Issue1535 (#1536)

* Remove 'R' formatter
* Remove remote target type
* Remove function sos remote push and sos remote pull.
* Stop interpreting paths in configuration file.
* Stop supporting named path (e.g. #home because we now assume home will be the same across hosts`)
* Stop converting paths like workdir because they are supposed to be the same across hosts.

requirements_dev.txt

@@ -16,4 +16,5 @@ pytest
 pytest-cov
 pyzmq
 sos-pbs
+tabulate>=0.9.0
 tqdm

setup.py

@@ -112,7 +112,6 @@ def run(self):
 file_target = sos.targets:file_target
 sos_tempfile = sos.targets:sos_tempfile
 dynamic = sos.targets:dynamic
-remote = sos.targets:remote
 executable = sos.targets:executable
 sos_variable = sos.targets:sos_variable
 sos_step = sos.targets:sos_step
@@ -126,14 +125,8 @@ def run(self):
 [sos_actions]
 script = sos.actions:script
 sos_run = sos.actions:sos_run
-fail_if = sos.actions:fail_if
-warn_if = sos.actions:warn_if
-stop_if = sos.actions:stop_if
-done_if = sos.actions:done_if
-skip_if = sos.actions:skip_if
 download = sos.actions:download
 run = sos.actions:run
-
 bash = sos.actions_bash:bash
 csh = sos.actions_bash:csh
 tcsh = sos.actions_bash:tcsh

src/sos/__main__.py

@@ -1057,22 +1057,6 @@ def cmd_remote(args, workflow_args):
             from .remote import run_command_on_hosts
 
             run_command_on_hosts(cfg, args.hosts, args.cmd, args.verbosity)
-        elif args.action == "push":
-            if not args.files:
-                raise ValueError(
-                    "Please specify files to push to remote host with option --files"
-                )
-            from .remote import push_to_hosts
-
-            push_to_hosts(cfg, args.hosts, args.files, args.verbosity)
-        elif args.action == "pull":
-            if not args.files:
-                raise ValueError(
-                    "Please specify files to pull from remote host with option --files"
-                )
-            from .remote import pull_from_host
-
-            pull_from_host(cfg, args.hosts, args.files, args.verbosity)
         else:
             raise ValueError(
                 "Unacceptable remote action. Use command 'sos remote -h' to check allowable actions."

src/sos/actions.py

@@ -2,7 +2,6 @@
 #
 # Copyright (c) Bo Peng and the University of Texas MD Anderson Cancer Center
 # Distributed under the terms of the 3-clause BSD License.
-
 import copy
 import gzip
 import os
@@ -33,18 +32,13 @@
 from .parser import SoS_Script
 from .syntax import SOS_ACTION_OPTIONS
 from .targets import executable, file_target, path, paths, sos_targets
-from .utils import (StopInputGroup, TerminateExecution,
-                    TimeoutInterProcessLock, env, fileMD5, get_traceback,
+from .utils import (TimeoutInterProcessLock, env, fileMD5, get_traceback,
                     load_config_files, short_repr, textMD5, transcribe)
 
 __all__ = [
     "SoS_Action",
     "script",
     "sos_run",
-    "fail_if",
-    "warn_if",
-    "stop_if",
-    "download",
     "run",
     "perl",
     "report",
@@ -129,8 +123,7 @@ def action_wrapper(*args, **kwargs):
                             "shub",
                             "oras",
                     ):
-                        env.logger.warning(
-                            f"Container type {cty} might not be supported.")
+                        env.logger.warning(f"Container type {cty} might not be supported.")
                 elif engine is not None and engine != "local":
                     raise ValueError(f"Only docker and singularity container engines are supported: {engine} specified")
                 else:
@@ -412,8 +405,9 @@ def run(self, **kwargs):
             else:
                 raise RuntimeError(f"Unacceptable interpreter {self.interpreter}")
 
