updating docker tests; fixing issue with working directory for docker

pydra/engine/environments.py

@@ -60,8 +60,11 @@ def execute(self, task, root="/mnt/pydra"):
         # todo adding xargsy etc
         docker_args = ["docker", "run", "-v", self.bind(task.cache_dir, "rw")]
         docker_args.extend(
-            " ".join([f"-v {self.bind(mount)}" for mount in mounts]).split()
+            " ".join(
+                [f"-v {key}:{val[0]}:{val[1]}" for (key, val) in mounts.items()]
+            ).split()
         )
+        docker_args.extend(["-w", f"{root}{task.output_dir}"])
         keys = ["return_code", "stdout", "stderr"]
         # print("\n Docker args", docker_args)
 

pydra/engine/task.py

@@ -345,7 +345,7 @@ def get_inputs_in_root(self, root=None):
             return []
         else:
             self._check_inputs(root=root)
-            return self.bindings.keys()
+            return self.bindings
 
     def command_args(self, root=None):
         """Get command line arguments"""
@@ -609,9 +609,13 @@ def _check_inputs(self, root):
                 # TODO: what if it's a directory? add tests
                 elif file.exists():  # is it ok if two inputs have the same parent?
                     # todo: probably need only keys
+                    if fld.metadata.get("mandatory"):
+                        mod = "rw"
+                    else:
+                        mod = "ro"
                     self.bindings[Path(file.parent)] = (
                         Path(f"{root}{file.parent}"),
-                        "ro",
+                        mod,
                     )
                     self.inputs_mod_root[fld.name] = f"{root}{Path(file).absolute()}"
                 # error should be raised only if the type is strictly File or Directory