -1,4 +1,3 @@
-from ..core import Workflow
 from ..helpers import load_task
 from pydra import mark
 

pydra/engine/tests/test_shelltask.py

@@ -1,22 +1,23 @@
 import attr
 import typing as ty
-import os, sys
-import subprocess as sp
+import os
+import sys
 import pytest
 from pathlib import Path
 import re
 import stat
 
 from ..task import ShellTask
 from ..submitter import Submitter
-from ..core import Workflow
 from ..specs import (
     ShellOutputs,
     ShellSpec,
-    SpecInfo,
+)
+from fileformats.generic import (
     File,
     Directory,
-    MultiInputFile,
+)
+from pydra.utils.typing import (
     MultiOutputFile,
     MultiInputObj,
 )