From b5959a1ea2b2a9095b1a0de1ff14a454dc52bfb7 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 5 May 2025 09:50:46 +1000
Subject: [PATCH 1/8] rolled "base.execute" into "read_and_display" including
 error common handling performed in Environment.execute

---
 pydra/environments/base.py        | 70 ++++++++++++++-----------------
 pydra/environments/docker.py      | 12 +-----
 pydra/environments/native.py      | 12 +-----
 pydra/environments/singularity.py | 11 +----
 4 files changed, 36 insertions(+), 69 deletions(-)

diff --git a/pydra/environments/base.py b/pydra/environments/base.py
index 96914224e..c1c217d58 100644
--- a/pydra/environments/base.py
+++ b/pydra/environments/base.py
@@ -200,52 +200,46 @@ def map_path(fileset: os.PathLike | FileSet) -> Path:
         return bindings, values
 
 
-def execute(cmd, strip=False):
-    """
-    Run the event loop with coroutine.
-
-    Uses :func:`read_and_display_async` unless a loop is
-    already running, in which case :func:`read_and_display`
-    is used.
+def read_and_display(
+    *cmd: str, strip: bool = False, hide_display: bool = False
+) -> dict[str, int | str]:
+    """Capture a process' standard output.
 
     Parameters
     ----------
-    cmd : :obj:`list` or :obj:`tuple`
-        The command line to be executed.
-    strip : :obj:`bool`
-        TODO
-
-    """
-    rc, stdout, stderr = read_and_display(*cmd, strip=strip)
-    """
-    loop = get_open_loop()
-    if loop.is_running():
-        rc, stdout, stderr = read_and_display(*cmd, strip=strip)
-    else:
-        rc, stdout, stderr = loop.run_until_complete(
-            read_and_display_async(*cmd, strip=strip)
-        )
+    cmd : str
+        The command to execute, as a list of strings.
+    strip : bool, optional
+        If True, the output will be stripped of leading and trailing whitespace.
+    hide_display : bool, optional
+        If True, the output will not be displayed.
+
+    Returns
+    -------
+        dict[str, Any]
+            A dictionary containing the return code, standard output, and standard error.
+
+    Raises
+    ------
+        RuntimeError
+            If the return code is not 0, a RuntimeError is raised with a formatted
+            error message.
     """
-    return rc, stdout, stderr
-
-
-def read_and_display(*cmd, strip=False, hide_display=False):
-    """Capture a process' standard output."""
     try:
         process = sp.run(cmd, stdout=sp.PIPE, stderr=sp.PIPE)
     except Exception:
         # TODO editing some tracing?
         raise
 
+    stdout = process.stdout.decode("utf-8")
     if strip:
-        return (
-            process.returncode,
-            process.stdout.decode("utf-8").strip(),
-            process.stderr.decode("utf-8"),
-        )
-    else:
-        return (
-            process.returncode,
-            process.stdout.decode("utf-8"),
-            process.stderr.decode("utf-8"),
-        )
+        stdout = stdout.strip()
+    stderr = process.stderr.decode("utf-8")
+    if process.returncode:
+        msg = f"Error executing command {cmd} (code: {process.returncode}):"
+        if stdout:
+            msg += "\n\nstderr:\n" + stderr
+        if stdout:
+            msg += "\n\nstdout:\n" + stdout
+        raise RuntimeError(msg)
+    return {"return_code": process.returncode, "stdout": stdout, "stderr": stderr}
diff --git a/pydra/environments/docker.py b/pydra/environments/docker.py
index 03179f0da..bee66e25f 100644
--- a/pydra/environments/docker.py
+++ b/pydra/environments/docker.py
@@ -28,19 +28,11 @@ def execute(self, job: "Job[shell.Task]") -> dict[str, ty.Any]:
             ).split()
         )
         docker_args.extend(["-w", f"{self.root}{job.cache_dir}"])
-        keys = ["return_code", "stdout", "stderr"]
 
         job.cache_dir.mkdir(exist_ok=True)
-        values = base.execute(
-            docker_args + [docker_img] + job.task._command_args(values=values),
+        return base.read_and_display(
+            *(docker_args + [docker_img] + job.task._command_args(values=values)),
         )
-        output = dict(zip(keys, values))
-        if output["return_code"]:
-            if output["stderr"]:
-                raise RuntimeError(output["stderr"])
-            else:
-                raise RuntimeError(output["stdout"])
-        return output
 
