added test for executable=None (i.e. use entrypoint)

Author: tclose

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,
         )
 

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:

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="",

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:

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"