-            debug_script_path = os.path.dirname(os.path.abspath(kwargs["stderr"])) if ("stderr" in kwargs and kwargs["stderr"] is not False and
-                                os.path.isdir(os.path.dirname(os.path.abspath(kwargs["stderr"])))) else env.exec_dir
+            debug_script_path = os.path.dirname(os.path.abspath(kwargs["stderr"])) if (
+                "stderr" in kwargs and kwargs["stderr"] is not False and
+                os.path.isdir(os.path.dirname(os.path.abspath(kwargs["stderr"])))) else env.exec_dir
             debug_script_file = os.path.join(
                 debug_script_path,
                 f'{env.sos_dict["step_name"]}_{env.sos_dict["_index"]}_{str(uuid.uuid4())[:8]}{self.suffix}',
@@ -769,49 +763,6 @@ def script(script, interpreter="", suffix="", args="", entrypoint="", **kwargs):
     return SoS_ExecuteScript(script, interpreter, suffix, args, entrypoint).run(**kwargs)
 
 
-@SoS_Action(acceptable_args=["expr", "msg"])
-def fail_if(expr, msg=""):
-    """Raise an exception with `msg` if condition `expr` is False"""
-    if expr:
-        raise TerminateExecution(msg if msg else "error triggered by action fail_if")
-    return 0
-
-
-@SoS_Action(acceptable_args=["expr", "msg"])
-def warn_if(expr, msg=""):
-    """Yield an warning message `msg` if `expr` is False """
-    if expr:
-        env.logger.warning(msg)
-    return 0
-
-
-@SoS_Action(acceptable_args=["expr", "msg", "no_output"])
-def stop_if(expr, msg="", no_output=False):
-    """Abort the execution of the current step or loop and yield
-    an warning message `msg` if `expr` is False"""
-    if expr:
-        raise StopInputGroup(msg=msg, keep_output=not no_output)
-    return 0
-
-
-@SoS_Action(acceptable_args=["expr", "msg"])
-def done_if(expr, msg=""):
-    """Assuming that output has already been generated and stop
-    executing the rest of the substep"""
-    if expr:
-        raise StopInputGroup(msg=msg, keep_output=True)
-    return 0
-
-
-@SoS_Action(acceptable_args=["expr", "msg", "no_output"])
-def skip_if(expr, msg=""):
-    """Skip the current substep and set _output to empty. Output
-    will be removed if already generated."""
-    if expr:
-        raise StopInputGroup(msg=msg, keep_output=False)
-    return 0
-
-
 #
 # download file with progress bar
 #

src/sos/functions.py

@@ -0,0 +1,65 @@
+from .utils import (StopInputGroup, TerminateExecution, env)
+
+# g_action_map = {}
+
+# def _load_actions():
+#     global g_action_map  # pylint: disable=global-variable-not-assigned
+#     for _entrypoint in pkg_resources.iter_entry_points(group="sos_actions"):
+#         # import actions from entry_points
+#         # Grab the function that is the actual plugin.
+#         _name = _entrypoint.name
+#         try:
+#             _plugin = _entrypoint.load()
+#             g_action_map[_name] = _plugin
+#         except Exception as e:
+#             from .utils import get_logger
+
+#             # look for sos version requirement
+#             get_logger().warning(f"Failed to load script running action {_entrypoint.name}: {e}")
+
+# def sos_run_script(action, script, *args, **kwargs):
+#     '''Call script-execution actions.'''
+#     if not g_action_map:
+#         _load_actions()
+#     try:
+#         g_action_map[action](script, *args, **kwargs)
+#     except KeyError as e:
+#         raise RuntimeError(f'Undefined script running action {action}') from e
+
+
+def stop_if(expr, msg="", no_output=False):
+    """Abort the execution of the current step or loop and yield
+    an warning message `msg` if `expr` is False"""
+    if expr:
+        raise StopInputGroup(msg=msg, keep_output=not no_output)
+    return 0
+
+
+def done_if(expr, msg=""):
+    """Assuming that output has already been generated and stop
+    executing the rest of the substep"""
+    if expr:
+        raise StopInputGroup(msg=msg, keep_output=True)
+    return 0
+
+
+def skip_if(expr, msg=""):
+    """Skip the current substep and set _output to empty. Output
+    will be removed if already generated."""
+    if expr:
+        raise StopInputGroup(msg=msg, keep_output=False)
+    return 0
+
+
+def fail_if(expr, msg=""):
+    """Raise an exception with `msg` if condition `expr` is False"""
+    if expr:
+        raise TerminateExecution(msg if msg else "error triggered by action fail_if")
+    return 0
+
+
+def warn_if(expr, msg=""):
+    """Yield an warning message `msg` if `expr` is False """
+    if expr:
+        env.logger.warning(msg)
+    return 0