 
 # Alias so it can be referred to as docker.Environment
diff --git a/pydra/environments/native.py b/pydra/environments/native.py
index fa51108d0..199a25c8c 100644
--- a/pydra/environments/native.py
+++ b/pydra/environments/native.py
@@ -15,18 +15,8 @@ class Native(base.Environment):
     """
 
     def execute(self, job: "Job[shell.Task]") -> dict[str, ty.Any]:
-        keys = ["return_code", "stdout", "stderr"]
         cmd_args = job.task._command_args(values=job.inputs)
-        values = base.execute(cmd_args)
-        output = dict(zip(keys, values))
-        if output["return_code"]:
-            msg = f"Error running '{job.name}' job with {cmd_args}:"
-            if output["stderr"]:
-                msg += "\n\nstderr:\n" + output["stderr"]
-            if output["stdout"]:
-                msg += "\n\nstdout:\n" + output["stdout"]
-            raise RuntimeError(msg)
-        return output
+        return base.read_and_display(cmd_args)
 
 
 # Alias so it can be referred to as native.Environment
diff --git a/pydra/environments/singularity.py b/pydra/environments/singularity.py
index a7fc0efff..4ce57a536 100644
--- a/pydra/environments/singularity.py
+++ b/pydra/environments/singularity.py
@@ -31,21 +31,12 @@ def execute(self, job: "Job[shell.Task]") -> dict[str, ty.Any]:
         singularity_args.extend(
             ["--pwd", f"{self.root.rstrip('/')}{job.cache_dir.absolute()}"]
         )
-        keys = ["return_code", "stdout", "stderr"]
-
         job.cache_dir.mkdir(exist_ok=True)
-        values = base.execute(
+        return base.read_and_display(
             singularity_args
             + [singularity_img]
             + job.task._command_args(values=values),
         )
-        output = dict(zip(keys, values))
-        if output["return_code"]:
-            if output["stderr"]:
-                raise RuntimeError(output["stderr"])
-            else:
-                raise RuntimeError(output["stdout"])
-        return output
 
 
 # Alias so it can be referred to as singularity.Environment

From 49a1f8dc4808c598fd55c87022d439a8059827da Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 5 May 2025 09:51:12 +1000
Subject: [PATCH 2/8] allow executable to be None if environment is a Container

---
 pydra/compose/shell/builder.py | 16 ++++++++++------
 pydra/compose/shell/task.py    | 18 ++++++++++++------
 2 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/pydra/compose/shell/builder.py b/pydra/compose/shell/builder.py
index 82030403e..22bacf0e3 100644
--- a/pydra/compose/shell/builder.py
+++ b/pydra/compose/shell/builder.py
@@ -130,13 +130,17 @@ def make(
                         f"Shell task class {wrapped} must have an `executable` "
                         "attribute that specifies the command to run"
                     ) from None
-            if not isinstance(executable, str) and not (
-                isinstance(executable, ty.Sequence)
-                and all(isinstance(e, str) for e in executable)
+            if (
+                executable is not None
+                and not isinstance(executable, str)
+                and not (
+                    isinstance(executable, ty.Sequence)
+                    and all(isinstance(e, str) for e in executable)
+                )
             ):
                 raise ValueError(
-                    "executable must be a string or a sequence of strings"
-                    f", not {executable!r}"
+                    "executable must be a string or a sequence of strings or None if "
+                    f"the command run is the entrypoint of a container, not {executable!r}"
                 )
             class_name = klass.__name__
             check_explicit_fields_are_none(klass, inputs, outputs)
@@ -199,7 +203,7 @@ def make(
         )
         parsed_inputs["executable"] = field.arg(
             name="executable",
-            type=str | ty.Sequence[str],
+            type=str | ty.Sequence[str] | None,
             argstr="",
             position=0,
             default=executable,
diff --git a/pydra/compose/shell/task.py b/pydra/compose/shell/task.py
index 3bdce0788..60fd35139 100644
--- a/pydra/compose/shell/task.py
+++ b/pydra/compose/shell/task.py
@@ -26,6 +26,7 @@
 )
 from pydra.compose import base
 from pydra.compose.base.field import RequirementSet
+from pydra.environments.base import Container
 from pydra.compose.base.helpers import is_set
 from . import field
 from .templating import (
@@ -254,6 +255,11 @@ class ShellTask(base.Task[ShellOutputsType]):
 
