removing temporary old env, some renaming

Author: djarecka

pydra/engine/environments.py

@@ -55,7 +55,7 @@ def execute(self, task, root="/mnt/pydra"):
         # Skips over any inputs in task.cache_dir
         # Needs to include `out_file`s when not relative to working dir
         # Possibly a `TargetFile` type to distinguish between `File` and `str`?
-        mounts = task.get_inputs_in_root(root=root)
+        mounts = task.get_bindings(root=root)
 
         # todo adding xargsy etc
         docker_args = ["docker", "run", "-v", self.bind(task.cache_dir, "rw")]

pydra/engine/task.py

@@ -38,6 +38,8 @@
       <https://colab.research.google.com/drive/1RRV1gHbGJs49qQB1q1d5tQEycVRtuhw6>`__
 
 """
+from __future__ import annotations
+
 import platform
 import re
 import attr
@@ -62,7 +64,6 @@
 )
 from .helpers import (
     ensure_list,
-    execute,
     position_sort,
     argstr_formatting,
     output_from_inputfields,
@@ -354,7 +355,7 @@ def get_bindings(self, root: str | None = None) -> dict[str, tuple[str, str]]:
         if root is None:
             return {}
         else:
-            self._check_inputs(root=root)
+            self._prepare_bindings(root=root)
             return self.bindings
 
     def command_args(self, root=None):
@@ -574,29 +575,7 @@ def cmdline(self):
     def _run_task(self, environment=None):
         if environment is None:
             environment = self.environment
-
-        if (
-            environment == "old"
-        ):  # TODO this is just temporarily for testing, remove this part
-            if isinstance(self, ContainerTask):
-                args = self.container_args + self.command_args()
-            else:
-                args = self.command_args()
-            if args:
-                # removing empty strings
-                args = [str(el) for el in args if el not in ["", " "]]
-                keys = ["return_code", "stdout", "stderr"]
-                values = execute(args, strip=self.strip)
-                self.output_ = dict(zip(keys, values))
-                if self.output_["return_code"]:
-                    msg = f"Error running '{self.name}' task with {args}:"
-                    if self.output_["stderr"]:
-                        msg += "\n\nstderr:\n" + self.output_["stderr"]
-                    if self.output_["stdout"]:
-                        msg += "\n\nstdout:\n" + self.output_["stdout"]
-                    raise RuntimeError(msg)
-        else:
-            self.output_ = environment.execute(self)
+        self.output_ = environment.execute(self)
 
     def _prepare_bindings(self, root: str):
         """Prepare input files to be passed to the task
@@ -721,7 +700,7 @@ def bind_paths(self):
         mount points: dict
             mapping from local path to tuple of container path + mode
         """
-        self._check_inputs()
+        self._prepare_bindings()
         return {**self.bindings, **{self.output_dir: (self.output_cpath, "rw")}}
 
     def binds(self, opt):
@@ -736,7 +715,7 @@ def binds(self, opt):
             bargs.extend([opt, f"{lpath}:{cpath}:{mode}"])
         return bargs
 
-    def _check_inputs(self):
+    def _prepare_bindings(self):
         fields = attr_fields(self.inputs)
         for fld in fields:
             if TypeParser.contains_type(FileSet, fld.type):

pydra/engine/tests/test_dockertask.py

@@ -17,13 +17,13 @@ def test_docker_1_nosubm():
     no submitter
     """
     cmd = "whoami"
-    docky = DockerTask(name="docky", executable=cmd, image="busybox", environment="old")
-    assert docky.inputs.image == "busybox"
-    assert docky.inputs.container == "docker"
-    assert (
-        docky.cmdline
-        == f"docker run --rm -v {docky.output_dir}:/output_pydra:rw -w /output_pydra {docky.inputs.image} {cmd}"
+    docky = ShellCommandTask(
+        name="docky", executable=cmd, environment=Docker(image="busybox")
     )
+    assert docky.environment.image == "busybox"
+    assert docky.environment.tag == "latest"
+    assert isinstance(docky.environment, Docker)
+    assert docky.cmdline == cmd
 
     res = docky()
     assert res.output.stdout == "root\n"

pydra/engine/tests/test_environments.py

@@ -46,13 +46,6 @@ def test_native_1(tmp_path):
         shelly_subm(submitter=sub, environment=Native())
     assert env_res == shelly_subm.result().output.__dict__
 
-    # TODO: should be removed at the end
-    shelly_old = ShellCommandTask(
-        name="shelly_old", executable=cmd, cache_dir=tmp_path, environment="old"
-    )
-    shelly_old()
-    assert env_res == shelly_old.result().output.__dict__
-
 
 @no_win
 @need_docker