Add sudo_options & 'env' parameters to run_command (#167)

cceyda · Ceyda Cinarel · web-flow · commit 4542532f96bd · 2020-09-16T22:38:43.000-06:00
* add sudo_options kwarg, add env kwarg to run_command
* add sudo_options to instance stop
* add environment parameter to run_command
* lint code
* rename env to environ
* lint

Co-authored-by: Ceyda Cinarel &lt;snu-ceyda@users.noreply.github.com&gt;
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,8 @@ The client here will eventually be released as "spython" (and eventually to
 singularity on pypi), and the versions here will coincide with these releases.
 
 ## [master](https://github.com/singularityhub/singularity-cli/tree/master)
+ - add sudo_options option to Instance.start/stop and Client.execute (0.0.85)
+   - add environ option to Instance.start and Client.execute for passing env variables
  - Small bugfix for docker writer and adding pyflakes for unused imports (0.0.84)
  - Adding support for multistage build parsing (0.0.83)
  - Singularity Python does not yet support multistage builds (0.0.82)
diff --git a/spython/instance/cmd/start.py b/spython/instance/cmd/start.py
@@ -14,9 +14,11 @@ def start(
     name=None,
     args=None,
     sudo=False,
+    sudo_options=None,
     options=None,
     capture=False,
     singularity_options=None,
+    environ=None,
 ):
     """start an instance. This is done by default when an instance is created.
 
@@ -77,7 +79,14 @@ def start(
     self.args = args
     self.cmd = cmd
 
-    output = run_command(cmd, sudo=sudo, quiet=True, capture=capture)
+    output = run_command(
+        cmd,
+        sudo=sudo,
+        sudo_options=sudo_options,
+        quiet=True,
+        capture=capture,
+        environ=environ,
+    )
 
     if output["return_code"] == 0:
         self._update_metadata()
diff --git a/spython/instance/cmd/stop.py b/spython/instance/cmd/stop.py
@@ -8,7 +8,14 @@
 from spython.logger import bot
 
 
-def stop(self, name=None, sudo=False, timeout=None, singularity_options=None):
+def stop(
+    self,
+    name=None,
+    sudo=False,
+    sudo_options=None,
+    timeout=None,
+    singularity_options=None,
+):
     """stop an instance. This is done by default when an instance is created.
 
     Parameters
@@ -42,7 +49,7 @@ def stop(self, name=None, sudo=False, timeout=None, singularity_options=None):
         instance_name = name
     cmd = cmd + [instance_name]
 
-    output = run_command(cmd, sudo=sudo, quiet=True)
+    output = run_command(cmd, sudo=sudo, sudo_options=sudo_options, quiet=True)
 
     if output["return_code"] != 0:
         message = "%s : return code %s" % (output["message"], output["return_code"])
diff --git a/spython/main/base/command.py b/spython/main/base/command.py
@@ -108,6 +108,7 @@ def run_command(
     quiet=None,
     return_result=False,
     sudo_options=None,
+    environ=None,
 ):
 
     """run_command is a wrapper for the global run_command, checking first
@@ -130,7 +131,12 @@ def run_command(
         quiet = self.quiet
 
     result = run_cmd(
-        cmd, sudo=sudo, capture=capture, quiet=quiet, sudo_options=sudo_options
+        cmd,
+        sudo=sudo,
+        capture=capture,
+        quiet=quiet,
+        sudo_options=sudo_options,
+        environ=environ,
     )
 
     # If one line is returned, squash dimension
diff --git a/spython/main/execute.py b/spython/main/execute.py
@@ -25,7 +25,9 @@ def execute(
     options=None,
     singularity_options=None,
     sudo=False,
+    sudo_options=None,
     quiet=True,
+    environ=None,
 ):
     """execute: send a command to a container
 
@@ -99,9 +101,14 @@ def execute(
 
         if not stream:
             return self._run_command(
-                cmd, sudo=sudo, return_result=return_result, quiet=quiet
+                cmd,
+                sudo=sudo,
+                sudo_options=sudo_options,
+                return_result=return_result,
+                quiet=quiet,
+                environ=environ,
             )
-        return stream_command(cmd, sudo=sudo)
+        return stream_command(cmd, sudo=sudo, sudo_options=sudo_options)
 
     bot.exit("Please include a command (list) to execute.")
 
diff --git a/spython/main/instances.py b/spython/main/instances.py
@@ -15,6 +15,7 @@ def list_instances(
     return_json=False,
     quiet=False,
     sudo=False,
+    sudo_options=None,
     singularity_options=None,
 ):
     """list instances. For Singularity, this is provided as a command sub
@@ -53,7 +54,7 @@ def list_instances(
     if name is not None:
         cmd.append(name)
 
-    output = run_command(cmd, quiet=True, sudo=sudo)
+    output = run_command(cmd, quiet=True, sudo=sudo, sudo_options=sudo_options)
     instances = []
 
     # Success, we have instances
diff --git a/spython/utils/terminal.py b/spython/utils/terminal.py
@@ -149,6 +149,7 @@ def run_command(
     no_newline_regexp="Progess",
     quiet=False,
     sudo_options=None,
+    environ=None,
 ):
 
     """run_command uses subprocess to send a command to the terminal. If
@@ -174,7 +175,8 @@ def run_command(
         stdout = subprocess.PIPE
 
     # Use the parent stdout and stderr
-    process = subprocess.Popen(cmd, stderr=subprocess.PIPE, stdout=stdout)
+
+    process = subprocess.Popen(cmd, stderr=subprocess.PIPE, stdout=stdout, env=environ)
     lines = []
     found_match = False
 
diff --git a/spython/version.py b/spython/version.py
@@ -5,7 +5,7 @@
 # with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
 
 
-__version__ = "0.0.84"
+__version__ = "0.0.85"
 AUTHOR = "Vanessa Sochat"
 AUTHOR_EMAIL = "vsochat@stanford.edu"
 NAME = "spython"