     def _run(self, job: "Job[ShellTask]", rerun: bool = True) -> None:
         """Run the shell command."""
+        if self.executable is None and not isinstance(job.environment, Container):
+            raise ValueError(
+                "executable is not set, and the environment is not a container "
+                f"({job.environment}) with an entrypoint"
+            )
         job.return_values = job.environment.execute(job)
 
     @property
@@ -291,9 +297,9 @@ def _command_args(self, values: dict[str, ty.Any]) -> list[str]:
         del values["executable"]
         del values["append_args"]
         # Add executable
-        pos_args = [
-            self._command_shelltask_executable(fld, self.executable),
-        ]  # list for (position, command arg)
+        pos_args = []
+        if self.executable is not None:
+            pos_args.append(self._executable_pos_arg(fld, self.executable))
         positions_provided = [0]
         fields = {f.name: f for f in get_fields(self)}
         for field_name in values:
@@ -312,9 +318,9 @@ def _command_args(self, values: dict[str, ty.Any]) -> list[str]:
         command_args += self.append_args
         return command_args
 
-    def _command_shelltask_executable(
-        self, fld: field.arg, value: ty.Any
-    ) -> tuple[int, ty.Any]:
+    def _executable_pos_arg(
+        self, fld: field.arg, value: str | list[str] | None
+    ) -> tuple[int, str | list[str] | None]:
         """Returning position and value for executable Task input"""
         pos = 0  # executable should be the first el. of the command
         assert value

From 6aa32fcc0933eb419dc1057c303d77c2a2c27d99 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 5 May 2025 11:55:57 +1000
Subject: [PATCH 3/8] fixed call to read_and_display

---
 pydra/environments/native.py      | 2 +-
 pydra/environments/singularity.py | 8 +++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/pydra/environments/native.py b/pydra/environments/native.py
index 199a25c8c..04e02aa8a 100644
--- a/pydra/environments/native.py
+++ b/pydra/environments/native.py
@@ -16,7 +16,7 @@ class Native(base.Environment):
 
     def execute(self, job: "Job[shell.Task]") -> dict[str, ty.Any]:
         cmd_args = job.task._command_args(values=job.inputs)
-        return base.read_and_display(cmd_args)
+        return base.read_and_display(*cmd_args)
 
 
 # Alias so it can be referred to as native.Environment
diff --git a/pydra/environments/singularity.py b/pydra/environments/singularity.py
index 4ce57a536..9e1157459 100644
--- a/pydra/environments/singularity.py
+++ b/pydra/environments/singularity.py
@@ -33,9 +33,11 @@ def execute(self, job: "Job[shell.Task]") -> dict[str, ty.Any]:
         )
         job.cache_dir.mkdir(exist_ok=True)
         return base.read_and_display(
-            singularity_args
-            + [singularity_img]
-            + job.task._command_args(values=values),
+            *(
+                singularity_args
+                + [singularity_img]
+                + job.task._command_args(values=values)
+            )
         )
 
 

From a9481506ff3eb2b06b90cf8e5349ff6a52ada47a Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 5 May 2025 12:22:58 +1000
Subject: [PATCH 4/8] added test for executable=None (i.e. use entrypoint)

---
 pydra/compose/shell/builder.py                | 14 +++++-
 pydra/compose/shell/task.py                   |  2 +-
 .../compose/shell/tests/test_shell_fields.py  | 18 ++++----
 pydra/environments/base.py                    |  2 +-
 pydra/environments/tests/test_environments.py | 46 +++++++++++++++++++
 5 files changed, 70 insertions(+), 12 deletions(-)

diff --git a/pydra/compose/shell/builder.py b/pydra/compose/shell/builder.py
index 22bacf0e3..def514ef5 100644
--- a/pydra/compose/shell/builder.py
+++ b/pydra/compose/shell/builder.py
@@ -33,6 +33,18 @@
 from .task import Task, Outputs
 
 
+def executable_validator(_, __, value):
+    """Validator for the executable attribute of a task"""
+    if value is None:
+        return
+    if not isinstance(value, (str, list)):
+        raise TypeError(
+            f"executable must be a string or a list of strings, not {value!r}"
+        )
+    if len(value) == 0:
+        raise ValueError("executable must be a non-empty string or a list of strings")
+
+
 @dataclass_transform(
     kw_only_default=True,
     field_specifiers=(field.out, field.outarg),
@@ -207,7 +219,7 @@ def make(
             argstr="",
             position=0,
             default=executable,
-            validator=attrs.validators.min_len(1),
+            validator=executable_validator,
             help=Task.EXECUTABLE_HELP,
         )
 
diff --git a/pydra/compose/shell/task.py b/pydra/compose/shell/task.py
index 60fd35139..f6ea4b4db 100644
--- a/pydra/compose/shell/task.py
+++ b/pydra/compose/shell/task.py
@@ -294,12 +294,12 @@ def _command_args(self, values: dict[str, ty.Any]) -> list[str]:
             if is_fileset_or_union(fld.type) and type(fld_value) is bool:
                 del values[fld.name]
         # Drop special fields that are added separately
-        del values["executable"]
         del values["append_args"]
         # Add executable
         pos_args = []
         if self.executable is not None:
             pos_args.append(self._executable_pos_arg(fld, self.executable))
+            del values["executable"]
         positions_provided = [0]
         fields = {f.name: f for f in get_fields(self)}
         for field_name in values:
diff --git a/pydra/compose/shell/tests/test_shell_fields.py b/pydra/compose/shell/tests/test_shell_fields.py
index 96189c602..528da8995 100644
--- a/pydra/compose/shell/tests/test_shell_fields.py
+++ b/pydra/compose/shell/tests/test_shell_fields.py
@@ -6,7 +6,7 @@
 import cloudpickle as cp
 from pydra.compose import shell
 from pydra.utils.general import get_fields, task_help, wrap_text
-from pydra.compose.shell.builder import _InputPassThrough
+from pydra.compose.shell.builder import _InputPassThrough, executable_validator
 from fileformats.generic import File, Directory, FsObject
 from fileformats import text, image
 from pydra.utils.typing import MultiInputObj
@@ -26,7 +26,7 @@ def test_interface_template():
     assert sorted_fields(Cp) == [
         shell.arg(
             name="executable",
-            validator=attrs.validators.min_len(1),
+            validator=executable_validator,
             default="cp",
             type=str | ty.Sequence[str],
             position=0,
@@ -81,7 +81,7 @@ def test_interface_template_w_types_and_path_template_ext():
     assert sorted_fields(TrimPng) == [
         shell.arg(
             name="executable",
-            validator=attrs.validators.min_len(1),
+            validator=executable_validator,
             default="trim-png",
             type=str | ty.Sequence[str],
             position=0,
@@ -122,7 +122,7 @@ def test_interface_template_w_modify():
     assert sorted_fields(TrimPng) == [
         shell.arg(
             name="executable",
-            validator=attrs.validators.min_len(1),
+            validator=executable_validator,
             default="trim-png",
             type=str | ty.Sequence[str],
             position=0,
@@ -181,7 +181,7 @@ def test_interface_template_more_complex():
     assert sorted_fields(Cp) == [
         shell.arg(
             name="executable",
-            validator=attrs.validators.min_len(1),
+            validator=executable_validator,
             default="cp",
             type=str | ty.Sequence[str],
             position=0,
@@ -281,7 +281,7 @@ def test_interface_template_with_overrides_and_optionals():
     assert sorted_fields(Cp) == [
         shell.arg(
             name="executable",
-            validator=attrs.validators.min_len(1),
+            validator=executable_validator,
             default="cp",
             type=str | ty.Sequence[str],
             position=0,
@@ -353,7 +353,7 @@ def test_interface_template_with_defaults():
     assert sorted_fields(Cp) == [
         shell.arg(
             name="executable",
-            validator=attrs.validators.min_len(1),
+            validator=executable_validator,
             default="cp",
             type=str | ty.Sequence[str],
             position=0,
@@ -421,7 +421,7 @@ def test_interface_template_with_type_overrides():
     assert sorted_fields(Cp) == [
         shell.arg(
             name="executable",
-            validator=attrs.validators.min_len(1),
+            validator=executable_validator,
             default="cp",
             type=str | ty.Sequence[str],
             position=0,
@@ -738,7 +738,7 @@ class Outputs(shell.Outputs):
     assert sorted_fields(A) == [
         shell.arg(
             name="executable",
-            validator=attrs.validators.min_len(1),
+            validator=executable_validator,
             default="cp",
             type=str | ty.Sequence[str],
             argstr="",
diff --git a/pydra/environments/base.py b/pydra/environments/base.py
index c1c217d58..6acc09dfa 100644
--- a/pydra/environments/base.py
+++ b/pydra/environments/base.py
@@ -236,7 +236,7 @@ def read_and_display(
         stdout = stdout.strip()
     stderr = process.stderr.decode("utf-8")
     if process.returncode:
-        msg = f"Error executing command {cmd} (code: {process.returncode}):"
+        msg = f"Error executing command {' '.join(cmd)!r} (code: {process.returncode}):"
         if stdout:
             msg += "\n\nstderr:\n" + stderr
         if stdout:
diff --git a/pydra/environments/tests/test_environments.py b/pydra/environments/tests/test_environments.py
index b39ed8ee8..f0a749085 100644
--- a/pydra/environments/tests/test_environments.py
+++ b/pydra/environments/tests/test_environments.py
@@ -1,5 +1,6 @@
 from pathlib import Path
 import typing as ty
+import docker as docker_engine
 from pydra.environments import native, docker, singularity
 from pydra.engine.submitter import Submitter
 from fileformats.generic import File
@@ -503,3 +504,48 @@ def newcache(x):
         "file_1_copy.txt",
         "file_2_copy.txt",
     ]
+
+
+@no_win
+@need_docker
+def test_entrypoint(tmp_path):
+    """docker env: task with a file in the output"""
+
+    dc = docker_engine.from_env()
+
+    # Create executable that runs validator then produces some mock output
+    # files
+    build_dir = tmp_path / "build"
+    build_dir.mkdir()
+    entrypoint = build_dir / "entrypoint.sh"
+    with open(entrypoint, "w") as f:
+        f.write("#!/bin/sh\necho hello $1")
+
+    IMAGE_TAG = "pydra-test-entrypoint"
+
+    # Build mock BIDS app image
+    with open(build_dir / "Dockerfile", "w") as f:
+        f.write(
+            """FROM busybox
+ADD ./entrypoint.sh /entrypoint.sh
+RUN chmod +x /entrypoint.sh
+ENTRYPOINT ["/entrypoint.sh"]"""
+        )
+
+    dc.images.build(path=str(build_dir), tag=IMAGE_TAG + ":latest")
+
+    @shell.define
+    class TestEntrypoint(shell.Task):
+        """task with a file in the output"""
+
+        executable = None
+        persons_name: str = shell.arg(help="the name of the person to say hello to")
+
+        class Outputs(shell.Outputs):
+            pass
+
+    test_entrypoint = TestEntrypoint(persons_name="Guido")
+
+    outputs = test_entrypoint(environment=docker.Environment(image=IMAGE_TAG))
+
+    assert outputs.stdout == "hello Guido\n"

From 0fa02d41cafcb8e9ca5c7a0002cfac99b59ccab7 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 5 May 2025 12:39:16 +1000
Subject: [PATCH 5/8] added line to docs about executable=None for entrypoints

---
 docs/source/tutorial/2-advanced-execution.ipynb | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/docs/source/tutorial/2-advanced-execution.ipynb b/docs/source/tutorial/2-advanced-execution.ipynb
index 164ab87fd..e09ea94e7 100644
--- a/docs/source/tutorial/2-advanced-execution.ipynb
+++ b/docs/source/tutorial/2-advanced-execution.ipynb
@@ -345,11 +345,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Of course for this to work Docker needs to work and be configured for\n",
-    "[sudo-less execution](https://docs.docker.com/engine/install/linux-postinstall/).\n",
+    "Note that for this to work Docker needs to work and be configured for\n",
+    "[sudo-less execution](https://docs.docker.com/engine/install/linux-postinstall/). If\n",
+    "the command you want to execute is the entrypoint of the container, you can set the\n",
+    "`executable` field to None, e.g.\n",
+    "`MrGrid(executable=None, in_file=nifti_file, operation=\"regrid\", voxel=(0.5, 0.5, 0.5))(environment=docker.Environment(\"mrgrid-image-with-entrypoint\"))`.\n",
     "See [Containers and Environments](../explanation/environments.rst) for more details on\n",
     "how to utilise containers and add support for other software environments.\n",
     "\n",
+    "\n",
     "It is also possible to specify functions to run at hooks that are immediately before and after\n",
     "the task is executed by passing a `pydra.engine.hooks.TaskHooks` object to the `hooks`\n",
     "keyword arg. The callable should take the `pydra.engine.job.Job` object as its only\n",

From 23a17ccae35416449a6ef81ab4df9555b8fb7a08 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 5 May 2025 12:42:42 +1000
Subject: [PATCH 6/8] fixed broken unittests

---
 pydra/compose/shell/tests/test_shell_fields.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/pydra/compose/shell/tests/test_shell_fields.py b/pydra/compose/shell/tests/test_shell_fields.py
index 528da8995..15b33fa3c 100644
--- a/pydra/compose/shell/tests/test_shell_fields.py
+++ b/pydra/compose/shell/tests/test_shell_fields.py
@@ -28,7 +28,7 @@ def test_interface_template():
             name="executable",
             validator=executable_validator,
             default="cp",
-            type=str | ty.Sequence[str],
+            type=str | ty.Sequence[str] | None,
             position=0,
             help=shell.Task.EXECUTABLE_HELP,
         ),
@@ -83,7 +83,7 @@ def test_interface_template_w_types_and_path_template_ext():
             name="executable",
             validator=executable_validator,
             default="trim-png",
-            type=str | ty.Sequence[str],
+            type=str | ty.Sequence[str] | None,
             position=0,
             help=shell.Task.EXECUTABLE_HELP,
         ),
@@ -124,7 +124,7 @@ def test_interface_template_w_modify():
             name="executable",
             validator=executable_validator,
             default="trim-png",
-            type=str | ty.Sequence[str],
+            type=str | ty.Sequence[str] | None,
             position=0,
             help=shell.Task.EXECUTABLE_HELP,
         ),
@@ -183,7 +183,7 @@ def test_interface_template_more_complex():
             name="executable",
             validator=executable_validator,
             default="cp",
-            type=str | ty.Sequence[str],
+            type=str | ty.Sequence[str] | None,
             position=0,
             help=shell.Task.EXECUTABLE_HELP,
         ),
@@ -283,7 +283,7 @@ def test_interface_template_with_overrides_and_optionals():
             name="executable",
             validator=executable_validator,
             default="cp",
-            type=str | ty.Sequence[str],
+            type=str | ty.Sequence[str] | None,
             position=0,
             help=shell.Task.EXECUTABLE_HELP,
         ),
@@ -355,7 +355,7 @@ def test_interface_template_with_defaults():
             name="executable",
             validator=executable_validator,
             default="cp",
-            type=str | ty.Sequence[str],
+            type=str | ty.Sequence[str] | None,
             position=0,
             help=shell.Task.EXECUTABLE_HELP,
         ),
@@ -423,7 +423,7 @@ def test_interface_template_with_type_overrides():
             name="executable",
             validator=executable_validator,
             default="cp",
-            type=str | ty.Sequence[str],
+            type=str | ty.Sequence[str] | None,
             position=0,
             help=shell.Task.EXECUTABLE_HELP,
         ),
@@ -740,7 +740,7 @@ class Outputs(shell.Outputs):
             name="executable",
             validator=executable_validator,
             default="cp",
-            type=str | ty.Sequence[str],
+            type=str | ty.Sequence[str] | None,
             argstr="",
             position=0,
             help=shell.Task.EXECUTABLE_HELP,
@@ -1004,7 +1004,7 @@ def test_shell_help1():
         "----------------------------",
         "",
         "Inputs:",
-        "- executable: str | Sequence[str]; default = 'shelly'",
+        "- executable: str | Sequence[str] | None; default = 'shelly'",
         "    the first part of the command, can be a string, e.g. 'ls', or a list, e.g.",
         "    ['ls', '-l', 'dirname']",
         "- in_file: generic/file",

From abebc2fe5d641e4015084239ad78a28b612c8234 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 5 May 2025 12:56:05 +1000
Subject: [PATCH 7/8] moved docker import inside test

---
 pydra/environments/tests/test_environments.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pydra/environments/tests/test_environments.py b/pydra/environments/tests/test_environments.py
index f0a749085..2573faae3 100644
--- a/pydra/environments/tests/test_environments.py
+++ b/pydra/environments/tests/test_environments.py
@@ -1,6 +1,5 @@
 from pathlib import Path
 import typing as ty
-import docker as docker_engine
 from pydra.environments import native, docker, singularity
 from pydra.engine.submitter import Submitter
 from fileformats.generic import File
@@ -511,6 +510,8 @@ def newcache(x):
 def test_entrypoint(tmp_path):
     """docker env: task with a file in the output"""
 
+    import docker as docker_engine
+
     dc = docker_engine.from_env()
 
     # Create executable that runs validator then produces some mock output

From b913f30e63d5dda0c4f758ca5499988735906e43 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Tue, 13 May 2025 14:50:11 +1000
Subject: [PATCH 8/8] removed circular import issue checking for container
 entrypoint

---
 pydra/compose/shell/task.py | 4 ++--
 pydra/environments/base.py  | 4 ++++
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/pydra/compose/shell/task.py b/pydra/compose/shell/task.py
index f6ea4b4db..60433f6c4 100644
--- a/pydra/compose/shell/task.py
+++ b/pydra/compose/shell/task.py
@@ -26,7 +26,6 @@
 )
 from pydra.compose import base
 from pydra.compose.base.field import RequirementSet
-from pydra.environments.base import Container
 from pydra.compose.base.helpers import is_set
 from . import field
 from .templating import (
@@ -255,7 +254,8 @@ class ShellTask(base.Task[ShellOutputsType]):
 
     def _run(self, job: "Job[ShellTask]", rerun: bool = True) -> None:
         """Run the shell command."""
-        if self.executable is None and not isinstance(job.environment, Container):
+
+        if self.executable is None and not job.environment.has_entrypoint:
             raise ValueError(
                 "executable is not set, and the environment is not a container "
                 f"({job.environment}) with an entrypoint"
diff --git a/pydra/environments/base.py b/pydra/environments/base.py
index 6acc09dfa..aae77ff33 100644
--- a/pydra/environments/base.py
+++ b/pydra/environments/base.py
@@ -26,6 +26,8 @@ class Environment:
     TODO: add setup and teardown methods
     """
 
+    has_entrypoint = False
+
     def setup(self):
         pass
 
@@ -107,6 +109,8 @@ class Container(Environment):
         Extra arguments to be passed to the container
     """
 
+    has_entrypoint = True
+
     image: str
     tag: str = "latest"
     root: str = "/mnt/pydra"